WorldWideScience

Sample records for ancestral pacific gondwana

  1. Paleozoic paleogeographic and depositional developments on the central proto-Pacific margin of Gondwana: Their importance to hydrocarbon accumulation

    Science.gov (United States)

    Gohrbandt, K. H. A.

    1992-11-01

    During the Paleozoic Era, the western portion of the Gondwana continent between the equator and latitude 27°S of present-day South America bordered the proto-Pacific Ocean as a predominantly convergent margin. Following the Middle Cambrian accretion of the Arequipa-Belen-Antofalla Terrane, an epicontinental sea with communication to the proto-Pacific Ocean established itself along the length of the western margin of Gondwana during Late Cambrian and Early Ordovician time. The emergence of a proto-Cordillera led to significant separation of the epicontinental sea from the proto-Pacific Ocean during Silurian and Devonian times. Gradual erosion of that proto-Cordillera during Carboniferous and Early Permian time once again facilitated widespread transgression of the proto-Pacific Ocean into the epicontinental domain. At the end of the Early Permian, the sea retreated from Gondwana and a proto-Cordillera was re-established. The proto-Cordillera and the craton of Gondwana controlled sediment type and distribution in the epicontinental sea. Deposition occurred in five tectono-sedimentary cycles, which were separated by orogenic pulses that resulted in regional erosion of the previously deposited section. Oil and gas have been produced from the Paleozoic epicontinental sediments of Argentina, Bolivia, Peru, and Brazil, in an area in which exploration efforts are ongoing. Sandstone reservoirs and argillaceous source rocks of commercial importance formed during the episodes of sedimentation, but carbonates do not contribute to commercial hydrocarbon generation and accumulation. Cap rocks are provided by shales or evaporites.

  2. Duration of convergence at the Pacific-Gondwana plate margin: insights from accessory phase petrochronology of the Alpine Schist, New Zealand

    Science.gov (United States)

    Briggs, S. I.; Cottle, J. M.; Smit, M. A.; Arnush, N. F.

    2016-12-01

    The timing, duration and along-strike synchroneity of metamorphism and anataxis in the Alpine Schist of New Zealand is a matter of considerable debate. Our preliminary data indicate that metamorphism resulting in garnet growth occurred from 97 - 75 Ma, and anatectic melting occurred from 80 - 51 Ma. These events are contemporaneous with rifting of Zealandia from East Gondwana, and Tasman Sea spreading from 83 - 52 Ma. An important implication of these results is that Late Cretaceous convergence along the Zealandia segment of the Pacific-Gondwana plate margin may have persisted much later than previously thought, and that convergence and extension occurred coevally in adjacent areas. This poses the question: for how long did convergence continue along the Pacific-Gondwana plate margin during East Gondwana breakup? To fully decipher the multiple stages of the complex metamorphic history recorded in the Alpine Schist, we combine Lu-Hf garnet geochronology with U-Th/Pb and REE analyses of zircon and monazite. We use the newly developed `single-shot laser ablation split stream' (SS-LASS) analysis method to obtain depth profiles through 5-10 µm metamorphic zircon overgrowths at 100 nm depth resolution to constrain both the timing and petrological context of discrete metamorphic zircon (re-)crystallization events recorded in the Alpine Schist. We also employ high spatial resolution LASS analysis to target rare 5 - 20 µm monazite in thin section to augment garnet and zircon data. Our multi-accessory phase petrochronology approach is capable of resolving discrete short-duration thermal events, strengthening the geological interpretation of `mean' Lu-Hf garnet ages and discerning between an episodic versus a prolonged history of metamorphism. In addition, comparison with geochronology from anatectic pegmatites clarifies the temporal relationship between metamorphism and melting in the Alpine Schist, while providing direct constraints on the timing and duration of

  3. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    International Nuclear Information System (INIS)

    Rapacz, J.; Hasler-Rapacz, J.O.; Chen, L.; Wu, Mingjiuan; Schumaker, V.N.; Butler-Brunner, E.; Butler, R.

    1991-01-01

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes

  4. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Energy Technology Data Exchange (ETDEWEB)

    Rapacz, J.; Hasler-Rapacz, J.O. (Univ. of Wisconsin, Madison (United States)); Chen, L.; Wu, Mingjiuan; Schumaker, V.N. (Univ. of California, Los Angeles (United States)); Butler-Brunner, E.; Butler, R. (Swiss Red Cross Blood Transfusion Service, Bern (Switzerland))

    1991-02-15

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes.

  5. Circum-Pacific accretion of oceanic terranes to continental blocks: accretion of the Early Permian Dun Mountain ophiolite to the E Gondwana continental margin, South Island, New Zealand

    Science.gov (United States)

    Robertson, Alastair

    2016-04-01

    Accretionary orogens, in part, grow as a result of the accretion of oceanic terranes to pre-existing continental blocks, as in the circum-Pacific and central Asian regions. However, the accretionary processes involved remain poorly understood. Here, we consider settings in which oceanic crust formed in a supra-subduction zone setting and later accreted to continental terranes (some, themselves of accretionary origin). Good examples include some Late Cretaceous ophiolites in SE Turkey, the Jurassic Coast Range ophiolite, W USA and the Early Permian Dun Mountain ophiolite of South Island, New Zealand. In the last two cases, the ophiolites are depositionally overlain by coarse clastic sedimentary rocks (e.g. Permian Upukerora Formation of South Island, NZ) that then pass upwards into very thick continental margin fore-arc basin sequences (Great Valley sequence, California; Matai sequence, South Island, NZ). Field observations, together with petrographical and geochemical studies in South Island, NZ, summarised here, provide evidence of terrane accretion processes. In a proposed tectonic model, the Early Permian Dun Mountain ophiolite was created by supra-subduction zone spreading above a W-dipping subduction zone (comparable to the present-day Izu-Bonin arc and fore arc, W Pacific). The SSZ oceanic crust in the New Zealand example is inferred to have included an intra-oceanic magmatic arc, which is no longer exposed (other than within a melange unit in Southland), but which is documented by petrographic and geochemical evidence. An additional subduction zone is likely to have dipped westwards beneath the E Gondwana margin during the Permian. As a result, relatively buoyant Early Permian supra-subduction zone oceanic crust was able to dock with the E Gondwana continental margin, terminating intra-oceanic subduction (although the exact timing is debatable). The amalgamation ('soft collision') was accompanied by crustal extension of the newly accreted oceanic slab, and

  6. Timing of the magmatism of the paleo-Pacific border of Gondwana: U-Pb geochronology of Late Paleozoic to Early Mesozoic igneous rocks of the north Chilean Andes between 20o and 31oS

    International Nuclear Information System (INIS)

    Maksaev, Victor; Munizaga, Francisco; Tassinari, Colombo

    2014-01-01

    U-Pb zircon geochronological data provide record of about 130 Ma of igneous activity in the Andes of northern Chile, which extended episodically from the latest Early Carboniferous to Early Jurassic (328-194 Ma). The overall U-Pb data show that volcanism and plutonism were essentially synchronous and major episodes of igneous activity developed during the Late Carboniferous to Mid-Permian (310 to 260 Ma) and from Late Permian to Late Triassic (255-205 Ma), with less prominent episodes in the mid-Carboniferous (330 to 320 Ma), and Early Jurassic (200-190 Ma). Thus, from the Carboniferous to the Early Triassic dominantly silicic magmatism developed along the Chilean segment of the southwestern border of Gondwana supercontinent. Further magmatism developed during the Mid-Late Triassic (250-194 Ma) was bimodal and synchronous with rift-related, continental and/or marine sedimentary strata related to the early stages of break-up of Gondwana. Most of the silicic volcanic rocks of the Precordillera and Domeyko Cordillera of northern Chile (21 o 30 o to 25 o 30 o S) are older than the silicic rocks assigned to the Choiyoi succession in Argentina, being instead equivalent in age to Carboniferous to Early Permian marine sedimentary sequences present in the eastern Argentinean foreland. On the other hand, silicic volcanic successions exposed in the easternmost part of northern Chile are equivalent in age to the Choiyoi succession of the San Rafael Block of Argentina. An eastward expansion or migration of the volcanism during the Mid-Permian to Early Triassic is inferred, interpretation that is consistent with expansion of the volcanism at that time in Argentina. The timing of the Late Paleozoic to Early Jurassic magmatism is coincident with that of the Andes of Peru and of western Argentina according to the available U-Pb data, revealing a rather consistent evolution in time of the magmatism along the southwestern, paleo-Pacific border of Gondwana

  7. STAGE MODEL FOR GONDWANA ASSEMBLY

    African Journals Online (AJOL)

    and the Kalahari craton (IMSLEK terranes) with the Congo craton and the Arabian Nubian Shield (ANS). The younger granulite event recorded in the Kitumbi area could then mark a younger collision between Australo-Antarctica and the combined IMSLEK-Conga. ANS collage marking the final assembly of Gondwana.

  8. Geological environment of Gondwana coals of Mozambique

    Energy Technology Data Exchange (ETDEWEB)

    Afonso, R.S.

    1984-01-01

    Coal deposition in the different Gondwana basins from Mozambique is discussed. The Productive Series position within the Gondwana Group and the Karoo System is determined. Coal seams of the different basins, as well as sedimentary environments and tectonics are also described. 52 refs.

  9. Ancestral Relationships Using Metafounders

    DEFF Research Database (Denmark)

    Legarra, Andres; Christensen, Ole Fredslund; Vitezica, Zulma G

    2015-01-01

    due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships....... We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view where each population is considered as an infinite, unrelated pool. Several ancestral populations may...... be connected and therefore related. Each ancestral population can be represented as a "metafounder", a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group". Metafounders have self- and across- relationships according to a set of parameters, which measure ancestral...

  10. Hypothesis for Cretaceous rifting of east Gondwana caused by subducted slab capture

    Science.gov (United States)

    Luyendyk, Bruce P.

    1995-04-01

    In the process of subducted slab capture, a spreading ridge approaches subparallel to a subduction zone following the trailing edge of a downgoing plate. Eventually the downgoing plate is too young and small to subduct, and spreading stops. The spreading ridge stalls many tens of kilometres outboard of the subduction zone. The subducted plate welds to the outboard plate across the dormant spreading center and is captured by it. The captured plate then acquires the motion of the plate it welded to. In the southwest Pacific the Pacific-Phoenix ridge approached the east Gondwana margin as the Phoenix plate subducted beneath New Zealand, the Chatham Rise and Campbell Plateau, the Lord Howe Rise (collectively, Zealandia), and Marie Byrd Land in Cretaceous time. Spreading and subduction shut down here between 110 and 105 Ma, and some sections of the Phoenix plate became welded to (captured by) the Pacific plate. Pacific plate northward motion began in Aptian time, pulling the captured subducted microplates with it. This movement exerted a basal traction on the overlying east Gondwana margin and resulted in extension of Zealandia and Marie Byrd Land. Continued Pacific northward motion rifted Zealandia from Marie Byrd Land at about 85 Ma.

  11. Detrital Zircons Split Sibumasu in East Gondwana

    Science.gov (United States)

    Zhang, X.; Chung, S. L.

    2017-12-01

    It is widely accepted that Sibumasu developed as a united terrane and originated from NW Australian margin in East Gondwana. Here we report new detrital zircon U-Pb-Hf isotopic data from Sumatra that, in combination with literature data, challenge and refute the above long-held view. In particular, the East and West Sumatra terranes share nearly identical Precambrian to Paleozoic detrital zircon age distributions and Hf isotopes, indicating a common provenance/origin for them. The Sumatra detrital zircons exhibit a prominent population of ca. 1170-1070 Ma, indistinguishable from those of the Lhasa and West Burma terranes, with detritus most probably sourcing from western Australia. By contrast, Sibuma (Sibumasu excluding Sumatra) detrital zircons display a prevailing population of ca. 980-935 Ma, strongly resembling those of the western Qiangtang terrane, with detrital materials most likely derived from Greater India and Himalayas. Such markedly distinct detrital zircon age profiles between Sumatra and Sibuma require disparate sources/origin for them, provoking disintegration of the widely-adopted, but outdated, term Sibumasu and thus inviting a new configuration of East Gondwana in the early Paleozoic, with Sumatra and West Burma lying outboard the Lhasa terrane in the NW Australian margin and Sibuma situated in the northern Greater Indian margin. More future investigations are needed to establish the precise rifting and drifting histories of Sumatra and Sibuma, as two separated terranes, during the breakup of Gondwana.

  12. Are palaeoscolecids ancestral ecdysozoans?

    Science.gov (United States)

    Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

    2010-01-01

    The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

  13. Scent of a supercontinent: Gondwana's ores as chemical tracers—tin, tungsten and the Neoproterozoic Laurentia-Gondwana connection

    Science.gov (United States)

    De Wit, Maarten J.; Thiart, Christien; Doucouré, Moctar; Wilsher, Wendy

    The birth of Gondwana is inextricably linked to the break-up of the earlier Neoproterozoic supercontinent Rodinia. In detail, the Neoproterozoic reconstructions of Rodinia are unsolved and without them a detailed kinematic history of the birth of Gondwana cannot be constructed. This paper shows that Gondwana's ore deposits provide chemical "scents" that can be effectively used to trace the tectonic history of Gondwana; and the heterogenous distribution of Gondwana's ore deposits are used to evaluate Late Neoproterozoic reconstructions, which place Laurentia against West Gondwana along a common belt of Grenville age rocks. West Gondwana (including its Grenville-like rocks) is anomalously enriched in Sn and W relative to the rest of Gondwana. The Grenville Province of Laurentia and its immediate hinterland are devoid of Sn-W deposits and even occurrences of any significance. Therefore, Rodinia reconstructions which juxtapose East Laurentia against the west coast of South America result in juxtaposition of distinctly different metalliferous crustal blocks. These reconstructions may not be correct, and other models should be (re-)explored.

  14. High-resolution seismic imaging of the Sohagpur Gondwana basin ...

    Indian Academy of Sciences (India)

    resolution seismic imaging of the Sohagpur Gondwana basin, central India: Evidence for syn-sedimentary subsidence and faulting. K Dhanam P Senthil Kumar D Mysaiah P Prabhakara Prasad T Seshunarayana. Volume 122 Issue 6 December ...

  15. Integrating Principles Underlying Ancestral Spirits Belief in ...

    African Journals Online (AJOL)

    , associated with ancestral spirits and its use as powerful therapeutic agent for influencing behavior or lifestyle changes. Explanatory models of attachment to ancestral spirits by living descendants are first discussed, followed by a discussion ...

  16. Patterns of Gondwana plant colonisation anddiversification

    Science.gov (United States)

    Anderson, J. M.; Anderson, H. M.; Archangelsky, S.; Bamford, M.; Chandra, S.; Dettmann, M.; Hill, R.; McLoughlin, S.; Rösler, O.

    Charting the broad patterns of vascular plant evolution for Gondwana againstthe major global environmental shifts and events is attempted here for the first time. This is based on the analysis of the major vascular plant-bearing formations of the southern continents (plus India) correlated against the standard geological time-scale. Australia, followed closely by South America, are shown to yield by far the most complete sequences of productive strata. Ten seminal turnover pulses in the unfolding evolutionary picture are identified and seen to be linked to continental drift, climate change and mass global extinctions. The rise of vascular plants along the tropical belt, for instance, followed closely after the end-Ordovician warming and extinction. Equally remarkable is that the Late Devonian extinction may have caused both the terrestrialisation of the vertebrates and the origin of the true gymnosperms. The end-Permian extinction, closure of Iapetus, together with warming, appears to have set in motion an unparalleled, explosive, gymnosperm radiation; whilst the Late Triassic extinction dramatically curtailed it. It is suggested that the latitudinal diversity gradient clearly recognised today, where species richness increases towards the tropics, may have been partly reversed during phases of Hot House climate. Evidence hints at this being particularly so at the heyday of the gymnosperms in the Late Triassic super-Hot House world. As for the origin of terrestrial, vascular, plant life, the angiosperms seem closely linked to a phase of marked shift from Ice House to Hot House. Insect and tetrapod evolutionary patterns are discussed in the context of the plants providing the base of the ever-changing ecosystems. Intimate co-evolution is often evident. This isn't always the case, for example the non-linkage between the dominant, giant, long-necked, herbivorous sauropod dinosaurs and the dramatic radiation of the flowering plants in the Mid Cretaceous.

  17. Early Palaeozoic orogenesis along the Indian margin of Gondwana: Tectonic response to Gondwana assembly

    Science.gov (United States)

    Cawood, Peter A.; Johnson, Michael R. W.; Nemchin, Alexander A.

    2007-03-01

    SHRIMP U-Pb dating of zircons from a peralkaline S-type Lesser Himalayan granite from the Kathmandu region, Nepal indicate an age of emplacement of 475 Ma. The granites along with metasedimentary xenoliths show a similar signature of inherited detrital zircon ages ranging from Archaean to early Palaeozoic with prominent late Mesoproterozoic (Grenvillian) and Neoproterozoic (Pan-African) age peaks and have a maximum age of 500 Ma based on the youngest detrital grains. Deformation structures in xenoliths are truncated by the granite and along with the granites are assigned to a Cambro-Ordovician orogenic event, herein termed the Bhimphedian Orogeny that can be traced across the Himalaya from Pakistan to the eastern Himalaya and possibly extends west into Afghanistan. We interpret the orogeny as being related to Andean-type orogenic activity on the northern margin of the Indian continent, following Gondwana assembly. The magmatic arc was associated with andesitic and basaltic volcanism and was active from c. 530 to 490 Ma. The arc activity overlaps with, and is succeeded by, regional deformation, crustal melting and S-type granite emplacement that extended to 470 Ma. Orogenic activity was driven by coupling across the plate margin either during on-going subduction or through accretion of microcontinental ribbons, possibly represented by the Lhasa and Qiangtang blocks. It represents the termination of an orogenic cycle, termed the North Indian Orogen that commenced with Neoproterozoic rifting and passive margin development and terminated with the Bhimphedian Orogeny. This was succeeded by a return to passive margin setting along the northern Indian margin of Gondwana which continued until the Cenozoic Himalayan Orogeny.

  18. Kinematics of late paleozoic continental collision between laurentia and gondwana.

    Science.gov (United States)

    Sacks, P E; Secor, D T

    1990-12-21

    In the Appalachians, late Paleozoic Alleghanian orogenesis is widely regarded as resulting from dextral oblique collision between irregular margins of Gondwana and Laurentia. However, this relative plate motion cannot account for coeval convergence in the Ouachitas and Variscides and is incompatible with some tectonic transport indicators in the Appalachians. An alternative kinematic model is proposed in which early sinistral transpression in the Appalachians is followed by counterclockwise rotation of Gondwana and the development of a system of dextral strike-slip faults extending from southern Europe to Alabama.

  19. REGEN: Ancestral Genome Reconstruction for Bacteria

    OpenAIRE

    Yang, Kuan; Heath, Lenwood S.; Setubal, João C.

    2012-01-01

    Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deleti...

  20. The P-T-t History of the Alpine Schist, New Zealand: Constraining Tectonic Processes During the Late Stages of Gondwana Breakup

    Science.gov (United States)

    Briggs, S. I.; Smit, M. A.; Cottle, J. M.; Hagen-Peter, G.

    2015-12-01

    Separation of the microcontinent Zealandia from the Marie Byrd Land sector of Antarctica in the Late Cretaceous marked the final stage in the breakup of Gondwana. Two contrasting ideas for the Late Cretaceous rifting of Zealandia from Gondwana have been proposed. One is that subduction at the paleo-Pacific - Gondwana convergent margin ceased after the last pulse of batholith emplacement at ~100 Ma, followed by a rapid transition to extension and seafloor spreading at 82 Ma. The other hypothesis is that convergence continued along Zealandia simultaneously with back-arc extension until ~85 M. This hypothesis is based on recently reported Late Cretaceous ages from the Alpine Schist, a metamorphosed accretionary wedge assemblage. Without accompanying pressure-temperature (P-T) information, the significance of Late Cretaceous ages from the Alpine Schist in terms of the orogenic processes that occurred during cessation of subduction at the paleo-Pacific - Gondwana margin remains unclear. In this study, Lu-Hf geochronology of Alpine Schist garnet is paired with phase equilibria modelling to elucidate the P-T-t history of the orogen and clarify the mechanisms behind Zealandia-Gondwana rifting. Garnet Lu-Hf dates have been obtained from 9 samples ranging in bulk composition from quartzo-feldspathic schists to mafic amphibolites. Garnet yields Early Cretaceous ages from the southern Alpine Schist, whereas northern Alpine Schist garnet yields Late Cretaceous ages. Garnet textures and major and trace element compositional zoning suggest that an additional, later period of garnet growth or recrystallization may be recorded in the northern samples. P-T-t data from each dated sample is supplemented with thermobarometric analysis from an adjacent sample of different lithology, with the advantage of providing more complete local P-T-t paths. The P-T-t paths define whether garnet grew during increasing P-T (prograde early), decreasing P and increasing T (prograde late), and

  1. Ancestral sequence reconstruction with Maximum Parsimony

    OpenAIRE

    Herbst, Lina; Fischer, Mareike

    2017-01-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...

  2. Ancestral sequence alignment under optimal conditions

    Directory of Open Access Journals (Sweden)

    Brown Daniel G

    2005-11-01

    Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

  3. Assessment of Hydrocarbon Generation Potential of Permian Gondwana Coals, Bangladesh

    Directory of Open Access Journals (Sweden)

    H. M. Zakir Hossain

    2013-06-01

    Full Text Available This paper represents the geochemical characteristics of Gondwana coals from the Barapukuria coal mine, Bangladesh in order to investigate the potential for hydrocarbon generation. A total number of twenty three coal samples were analyzed Rock-Eval pyrolysis, CHNS elemental analyses, maceral analysis and vitrinite reflectance. The samples were collected from drill hole GDH-40 of the Barapukuria coal mine encountered within Gondwana succession of Permian age. The TOC contents of the coal samples range between ~50 and 76 wt.% and the organic matter consists predominantly of type III and type IV kerogen with respect to hydrocarbon generation. The GP, HI, PI and Tmax values range between 7 and 35 mg HC/g rock, 20 and 62 mg HC/g TOC, 0.02 and 0.04, and 430 and 437oC, respectively. The organic matter is mainly gas prone and thermally immature to early mature level. The potential coal bed methane (CBM generation of the Barapukuria basin is estimated to be 11 Gm3. Thus, underground coal gasification (UCG is helpful for better development of subsurface coals at the Barapukuria basin, Bangladesh.

  4. Wildfires in the Triassic of Gondwana Paraná Basin

    Science.gov (United States)

    Cardoso, Daiane dos Santos; Mizusaki, Ana Maria Pimentel; Guerra-Sommer, Margot; Menegat, Rualdo; Barili, Rosalia; Jasper, André; Uhl, Dieter

    2018-03-01

    This first report of wildfires from an association of facies containing a Dicroidium flora is made from the Upper Triassic (Carnian age) in the southern part of the Paraná Basin (Santa Maria Supersequence, Rio Grande do Sul state). The geographical extension of the Dicroidium plant assemblage is augmented in Brazilian Gondwana. Field work followed by organic petrography (inertinite reflectance), scanning electron microscopy (SEM) and field emission gun scanning electron microscopy (FEG-SEM), revealed charcoal presence in a section located in Pinheiro Machado town. Macroscopic charcoal is represented by three-dimensional wood specimens assigned to gymnosperms, with coniferous affinities and by flattened, thin, elongated remains corresponding to rachises of Dicroidium. Average reflectance values between 2.80 and 6.61 %Ro measured in the macroscopic charcoals evidence high temperature burning processes, involving fires both in the crown and in the crown-surface interface. The occurrence of charcoal in distinct and subsequent facies of the studied section indicates wildfires, which affected hinterland, meso-xerophyllous coniferous assemblages and marginal hygro-mesophyllous Dicroidium-like assemblages. The integration of results from the charcoal analyses is consistent with an atmospheric oxygen content higher than 18.5% and fuel enough to generate wildfires during the Triassic of Gondwana.

  5. Gondwana basins and their coal resources in Bangladesh

    International Nuclear Information System (INIS)

    Nehaluddin, M.; Sultan-ul-Islam, M.

    1994-01-01

    Fault bounded five Gondwana basins have been discovered in the north western Bangladesh. Among these basins show considerable amount of coal deposits. The Gondwana rocks are highly formed during the Permo-carboniferous diastrophism and later on acquired dynamic characters. In almost all basins, the Permian rocks overlie the Precambrian basement and underlie either the Tertiary or the Cretaceous sediments, structural, stratigraphic, and depositional history of these basins is more or less similar. The sedimentary sequences are composed of light to dark gray, fine to very coarse grained, sub angular to sub rounded felspathic sandstone, dark grey carbonaceous shale and sandstone, variegated conglomerate and thick coal seams (single seam max. 42.38m). The rocks are often alternated and bear the characteristics of cyclic sedimentation. The depositional environments varied from restricted drainage to open fluvial dominated low to moderate sinuous drainage system. The coal bearing basins were flanked by vegetated and swampy over bank. Age of these coals is suggested to be the late permian. Proved and probable reserves of coal in Jamalganj-Paharpur basin are 670 and 1,460 million metric tons, in Barapukuria basin 303 and 3899 million metric tons; in Barapukuria basin 303 and 389 million metric tons; and in Khalaspir basin 143 and 685 million metric tons respectively. The coal is high volatile, low sulphur, bituminous type. It can be used for different forms of thermal conversion. (author)

  6. REGEN: Ancestral Genome Reconstruction for Bacteria

    Directory of Open Access Journals (Sweden)

    João C. Setubal

    2012-07-01

    Full Text Available Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  7. REGEN: Ancestral Genome Reconstruction for Bacteria.

    Science.gov (United States)

    Yang, Kuan; Heath, Lenwood S; Setubal, João C

    2012-07-18

    Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  8. Staging Sacrifice: Performing History, Memory, and Ancestral ...

    African Journals Online (AJOL)

    Returning and recurring cultural forms, ancestral incarnations, theatrical imaginations, and racial memories in African plays construct a specific kind of historicity - the conjuring of the dead and the revitalization of cosmic energy or spiritual power. These formations perpetuate the construction of Africa and African-ness ...

  9. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  10. Early breakup of Gondwana: constraints from global plate motion models

    Science.gov (United States)

    Seton, Maria; Zahirovic, Sabin; Williams, Simon; Whittaker, Joanne; Gibbons, Ana; Muller, Dietmar; Brune, Sascha; Heine, Christian

    2015-04-01

    Supercontinent break-up and amalgamation is a fundamental Earth cycle, contributing to long-term sea-level fluctuations, species diversity and extinction events, long-term greenhouse-icehouse cycles and changes in the long-wavelength density structure of the mantle. The most recent and best-constrained example involves the fragmentation of Gondwana, starting with rifting between Africa/Madagascar and Antarctica in the Early Jurassic and ending with the separation of the Lord Howe microcontinental blocks east of Australia in the Late Cretaceous. Although the first order configuration of Gondwana within modern reconstructions appears similar to that first proposed by Wegener a century ago, recent studies utilising a wealth of new geophysical and geological data provide a much more detailed picture of relative plate motions both during rifting and subsequent seafloor spreading. We present our latest global plate motion model that includes extensive, new regional analyses. These include: South Atlantic rifting, which started at 150 Ma and propagated into cratonic Africa by 145 Ma (Heine et al., 2013); rifting and early seafloor spreading between Australia, India and Antarctica, which reconciles the fit between Broken Ridge-Kergulean Plateau and the eastern Tasman region (Whittaker et al., 2013); rifting of continental material from northeastern Gondwana and its accretion onto Eurasia and SE Asia including a new model of microcontinent formation and early seafloor spreading in the eastern Indian Ocean (Gibbons et al., 2012; 2013; in review; Williams et al., 2013; Zahirovic et al., 2014); and a new model for the isolation of Zealandia east of Australia, with rifting initiating at 100 Ma until the start of seafloor spreading in the Tasman Sea at ~85 Ma (Williams et al., in prep). Using these reconstructions within the open-source GPlates software, accompanied by a set of evolving plates and plate boundaries, we can explore the factors that govern the behavior of plate

  11. Assessing the Accuracy of Ancestral Protein Reconstruction Methods

    OpenAIRE

    Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A

    2006-01-01

    The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolu...

  12. Contemporaneous assembly of Western Gondwana and final Rodinia break-up: Implications for the supercontinent cycle

    Directory of Open Access Journals (Sweden)

    Sebastián Oriolo

    2017-11-01

    Full Text Available Geological, geochronological and isotopic data are integrated in order to present a revised model for the Neoproterozoic evolution of Western Gondwana. Although the classical geodynamic scenario assumed for the period 800–700 Ma is related to Rodinia break-up and the consequent opening of major oceanic basins, a significantly different tectonic evolution can be inferred for most Western Gondwana cratons. These cratons occupied a marginal position in the southern hemisphere with respect to Rodinia and recorded subduction with back-arc extension, island arc development and limited formation of oceanic crust in internal oceans. This period was thus characterized by increased crustal growth in Western Gondwana, resulting from addition of juvenile continental crust along convergent margins. In contrast, crustal reworking and metacratonization were dominant during the subsequent assembly of Gondwana. The Río de la Plata, Congo-São Francisco, West African and Amazonian cratons collided at ca. 630–600 Ma along the West Gondwana Orogen. These events overlap in time with the onset of the opening of the Iapetus Ocean at ca. 610–600 Ma, which gave rise to the separation of Baltica, Laurentia and Amazonia and resulted from the final Rodinia break-up. The East African/Antarctic Orogen recorded the subsequent amalgamation of Western and Eastern Gondwana after ca. 580 Ma, contemporaneously with the beginning of subduction in the Terra Australis Orogen along the southern Gondwana margin. However, the Kalahari Craton was lately incorporated during the Late Ediacaran–Early Cambrian. The proposed Gondwana evolution rules out the existence of Pannotia, as the final Gondwana amalgamation postdates latest connections between Laurentia and Amazonia. Additionally, a combination of introversion and extroversion is proposed for the assembly of Gondwana. The contemporaneous record of final Rodinia break-up and Gondwana assembly has major implications for the

  13. Contemporaneous assembly of Western Gondwana and final Rodinia break-up: Implications for the supercontinent cycle

    OpenAIRE

    Oriolo, Sebastián; Oyhantçabal, Pedro; Wemmer, Klaus; Siegesmund, Siegfried

    2017-01-01

    Geological, geochronological and isotopic data are integrated in order to present a revised model for the Neoproterozoic evolution of Western Gondwana. Although the classical geodynamic scenario assumed for the period 800–700 Ma is related to Rodinia break-up and the consequent opening of major oceanic basins, a significantly different tectonic evolution can be inferred for most Western Gondwana cratons. These cratons occupied a marginal position in the southern hemisphere with respect to Rod...

  14. 40Ar-39Ar age studies for tectonics of the Gondwana land

    International Nuclear Information System (INIS)

    Takigami, Yutaka; Sugiura, Naoji.

    1997-01-01

    40 Ar- 39 Ar age studies have been performed for samples from Antarctica and India which were parts of the Gondwana land at Mesozoic and Paleozoic time in order to investigate their thermal history and tectonic movement. From the both areas, ages of about 500 Ma which have been considered to be the age of Pan-African Orogeny were obtained, which represents that this thermal event spread widely over the Gondwana land. (author)

  15. ^<40>Ar-^<39>Ar Age Studies for Tectonics of the Gondwana Land

    OpenAIRE

    Takigami, Yutaka; Sugiura, Naoji

    1997-01-01

    ^Ar-^Ar age studies have been performed for samples from Antarctica and India which were parts of the Gondwana land at Mesozoic and Paleozoic time in order to investigate their thermal history and tectonic movement. From the both areas, ages of about 500 Ma which have been considered to be the age of Pan-African Orogeny were obtained, which represents that this thermal event spread widely over the Gondwana land.

  16. Plate motions, Gondwana Dinosaurs, Noah's Arks, Beached Viking Funeral Ships, Ghost Ships, and Landspans

    Directory of Open Access Journals (Sweden)

    Louis L. Jacobs

    2011-03-01

    Full Text Available Gondwana landmasses have served as large-scale biogeographic Noah's Arks and Beached Viking Funeral Ships, as defined by McKenna. The latitudinal trajectories of selected Gondwana dinosaur localities were traced through time in order to evaluate their movement through climate zones relative to those in which they originally formed. The dispersal of fauna during the breakup of Gondwana may have been facilitated by the presence of offshelf islands forming landspans (sensu Iturralde-Vinent and MacPhee in the Equatorial Atlantic Gateway and elsewhere.As massas de terra do Gondwana serviram como Arcas de Noe biogeograficas de grande escala e Navios Funerarios Vikings encalhados, conforme definido por McKenna. As trajetorias latitudinais de areas selecionadas de dinossauros do Gondwana foram tracadas ao longo do tempo a fim de avaliar seu movimento atraves de zonas climaticas relativas aquelas nas quais elas foram originalmente formadas. A dispersao da fauna durante a quebra do Gondwana pode ter sido facilitada pela presenca de ilhas oceanicas formando extensoes de terra (sensu Iturralde-Vinent e MacPhee na entrada do Atlantico Equatorial e em outros lugares.

  17. The ancestral complement system in sea urchins.

    Science.gov (United States)

    Smith, L C; Clow, L A; Terwilliger, D P

    2001-04-01

    The origin of adaptive immunity in the vertebrates can be traced to the appearance of the ancestral RAG genes in the ancestral jawed vertebrate; however, the innate immune system is more ancient. A central subsystem within innate immunity is the complement system, which has been identified throughout and seems to be restricted to the deuterostomes. The evolutionary history of complement can be traced from the sea urchins (members of the echinoderm phylum), which have a simplified system homologous to the alternative pathway, through the agnathans (hagfish and lamprey) and the elasmobranchs (sharks and rays) to the teleosts (bony fish) and tetrapods, with increases in the numbers of complement components and duplications in complement pathways. Increasing complexity in the complement system parallels increasing complexity in the deuterostome animals. This review focuses on the simplest of the complement systems that is present in the sea urchin. Two components have been identified that show significant homology to vertebrate C3 and factor B (Bf), called SpC3 and SpBf, respectively. Sequence analysis from both molecules reveals their ancestral characteristics. Immune challenge of sea urchins indicates that SpC3 is inducible and is present in coelomic fluid (the body fluids) in relatively high concentrations, while SpBf expression is constitutive and is present in much lower concentrations. Opsonization of foreign cells and particles followed by augmented uptake by phagocytic coelomocytes appears to be a central function for this simpler complement system and important for host defense in the sea urchin. These activities are similar to some of the functions of the homologous proteins in the vertebrate complement system. The selective advantage for the ancestral deuterostome may have been the amplification feedback loop that is still of central importance in the alternative pathway of complement in higher vertebrates. Feedback loop functions would quickly coat

  18. Cordillera Zealandia: A Mesozoic arc flare-up on the palaeo-Pacific Gondwana Margin

    OpenAIRE

    Milan, L. A.; Daczko, N. R.; Clarke, G. L.

    2017-01-01

    Two geochemically and temporally distinct components of the Mesozoic Zealandia Cordilleran arc indicate a shift from low to high Sr/Y whole rock ratios at c. 130?Ma. Recent mapping and a reappraisal of published Sr-Nd data combined with new in-situ zircon Hf isotope analyses supports a genetic relationship between the two arc components. A reappraisal of geophysical, geochemical and P-T estimates demonstrates a doubling in thickness of the arc to at least 80?km at c. 130?Ma. Contemporaneously...

  19. Cordillera Zealandia: A Mesozoic arc flare-up on the palaeo-Pacific Gondwana Margin.

    Science.gov (United States)

    Milan, L A; Daczko, N R; Clarke, G L

    2017-03-21

    Two geochemically and temporally distinct components of the Mesozoic Zealandia Cordilleran arc indicate a shift from low to high Sr/Y whole rock ratios at c. 130 Ma. Recent mapping and a reappraisal of published Sr-Nd data combined with new in-situ zircon Hf isotope analyses supports a genetic relationship between the two arc components. A reappraisal of geophysical, geochemical and P-T estimates demonstrates a doubling in thickness of the arc to at least 80 km at c. 130 Ma. Contemporaneously, magmatic addition rates shifted from ~14 km 3 /my per km of arc to a flare-up involving ~100 km 3 /my per km of arc. Excursions in Sr-Nd-Hf isotopic ratios of flare-up rocks highlight the importance of crust-dominated sources. This pattern mimics Cordilleran arcs of the Americas and highlights the importance of processes occurring in the upper continental plates of subduction systems that are incompletely reconciled with secular models for continental crustal growth.

  20. Approximate maximum parsimony and ancestral maximum likelihood.

    Science.gov (United States)

    Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

    2010-01-01

    We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

  1. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty.

    Science.gov (United States)

    Hanson-Smith, Victor; Kolaczkowski, Bryan; Thornton, Joseph W

    2010-09-01

    Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and a specific phylogeny--typically the tree with the ML. The true phylogeny is seldom known with certainty, however. ML methods ignore this uncertainty, whereas Bayesian methods incorporate it by integrating the likelihood of each ancestral state over a distribution of possible trees. It is not known whether Bayesian approaches to phylogenetic uncertainty improve the accuracy of inferred ancestral sequences. Here, we use simulation-based experiments under both simplified and empirically derived conditions to compare the accuracy of ASR carried out using ML and Bayesian approaches. We show that incorporating phylogenetic uncertainty by integrating over topologies very rarely changes the inferred ancestral state and does not improve the accuracy of the reconstructed ancestral sequence. Ancestral state reconstructions are robust to uncertainty about the underlying tree because the conditions that produce phylogenetic uncertainty also make the ancestral state identical across plausible trees; conversely, the conditions under which different phylogenies yield different inferred ancestral states produce little or no ambiguity about the true phylogeny. Our results suggest that ML can produce accurate ASRs, even in the face of phylogenetic uncertainty. Using Bayesian integration to incorporate this uncertainty is neither necessary nor beneficial.

  2. Ancestral genome organization: an alignment approach.

    Science.gov (United States)

    Holloway, Patrick; Swenson, Krister; Ardell, David; El-Mabrouk, Nadia

    2013-04-01

    We present a comparative genomics approach for inferring ancestral genome organization and evolutionary scenarios, based on present-day genomes represented as ordered gene sequences with duplicates. We develop our methodology for a model of evolution restricted to duplication and loss, and then show how to extend it to other content-modifying operations, and to inversions. From a combinatorial point of view, the main consequence of ignoring rearrangements is the possibility of formulating the problem as an alignment problem. On the other hand, duplications and losses are asymmetric operations that are applicable to one of the two aligned sequences. Consequently, an ancestral genome can directly be inferred from a duplication-loss scenario attached to a given alignment. Although alignments are a priori simpler to handle than rearrangements, we show that a direct approach based on dynamic programming leads, at best, to an efficient heuristic. We present an exact pseudo-boolean linear programming algorithm to search for the optimal alignment along with an optimal scenario of duplications and losses. Although exponential in the worst case, we show low running times on real datasets as well as synthetic data. We apply our algorithm (*) in a phylogenetic context to the evolution of stable RNA (tRNA and rRNA) gene content and organization in Bacillus genomes. Our results lead to various biological insights, such as rates of ribosomal RNA proliferation among lineages, their role in altering tRNA gene content, and evidence of tRNA class conversion.

  3. The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid.

    Science.gov (United States)

    Smith, Andrew B; Zamora, Samuel; Álvaro, J Javier

    2013-01-01

    The earliest fossil echinoderms have, until now, come almost exclusively from North America and are represented by few taxa, all of which have a radiate body plan. Here we report the discovery of two new echinoderm faunas from the early part of the Cambrian of Morocco (West Gondwana). The former represents the oldest echinoderm fauna from Gondwana, approximately equivalent in age to those from North America, and the latter the oldest diversified fauna from Gondwana. In both cases, the appearance of well-preserved echinoderms coincides with a change in palaeogeographic regime. The presence of four markedly different echinoderm body plans in these earliest faunas indicates that considerable diversification had already taken place by 510 Ma. Yet all share the same distinctive biomineralized skeleton that, based on the fossil record and ocean geochemistry, probably evolved just 10-15 my earlier. This suggests that a rapid rate of morphological divergence took place during the initial stages of echinoderm evolution.

  4. Isotopic characterisation of the sub-continental lithospheric mantle beneath Zealandia, a rifted fragment of Gondwana

    Science.gov (United States)

    Waight, Tod E.; Scott, James M.; van der Meer, Quinten H. A.

    2013-04-01

    The greater New Zealand region, known as Zealandia, represents an amalgamation of crustal fragments accreted to the paleo-Pacific Gondwana margin and which underwent significant thinning during the subsequent split from Australia and Antarctica in the mid-Cretaceous following opening of the Tasman Sea and the Southern Ocean. We present Sr, Nd and Pb isotopes and laser ablation trace element data for a comprehensive suite of clinopyroxene separates from spinel peridotite xenoliths (lherzolite to harzburgite) from the sub-continental lithospheric mantle across southern New Zealand. These xenoliths were transported to the surface in intra-plate alkaline volcanics that erupted across the region in the Eocene and Miocene (33-10 m.y.a.). Most of the volcanic suites have similar geochemical and isotopic properties that indicate melting of an OIB-like mantle source in the garnet stability zone and that contained a HIMU component. The volcanics have tapped two adjacent but chemically contrasting upper mantle domains: a fertile eastern domain and an extremely depleted western domain. Both domains underlie Mesozoic metasedimentary crust. Radiogenic isotope compositions of the clinopyroxene have 87Sr/86Sr between 0.7023 to 0.7035, 143Nd/144Nd between 0.5128 and 0.5132 (corresponding to ?Nd between +3 and +13) with a few samples extending to even more depleted compositions, 206Pb/204 Pb between ca. 19.5 to 21.5 and 208Pb/204 Pb between ca. 38.5 to 40.5. No correlations are observed between isotopic composition, age or geographical separation. These isotopic compositions indicate that the sub-continental lithospheric mantle under southern New Zealand has a regionally distinct and pervasive FOZO to HIMU - like signature. The isotopic signatures are also similar to those of the alkaline magmas that transported the xenoliths and suggest that most of the HIMU signature observed in the volcanics could be derived from a major source component in the sub-continental lithospheric mantle

  5. Magma sources during Gondwana breakup: chemistry and chronology of Cretaceous magmatism in Westland, New Zealand

    DEFF Research Database (Denmark)

    van der Meer, Quinten Har Adriaan; Waight, Tod Earle; Scott, James M.

    2013-01-01

    Cretaceous-Paleogene rifting of the Eastern Gondwana margin thinned the continental crust of Zealandia and culminated in the opening of the Tasman Sea between Australia and New Zealand and the Southern Ocean, separating both from Antarctica. The Western Province of New Zealand consists of a succe......Cretaceous-Paleogene rifting of the Eastern Gondwana margin thinned the continental crust of Zealandia and culminated in the opening of the Tasman Sea between Australia and New Zealand and the Southern Ocean, separating both from Antarctica. The Western Province of New Zealand consists...

  6. Assessing the accuracy of ancestral protein reconstruction methods.

    Directory of Open Access Journals (Sweden)

    Paul D Williams

    2006-06-01

    Full Text Available The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.

  7. Assessing the accuracy of ancestral protein reconstruction methods.

    Science.gov (United States)

    Williams, Paul D; Pollock, David D; Blackburne, Benjamin P; Goldstein, Richard A

    2006-06-23

    The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of "ancestral sequences" inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a "best guess" amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.

  8. Heat flow in Indian Gondwana basins and heat production of their basement rocks

    Energy Technology Data Exchange (ETDEWEB)

    Rao, G.V.; Rao, R.U.M.

    1983-01-01

    Temperatures have been measured in eight boreholes (ranging from 260 to 800 m in depth) in five Gondwana basins of the Damodar and Son valleys. With the aid of about 250 thermal conductivity determinations on core samples from these holes, heat flow has been evaluated. Measurements of radioactive heat generation have been made on samples of Precambrian gneisses constituting the basement for the Sonhat (Son valley) and Chintalapudi (Godavari valley) basins. Heat-flow values from all of the Damodar valley basins are within the narrow range of 69-79 mW/m exp(2). The value from the Sonhat basin (107 mW/m exp(2)) is significantly higher. The generally high heat flows observed in Gondwana basins of India cannot be attributed to the known tectonism or igneous activity associated with these basins. The plots of heat flow vs. heat generation for three Gondwana basins (Jharia, Sonhat and Chintalapudi) are on the same line as those of three regions in the exposed Precambrian crystalline terrains in the northern part of the Indian shield. This indicates that the crust under exposed regions of the Precambrian crystalline rocks as well as the Gondwana basins, form an integral unit as far as the present-day geothermal character is concerned. (5 figs., 14 refs., 4 tables).

  9. Heat flow in Indian Gondwana basins and heat production of their basement rocks

    Science.gov (United States)

    Rao, G. V.; Rao, R. U. M.

    1983-01-01

    Temperatures have been measured in eight boreholes (ranging from 260 to 800 m in depth) in five Gondwana basins of the Damodar and Son valleys. With the aid of about 250 thermal conductivity determinations on core samples from these holes, heat flow has been evaluated. Measurements of radioactive heat generation have been made on samples of Precambrian gneisses constituting the basement for the Sonhat (Son valley) and Chintalapudi (Godavari valley) basins. Heat-flow values from all of the Damodar valley basins are within the narrow range of 69-79 mW/m 2. The value from the Sonhat basin (107 mW/m 2) is significantly higher. The generally high heat flows observed in Gondwana basins of India cannot be attributed to the known tectonism or igneous activity associated with these basins. The plots of heat flow vs. heat generation for three Gondwana basins (Jharia, Sonhat and Chintalapudi) are on the same line as those of three regions in the exposed Precambrian crystalline terrains in the northern part of the Indian shield. This indicates that the crust under exposed regions of the Precambrian crystalline rocks as well as the Gondwana basins, form an integral unit as far as the present-day geothermal character is concerned.

  10. Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases.

    Science.gov (United States)

    Devamani, Titu; Rauwerdink, Alissa M; Lunzer, Mark; Jones, Bryan J; Mooney, Joanna L; Tan, Maxilmilien Alaric O; Zhang, Zhi-Jun; Xu, Jian-He; Dean, Antony M; Kazlauskas, Romas J

    2016-01-27

    Catalytic promiscuity is a useful, but accidental, enzyme property, so finding catalytically promiscuous enzymes in nature is inefficient. Some ancestral enzymes were branch points in the evolution of new enzymes and are hypothesized to have been promiscuous. To test the hypothesis that ancestral enzymes were more promiscuous than their modern descendants, we reconstructed ancestral enzymes at four branch points in the divergence hydroxynitrile lyases (HNL's) from esterases ∼ 100 million years ago. Both enzyme types are α/β-hydrolase-fold enzymes and have the same catalytic triad, but differ in reaction type and mechanism. Esterases catalyze hydrolysis via an acyl enzyme intermediate, while lyases catalyze an elimination without an intermediate. Screening ancestral enzymes and their modern descendants with six esterase substrates and six lyase substrates found higher catalytic promiscuity among the ancestral enzymes (P promiscuous and catalyzed both hydrolysis and lyase reactions with many substrates. A broader screen tested mechanistically related reactions that were not selected for by evolution: decarboxylation, Michael addition, γ-lactam hydrolysis and 1,5-diketone hydrolysis. The ancestral enzymes were more promiscuous than their modern descendants (P = 0.04). Thus, these reconstructed ancestral enzymes are catalytically promiscuous, but HNL1 is especially so.

  11. Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

    Directory of Open Access Journals (Sweden)

    Ciprian Jeler

    2014-12-01

    Full Text Available This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the consequences are not very promising: very much like correlationism, speculative materialism explicitly denies what I call the “generalized version of the realistic assumption of science” and, in so doing, renders scientific ancestral statements de jure unverifiable. Therefore, if correlationism is rendered suspicious by the issue of ancestrality, the same can be said of speculative materialism.

  12. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States.

    Science.gov (United States)

    Gruenstaeudl, Michael

    2016-02-01

    Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. A set of command line-based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion.

  13. Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

    OpenAIRE

    Ciprian Jeler

    2014-01-01

    This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the...

  14. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana

    OpenAIRE

    Beaulieu, Jeremy M; Tank, David C; Donoghue, Michael J

    2013-01-01

    Background New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time informat...

  15. Paleomagnetism of Early Cambrian Itabaiana mafic dikes (NE Brazil) and the final assembly of Gondwana

    Science.gov (United States)

    Trindade, Ricardo I. F.; D'Agrella-Filho, Manoel S.; Epof, Igor; Brito Neves, Benjamim B.

    2006-04-01

    Paleomagnetic analysis on 15 early Cambrian mafic dikes from Itabaiana (Paraíba State) yielded a southern (northwestern) direction with steep upward (downward) inclination ( Dm = 167.5°, Im = - 63.7°, α95 = 7.3°). AF and Thermal demagnetization, thermomagnetic curves, and hysteresis results suggest that this component is dominantly carried by fine-grained SD magnetite. The high stability of this component and positive baked contact tests on three dikes indicate it represents a primary thermoremanent magnetization. Ar-Ar analysis on whole-rock samples from two sites provides a strong constraint on the age of the Itabaiana paleomagnetic pole (134.6° E, 34.9° S; A95 = 7.3, K = 28) defined by plateau ages of 525 ± 5 and 526 ± 4 Ma. This pole completely satisfies six out of the seven quality criteria proposed by Van der Voo [R. Van der Voo, The reliability of paleomagnetic data, Tectonophysics 184 (1990) 1-9.] and permits a tight constraint on the Early Cambrian sector of the Gondwana apparent polar wander path. Paleogeographic reconstructions consistent with the available paleomagnetic and geological record show that Gondwana was sutured along three major orogenies, the Mozambique (Brasilano/Pan-African) Orogeny (800-650 Ma), the Kuunga Orogeny (570-530 Ma) and the Pampean-Araguaia Orogeny (540-520 Ma). We suggest that after rifting away from Laurentia at the end of the Neoproterozoic, opening the Iapetus ocean, the Amazonian craton and minor adjoining blocks, such as Rio Apa and Pampia, collided with the proto-Gondwana by Cambrian times at ca. 530-520 Ma. Unless for small adjustments, Gondwana was completely formed by 525 Ma whose paleogeography is defined by the Itabaiana pole.

  16. Early Paleozoic paleogeography of the northern Gondwana margin: new evidence for Ordovician-Silurian glaciation

    Science.gov (United States)

    Semtner, A.-K.; Klitzsch, E.

    1994-12-01

    During the Early Paleozoic, transgressions and the distribution of sedimentary facies on the northern Gondwana margin were controlled by a regional NNW-SSE to almost north-south striking structural relief. In Early Silurian times, a eustatic highstand enabled the sea to reach its maximum southward extent. The counterclockwise rotation of Gondwana during the Cambrian and Early Ordovician caused the northern Gondwana margin to shift from intertropical to southern polar latitudes in Ordovician times. Glacial and periglacial deposits are reported from many localities in Morocco, Algeria, Niger, Libya, Chad, Sudan, Jordan and Saudi Arabia. The Late Ordovician glaciation phase was followed by a period of a major glacioeustatic sea-level rise in the Early Silurian due to the retreat of the ice-cap. As a consequence of the decreasing water circulation in the basin centers (Central Arabia, Murzuk- and Ghadames basins), highly bituminous euxinic shales were deposited. These shales are considered to be the main source rock of Paleozoic oil and gas deposits in parts of Saudi Arabia, Libya and Algeria. The following regression in the southern parts of the Early Silurian sea was probably caused by a second glacial advance, which was mainly restricted to areas in Chad, Sudan and Niger. Evidence for glacial activity and fluvioglacial sedimentation is available from rocks overlying the basal Silurian shale in north-east Chad and north-west Sudan. The Early Silurian ice advance is considered to be responsible for the termination of euxinic shale deposition in the basin centers.

  17. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana.

    Science.gov (United States)

    Beaulieu, Jeremy M; Tank, David C; Donoghue, Michael J

    2013-04-08

    New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time information with a likelihood-based biogeographic model focused on the Gondwanan landmasses. Our analyses imply that campanulids likely originated in the middle Albian (~105 Ma), and that a substantial portion of the early evolutionary history of campanulids took place in the Southern Hemisphere, despite their greater species richness in the Northern Hemisphere today. We also discovered several disjunctions that show biogeographic and temporal correspondence with the break-up of Gondwana. While it is possible to discern traces of the break-up of Gondwana in clades that are old enough, it will generally be difficult to be confident in continental movement as the prime cause of geographic disjunctions. This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.

  18. Reconstruction of the ancestral marsupial karyotype from comparative gene maps

    Science.gov (United States)

    2013-01-01

    Background The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome. PMID:24261750

  19. A Cenozoic diffuse alkaline magmatic province (DAMP) in the southwest Pacific without rift or plume origin

    Science.gov (United States)

    Finn, Carol A.; Müller, R. Dietmar; Panter, Kurt S.

    2005-02-01

    Common geological, geochemical, and geophysical characteristics of continental fragments of East Gondwana and adjacent oceanic lithosphere define a long-lived, low-volume, diffuse alkaline magmatic province (DAMP) encompassing the easternmost part of the Indo-Australian Plate, West Antarctica, and the southwest portion of the Pacific Plate. A key to generating the Cenozoic magmatism is the combination of metasomatized lithosphere underlain by mantle at only slightly elevated temperatures, in contrast to large igneous provinces where mantle temperatures are presumed to be high. The SW Pacific DAMP magmatism has been conjecturally linked to rifting, strike-slip faulting, mantle plumes, or hundreds of hot spots, but all of these associations have flaws. We suggest instead that sudden detachment and sinking of subducted slabs in the late Cretaceous induced Rayleigh-Taylor instabilities along the former Gondwana margin that in turn triggered lateral and vertical flow of warm Pacific mantle. The interaction of the warm mantle with metasomatized subcontinental lithosphere that characterizes much of the SW Pacific DAMP concentrates magmatism along zones of weakness. The model may also provide a mechanism for warming south Pacific mantle and resulting Cenozoic alkaline magmatism, where the oceanic areas are characterized primarily, but not exclusively, by short-lived hot spot tracks not readily explained by conventional mantle plume theory. This proposed south Pacific DAMP is much larger and longer-lived than previously considered.

  20. Reproductive function in mice exposed to ancestral and direct irradiation

    International Nuclear Information System (INIS)

    Nash, D.J.; Sprackling, L.S.

    1978-01-01

    Reproduction was studied in 13 inbred strains of mice that had been exposed continuously to 60 Co gamma radiation for varying numbers of generations. At weaning the mice were removed from the irradiation chamber and were tested for reproductive performance. Ancestral and direct levels of irradiation were determined for each animal. Each irradiated or control female was scored as fertile or sterile, and in utero litter counts were made in pregnant females that were dissected past the 10th day of pregnancy. The number of resorptions, dead embryos, and live embryos were counted, and the ratio of living embryos to the total number of embryos was determined for each litter. The overall fertility curves were sigmoid in the range of doses below those which caused complete sterility, which indicated some sort of cumulative damage. In 11 of the 13 strains studied, an increase in ancestral and/or direct irradiation led to significant decreases in fertility. The means of the number alive in the litters for the control and irradiated mice in each strain showed a definite trend toward fewer live mice in utero after irradiation. Least-squares analyses of variance were made to detect possible effects of any of six irradiation variables (ancestral linear, ancestral quadratic, ancestral cubic, direct linear, direct quadratic, or direct cubic) or of strain differences on total litter size and on ratio. Strain effects were significant in each instance. Litter size was more likely to be affected by radiation variables than ratios were

  1. Ancestrality and evolution of trait syndromes in finches (Fringillidae).

    Science.gov (United States)

    Ponge, Jean-François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre-Yves; Théry, Marc; Guilbert, Éric

    2017-12-01

    Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from "ancestral" to "derived" strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabilized (collectively called B strategy). We analyzed the correlated evolution of four syndromes, summarizing the covariation between 53 traits, respectively, involved in ecological specialization, r-K gradient, sexual selection, and dispersal/social behaviors in 81 species representative of Fringillidae, a bird family with available natural history information and that shows variability for all these traits. The ancestrality of strategy A was supported for three of the four syndromes, the ancestrality of generalism having a weaker support, except for the core group Carduelinae (69 species). It appeared that two different B-strategies evolved from the ancestral state A, both associated with highly predictable environments: one in poorly seasonal environments, called B1, with species living permanently in lowland tropics, with "slow pace of life" and weak sexual dimorphism, and one in highly seasonal environments, called B2, with species breeding out-of-the-tropics, migratory, with a "fast pace of life" and high sexual dimorphism.

  2. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

    Science.gov (United States)

    Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J.

    2012-01-01

    In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (kcat/KM) for competing substrates, even though adaptive substitutions may affect KM and kcat separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities. PMID:22315396

  3. Intraplate mountain building in response to continent continent collision—the Ancestral Rocky Mountains (North America) and inferences drawn from the Tien Shan (Central Asia)

    Science.gov (United States)

    Dickerson, Patricia Wood

    2003-04-01

    Miocene time when full coupling of the colliding plates had occurred. As in the Laurentia-Gondwana case, structures of similar magnitude and spacing to those in Eurasia have developed in the Indian plate. Within the present orogen two ancient suture zones have been reactivated—the early Paleozoic Terskey zone and the late Paleozoic Turkestan suture between the Siberian and East Gondwanan cratons. Inverted Proterozoic to early Paleozoic rift structures and passive-margin deposits are exposed north of the Terskey zone. In the Alay and Tarim complexes, Vendian to mid-Carboniferous passive-margin strata and the subjacent Proterozoic crystalline basement have been uplifted. Data on Tien Shan uplifts, basins, structural arrays, and deformation rates guide paleotectonic interpretations of ancient intraplate mountain belts. Similarly, exhumed deep crustal shear zones in the Ancestral Rockies offer insight into partitioning and reorientation of strain during contemporary intraplate deformation.

  4. Lost Terranes of Zealandia: possible development of late Paleozoic and early Mesozoic sedimentary basins at the southwest Pacific margin of Gondwanaland, and their destination as terranes in southern South America Terrenos perdidos de Zealandia: posible desarrollo de cuencas sedimentarias del Paleozoico tardío y Mesozoico temprano en el margen suroccidental del Pacífico de Gondwana y su destino como terrenos en el sur de América del Sur

    Directory of Open Access Journals (Sweden)

    Christopher J Adams

    2010-07-01

    Full Text Available Latest Precambrian to Ordovician metasedimentary successions and Cambrian-Ordovician and Devonian-Carboniferous granitoids form the major part of the basement of southern Zealandia and adjacent sectors of Antarctica and southeast Australia. Uplift/cooling ages of these rocks, and local Devonian shallow-water cover sequences suggest that final consolidation of the basement occurred through Late Paleozoic time. A necessary consequence of this process would have been contemporaneous erosion and the substantial development of marine sedimentary basins at the Pacific margin of Zealandia. These are found nowhere at the present day, suggesting that the basins have been lost by tectonic erosion, perhaps in a margin-parallel dextral translation similar to late Paleozoic-Mesozoic suspect terranes of New Zealand. Aprobable detrital zircon age pattern is assembled for these lost Zealandia sediments, and then compared with those of pre-Jurassic (probable Triassic to Devonian metasedimentary rocks in the Chilean archipelago. Significant Mesoproterozoic, latest Neoproterozoic-Cambrian and Devonian-Carboniferous detrital zircon age components are common to both, thus supporting a possible Chilean terrane destination for these 'lost terranes of Zealandia'.Las sucesiones metasedimentarias del Precámbrico tardío al Ordovícico y granitoides del Cámbrico-Ordovícico y Devónico-Carbonífero constituyen la mayor parte del basamento del sur de Zealandia y sectores adyacentes de la Antartica y el sudeste de Australia. Las edades de enfriamiento/alzamiento de estas rocas y la cobertura local de secuencias de aguas someras del Devónico, sugieren que la consolidación definitiva del basamento se produjo durante el Paleozoico tardío. Una consecuencia necesaria de este proceso habría sido la erosion contemporánea y el desarrollo sustancial de cuencas sedimentarias marinas en el margen del Pacífico de Zealandia. Estas no se encuentran en ninguna parte en la

  5. Ancestral gene synteny reconstruction improves extant species scaffolding.

    Science.gov (United States)

    Anselmetti, Yoann; Berry, Vincent; Chauve, Cedric; Chateau, Annie; Tannier, Eric; Bérard, Sèverine

    2015-01-01

    We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.

  6. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.

    Science.gov (United States)

    Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A; Wang, Xiaowu

    2013-05-01

    The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.

  7. Musculature in sipunculan worms: ontogeny and ancestral states.

    Science.gov (United States)

    Schulze, Anja; Rice, Mary E

    2009-01-01

    Molecular phylogenetics suggests that the Sipuncula fall into the Annelida, although they are morphologically very distinct and lack segmentation. To understand the evolutionary transformations from the annelid to the sipunculan body plan, it is important to reconstruct the ancestral states within the respective clades at all life history stages. Here we reconstruct the ancestral states for the head/introvert retractor muscles and the body wall musculature in the Sipuncula using Bayesian statistics. In addition, we describe the ontogenetic transformations of the two muscle systems in four sipunculan species with different developmental modes, using F-actin staining with fluorescent-labeled phalloidin in conjunction with confocal laser scanning microscopy. All four species, which have smooth body wall musculature and less than the full set of four introvert retractor muscles as adults, go through developmental stages with four retractor muscles that are eventually reduced to a lower number in the adult. The circular and sometimes the longitudinal body wall musculature are split into bands that later transform into a smooth sheath. Our ancestral state reconstructions suggest with nearly 100% probability that the ancestral sipunculan had four introvert retractor muscles, longitudinal body wall musculature in bands and circular body wall musculature arranged as a smooth sheath. Species with crawling larvae have more strongly developed body wall musculature than those with swimming larvae. To interpret our findings in the context of annelid evolution, a more solid phylogenetic framework is needed for the entire group and more data on ontogenetic transformations of annelid musculature are desirable.

  8. A comparison of ancestral state reconstruction methods for quantitative characters.

    Science.gov (United States)

    Royer-Carenzi, Manuela; Didier, Gilles

    2016-09-07

    Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Modeling X-linked ancestral origins in multiparental populations

    NARCIS (Netherlands)

    Zheng, Chaozhi

    2015-01-01

    The models for the mosaic structure of an individual's genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes

  10. An Epistemological Analysis of the African Ontology of `Ancestral ...

    African Journals Online (AJOL)

    The paper explores the contemporary debate surrounding the idea of ancestral reincarnation in African society and philosophy. It analyzes various problem areas having to do with the physical and spiritual status of ancestors, their relationship with their societies of orientation, the philosophical contexts of their existence, ...

  11. Are survival processing memory advantages based on ancestral priorities?

    Science.gov (United States)

    Soderstrom, Nicholas C; McCabe, David P

    2011-06-01

    Recent research has suggested that our memory systems are especially tuned to process information according to its survival relevance, and that inducing problems of "ancestral priorities" faced by our ancestors should lead to optimal recall performance (Nairne & Pandeirada, Cognitive Psychology, 2010). The present study investigated the specificity of this idea by comparing an ancestor-consistent scenario and a modern survival scenario that involved threats that were encountered by human ancestors (e.g., predators) or threats from fictitious creatures (i.e., zombies). Participants read one of four survival scenarios in which the environment and the explicit threat were either consistent or inconsistent with ancestrally based problems (i.e., grasslands-predators, grasslands-zombies, city-attackers, city-zombies), or they rated words for pleasantness. After rating words based on their survival relevance (or pleasantness), the participants performed a free recall task. All survival scenarios led to better recall than did pleasantness ratings, but recall was greater when zombies were the threat, as compared to predators or attackers. Recall did not differ for the modern (i.e., city) and ancestral (i.e., grasslands) scenarios. These recall differences persisted when valence and arousal ratings for the scenarios were statistically controlled as well. These data challenge the specificity of ancestral priorities in survival-processing advantages in memory.

  12. A review of the Late Cambrian (Furongian) palaeogeography in the western Mediterranean region, NW Gondwana

    Science.gov (United States)

    Álvaro, J. Javier; Ferretti, Annalisa; González-Gómez, Cristina; Serpagli, Enrico; Tortello, M. Franco; Vecoli, Marco; Vizcaïno, Daniel

    2007-11-01

    The Cambrian-Ordovician transition of the western Mediterranean region (NW Gondwana) is characterized by the record of major erosive unconformities with gaps that range from a chronostratigraphic stage to a series. The hiatii are diachronous and involved progressively younger strata along the Gondwanan margin, from SW (Morocco) to NE (Montagne Noire). They can be related to development of a multi-stage rifting (further North), currently connected to the opening of the Rheic Ocean, and concomitant erosion on southern rift shoulders. The platforms of this margin of Gondwana occupied temperate-water, mid latitudes and were dominated by siliciclastic sedimentation, while carbonate factories were only episodically active in the Montagne-Noire platform. The Upper Cambrian is devoid of significant gaps in the southern Montagne Noire and the Iberian Chains. There, the sedimentation took place in a transgressive-dominated depositional system, with common offshore deposits and clayey substrates, and was bracketed by two major regressive trends. The Late Cambrian is also associated with the record of volcanic activity ( e.g., in the Cantabrian and Ossa-Morena zones, and the northern Montagne Noire), and widespread development of a tectonic instability that led to the episodic establishment of palaeotopographies and record of slope-related facies associations. Several immigration events are recognized throughout the latest Middle Cambrian, Late Cambrian and Tremadocian. The trilobites show a stepwise replacement of Acado-Baltic-type families ( e.g., the conocoryphid-paradoxidid-solenopleurid assemblage) characterized by: (i) a late Languedocian (latest Middle Cambrian) co-occurrence of Middle Cambrian trilobite families with the first anomocarid, dorypygid and proasaphiscid invaders; (ii) a Late Cambrian immigration replacing previous faunas, composed of trilobites (aphelaspidids, catillicephalids, ceratopygids, damesellids, eulomids, idahoiids, linchakephalids, lisariids

  13. Radiizonates arcuatus, a distinctive new miospore species from the Lower Carboniferous of Western Gondwana.

    Science.gov (United States)

    Loboziak; Playford; Melo

    2000-05-01

    A new species of trilete zonate miospores, Radiizonates arcuatus, is established for Lower Carboniferous Western Gondwanan forms hitherto ascribed misguidedly to Radiizonates genuinus (Jushko) Loboziak and Alpern (1978), a Russian Lower Carboniferous species. The latter binomen is, moreover, not a valid combination and is more correctly designated as Vallatisporites genuinus (Jushko) Byvsheva, 1980. R. arcuatus is, from records to date, confined to westerly parts of Gondwana (Brazil, North Africa and Middle East), in which it is characteristic of Early Carboniferous strata, albeit with some slightly older and slightly younger occurrences.

  14. A palynostratigraphic study of Lower Gondwana sediments from Bandar coalfield, Nagpur district, Maharashtra

    Energy Technology Data Exchange (ETDEWEB)

    Sabina, K.P.; Mahesh, S.; Bilwa, L.M. [University of Mysore, Mysore (India)

    2007-04-15

    Core samples of Borehole MBG-23 of Gokul Block, Bandar Coalfield have been analyzed palynologically. Shaly coal and shale occurring between the depth 52.3 43 m have been found to be rich in miospores and a statistical analysis of these samples have revealed the abundance of non-striate disaccate genera based on which Scheuringipollenites assemblage zone has been recognised which suggests Lower Barakar affinity (Early Permian). This assemblage zone shows broad similarities with the Lower Barakar mioflora of other Lower Gondwana basins of India.

  15. Gondwana sedimentation in the Chintalapudi sub-basin, Godavari Valley, Andhra Pradesh

    Energy Technology Data Exchange (ETDEWEB)

    Lakshminarayana, G. [Geological Survey of India, Calcutta (India). Division of Monitoring

    1995-10-01

    A 3000 m thick Gondwana lithic fill consisting of multifacies associations were preserved in a NW-SE oriented intracratonic Chintalapudi sub-basin set across the Eastern Chat Complex (EGC). Sedimentation commenced with the deposition of diamictite-rhythmite sequence of the Talchir Formation in glacio-lacustrine environment. The succeeding sandstone-coal cyclothems of the Barakar Formation were formed in fluvial-coal swamps complex. The fluvial streams flowed across the EGC, originating somewhere in the southeast beyond the East Coast of India. Phase wise upliftment of the EGC during Mesozoic imparted changes to the Permian intercontinental drainage system which started supplying increased amount of detritus to the basin. Basin marginal faults were first formed at the beginning of Triassic. Alluvial fans originated in the east and southeast and northwesterly flowing braided streams deposited the conglomerate sandstone sequence of the Kamthi Formation. The Early Jurassic uplift of the Mailaram high in the north imparted westerly shift to the braided rivers during the Kota sedimentation. Due to prominence of Kamavarapukota ridge in the south by Early Cretaceous, the drainage pattern became centripetal and short-lived high sinuous rivers debouched into the basin. The silting up of the Chintalapudi sub-basin with the sandstone-claystone sequence of the Gangapur Formation marks the culmination of the Gondwana sedimentation, perhaps, coinciding with the breakup of India from the Gondwanaland.

  16. Geochemical characteristics of Proterozoic granite magmatism from Southern Granulite Terrain, India: Implications for Gondwana

    Science.gov (United States)

    Yellappa, T.; Rao, J. Mallikharjuna

    2018-03-01

    Granitoid intrusions occur widely in the Southern Granulite Terrain (SGT) of India, particularly within the Cauvery Suture Zone (CSZ), which is considered as the trace of the Neoproterozoic Mozambique ocean closure. Here we present the petrological and geochemical features of 19 granite plutons across the three major tectonic blocks of the terrain. Our data show a wide variation in the compositions of these intrusions from alkali feldspathic syenite to granite. The whole rock geochemistry of these intrusions displays higher concentrations of SiO2, FeO*, K2O, Ba, Zr, Th, LREE and low MgO, Na2O, Ti, P, Nb, Y and HREE's. The granitoids are metaluminous to slightly peraluminous in nature revealing both I-type and A-type origin. In tectonic discrimination plots, the plutons dominantly show volcanic arc and syn-collisional as well as post-collisional affinity. Based on the available age data together with geochemical constrains, we demonstrate that the granitic magmatism in the centre and south of the terrain is mostly associated with the Neoproterozoic subduction-collision-accretion-orogeny, followed by extensional mechanism of Gondwana tectonics events. Similar widespread granitic activity has also been documented in the Arabian Nubian shield, Madagascar, Sri Lanka and Antarctica, providing similarities for the reconstruction of the crustal fragments of Gondwana supercontinent followed by Pan-African orogeny.

  17. Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

    Directory of Open Access Journals (Sweden)

    Asunción Delgado

    2017-05-01

    Full Text Available Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance.

  18. Perianth evolution in Ranunculaceae: are petals ancestral in the family?

    Directory of Open Access Journals (Sweden)

    Sophie Nadot

    2016-04-01

    Full Text Available Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales as a whole. Here, we present ancestral state reconstructions for several perianth characters, such as differentiation into sepals and petals, shape of petals, presence/absence of nectaries, and petaloid or sepaloid aspect of sepals. Characters were scored using the PROTEUS database and optimized on the most recent phylogeny of Ranunculaceae using parsimony and maximum likelihood methods. The results are discussed with regard to recent evo-devo studies focused on identifying genes involved in floral organs identity (the so-called ABC model in Ranunculales.

  19. Prenatal effects of ancestral irradiation in inbred mice

    International Nuclear Information System (INIS)

    Sprackling, L.E.S.

    1975-01-01

    Mice from 13 inbred strains (S, Z, E, Bab, BaB, BrR, C, K, N, Q, G, CFW, CF1) received continuous cobalt 60 irradiation at low dose rates for varying numbers of consecutive generations. Some Bab and BaB mice had received continuous irradiation for from 24 to 31 generations and the other mice had up to six generations of continuous irradiation in their ancestry. At weaning, the mice were removed from the irradiation room and were mated within strains either to sibs or nonsibs. Ancestral and direct irradiation doses were calculated. The ancestral dose was the effective accumulated dose to the progeny of the mated mice. The direct dose was the amount of irradiation received by any mated female from her conception to her weaning. Each irradiated or control female was scored as fertile or sterile and in utero litter counts were made in pregnant females that were dissected past the tenth day of pregnancy; the sum of moles, dead embryos, and live embryos was the total in utero litter size. A ratio of the living embryos to the total number of embryos in utero was determined for each litter. An increase in ancestral or direct irradiation dose significantly decreased fertility in 11 of the 13 strains. The fertility curves for the pooled data were sigmoid in the area of the doses below those that caused complete sterility. Among the controls, there were significant strain differences in total litter size and in the ratio. Strain X--Y plots, with ancestral or direct doses plotted against total litter size or ratio, revealed the tendency for litter size to decrease as dose increased. The only trend shown for ratio was for the litters with ratios of 0.50 or less to appear more frequently among the irradiated mice. The few corpora lutea counts revealed nothing of significance. Generally, there was a definite trend toward fewer mice alive in utero among the irradiated mice

  20. Ancestrality and evolution of trait syndromes in finches (Fringillidae)

    OpenAIRE

    Ponge, Jean‐François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre‐Yves; Théry, Marc; Guilbert, Éric

    2017-01-01

    International audience; Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from “ancestral” to “derived” strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabil...

  1. Reconstruction of ancestral RNA sequences under multiple structural constraints

    OpenAIRE

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

    2016-01-01

    Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

  2. Molecular paleontology: a biochemical model of the ancestral ribosome.

    Science.gov (United States)

    Hsiao, Chiaolong; Lenz, Timothy K; Peters, Jessica K; Fang, Po-Yu; Schneider, Dana M; Anderson, Eric J; Preeprem, Thanawadee; Bowman, Jessica C; O'Neill, Eric B; Lie, Lively; Athavale, Shreyas S; Gossett, J Jared; Trippe, Catherine; Murray, Jason; Petrov, Anton S; Wartell, Roger M; Harvey, Stephen C; Hud, Nicholas V; Williams, Loren Dean

    2013-03-01

    Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting experiments support formation of predicted secondary and tertiary structure. Gel shift, spectroscopic and yeast three-hybrid assays show specific interactions between ancestral rRNA and ribosomal protein fragments, independent of other, more recent, components of the ribosome. This robustness suggests that the catalytic core of the ribosome is an ancient construct that has survived billions of years of evolution without major changes in structure. Collectively, the data here support a model in which ancestors of the large and small subunits originated and evolved independently of each other, with autonomous functionalities.

  3. Cases in which ancestral maximum likelihood will be confusingly misleading.

    Science.gov (United States)

    Handelman, Tomer; Chor, Benny

    2017-05-07

    Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.

  4. Choosing the best ancestral character state reconstruction method.

    Science.gov (United States)

    Royer-Carenzi, Manuela; Pontarotti, Pierre; Didier, Gilles

    2013-03-01

    Despite its intrinsic difficulty, ancestral character state reconstruction is an essential tool for testing evolutionary hypothesis. Two major classes of approaches to this question can be distinguished: parsimony- or likelihood-based approaches. We focus here on the second class of methods, more specifically on approaches based on continuous-time Markov modeling of character evolution. Among them, we consider the most-likely-ancestor reconstruction, the posterior-probability reconstruction, the likelihood-ratio method, and the Bayesian approach. We discuss and compare the above-mentioned methods over several phylogenetic trees, adding the maximum-parsimony method performance in the comparison. Under the assumption that the character evolves according a continuous-time Markov process, we compute and compare the expectations of success of each method for a broad range of model parameter values. Moreover, we show how the knowledge of the evolution model parameters allows to compute upper bounds of reconstruction performances, which are provided as references. The results of all these reconstruction methods are quite close one to another, and the expectations of success are not so far from their theoretical upper bounds. But the performance ranking heavily depends on the topology of the studied tree, on the ancestral node that is to be inferred and on the parameter values. Consequently, we propose a protocol providing for each parameter value the best method in terms of expectation of success, with regard to the phylogenetic tree and the ancestral node to infer. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Detrital zircon geochronology of quartzites from the southern Madurai Block, India: Implications for Gondwana reconstruction

    Directory of Open Access Journals (Sweden)

    Shan-Shan Li

    2017-07-01

    Full Text Available Detrital zircons are important proxies for crustal provenance and have been widely used in tracing source characteristics and continental reconstructions. Southern Peninsular India constituted the central segment of the late Neoproterozoic supercontinent Gondwana and is composed of crustal blocks ranging in age from Mesoarchean to late Neoproterozoic–Cambrian. Here we investigate detrital zircon grains from a suite of quartzites accreted along the southern part of the Madurai Block. Our LA-ICPMS U-Pb dating reveals multiple populations of magmatic zircons, among which the oldest group ranges in age from Mesoarchean to Paleoproterozoic (ca. 2980–1670 Ma, with peaks at 2900–2800 Ma, 2700–2600 Ma, 2500–2300 Ma, 2100–2000 Ma. Zircons in two samples show magmatic zircons with dominantly Neoproterozoic (950–550 Ma ages. The metamorphic zircons from the quartzites define ages in the range of 580–500 Ma, correlating with the timing of metamorphism reported from the adjacent Trivandrum Block as well as from other adjacent crustal fragments within the Gondwana assembly. The zircon trace element data are mostly characterized by LREE depletion and HREE enrichment, positive Ce, Sm anomalies and negative Eu, Pr, Nd anomalies. The Mesoarchean to Neoproterozoic age range and the contrasting petrogenetic features as indicated from zircon chemistry suggest that the detritus were sourced from multiple provenances involving a range of lithologies of varying ages. Since the exposed basement of the southern Madurai Block is largely composed of Neoproterozoic orthogneisses, the data presented in our study indicate derivation of the detritus from distal source regions implying an open ocean environment. Samples carrying exclusive Neoproterozoic detrital zircon population in the absence of older zircons suggest proximal sources in the southern Madurai Block. Our results suggest that a branch of the Mozambique ocean might have separated the

  6. South China connected to north India in Gondwana: sedimentary basin and detrital provenance analyses

    Science.gov (United States)

    Yao, W.; Li, Z. X.; Li, W. X.; Li, X. H.; Yang, J. H.

    2015-12-01

    The paleoposition of South China during the Ediacaran-Silurian is important for understanding the assembly of Gondwana. We report here the tectonostratigraphic evolution of the Ediacaran-Silurian Nanhua foreland basin in South China, and discuss South China's connection with Gondwana and potential tectonic triggers for both the Wuyi-Yunkai orogeny in South China and the Bhimphedian orogeny in north India. The Nanhua basin was involved in a three-stage evolution, which are: Stage 1 (the Ediacaran-Cambrian) recording the start of tectonic subsidence with turbiditic marine clastic deposition, fed by exotic orogens outboard South China; Stage 2 (the Ordovician to earliest-Silurian) featured by migrating depocentres with dominant shallow marine to deltaic clastic deposition, fed by the local Wuyi-Yunkai orogen; and Stage 3 (the Silurian) showing the arrival of depocentre in the Yangtze Block during the waning stage of the Wuyi-Yunkai orogeny with deltaic deposition in the remanent foreland basin. Detrital zircon analyses of the Ediacaran-Silurian sandstones across the Nanhua basin reveal a prominent age population of 1100-900 Ma (with a peak age at ~980 Ma) and moderate populations of Archean-Paleozoic ages, grossly matching that of crystalline and sedimentary rocks in northern India. Zircon isotopes of the Stage 1 samples suggest three Precambrian episodes of juvenile crustal growth at 3.0 Ga, 2.5 Ga and 1.0 Ga, and a major crustal reworking at 580-500 Ma for the source areas, which are constraint to be northwestern India and its surrounding orogens. Together with other evidence, we propose that South China likely collided with northwestern India during the Gondwana assembly, generated the Bhimphedian orogeny in north India and formed two foreland basins on both the north India and South China sides. Far-field stress of the collision triggered the Ordovician-Silurian Wuyi-Yunkai orogeny in South China. The Stage 2-3 samples in the Nanhua basin of South China were shed

  7. Amálgamas do W-Gondwana na província Tocantins

    OpenAIRE

    Frasca, Antonio Augusto Soares

    2016-01-01

    Os orógenos Brasília e Araguaia são cinturões Neoproterozoicos da Província Tocantins. Desenvolveram-se durante a amálgama do W-Gondwana, como consequência da colisão e colagem de blocos alóctones, arcos acrescionários e sequências metavulcanossedimentares correlatas entre os crátons Amazônico e São Francisco-Congo. Na porção setentrional do Orógeno Brasília rochas plutônicas calci-alcalinas de arco magmático se estendem por mais de 250 km e constituem a extensão do Arco Magmático de Goiás (A...

  8. Preliminary environmental analysis of Gondwana in Candiota Region, Rio Grande do Sul

    International Nuclear Information System (INIS)

    Silveira Fontes, L.C. da; Cava, L.T.

    1980-10-01

    The geological results obtained in the Candiota Region by NUCLEBRAS, during the evaluation of the uranium economic potential from basal Gondwana Sequence - Itarare Group and Rio Bonito Formation - at South-East of the Parana Sedimentary Basin, are studied. The analysis of 18 geologic sections (scales 1:5.000 x 1:500), 21 drill holes and fotogeologic interpretation in the scale 1:50.000, are included. The Itarare Group sedimentation was conditioned by paleo - relief with valleys formed from differential erosion on 'horst - graben' structures. The deposition of its rhythmites, diamictites and siltstones was made in periglacial and marine environments. The sedimentation of the Rio Bonito Formation is related to the main Itarare Group depositional axes. The typical lithologies are: sandstones, siltstones, mudstones and coals, representing progradational fluvial sediments over coastal - plain areas. (Author) [pt

  9. Evolução paleozóica da Gondwana

    OpenAIRE

    Dias, Rui; Schmitt, Renata

    2012-01-01

    Durante o Paleozóico a actuação de diversos ciclos de Wilson levaram, não só à unificação da Gondwana mas também da própria Pangeia. Se alguns destes ciclos são exclusivamente paleozóicos (é o caso do orógeno Varisco nos sectores setentrionais), outros resultam de processos extensivos iniciados no final do Neoproterozóico e cujas fases colisionais só ocorreram no Paleozóico inferior (e.g. orogenia Búzios - SE do Brasil). Neste simpósio serão abordados os processos e mecanismos associados à ev...

  10. Gondwana and Cathaysian blocks, palaeotethys sutures and cenozoic tectonics in South-east Asia

    Science.gov (United States)

    Hutchison, Charles S.

    1994-07-01

    The Triassic Indosinian Orogeny followed extinction of the Palaeotethys Ocean resulting in suturing of Gondwana affinity and Cathaysian blocks. The Gondwana affinity Sinoburmalaya block of Peninsular Malaysia, characterized by Carboniferous—Permian mudstones containing glacial dropstones and sparse fauna and flora, is traced extensively into Sumatra. This mudstone facies is flanked on the east by a sandstone-dominated facies and by carbonate localized in the Kinta Valley. The muddy and sandy facies both begin with a basal Carboniferous condensed red bed sequence, which unconformably overlies the older formations of Sinoburmalaya. Both facies also demonstrate a Late Permian conformable transition into overlying limestone. The Cathaysian block of East Malaya is characterized by Late Permian Gigantopteris flora and fusulinid limestones associated with andesitic volcanism. It is similar but not identical to the West Sumatra Carboniferous—Permian block, characterized by Early Permian volcanism, fusulinid limestones and early Cathaysian Jambi flora. The South to SSE trending central Peninsular Malaysian Triassic orogenic belt swings south-east from Singapore to Bangka, then east to Billiton. The Palaeotethys suture (Bentong—Raub Line) forms the western margin of this belt and is therefore unlikely to continue south along the Palaeogene Bengkalis Graben, which transects the north-west—south-east orogenic fabric of Sumatra. The oroclinal bending of the Indosinian Orogen, from a north-west—south-east grain in Sumatra to a northerly grain through Peninsular Malaysia, is attributed to the Palaeocene collision of India and its subsequent indentation into Eurasia. The bending was accomplished by clockwise rotation and right-lateral shear parallel to the orogenic grain. The Mesozoic Palaeotethyan sutures were transformed into Palaeocene and younger shear zones. The outer zones of the orocline experienced pull apart tectonics (Andaman Sea and Sumatra basins) while the

  11. Uranium exploration by geophysical techniques in Upper Gondwanas of Satpura Gondwana Basin - a case study from Jhirpa area, Chhindwara district, Madhya Pradesh, India

    International Nuclear Information System (INIS)

    Markandeyulu, A.; Kumar, B.V.L.; Jain, S.K.; Israeli, I.H.; Yadav, O.P.; Roy, M.K.

    2009-01-01

    Reconnaissance geological, radiometric, regional hydro-geochemical and radon surveys conducted during the last decade by AMD, brought out several promising areas in Upper Gondwana formations. Further, detailed geological, structural mapping and geochemical surveys are conducted in the Jhipra-Kharatoria tract of Chhindwara district, MP. In this tract uranium mineralisation occurs along a major linement within the Middle Denwa formations. Detailed geophysical surveys comprising magnetic and resistivity/IP surveys are conducted over an area of about 12 sq. km for a strike length of 8.4 line km. Six vertical electrical resistivity soundings are also conducted. High amplitude and short wave length nature of magnetic anomalies indicate their strong magnetic character and shallow depth of occurrence. Magnetic image map clearly reflects the continuity of intrusive dykes in strike direction. Magnetic anomalous zones are marked at the intersection of magnetic anomaly trends and inferred structural features. Resistivity and IP surveys conducted employing Wenner-Schlumberger array with an effective current electrode separation of 500m indicated the highly conductive nature of Denwa sediments and reflected the trend and disposition of basic dykes. High resistivity (up to 30 ohm-m) and high chargeability (upto 8 mV/V) anomalies are recorded over the basic dykes. Vertical electrical sounding data helped in deciphering the vertical variations in resistivity of different beds of Denwa formations in the area. The maximum depth to sandstone, a high resistivity unit of Denwa formations as interpreted from VES and TEM soundings, is in the range of 215 to 275 m. (author)

  12. Visual system evolution and the nature of the ancestral snake.

    Science.gov (United States)

    Simões, B F; Sampaio, F L; Jared, C; Antoniazzi, M M; Loew, E R; Bowmaker, J K; Rodriguez, A; Hart, N S; Hunt, D M; Partridge, J C; Gower, D J

    2015-07-01

    The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  13. How Do Ancestral Traits Shape Family Trees Over Generations?

    Science.gov (United States)

    Fu, Siwei; Dong, Hao; Cui, Weiwei; Zhao, Jian; Qu, Huamin

    2018-01-01

    Whether and how does the structure of family trees differ by ancestral traits over generations? This is a fundamental question regarding the structural heterogeneity of family trees for the multi-generational transmission research. However, previous work mostly focuses on parent-child scenarios due to the lack of proper tools to handle the complexity of extending the research to multi-generational processes. Through an iterative design study with social scientists and historians, we develop TreeEvo that assists users to generate and test empirical hypotheses for multi-generational research. TreeEvo summarizes and organizes family trees by structural features in a dynamic manner based on a traditional Sankey diagram. A pixel-based technique is further proposed to compactly encode trees with complex structures in each Sankey Node. Detailed information of trees is accessible through a space-efficient visualization with semantic zooming. Moreover, TreeEvo embeds Multinomial Logit Model (MLM) to examine statistical associations between tree structure and ancestral traits. We demonstrate the effectiveness and usefulness of TreeEvo through an in-depth case-study with domain experts using a real-world dataset (containing 54,128 family trees of 126,196 individuals).

  14. Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance.

    Science.gov (United States)

    Delgado, Asunción; Arco, Rocio; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2017-05-09

    Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  15. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  16. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  17. Taphonomic analysis in lacustrine environments: Two different contexts for Triassic lake paleofloras from Western Gondwana (Argentina)

    Science.gov (United States)

    Mancuso, Adriana Cecilia

    2009-12-01

    During the earliest Triassic several rift basins developed along the western margin of Gondwana associated with the pre-breakup of Pangea. They were filled by exclusively non-marine sediments including alluvial, fluvial, and lacustrine deposits. In the Ischigualasto-Villa Unión Basin, the lacustrine-deltaic succession is placed in the Los Rastros Formation and consists of several coarsening-upward cycles of black shale, siltstone, and sandstone. The paleontologic content of the succession includes abundant floral remains (related to the Dicroidium-type flora), invertebrates (conchostracans, insects), and vertebrates (fishes, a temnospondyl amphibian, ichnites). At the Cerro Puntudo area in the Cuyana Basin, the lacustrine succession forms the upper part of the Cerro Puntudo Formation and consists of limestone, stromatolitic limestone, mudstone, sandstone, and tuff. The paleontologic content includes scarce floral remains and rhizoliths; invertebrates are represented exclusively by traces (associated with ichnofacies of Skolithos and Scoyenia), and vertebrates by a fragment of the pelvic girdle of a basal arcosaur. The taphonomic analysis performed in the two Triassic lacustrine successions allows recognition of two different taphonomic histories for the plant remains. The Los Rastros lake preserved both autochthonous (originated in the littoral zone) and allochthonous (originated in the upstream fluvial system) elements. The offshore lacustrine area was dominated by autochthonous well-preserved elements and allochthonous plant debris and wood, which formed time-averaged accumulations. The delta deposits are characterized by allochthonous elements with varied preservational conditions, usually showing evidence of mechanical degradation and accumulation within a short time. Autochthonous and allochthonous material were preserved in the Los Rastros Lake by means of anoxic conditions in the offshore lacustrine area and high sedimentation rates in the delta. In

  18. Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

    Science.gov (United States)

    Kacar, Betul; Guy, Lionel; Smith, Eric; Baross, John

    2017-11-01

    Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the

  19. A new theropod dinosaur from India with remarks on the Gondwana-Laurasia connection in the Late Triassic

    Science.gov (United States)

    Chatterjee, S.

    Walkeria maleriensis (n. g., n. sp.) from the Late Triassic Maleri Formation of the Godavari Valley of India is the earliest known dinosaur from Asia. It is a small podokesaurid theropod, very similar to Procompsognathus of Germany, Coelophysis of North America, and Syntarsus from Zimbabwe and North America. The podokesaurs are of particular interest to students of organic evolution because they are the earliest known theropods from which Archaeopteryx, the oldest known fossil bird, was probably evolved. Traditionally, India has been regarded as a part of Gondwana. It is generally believed that Gondwana remained an integral geographic unit throughout the Triassic. If this is so, a strong faunal correlation between India and other Gondwana continents should be expected in Late Triassic time. Contrary to this, the Maleri fauna is overwhelmingly "northern". Walkeria occurs in association with metoposaurs, parasuchids, protorosaurs, aetosaurs, rhynchosaurs, and traversodonts. Most of these taxa have been identified in the Dockum fauna of North America, indicating a close paleontologic link between India and Laurasia. Possibly the route of faunal migration between India and North America during the Late Triassic was via northern Africa.

  20. Basic features of the ancestral chordate brain: a protochordate perspective.

    Science.gov (United States)

    Lacalli, Thurston C

    2008-03-18

    Basic features of the anterior nerve cord in amphioxus larvae are summarized to highlight its essential similarity with the vertebrate brain. Except for a pineal homolog, the amphioxus brain consists of a much simplified version of the ventral brainstem, including a region probably homologous with the hypothalamus, and a locomotory control center roughly comparable to the vertebrate tegmentum and reticulospinal system. Amphioxus has direct pathways for activating its locomotory circuits in response to mechanical stimuli via epithelial sensory cells, but this response is evidently modulated by inputs from diverse sensory-type cells located in the putative hypothalamic homolog, and from the lamellar body, the pineal homolog. This implies that a basic function of the amphioxus brain is to switch between locomotory activities, of which there are several, and the principal non-locomotory one, namely feeding. A similar involvement in switching between behavioral modes may thus have been a core brain function in ancestral chordates. Currently, however, incomplete knowledge of the physiology and behavior of amphioxus limits how effectively it can be used as an evolutionary model. Eye evolution is briefly discussed to illustrate how a better understanding of living forms can inform the evolutionary debate. An account of recent data on dorsoventral inversion is also included, as this bears directly on the question of where the chordate brain originated in relation to other structures. It now appears likely that key components of the ancestral brain were originally located around the mouth. A secondary repositioning of the latter would therefore have been required before a unitary brain could be assembled and internalized. This association between the mouth and the evolving brain reinforces the idea of a fundamental early connection between core brain structures and the control of feeding activity.

  1. A history of Proterozoic terranes in southern South America: From Rodinia to Gondwana

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    C. Casquet

    2012-03-01

    Full Text Available The role played by Paleoproterozoic cratons in southern South America from the Mesoproterozoic to the Early Cambrian is reconsidered here. This period involved protracted continental amalgamation that led to formation of the supercontinent Rodinia, followed by Neoproterozoic continental break-up, with the consequent opening of Clymene and Iapetus oceans, and finally continental re-assembly as Gondwana through complex oblique collisions in the Late Neoproterozoic to Early Cambrian. The evidence for this is based mainly on a combination of precise U-Pb SHRMP dating and radiogenic isotope data for igneous and metamorphic rocks from a large area extending from the Rio de la Plata craton in the east to the Argentine Precordillera in the west and as far north as Arequipa in Peru. Our interpretation of the paleogeographical and geodynamic evolution invokes a hypothetical Paleoproterozoic block (MARA embracing basement ultimately older than 1.7 Ga in the Western Sierras Pampeanas (Argentina, the Arequipa block (Peru, the Rio Apa block (Brazil, and probably also the Paraguaia block (Bolivia.

  2. EVOLUTION. A four-legged snake from the Early Cretaceous of Gondwana.

    Science.gov (United States)

    Martill, David M; Tischlinger, Helmut; Longrich, Nicholas R

    2015-07-24

    Snakes are a remarkably diverse and successful group today, but their evolutionary origins are obscure. The discovery of snakes with two legs has shed light on the transition from lizards to snakes, but no snake has been described with four limbs, and the ecology of early snakes is poorly known. We describe a four-limbed snake from the Early Cretaceous (Aptian) Crato Formation of Brazil. The snake has a serpentiform body plan with an elongate trunk, short tail, and large ventral scales suggesting characteristic serpentine locomotion, yet retains small prehensile limbs. Skull and body proportions as well as reduced neural spines indicate fossorial adaptation, suggesting that snakes evolved from burrowing rather than marine ancestors. Hooked teeth, an intramandibular joint, a flexible spine capable of constricting prey, and the presence of vertebrate remains in the guts indicate that this species preyed on vertebrates and that snakes made the transition to carnivory early in their history. The structure of the limbs suggests that they were adapted for grasping, either to seize prey or as claspers during mating. Together with a diverse fauna of basal snakes from the Cretaceous of South America, Africa, and India, this snake suggests that crown Serpentes originated in Gondwana. Copyright © 2015, American Association for the Advancement of Science.

  3. A loess deposit in the Late Triassic of southern Gondwana, and its significance to global paleoclimate

    Science.gov (United States)

    Horn, Bruno Ludovico Dihl; Goldberg, Karin; Schultz, Cesar Leandro

    2018-01-01

    This work aims to characterize the depositional systems of the Santa Maria Supersequence (Middle to Late Triassic) in the Paraná Basin and discuss their paleoclimatic significance through the use of field, chemical and paleontologic data. Facies analysis led to the identification of two dominant facies associations: dry mudflat and sheet delta. The dry mudflat facies association dominates in the Pinheiros-Chiniquá and Santa Cruz Sequences, and sheetflood delta facies association occurs only in the Candelária Sequence. Loess deposits were recognized in the lowermost sequences. Evidence for loess deposits includes the absence of floodplain feeding channels, thick, structureless siltstone bodies, overwhelming dominance of grain-size mode in 0.0031 mm and age dispersion of dated zircons. Throughout the Santa Maria Supersequence, the chemical index of alteration indicates semi-arid climate, in agreement with global-scale paleoclimatic conditions. However, during the Carnian the abundance of calcrete decreased and the occurrence of aquatic and semi-aquatic fauna increased, implying an increase in humidity in this interval. Other fossiliferous basins in Gondwana recorded the same short-lived, humid event. The humid peak may be associated with the Carnian "Wet Intemezzo", related with the development of the Wrangellian large igneous province (LIP).

  4. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    Science.gov (United States)

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  5. A new Cretaceous terrestrial ecosystem from Gondwana with the description of a new sauropod dinosaur

    Directory of Open Access Journals (Sweden)

    Jorge O. Calvo

    2007-09-01

    Full Text Available A unique site at the northern area of Patagonia (Neuquén, Argentina reveals a terrestrial ecosystem preserved in a detail never reported before in a Late Cretaceous deposit. An extraordinary diversity and abundance of fossils was found concentrated in a 0.5 m horizon in the same quarry, including a new titanosaur sauropod, Futalognkosaurus dukei n.gen., n.sp, which is the most complete giant dinosaur known so far. Several plant leaves, showing a predominance of angiosperms over gymnosperms that likely constituted the diet of F. dukei were found too. Other dinosaurs (sauropods, theropods, ornithopods, crocodylomorphs, pterosaurs, and fishes were also discovered, allowing a partial reconstruction of this Gondwanan continental ecosystem.Um depósito fóssil na região norte da Patagônia (Neuquén, Argentina revela um ecossistema nunca antes registrado a este nível de detalhes em depósitos do Cretáceo Superior. Uma diversidade e abundância extraordinária de fósseis encontra-se concentrada em uma camada de 0,5 m no mesmo sítio, incluindo um novo saurópodo titanossaurídeo, Futalognkosaurus dukei n. gen, n. sp., que é o mais completo dinossauro gigante encontrado até a presente data. Foram descobertas váriasfolhas de plantas indicando a predominância de angiospermas sobre gimnospermas que possivelmente formavam a base da dieta de F. dukei. Outros dinossauros (saurópodes, terópodes, ornitópodes, crocodilomorfos, pterossauros e peixes foram também encontrados possibilitando a reconstrução parcialdeste ecossistema continental do Gondwana.

  6. Early to mid Cretaceous vegetation of northern Gondwana - the onset of angiosperm radiation and climatic implications

    Science.gov (United States)

    Coiffard, Clément; Mohr, Barbara

    2014-05-01

    Early Cretaceous Northern Gondwana seems to be the cradle of many early flowering plants, especially mesangiosperms that include magnoliids and monocots and basal eudicots. So far our knowledge was based mostly on dispersed pollen and small flowering structures. New fossil finds from Brazil include more complete plants with attached roots, leaves and flowers. Taxonomic studies show that these fossils belonged to clades which are, based on macroscopic characters and molecular data, also considered to be rather basal, such as several members of Nymphaeales, Piperales, Laurales, Magnoliales, monocots (Araliaceae) and Ranunculales. Various parameters can be used in order to understand the physiology and habitat of these plants. Adaptations to climate and habitat are partly mirrored in their root anatomy (evidence of tap roots), leaf size and shape, leaf anatomy including presence of glands, and distribution of stomata. An important ecophysiolocical parameter is vein density as an indicator for the plants' cabability to pump water, and the stomatal pore index, representing the proportion of stomatal pore area on the leaf surface, which is related to the water vapor resistance of the leaf epidermis. During the mid-Cretaceous leaf vein density started to surpass that of gymnosperms, one factor that made angiosperms very successful in conquering many kinds of new environments. Using data on these parameters we deduce that during the late Early to mid Cretaceous angiosperms were already diverse, being represented as both herbs, with aquatic members, such as Nymphaeles, helophytes (e.g. some monocots) and plants that may have grown in shady locations. Other life forms included shrubs and perhaps already small trees (e.g. Magnoliales). These flowering plants occupied various habitats, ranging from xeric (e.g. some Magnoliales) to mesic and shady (e.g. Piperales) or aquatic (e.g. Araceae, Nymphaeales). Overall, it seems that several of these plants clearly exhibited some

  7. Episodic growth of the Gondwana supercontinent from hafnium and oxygen isotopes in zircon.

    Science.gov (United States)

    Kemp, A I S; Hawkesworth, C J; Paterson, B A; Kinny, P D

    2006-02-02

    It is thought that continental crust existed as early as 150 million years after planetary accretion, but assessing the rates and processes of subsequent crustal growth requires linking the apparently contradictory information from the igneous and sedimentary rock records. For example, the striking global peaks in juvenile igneous activity 2.7, 1.9 and 1.2 Gyr ago imply rapid crustal generation in response to the emplacement of mantle 'super-plumes', rather than by the continuous process of subduction. Yet uncertainties persist over whether these age peaks are artefacts of selective preservation, and over how to reconcile episodic crust formation with the smooth crustal evolution curves inferred from neodymium isotope variations of sedimentary rocks. Detrital zircons encapsulate a more representative record of igneous events than the exposed geology and their hafnium isotope ratios reflect the time since the source of the parental magmas separated from the mantle. These 'model' ages are only meaningful if the host magma lacked a mixed or sedimentary source component, but the latter can be diagnosed by oxygen isotopes, which are strongly fractionated by rock-hydrosphere interactions. Here we report the first study that integrates hafnium and oxygen isotopes, all measured in situ on the same, precisely dated detrital zircon grains. The data reveal that crust generation in part of Gondwana was limited to major pulses at 1.9 and 3.3 Gyr ago, and that the zircons crystallized during repeated reworking of crust formed at these times. The implication is that the mechanisms of crust formation differed from those of crustal differentiation in ancient orogenic belts.

  8. Allatotropin: An Ancestral Myotropic Neuropeptide Involved in Feeding

    Science.gov (United States)

    Alzugaray, María Eugenia; Adami, Mariana Laura; Diambra, Luis Anibal; Hernandez-Martinez, Salvador; Damborenea, Cristina; Noriega, Fernando Gabriel; Ronderos, Jorge Rafael

    2013-01-01

    Background Cell-cell interactions are a basic principle for the organization of tissues and organs allowing them to perform integrated functions and to organize themselves spatially and temporally. Peptidic molecules secreted by neurons and epithelial cells play fundamental roles in cell-cell interactions, acting as local neuromodulators, neurohormones, as well as endocrine and paracrine messengers. Allatotropin (AT) is a neuropeptide originally described as a regulator of Juvenile Hormone synthesis, which plays multiple neural, endocrine and myoactive roles in insects and other organisms. Methods A combination of immunohistochemistry using AT-antibodies and AT-Qdot nanocrystal conjugates was used to identify immunoreactive nerve cells containing the peptide and epithelial-muscular cells targeted by AT in Hydra plagiodesmica. Physiological assays using AT and AT- antibodies revealed that while AT stimulated the extrusion of the hypostome in a dose-response fashion in starved hydroids, the activity of hypostome in hydroids challenged with food was blocked by treatments with different doses of AT-antibodies. Conclusions AT antibodies immunolabeled nerve cells in the stalk, pedal disc, tentacles and hypostome. AT-Qdot conjugates recognized epithelial-muscular cell in the same tissues, suggesting the existence of anatomical and functional relationships between these two cell populations. Physiological assays indicated that the AT-like peptide is facilitating food ingestion. Significance Immunochemical, physiological and bioinformatics evidence advocates that AT is an ancestral neuropeptide involved in myoregulatory activities associated with meal ingestion and digestion. PMID:24143240

  9. Modeling X-linked ancestral origins in multiparental populations.

    Science.gov (United States)

    Zheng, Chaozhi

    2015-03-04

    The models for the mosaic structure of an individual's genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes in a mapping population, which is necessary for developing hidden Markov models in the reconstruction of ancestry blocks for X-linked quantitative trait locus mapping. The model accounts for the joint recombination pattern, the asymmetry between maternally and paternally derived X chromosomes, and the finiteness of population size. The model can be applied to various mapping populations such as the advanced intercross lines (AIL), the Collaborative Cross (CC), the heterogeneous stock (HS), the Diversity Outcross (DO), and the Drosophila synthetic population resource (DSPR). We further derive the map expansion, density (per Morgan) of recombination breakpoints, in advanced intercross populations with L inbred founders under the limit of an infinitely large population size. The analytic results show that for X chromosomes the genetic map expands linearly at a rate (per generation) of two-thirds times 1 - 10/(9L) for the AIL, and at a rate of two-thirds times 1 - 1/L for the DO and the HS, whereas for autosomes the map expands at a rate of 1 - 1/L for the AIL, the DO, and the HS. Copyright © 2015 Zheng.

  10. Allatotropin: an ancestral myotropic neuropeptide involved in feeding.

    Directory of Open Access Journals (Sweden)

    María Eugenia Alzugaray

    Full Text Available Cell-cell interactions are a basic principle for the organization of tissues and organs allowing them to perform integrated functions and to organize themselves spatially and temporally. Peptidic molecules secreted by neurons and epithelial cells play fundamental roles in cell-cell interactions, acting as local neuromodulators, neurohormones, as well as endocrine and paracrine messengers. Allatotropin (AT is a neuropeptide originally described as a regulator of Juvenile Hormone synthesis, which plays multiple neural, endocrine and myoactive roles in insects and other organisms.A combination of immunohistochemistry using AT-antibodies and AT-Qdot nanocrystal conjugates was used to identify immunoreactive nerve cells containing the peptide and epithelial-muscular cells targeted by AT in Hydra plagiodesmica. Physiological assays using AT and AT- antibodies revealed that while AT stimulated the extrusion of the hypostome in a dose-response fashion in starved hydroids, the activity of hypostome in hydroids challenged with food was blocked by treatments with different doses of AT-antibodies.AT antibodies immunolabeled nerve cells in the stalk, pedal disc, tentacles and hypostome. AT-Qdot conjugates recognized epithelial-muscular cell in the same tissues, suggesting the existence of anatomical and functional relationships between these two cell populations. Physiological assays indicated that the AT-like peptide is facilitating food ingestion.Immunochemical, physiological and bioinformatics evidence advocates that AT is an ancestral neuropeptide involved in myoregulatory activities associated with meal ingestion and digestion.

  11. Possible rules for the ancestral origin of Hox gene collinearity.

    Science.gov (United States)

    Gaunt, Stephen J; Gaunt, Alexander L

    2016-12-07

    The Hox gene cluster is believed to have formed from a single ProtoHox gene by repeated cycles of the following events: tandem gene duplication, mutation to generate a new expression boundary along the embryonic axis, and acquisition of a new Hox patterning function. The Hox cluster in Bilateria evolved in compliance with the so-called collinearity rule. That is, the order of the genes along the chromosome corresponds with the order of their embryonic expression domains along the head-tail axis. Gaunt (2015) suggested that collinearity may have arisen as a mechanism to minimise the incidence of boundaries between active and inactive genes within the Hox cluster. We now attempt to clarify the model by presenting it in the form of three rules: 1) no two Hox genes may persist in the same cluster with the same anterior boundary of activity in the same tissue; 2) an inactive Hox gene must not be flanked by two active Hox genes; 3) an active Hox gene must not be flanked by two inactive genes. We provide evidence and illustrative computer simulations to show that these rules, which can apply only to partially overlapping patterns of Hox activity, may account for the ancestral origin of Hox gene collinearity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

    Science.gov (United States)

    Didier, Gilles

    2017-10-01

    The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

  13. Ancestral fertility in "Ponciá Vivêncio"

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    Ana Ximenes Gomes de Oliveira

    2015-12-01

    Full Text Available The literature of Conceição Evaristo presents in its characters a rescue and a sort of re­writing of Brazilian historical records, mainly experienced by the black skinned people. Therefore, a literature work as such goes beyond the intentions and canonical places to be destined, because it is a fictional production that acts interposing the discourse of literary authoritarianism. Conceição Evaristo is an author who symbolizes this multiplicity of inherited experiences of the slavery period and post-colonialism in Brazil. Whence, the purpose of this study is to explore the reflections on the historical memory in the novel Ponciá Vicêncio, as well as the issues of ancestrally and how it is con­figured in the maternity of two feminine characters in the novel: the protagonist Ponciá Vicêncio and the wise Nêngua Kainda. Therefore, the considerations of Verena Alberti (2004 on memory and orality; and Reginaldo Prandi (2001 on the representation of mythology of deities in this narrative, it will be used as theoretical framework.

  14. New early Eocene vertebrate assemblage from western India reveals a mixed fauna of European and Gondwana affinities

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    Thierry Smith

    2016-11-01

    Full Text Available The Ypresian Cambay Shale Formation at Vastan and Mangrol lignite mines in Gujarat, western India, has yielded a rich vertebrate fauna with numerous taxa of European affinities. Here we report a new, approximately contemporary vertebrate assemblage from two fossiliferous layers in the nearby mine of Tadkeshwar. These layers have yielded a similar mammal fauna with the co-occurrence of the perissodactyl-like cambaytheriid Cambaytherium thewissi, the adapoid primates Marcgodinotius indicus and cf. Asiadapis cambayensis, and the hyaenodontid Indohyaenodon raoi. The presence of these species in both Vastan and Tadkeshwar mines and at different levels suggests that the deposits between the two major lignite seams represent a single land mammal age. Apart from the aforementioned species there is a new, smaller species of Cambaytherium, and a new genus and species of esthonychid tillodont. This fauna also contains the first large early Eocene vertebrates from India, including an unidentified Coryphodon-like pantodont, a dyrosaurid crocodyliform and a new giant madtsoiid snake. Among the Tadkeshwar vertebrates several taxa are of Gondwana affinities, such as Pelomedusoides turtles, dyrosaurids, and large madtsoiids, attesting that the early Eocene was a crucial period in India during which Laurasian taxa of European affinities co-existed with relict taxa from Gondwana before the India-Asia collision. Our results suggest that terrestrial faunas could have dispersed to or from Europe during episodes of contact between the Indian subcontinent and different island blocks along the northern margin of the Neotethys, such as the Kohistan–Ladakh island-arc system. Gondwana taxa might represent remnants of ghost lineages shared with Madagascar, which reached the Indian subcontinent during the late Cretaceous; alternatively they might have come from North Africa and passed along the southern margin of the Neotethys to reach the Indian subcontinent. These

  15. The eoorthid brachiopod Apheoorthina in the Lower Ordovician of NW Argentina and the dispersal pathways along western Gondwana

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    Diego F. Muñoz

    2016-08-01

    Full Text Available The eoorthid brachiopod Apheoorthina is reported for the first time from the Lower Ordovician of NW Argentina. It is represented by a species similar to A. ferrigena from the Tremadocian of the Prague Basin, increasing the faunal affinities between the Central Andean Basin and the South European microcontinents, in particular the Bohemian region (Perunica. Nine out of the fourteen brachiopod genera reported from the Tremadocian of the Central Andean Basin (~64% are shared with the Mediterranean region, four of which (~28% have been recorded in the Prague Basin, and two (Kvania and Apheoorthina are restricted to the Central Andes and Perunica. Dispersal pathways around Gondwana are analyzed in the light of major factors affecting large-scale distribution of brachiopods (environment, larval capacity for dispersal, oceanic currents. The presence in Apheoorthina aff. ferrigena of a well-preserved larval protegulum measuring 420 μm in width and 210 μm in length strongly suggests that this species had planktotrophic larvae capable of long-distance dispersal. According to recent ocean-atmosphere general circulation models for the Ordovician Period, the Central Andean margin was dominated by the cold-water Antarctica Current. Despite the complex non-zonal pattern produced by current deflections around the peri-Gondwanan microcontinents, the general westward circulation sense favoured larval dispersal from the Andean region to North Africa, Avalonia, the Armorican Terrane Assemblage, and Perunica. On the other hand, the eastwards flowing Gondwana Current connected the North Gondwana waters with the South American epicontinental seas, which could explain the reversed migration of some brachiopods.

  16. First occurrence of a new Ocruranus-like helcionelloid mollusc from the lower Cambrian of East Gondwana

    DEFF Research Database (Denmark)

    Skovsted, Christian B.; Brock, Glenn A.; Topper, Timothy Paul

    2012-01-01

    A new cap-shaped mollusc, Emargimantus angulatus gen. et sp. nov. is described from the Arrowie Basin of South Australia. The new species is closely comparable to mollusc species from South China and North-East Greenland previously described under the generic name Ocruranus Liu, a genus recently...... reinterpreted as a multiplated, possibly polyplacophoran mollusc. Emargimantus is interpreted as a univalved helcionelloid mollusc and differs from Ocruranus in both morphology and function. E. angulatus represents the first discovery of Ocruranus-like helcionelloids in the lower Cambrian of eastern Gondwana...... and demonstrates that these molluscs had a global distribution during the early Cambrian....

  17. Fusion of cervical vertebrae from a basal archosauromorph from the Middle Triassic Denwa Formation, Satpura Gondwana Basin, India.

    Science.gov (United States)

    Sengupta, Saradee

    2018-03-01

    This report describes two adjacent, longitudinally-fused anterior cervical vertebrae from a basal archosauromorph. The specimen was collected from the Denwa Formation, Satpura Gondwana Basin, India. The differential diagnosis of the fusion includes genetic or environmentally-mediated congenital malformations, nonspecific spondyloarthopathy, and various infectious agents. These observations represent the first published recognition of archosauromorph vertebral pathology from specimens that were discovered in India. The observations affirm that basal archosauromorphs suffered from disorders that have been observed in later dinosaurs and modern-day vertebrates. Considering the process of orderly differential diagnosis is an important aspect of understanding lesions of ancient bones. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.

    Science.gov (United States)

    Akanuma, Satoshi

    2017-08-06

    Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth's early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth's surface temperature gradually decreased over time, from Archean to present.

  19. "I Ulu No Ka Lala I Ke Kumu", The Branches Grow Because of the Trunk: Ancestral Knowledge as Refusal

    Science.gov (United States)

    Chandler, Kapua L.

    2018-01-01

    This paper will discuss the ways that Native Hawaiian scholars are engaging in innovative strategies that incorporate ancestral knowledges into the academy. Ancestral knowledges are highly valued as Indigenous communities strive to pass on such wisdom and lessons from generation to generation. Ancestral knowledges are all around us no matter where…

  20. Genome-wide inference of ancestral recombination graphs.

    Directory of Open Access Journals (Sweden)

    Matthew D Rasmussen

    Full Text Available The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG, a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective

  1. Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids.

    Science.gov (United States)

    Mims, Meryl C; Darrin Hulsey, C; Fitzpatrick, Benjamin M; Streelman, J Todd

    2010-03-01

    Phenotypically diverse Lake Malawi cichlids exhibit similar genomes. The extensive sharing of genetic polymorphism among forms has both intrigued and frustrated biologists trying to understand the nature of diversity in this and other rapidly evolving systems. Shared polymorphism might result from hybridization and/or the retention of ancestrally polymorphic alleles. To examine these alternatives, we used new genomic tools to characterize genetic differentiation in widespread, geographically structured populations of Labeotropheus fuelleborni and Metriaclima zebra. These phenotypically distinct species share mitochondrial DNA (mtDNA) haplotypes and show greater mtDNA differentiation among localities than between species. However, Bayesian analysis of nuclear single nucleotide polymorphism (SNP) data revealed two distinct genetic clusters corresponding perfectly to morphologically diagnosed L. fuelleborni and M. zebra. This result is a function of the resolving power of the multi-locus dataset, not a conflict between nuclear and mitochondrial partitions. Locus-by-locus analysis showed that mtDNA differentiation between species (F(CT)) was nearly identical to the median single-locus SNP F(CT). Finally, we asked whether there is evidence for gene flow at sites of co-occurrence. We used simulations to generate a null distribution for the level of differentiation between co-occurring populations of L. fuelleborni and M. zebra expected if there was no hybridization. The null hypothesis was rejected for the SNP data; populations that co-occur at rock reef sites were slightly more similar than expected by chance, suggesting recent gene flow. The coupling of numerous independent markers with extensive geographic sampling and simulations utilized here provides a framework for assessing the prevalence of gene flow in recently diverged species.

  2. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  3. The microcephalin ancestral allele in a Neanderthal individual.

    Directory of Open Access Journals (Sweden)

    Martina Lari

    Full Text Available BACKGROUND: The high frequency (around 0.70 worldwide and the relatively young age (between 14,000 and 62,000 years of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1 locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1 locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy. We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

  4. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  5. Is the Palaeozoic of Istanbul a part of Gondwana-Land or Laurasia, or both?

    Science.gov (United States)

    Lom, Nalan; Ülgen, Semih Can; Özgül, Necdet; Celal Şengör, A. M.

    2014-05-01

    The Istanbul Zone, northwestern Turkey, located along the southwestern Black Sea coast, consists of a Neoproterozoic (almost entirely Ediacaran) middle to high-grade crystalline basement with relicts of oceanic lithosphere, volcanic arc and continental crust of unknown affinity and it is overlain by a continuous, well-developed transgressive sedimentary sequence extending from the late Ordovician to the Carboniferous. The Palaeozoic sequence was folded and thrust-faulted during the Carboniferous Hercynian orogeny, and is unconformably overlain by Lower Triassic and younger sedimentary strata. The Istanbul Zone is separated from the Sakarya Zone by the Intra- Pontide suture of early to medial Eocene and from the Strandja Massif by an inferred right-lateral strike-slip West Black Sea Fault. The Sakarya and Strandja fragments exhibit late Triassic and late Jurassic-Early Cretaceous metamorphism and deformation, respectively, which are not observed in the Istanbul Zone. The Palaeozoic sequences of Istanbul and Zonguldak have been compared and correlated with similar sequences in Europe, including the Moesian platform in Romania and Bulgaria, Moravo-Silesia (Brunovistulian) in the Czech Republic and the Rhenohercynian zone in Germany and Belgium, all deposited on the northern passive margin of the Rheic ocean. However, these correlations are based on insufficient knowledge of the correlated rock sequences. By contrast, the İstanbul sequence resembles the Carnic Alps, the Montaigne Noir, the Bohemian (Saxo-Thuringian), the Morocco, the Pyrenean sequences and thus northern Gondwana-Land of the Palaeozoic times. Istanbul Zone thus combines the characteristics of both the north and south Hercynian margins! The Istanbul Zone shows characteristics of graben-facies deposits during the Ordovician-early Silurian followed by Atlantic-type continental margin sediments of late Silurian- late Devonian age. Since the arc is missing, the ocean facing İstanbul must have been consumed

  6. Magma sources during Gondwana breakup: chemistry and chronology of Cretaceous magmatism in Westland, New Zealand

    Science.gov (United States)

    van der Meer, Quinten H. A.; Waight, Tod E.; Scott, James M.

    2013-04-01

    Cretaceous-Paleogene rifting of the Eastern Gondwana margin thinned the continental crust of Zealandia and culminated in the opening of the Tasman Sea between Australia and New Zealand and the Southern Ocean, separating both from Antarctica. The Western Province of New Zealand consists of a succession of metasedimentary rocks intruded by Palaeozoic and Mesozoic granitoids that formed in an active margin setting through the Phanerozoic. Upon cessation of subduction, the earliest stages of extension (~110-100 Ma) were expressed in the formation of metamorphic core complexes, followed by emplacement of granitoid plutons, the deposition of terrestrial Pororari Group sediments in extensional half-grabens across on- and offshore Westland, and the intrusion of mafic dikes from ~90 Ma. These dikes are concentrated in the swarms of the Paparoa and Hohonu Ranges and were intruded prior to and simultaneous with volumetrically minor A-type plutonism at 82 Ma. The emplacement of mafic dikes and A-type plutonism at ~82 Ma is significant as it coincides with the age of the oldest seafloor in the Tasman Sea, therefore it represents magmatism coincident with the initiation of seafloor spreading which continued until ~53 Ma. New 40Ar-39Ar ages indicate that the intrusion of mafic dikes in basement lithologies both preceded and continued after the initial opening of the Tasman Sea, including an additional population of ages at ~70 Ma. This indicates either a prolonged period of extension-related magmatism that continued >10 Ma after initial breakup, or two discrete episodes of magmatism during Tasman Sea spreading. Volumetrically minor Cenozoic within-plate magmatism continued sporadically throughout the South Island and bears a characteristic HIMU (high time integrated U/Pb) signature. A detailed geochemistry and chronological study of Cretaceous mafic and felsic magmatism is currently in progress and aims to better understand the transition of magma sources from a long lived active

  7. Global deglaciation and the re-appearance of microbial matground-dominated ecosystems in the late Paleozoic of Gondwana.

    Science.gov (United States)

    Buatois, L A; Netto, R G; Gabriela Mángano, M; Carmona, N B

    2013-07-01

    The extensive matgrounds in Carboniferous-Permian open-marine deposits of western Argentina constitute an anachronistic facies, because with the onset of penetrative bioturbation during the early Paleozoic microbial mats essentially disappeared from these settings. Abundant microbially induced sedimentary structures in the Argentinean deposits are coincident with the disappearance of trace and body fossils in the succession and with a landward facies shift indicative of transgressive conditions. Deposits of the Late Carboniferous-Early Permian glacial event are well developed in adjacent basins in eastern Argentina, Brazil, South Africa and Antarctica, but do not occur in the western Andean basins of Argentina. However, the deglaciation phase is indirectly recorded in the studied region by a rapid rise in sea level referred to as the Stephanian-Asselian transgression. We suggest that an unusual release of meltwater during the final deglaciation episode of the Gondwana Ice Age may have dramatically freshened peri-Gondwanan seas, impacting negatively on coastal and shallow-marine benthic faunas. Suppression of bioturbation was therefore conducive to a brief re-appearance of matground-dominated ecosystems, reminiscent of those in the precambrian. Bioturbation is essential for ecosystem performance and plays a major role in ocean and sediment geochemistry. Accordingly, the decimation of the mixed layer during deglaciation in the Gondwana basins may have altered ecosystem functioning and geochemical cycling. © 2013 John Wiley & Sons Ltd.

  8. Isotopic (U-Pb, Nd) and geochemical constraints on the origins of the Aileu and Gondwana sequences of Timor

    Science.gov (United States)

    Boger, S. D.; Spelbrink, L. G.; Lee, R. I.; Sandiford, M.; Maas, R.; Woodhead, J. D.

    2017-02-01

    Detrital zircon U-Pb age data collected from the argillitic sedimentary rocks of the Timorese Aileu Complex and Gondwana Sequence indicate that both units were derived from a common source containing 200-600 Ma, 900-1250 Ma and 1450-1900 Ma zircon. The modally most significant age population within this range of ages dates to c. 260 Ma. The observed spectrum of ages can be traced to the eastern active margin of Pangaea and its immediate foreland, which today is best exposed along the northeast coast of Australia. Compared to the relative homogeneity of the detrital zircon age data, geochemical and Nd isotopic data show that the mudstones of the Aileu Complex are on average more siliceous, have higher K2O/Na2O, Rb/Sr, Th/Sc and yield notably older Nd TDM model ages when compared to those from the Gondwana Sequence. These data are interpreted to suggest that, although both sequences share a common east Pangaea provenance, they were eroded from different sections of this active margin and deposited in spatially separated basins. The present proximity of these units is a result of their tectonic juxtaposition during the Pliocene to Recent collision between the northern edge of the Indo-Australia plate and the Banda Arc.

  9. Control on frontal thrust progression by the mechanically weak Gondwana horizon in the Darjeeling-Sikkim Himalaya

    Science.gov (United States)

    Ghosh, Subhajit; Bose, Santanu; Mandal, Nibir; Das, Animesh

    2018-03-01

    This study integrates field evidence with laboratory experiments to show the mechanical effects of a lithologically contrasting stratigraphic sequence on the development of frontal thrusts: Main Boundary Thrust (MBT) and Daling Thrust (DT) in the Darjeeling-Sikkim Himalaya (DSH). We carried out field investigations mainly along two river sections in the DSH: Tista-Kalijhora and Mahanadi, covering an orogen-parallel stretch of 20 km. Our field observations suggest that the coal-shale dominated Gondwana sequence (sandwiched between the Daling Group in the north and Siwaliks in the south) has acted as a mechanically weak horizon to localize the MBT and DT. We simulated a similar mechanical setting in scaled model experiments to validate our field interpretation. In experiments, such a weak horizon at a shallow depth perturbs the sequential thrust progression, and causes a thrust to localize in the vicinity of the weak zone, splaying from the basal detachment. We correlate this weak-zone-controlled thrust with the DT, which accommodates a large shortening prior to activation of the weak zone as a new detachment with ongoing horizontal shortening. The entire shortening in the model is then transferred to this shallow detachment to produce a new sequence of thrust splays. Extrapolating this model result to the natural prototype, we show that the mechanically weak Gondwana Sequence has caused localization of the DT and MBT in the mountain front of DSH.

  10. Evidence of Gondwana early rifting process recorded by Resende-Ilha Grande Dike Swarm, southern Rio de Janeiro, Brazil

    Science.gov (United States)

    Guedes, Eliane; Heilbron, Monica; de Morisson Valeriano, Claudio; de Almeida, Julio César Horta; Szatmari, Peter

    2016-04-01

    Continental flood basalts and dike swarm have been related to continental breakup process through geological time. The Resende - Ilha Grande Dike swarm (RIGDS) located in the southeast Brazil, is related the Gondwana breakup and composed of dikes/sills intruded in Precambrian gneiss. The dikes have three distinguish orientations: NNW more inland; NS-NNE in the central segment and NE orientation in the coast line, consistent with Precambrian structural lineaments. The swarm comprises high-TiO2 tholeiitic basalts divided into three suites based on REE and Sr and Nd isotope data. The Resende and Volta Redonda suites present higher initial 87Sr/86Sr ratios between 0.7077 and 0.7065, while Angra dos Reis suite presents values of 0.7066 to 0.7057. Geochemical and isotopic data support the sub-continental lithospheric mantle (SCLM) as the main source for the high-TiO2 basalts. The suites heterogeneities are explained by different compositions of SCLM in accreted Precambrian terranes and/or different degree of partial melting and fractional. 40Ar/39Ar data indicate age interval between ca. 156 to 144 Ma for the swarm, older than the average for Gondwana breakup (ca. 130-120 Ma). The age interval places the RIGDS between the Karoo magmatism (181-178 Ma) and the Paraná-Etendeka magmatism (133-134 Ma) and indicates that extensional process affected the supercontinent prior the break-up.

  11. An ancestral role for the mitochondrial pyruvate carrier in glucose-stimulated insulin secretion

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    Kyle S. McCommis

    2016-08-01

    Conclusions: Altogether, these studies suggest that the MPC plays an important and ancestral role in insulin-secreting cells in mediating glucose sensing, regulating insulin secretion, and controlling systemic glycemia.

  12. Are hybrid species more fit than ancestral parent species in the current hybrid species habitats?

    NARCIS (Netherlands)

    Donovan, L.A.; Rosenthal, D.R.; Sanchez-Velenosi, M.; Rieseberg, L.H.; Ludwig, F.

    2010-01-01

    Hybrid speciation is thought to be facilitated by escape of early generation hybrids into new habitats, subsequent environmental selection and adaptation. Here, we ask whether two homoploid hybrid plant species (Helianthus anomalus, H. deserticola) diverged sufficiently from their ancestral parent

  13. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States1

    Science.gov (United States)

    Gruenstaeudl, Michael

    2016-01-01

    Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. Conclusions: WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion. PMID:26949580

  14. Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm.

    Science.gov (United States)

    Goolsby, Eric W

    2017-04-01

    Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000-species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within-species variation, non-Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time-consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation-Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars

  15. An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product

    OpenAIRE

    Chen, H. Deborah; Jewett, Mollie W.; Groisman, Eduardo A.

    2012-01-01

    Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the...

  16. Influence of Late Paleozoic Gondwana glaciations on the depositional evolution of the northern Pangean shelf, North Greenland, Svalbard and the Barents Sea

    DEFF Research Database (Denmark)

    Stemmerik, Lars

    2008-01-01

    Outcrop and subsurface data from the central northern margin of the Pangean shelf in North Greenland, Svalbard, and the Norwegian Barents Sea record the depositional response of a Northern Hemisphere subtropical shelf to Late Carboniferous-Early Permian (Bashkirian-Sakmarian) Gondwana glaciations...

  17. Upper Paleozoic glacigenic deposits of Gondwana: Stratigraphy and paleoenvironmental significance of a tillite succession in Northern Victoria Land (Antarctica)

    Science.gov (United States)

    Cornamusini, Gianluca; Talarico, Franco M.; Cirilli, Simonetta; Spina, Amalia; Olivetti, Valerio; Woo, Jusun

    2017-08-01

    Late Paleozoic glacial deposits are widespread in Gondwana. In Antarctica the best outcrops occur in the Central Transantarctic Mountains, Ellsworth Mountains, Pensacola Mountains, and in Southern Victoria Land, whereas they are rare and very scattered in Northern Victoria Land, which represents a linkage sector with Tasmania and eastern Australia. The aim of the present research is to define the stratigraphic setting and the environmental interpretation of a poorly studied Lower Permian glacigenic succession located near Orr Glacier in the Lanterman Range in Northern Victoria Land. It has great importance because it represents the only significant glacigenic succession for this wide area, marking and defining time and modality of a glacial-postglacial transition during the early Permian, a critical time-interval in the paleoenvironmental evolution of southern Gondwana. This succession, named here as the Lanterman Formation, lies directly on to crystalline basement, and is overlain by a thick Permian fluvial succession (Takrouna Formation). The results provided by sedimentological facies analysis and palynological analysis, integrated with a limited petrographic characterization, show a correlation framework between two isolated successions, outlining their stratigraphic architecture and subdivided into a lower glacial portion and an upper postglacial portion. The former, Asselian in age, is dominated by diamictite, sandstone, mudstone with lonestones, and carbonate deposits, suggesting repeated advance and retreat of a terrestrial glacier, with facies associations indicating environmental changes from subglacial to glaciofluvial, to glaciolacustrine. The latter is dominated by lacustrine mudstone with decreasing lonestones upward, thin bedded sandstone, conglomerate and a thick fluvial sandstone and pebbly sandstone succession at the top, signalling the transition to a fluvial system through time. The overall dataset suggests that the late Paleozoic glacigenic

  18. High-pressure granulite-facies metamorphism in central Dronning Maud Land (East Antarctica): Implications for Gondwana assembly

    Science.gov (United States)

    Palmeri, Rosaria; Godard, Gaston; Di Vincenzo, Gianfranco; Sandroni, Sonia; Talarico, Franco M.

    2018-02-01

    Central Dronning Maud Land (DML; East Antarctica) is located in a key region of the Gondwana supercontinent. The Conradgebirge area (central DML) consists of orthogneisses, derived from both volcanic and plutonic protoliths, and minor metasedimentary rocks, intruded by Cambrian syn- to post-metamorphic plutons and dykes. Mafic-ultramafic boudins in the metavolcanic and metaplutonic gneisses from Conradgebirge consist of amphibolites and high-grade garnet-bearing pyroxene- and amphibole-rich granofels. They occur either as discontinuous levels or as pods boudinaged within highly-strained and strongly-migmatized gneisses. Bulk-rock major and trace-element compositions, together with geochemical discriminant diagrams (e.g., Th/Yb versus Ta/Yb and V versus Ti), suggest derivation from enriched mantle source for the mafic rocks boudinaged in metaplutonic gneisses, whereas a calc-alkaline signature is common for the mafic boudins in metavolcanic rocks. The microstructural study and P-T modelling of an ultramafic metagabbroic rock reveal a prograde metamorphic evolution from amphibolite-facies (ca. 0.5 GPa; 500 °C) up to high-P granulite-facies conditions (ca. 1.5-1.7 GPa; 960-970 °C). Partial melting is testified by "nanogranitoid" inclusions enclosed in garnet. An almost isothermal decompression down to ca. 0.4 GPa and 750-850 °C produced well-developed An + Opx-bearing symplectites around garnet. A final isobaric cooling at nearly 0.4 GPa is testified by Grt coronas around high-T symplectites. The above reconstruction traces a clockwise loading-heating P-T evolution with a peak metamorphism at high-P granulite-facies conditions suggesting crustal thickening at nearly 570 Ma, followed by a tectonically assisted rapid exhumation, and then, by an isobaric cooling. 40Ar-39Ar dating of amphibole and biotite at 505-480 Ma testify mineral re-equilibration at upper crustal level (T < 650 °C) during the isobaric cooling. This tectono-metamorphic scenario seems

  19. Carbon isotope chemostratigraphy of the Llandovery in northern peri-Gondwana: new data from the Barrandian area, Czech Republic

    Directory of Open Access Journals (Sweden)

    Jiří Frýda

    2014-12-01

    Full Text Available The first complete δ13Corg record of the uppermost Hirnantian to lower Telychian strata of the Barrandian area (northern peri-Gondwana is presented based on 168 new samples. The new data from the study area reveal that the evolution of the Llandoverian organic carbon isotope reservoir was similar to that on other palaeoplates, but it differs from the development of the coeval carbonate carbon isotope reservoir in the absence of two δ13C excursions (i.e. the early Aeronian positive excursion in the upper part of the Demirastrites triangulatus graptolite Biozone and a negative excursion occurring close to the boundary between the Cystograptus vesiculosus and Coronograptus cyphus graptolite biozones.

  20. Gondwana Geodiversity and Geological Heritage: Examples from the North Coast of São Paulo State, Brazil

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    Maria da Glória Motta Garcia

    2012-01-01

    Full Text Available A região do Litoral Norte do Estado de São Paulo é caracterizada por registros de uma história geológica relacionada ao supercontinente Gondwana Ocidental, amalgamado durante o Ciclo Brasiliano, no Neoproterozoico-Cambriano e fragmentado no Jurássico-Cretáceo. Reativações durante o Cenozoico foram também responsáveis pela configuração atual da Serra do Mar e da linha de costa. Além disso, a região detém a mais importante área de Mata Atlântica preservada no Brasil, o que aumenta sua importância como zona protegida. A estes aspectos físicos somam-se registros de uma história que remonta a 2500 anos, além de inúmeras 101-11construções do período colonial que contam uma história de desafios entre os povos nativos e os conquistadores. O conjunto destes aspectos deu origem a uma cultura rica, caracterizada pela mistura de costumes de populações tradicionais diversas e que delinearam os valores culturais atuais. Este trabalho tem como escopo principal associar os principais eventos geológicos que ocorreram durante o Neoproterozoico-Paleógeno, incluindo fusão e separação do Supercontinente Gondwana e processos associados, aos valores da Geodiversidade da região. O objetivo destas ações é incluir locais com reconhecido valor geocientífico em programas de Geoturismo locais, incluindo apoio à sustentabilidade, preservação da história e da cultura tradicional, integração da população costeira e geração de emprego e renda.

  1. Silurian high-pressure granulites from Central Qiangtang, Tibet: Constraints on early Paleozoic collision along the northeastern margin of Gondwana

    Science.gov (United States)

    Zhang, Xiu-Zheng; Dong, Yong-Sheng; Li, Cai; Deng, Ming-Rong; Zhang, Le; Xu, Wang

    2014-11-01

    High-pressure (HP) granulites are commonly regarded as indicators of plate convergence and collision following the subduction of oceanic or continental crust. In this study we report the discovery of Silurian HP basic granulites from Central Qiangtang on the Tibetan Plateau. Detailed petrology and geochronology reveal a three-stage metamorphic history based on inclusions, reaction textures, and garnet zoning patterns. Peak metamorphism at 830-860 °C and 1.15-1.45 GPa (M1) is defined by high-Ca garnet cores, high-Al clinopyroxene, and high-Na plagioclase. Symplectites or coronas of orthopyroxene + plagioclase ± magnetite around garnet porphyroblasts indicate garnet breakdown reactions at ca. 810-830 °C and 0.65-0.85 GPa (M2). Kelyphites of amphibole + plagioclase around garnet formed during the cooling process at about 590-650 °C and 0.62-0.82 GPa (M3). These results help define a sequential P-T path containing near-isothermal decompression (ITD) and near-isobaric cooling (IBC) stages. Identification of mineral inclusion assemblages in zircons dated by U-Pb SHRIMP and LA-ICP-MS reveals peak HP metamorphism at ca. 427-422 Ma, subsequent near-isothermal decompression with associated retrograde reactions at ca. 392-389 Ma, and continued cooling at ca. 360 Ma. The P-T-t path of HP basic granulites reflects collision followed by extensional exhumation during early Paleozoic orogenesis. The present results indicate the occurrence of a collisional event along the northern margin of Indo-Australian Gondwana during the Silurian. Renewed Gondwana-directed subduction and subsequent collision probably led to the opening of the Paleo-Tethys Ocean.

  2. Mesozoic lacustrine system in the Parnaíba Basin, northeastern Brazil: Paleogeographic implications for west Gondwana

    Science.gov (United States)

    Cardoso, Alexandre Ribeiro; Nogueira, Afonso César Rodrigues; Abrantes, Francisco Romério; Rabelo, Cleber Eduardo Neri

    2017-03-01

    The fragmentation of the West Gondwana during Early Triassic to Cretaceous was marked by intense climatic changes, concomitant with the establishment of extensive desertic/lacustrine systems. These deposits succeeded the emplacement and extrusion of lava flows, related to the pre-rift phase and initial opening of the Equatorial Atlantic Ocean. The thermal phase is recorded in the Upper Jurassic-Lower Cretaceous Pastos Bons Formation, exposed mainly in southeast parts of the Parnaíba Basin, Northeastern Brazil. The sedimentary facies of this unit were grouped in two facies associations (FA), representative of a shallow lacustrine system, influenced by episodic hyperpycnal and oscillatory flows. Central lake facies association (FA1) is composed by laminated mudstone (Ml), sandstone/mudstone rhythmite (S/Mr) and sandstone with even-parallel lamination (Sel). Flysch-like delta front (FA2) consists in sandstones with wave structures (Sw), sandstones with even-parallel stratification (Ses), massive sandstones (Sm), sandstones with soft-sediment deformation structures (Sd) and laminated mudstones (Ml). FA1 was deposited in the deepest portions of the lake, characterized by low energy, episodically disturbed by siliciclastic influx. FA2 presents sandy deposits generated by unconfined flow, probably fed by ephemeral stream flows that generated thickening upward of tabular sandstone beds. The progressive filling of the lake resulted in recurrent shoaling up of the water level and reworking by wave action. The installation of Pastos Bons lakes was controlled by thermal subsidence, mainly in restricted depocenters. The siliciclastic fluvial inflow can be related to the adjacent humid desertic facies, formed under climatic attenuation, typical of post-Triassic period, with reduced biological activity. Smectite and abundant feldspars, in lacustrine facies, corroborate an arid climate, with incipient chemical weathering. The new facies and stratigraphic data present in this

  3. Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

    Science.gov (United States)

    Krishnan, Neeraja M; Seligmann, Hervé; Stewart, Caro-Beth; De Koning, A P Jason; Pollock, David D

    2004-10-01

    Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and

  4. Ancestral effect on HOMA-IR levels quantitated in an American population of Mexican origin.

    Science.gov (United States)

    Qu, Hui-Qi; Li, Quan; Lu, Yang; Hanis, Craig L; Fisher-Hoch, Susan P; McCormick, Joseph B

    2012-12-01

    An elevated insulin resistance index (homeostasis model assessment of insulin resistance [HOMA-IR]) is more commonly seen in the Mexican American population than in European populations. We report quantitative ancestral effects within a Mexican American population, and we correlate ancestral components with HOMA-IR. We performed ancestral analysis in 1,551 participants of the Cameron County Hispanic Cohort by genotyping 103 ancestry-informative markers (AIMs). These AIMs allow determination of the percentage (0-100%) ancestry from three major continental populations, i.e., European, African, and Amerindian. We observed that predominantly Amerindian ancestral components were associated with increased HOMA-IR (β = 0.124, P = 1.64 × 10(-7)). The correlation was more significant in males (Amerindian β = 0.165, P = 5.08 × 10(-7)) than in females (Amerindian β = 0.079, P = 0.019). This unique study design demonstrates how genomic markers for quantitative ancestral information can be used in admixed populations to predict phenotypic traits such as insulin resistance.

  5. On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2018-04-01

    We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

  6. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

    Science.gov (United States)

    Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; B�rard, S�verine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

    2017-01-01

    DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria. Availability: http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017). PMID:28402423

  7. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs

    International Nuclear Information System (INIS)

    Ma, Jing; Chen, Xi; Liu, Yanan; Xie, Qunhui; Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan; Zhao, Bin; Tang, Naijun

    2015-01-01

    Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8–14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue. - Highlights: • Ancestral TCDD exposure induces epigenetic transgenerational inheritance. • Ancestral TCDD exposure affects methylation status in ICR and DMR2 region of Igf2. • DNMTs play a role in TCDD induced epigenetic transgenerational changes of Igf2.

  8. Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

    Science.gov (United States)

    Chen, Hua; Chen, Kun

    2013-07-01

    The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by Tm the mth coalescent time, when m + 1 lineages coalesce into m lineages, and An(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, An(t), and the coalescence times, Tm, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n - An(t) follows a Poisson distribution, and as m → n, $$n\\left(n-1\\right){T}_{m}/2N\\left(0\\right)$$ follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.

  9. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

    Science.gov (United States)

    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

  10. Isotopic evidence for a large-scale plume-derived mantle domain between the Indian and Pacific mantles beneath the Southern Ocean.

    Science.gov (United States)

    Park, S. H.; Langmuir, C. H.; Scott, S. R.; Sims, K. W. W.; Lin, J.; Kim, S. S.; Blichert-Toft, J.; Choi, H.; Yang, Y. S.; Michael, P. J.

    2017-12-01

    Earth's upper mantle is characterized by Indian- and Pacific-type domains with distinctive isotope characteristics. The boundary between these two mantle regions has been hypothesized to be located at the Australian-Antarctic-Discordance (AAD), where regions west and east of the AAD are Indian- and Pacific-type, respectively. It was further posited that the Pacific mantle feeds into the Indian mantle as the boundary is moving westward. These scenarios have important implications for the dynamics of mantle convection in the area. In the present model, regions east of the AAD are assumed to be entirely Pacific-type mantle, but our recent recovery of basalts from a 2,000-km sampling gap along the Australian-Antarctic Ridge (AAR), located east of the AAD on the Pacific side, challenges this picture. Here we show that the Hf, Nd, Pb, and Sr isotopic compositions of AAR MORB are distinct from those of Pacific and Indian MORB. Rather, the AAR lavas show mixing relationships with volcanoes from the Hikurangi seamounts, the Balleney and Scott Islands, the West Antarctic Rift System, New Zealand, and east Australia. According to tectonic reconstruction models, these volcanoes are related to super-plume activity that caused Gondwana to break up at 90 Ma. These results imply that a large-scale plume-derived mantle domain exists between the Indian and Pacific mantle domains, and that mantle dynamics along the AAD should be reinterpreted in light of interaction with a super-plume.

  11. Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.

    Science.gov (United States)

    Wright, April M; Lyons, Kathleen M; Brandley, Matthew C; Hillis, David M

    2015-09-01

    Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollo's Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were

  12. Pacific Equatorial Transect

    OpenAIRE

    Pälike, Heiko; Nishi, Hiroshi; Lyle, Mitch; Raffi, Isabella; Klaus, Adam; Gamage, Kusali

    2009-01-01

    Integrated Ocean Drilling Program Expedition 320/321, "Pacific Equatorial Age Transect" (Sites U1331–U1338), was designed to recover a continuous Cenozoic record of the paleoequatorial Pacific by coring above the paleoposition of the Equator at successive crustal ages on the Pacific plate. These sediments record the evolution of the paleoequatorial climate system throughout the Cenozoic. As we gained more information about the past movement of plates and when in Earth's history "critical" cli...

  13. Inheritance of the 8.1 ancestral haplotype in recurrent pregnancy loss

    DEFF Research Database (Denmark)

    Kolte, Astrid M; Nielsen, Henriette S; Steffensen, Rudi

    2015-01-01

    BACKGROUND AND OBJECTIVES: The 8.1 ancestral haplotype (AH) (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2) is a remarkably long and conserved haplotype in the human major histocompatibility complex. It has been associated with both beneficial and detrimental effects, consistent with antagonistic...

  14. Inferring ancestral distribution area and survival vegetation of Caragana (Fabaceae) in Tertiary

    Science.gov (United States)

    Mingli Zhang; Juanjuan Xue; Qiang Zhang; Stewart C. Sanderson

    2015-01-01

    Caragana, a leguminous genus mainly restricted to temperate Central and East Asia, occurs in arid, semiarid, and humid belts, and has forest, grassland, and desert ecotypes. Based on the previous molecular phylogenetic tree and dating, biogeographical analyses of extant species area and ecotype were conducted by means of four ancestral optimization approaches: S-DIVA,...

  15. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

    DEFF Research Database (Denmark)

    Olalde, Inigo; Allentoft, Morten E.; Sanchez-Quinto, Federico

    2014-01-01

    to the Mesolithic. The La Brana individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated...

  16. Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa[C][W

    Science.gov (United States)

    Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A.; Wang, Xiaowu

    2013-01-01

    The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers. PMID:23653472

  17. A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, Patrícia; Moravec, Jiří C.; Martínková, Natália

    2015-01-01

    Roč. 64, č. 6 (2015), s. 1074-1088 ISSN 1063-5157 EU Projects: European Commission(XE) CZ.1.07/2.4.00/17.0138 Institutional support: RVO:68081766 Keywords : Sciurini * multilocus phylogeny * geometric morphometry * speciation * ancestral range reconstruction * diet modelling Subject RIV: EG - Zoology Impact factor: 8.225, year: 2015

  18. Language Shift and Maintenance in Multilingual Mauritius: The Case of Indian Ancestral Languages

    Science.gov (United States)

    Bissoonauth, Anu

    2011-01-01

    This paper reports on a research study conducted in Mauritius between June and July 2009. The aim of this research was to investigate the use of Indian ancestral languages in the domestic domain by the younger generations. The data were collected in the field by means of a questionnaire and interviews from a quota sample of secondary school…

  19. The middle and upper Lochkovian (Lower Devonian) conodont successions in key peri-Gondwana localities (Spanish Central Pyrenees and Prague Synform) and their relevance for global correlations

    Czech Academy of Sciences Publication Activity Database

    Valenzuela-Ríos, J. I.; Slavík, Ladislav; Liao, J.-Ch.; Calvo, H.; Hušková, Aneta; Chadimová, Leona

    2015-01-01

    Roč. 27, č. 6 (2015), s. 409-415 ISSN 0954-4879 R&D Projects: GA ČR GA14-18183S Grant - others:Rada Programu interní podpory projektů mezinárodní spolupráce AV ČR(CZ) M100131201 Institutional support: RVO:67985831 Keywords : Lochkovian * conodonts * peri-Gondwana localities Subject RIV: DB - Geology ; Mineralogy Impact factor: 2.758, year: 2015

  20. Eastern Gondwana breakup and the Lord Howe Rise continental ribbon from multi-channel seismic reflection data

    Science.gov (United States)

    Boston, Brian; Nakamura, Yasuyuki; Kodaira, Shuichi; Miura, Seiichi; Gallais, Flora; Fujie, Gou; Kaiho, Yuka; Hackney, Ron; Yamada, Yasuhiro; Saito, Saneatsu; Shiraishi, Kazuya; Nichol, Scott; Bernardel, George; Mitchell, Cameron

    2017-04-01

    The eastern Australian margin of Gondwana rifted during the Late Cretaceous, forming the Lord Howe Rise continental ribbon. This breakup is still poorly understood with only a few regional studies and suggested formation processes that range from a plume impinging on the lithosphere to upper-plate extension associated with slab rollback. This project uses data collected on a multi-leg geophysical cruise undertaken in 2016 to study the rifting processes at the Lord Howe Rise. This project uses a regional 900 km long east-west oriented profile at 27.2°S with both multi-channel seismic reflection and multibeam bathymetry datasets. We present processed pre-stack depth migrated seismic reflection images and interpretations to show the structure and evolution of this margin from the oceanic Tasman Basin in the west to the extended continental crust of the Lord Howe Rise in the east. The Tasman Basin contains buried basins only on its eastern side. These basins may be related to early transform faulting. The Lord Howe Rise contains both syn-rift and post-rift sedimentary sequences in multiple basins that record the breakup of the margin. Between these two regions are the Dampier Ridge and Middleton Basin. The boundary between the Dampier Ridge and Tasman Basin is a very sharp feature that is unlike any other boundary in the area. This sharp boundary may represent a transform segment. Within the Dampier Ridge, there are multiple rift basins up to 3 km deep that are similar to those on the Lord Howe Rise. In contrast, the Middleton Basin that separates the Dampier Ridge and the Lord Howe Rise is a broad, well-stratified sedimentary basin of up to 3.5 km thick and contains an unconformity that separates deeper sedimentary strata that are conformable with the basement and younger strata that filled the basin post-rifting. These new results indicate a dynamic process and history during the breakup of eastern Gondwana that led to the opening of the Tasman Basin and formation

  1. RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.

    Science.gov (United States)

    Kratsch, Christina; McHardy, Alice C

    2014-09-01

    Ancestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution. We suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  2. The Pacific University Alliance

    International Nuclear Information System (INIS)

    Peddicord, K.L.; Graham, J.A.

    1996-01-01

    The Pacific University Alliance represents a partnership between universities from the Pacific Rim countries in North America and Asia with international companies in the field of nuclear technology. This partnership builds on a strong academic base to address 'world problems' and to prepare students to meet the challenges for the global nuclear industry of the 21st century. (author)

  3. PACIFIC NORTHWEST CYBER SUMMIT

    Energy Technology Data Exchange (ETDEWEB)

    Lesperance, Ann M.; Matlock, Gordon W.; Becker-Dippmann, Angela S.; Smith, Karen S.

    2013-08-07

    On March 26, 2013, the Snohomish County Public Utility District (PUD) and the U.S. Department of Energy’s (DOE’s) Pacific Northwest National Laboratory (PNNL) jointly hosted the Pacific Northwest Cyber Summit with the DOE’s Office of Electricity Delivery and Energy Reliability, the White House, Washington State congressional delegation, Washington State National Guard, and regional energy companies.

  4. Asia Pacific energy derivatives

    International Nuclear Information System (INIS)

    Fusaro, P.C.

    1997-09-01

    Asia Pacific Energy Derivatives, from FT Energy, is the first report of its kind to examine the growth of energy derivatives within Asia Pacific and their increasing importance within this region. It provides a comprehensive overview of the subject, including analysis of: deregulation as a market driver; the impact of privatisation; the future for energy risk management tools; the unique characteristics of the Asia Pacific energy market; the role of futures exchanges in Asia; existing indexes and their performance; the differences between the Asia Pacific markets and their more mature counterparts in London and New York; non-oil derivatives, project finance and cross commodity arbitrage; the thriving Pacific Rim Over the Counter (OTC) markets. (author)

  5. Isotopic signature of Pan-African rejuvenation in the Kerala Khondalite belt, southern India: implications for east Gondwana reassembly

    International Nuclear Information System (INIS)

    Unnikrishnan Warrier, C.

    1997-01-01

    Sm-Nd isotope systematics on mineral separates from sillimanite-and cordierite-bearing metapelite (khondalite), and garnet-and biotite-bearing gneiss (leptynite) from the Kerala Khondalite Belt (KKB), southern India, yielded mineral isochron ages (wr-feld-bio-gar) of 537±27 Ma (MSWD=0.9) and 534±26 Ma (MSWD=1.23) respectively. Rb-Sr systematics in the same samples gave wr-feld-bio mineral isochron ages of 437±9 Ma (MSWD=0.67) and 467±9 Ma (MSWD=0.76). These results provide the first mineral isochron ages for the regional metasedimentaries in the KKB. The ε (Nd T) values at 550 Ma for khondalite and leptynite are -22.7 and -21.8 respectively. These results demonstrate a complete rejuvenation of the crust during Pan-African times. Coeval alkaline plutons emplaced along fault-lineaments in this area suggest an extensional tectonic regime. Geochronologic correlations with the Lutzow-Holm bay complexes in east Antarctica, and the highland and southwestern complex of Sri Lanka show that a similar Pan-African tectono-thermal event manifested in all the east Gondwana crustal fragments. (author)

  6. Signatures of Late Neoproterozoic Gondwana assembly and Maronian glaciation in Lesser Himalaya: a palaeogeographical and stratigraphical approach

    Science.gov (United States)

    Umar, Muhammad; Betts, Peter; Saud Khan, Malik Muhammad; Amjad Sabir, Muhammad; Farooq, Muhammad; Zeb, Asif; Khan Jadoon, Umair; Ali, Shoaib

    2015-03-01

    Stratigraphical and sedimentological analyses of Late Neoproterozoic successions in Lesser Himalaya are combined herein with palaeogeographical considerations and comparisons with equivalent successions in India and South China. The succession starts with the Hazara Formation, which contains complete and incomplete Bouma sequences suggesting its deposition in deep marine turbidite settings. The overlying Tanawal Formation, rich in massive sandstone, shale and siltstone, was deposited in shallow marine conditions, as indicated by the presence of parallel lamination, large scale tabular, trough cross- and hummocky cross-stratifications. The Tanawal Formation facies shift laterally from proximal (south-southeast) to distal (north-northwest). The glaciogenic Tanaki Boulder Bed, overlying the Tanawal Formation, was deposited during the Maronian glaciation. It is equivalent to the Blaini Formation of India, and to the Sinian diamictites of South China. The Abbottabad Formation of Cambrian age overlies the Tanaki Boulder Bed, and is composed of dolomite, chert nodules and phosphate-rich packages; similar successions are documented in India and South China at the same stratigraphical interval. The similarities of the Neoproterozoic successions of Lesser Himalaya (both in Pakistan and India) and South China suggests their possible proximity during the break-up of Rodinia and the assembly of the Gondwana Supercontinent.

  7. The late Paleozoic palynological diversity in southernmost Paraná (Uruguay), Claromecó and Paganzo basins (Argentina), Western Gondwana

    Science.gov (United States)

    Beri, Ángeles; Gutiérrez, Pedro R.; Balarino, M. Lucía

    2015-12-01

    This study explores the changes in palynoflora diversity of the late Paleozoic in boreholes DI.NA.MI.GE. 254 (26 samples) and DI.NA.MI.GE. 221 (14 samples) of the Paraná Basin in Uruguay and in 18 surface samples of the La Deheza Formation (Paganzo Basin) and 10 samples of borehole UTAL.CMM1.La Estrella.x-1 (Claromecó Basin) in Argentina. Possible relationships among biostratigraphic zones, diversity levels, facies and climatic evolution patterns in Western Gondwana are studied. Diversity curves of boreholes 221 and 254 and the La Deheza Formation outcrop exhibit similar diversity evolution patterns, i.e., an increase in lower strata diversity and a decrease in upper strata diversity. The disappearance events are determined to be more prominent in biozones of the Cisuralian to the Guadalupian age and less prominent in biozones of the early Cisuralian age. The number of genera raises from the glaciomarine facies, through the deltaic and the marine facies, up to the shallow marine or lagoon facies, in which the disappearance rates become more prominent. . The diversity of the lower part of the La Estrella borehole is lesser than that of the other sequences These diversity, disappearance and appearance behaviors may reflect post-glacial climatic amelioration patterns and the beginning of an arid phase.

  8. Ichnologic evidence of a Cambrian age in the southern Amazon Craton: Implications for the onset of the Western Gondwana history

    Science.gov (United States)

    Santos, Hudson P.; Mángano, M. Gabriela; Soares, Joelson L.; Nogueira, Afonso C. R.; Bandeira, José; Rudnitzki, Isaac D.

    2017-07-01

    Colonization of the infaunal ecospace by burrowing bilaterians is one of the most important behavioral innovations during the Ediacaran-Cambrian transition. The establishment of vertical burrows by suspension feeders in high-energy nearshore settings during Cambrian Age 2 is reflected by the appearance of the Skolithos Ichnofacies. For the first time, unquestionable vertical burrows typical of the Skolithos Ichnofacies, such as Skolithos linearis, Diplocraterion parallelum and Arenicolites isp., are recorded from nearshore siliciclastic deposits of the Raizama Formation, southeastern Amazon Craton, Brazil. Integration of ichnologic and sedimentologic datasets suggests that these trace fossils record colonization of high-energy and well-oxygenated nearshore sandy environments. Chronostratigraphically, the presence of these vertical burrows indicates an age not older than early Cambrian for the Raizama Formation, which traditionally has been regarded as Ediacaran. Therefore, the Raizama ichnofauna illustrates the advent of modern Phanerozoic ecology marked by the Agronomic Revolution. The discovery of the Skolithos Ichnofacies in these shallow-marine strata suggests possible connections between some central Western Gondwana basins.

  9. Linguistic Diversity in the Pacific.

    Science.gov (United States)

    Crowley, Terry

    1999-01-01

    Reviews Peter Muhlhausler's book "Linguistic Ecology: Language Change and Linguistic Imperialism in the Pacific Region." Discusses the linguistic diversity of the Pacific, the linguistic impact of colonialism in the Pacific, and the role of linguists in the evolving linguistic situation in the Pacific. (Author/VWL)

  10. Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

    Science.gov (United States)

    Onimaru, Koh; Kuraku, Shigehiro

    2018-03-16

    Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as 'chronological reconstruction of ohnolog functions (CHROF)'. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

  11. Temperature-dependent respiration-growth relations in ancestral maize cultivars

    Science.gov (United States)

    Bruce N. Smith; Jillian L. Walker; Rebekka L. Stone; Angela R. Jones; Lee D. Hansen

    2001-01-01

    Shoots from 4- to 6-day old seedlings of seven ancestral or old cultivars of Zea mays L. were placed in a calorimeter. Dark metabolic heat rate (q) and CO2 production rate (RCO2) were measured at nine temperatures (5, 10, 15, 20, 25, 30, 35, 40, and 45 °C). Temperature dependencies of q and RCO2 were used to model response of both growth and substrate carbon conversion...

  12. Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Carroll, Sean Michael; Ortlund, Eric A; Thornton, Joseph W. (Emory-MED); (Harvard); (Oregon)

    2012-03-16

    Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs - reduced sensitivity to all hormones and increased selectivity for glucocorticoids - are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR-MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and

  13. Ancestral genes can control the ability of horizontally acquired loci to confer new traits.

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    H Deborah Chen

    2011-07-01

    Full Text Available Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P, protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.

  14. Hermeneutic Inquiry: Paying Heed to History and Hermes An Ancestral, Substantive, and Methodological Tale

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    Nancy J. Moules

    2002-09-01

    Full Text Available Hermeneutic or interpretive inquiry is a living tradition of interpretation with a rich legacy of theory, philosophy, and practice. This paper is not intended to be a treatise on the right way to view and practice this tradition, but an exploration of the legacies that inform the philosophy of practice as the author has taken it up. In this explication, the author examines the ancestral, philosophical, and methodological histories that inform a current practice of hermeneutic inquiry.

  15. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    DEFF Research Database (Denmark)

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures...

  16. Preliminary appraisal of ground water in and near the ancestral Missouri River Valley, northeastern Montana

    Science.gov (United States)

    Levings, G.W.

    1986-01-01

    A preliminary appraisal was conducted in and near the ancestral Missouri River valley in northeastern Montana to describe the groundwater resources and to establish a data base for the area. The data base then could be used for future evaluation of possible changes in water levels or water quality. In this area, consolidated aquifers are the Upper Cretaceous Fox Hills-lower Hell Creek aquifer and the overlying Paleocene Fort Union Formation. Unconsolidated aquifers are Pleistocene terrace gravel and glacial deposits and Holocene alluvial deposits. Aquifers are recharged by precipitation, infiltration of streamflow, and possibly leakage from lakes and potholes. Groundwater moves from topographically higher areas to the ancestral valley, then along the ancestral valley to the southwest. Water is discharged from aquifers by evapotranspiration, springs and seeps, movement directly into streams and lakes, and from pumping wells. Average well yields are greatest for irrigation wells completed in outwash gravel (886 gallons/min). Eighteen wells were completed in various aquifers to monitor potential long-term changes in water levels and water quality. Measured water levels declined about 2 ft. or less during the study (1982-85). Chemical analysis of groundwater samples indicated that concentrations of some dissolved constituents exceeded U.S. Environmental Protection Agency standards for drinking water. (USGS)

  17. Something for nothing? Reconstruction of ancestral character states in asterinid sea star development.

    Science.gov (United States)

    Keever, Carson C; Hart, Michael W

    2008-01-01

    Traits from early development mapped onto phylogenetic trees can potentially offer insight into the evolutionary history of development by inferring the states of those characters among ancestors at nodes in the phylogeny. A key and often-overlooked aspect of such mapping is the underlying model of character evolution. Without a well-supported and realistic model ("nothing"), character mapping of ancestral traits onto phylogenetic trees might often return results ("something") that lack a sound basis. Here we reconsider a challenging case study in this area of evolutionary developmental biology: the inference of ancestral states for ecological and morphological characters in the reproduction and larval development of asterinid sea stars. We apply improved analytical methods to an expanded set of asterinid phylogenetic data and developmental character states. This analysis shows that the new methods might generally offer some independent insight into choice of a model of character evolution, but that in the specific case of asterinid sea stars the quantitative features of the model (especially the relative probabilities of different directions of change) have an important effect on the results. We suggest caution in applying ancestral state reconstructions in the absence of an independently corroborated model of character evolution, and highlight the need for such modeling in evolutionary developmental biology.

  18. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference.

    Science.gov (United States)

    Gao, Nan; Zhang, Yan; Feng, Bing; Tang, Jijun

    2015-01-01

    Recent advances of technology have made it easy to obtain and compare whole genomes. Rearrangements of genomes through operations such as reversals and transpositions are rare events that enable researchers to reconstruct deep evolutionary history among species. Some of the popular methods need to search a large tree space for the best scored tree, thus it is desirable to have a fast and accurate method that can score a given tree efficiently. During the tree scoring procedure, the genomic structures of internal tree nodes are also provided, which provide important information for inferring ancestral genomes and for modeling the evolutionary processes. However, computing tree scores and ancestral genomes are very difficult and a lot of researchers have to rely on heuristic methods which have various disadvantages. In this paper, we describe the first genetic algorithm for tree scoring and ancestor inference, which uses a fitness function considering co-evolution, adopts different initial seeding methods to initialize the first population pool, and utilizes a sorting-based approach to realize evolution. Our extensive experiments show that compared with other existing algorithms, this new method is more accurate and can infer ancestral genomes that are much closer to the true ancestors.

  19. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat

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    Ross eGillette

    2015-03-01

    Full Text Available Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area, lateral hypothalamus, and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the medial preoptic area. Epigenetic related genes were affected by stress in the ventromedial hypothalamus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the lateral hypothalamus showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  20. Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity.

    Science.gov (United States)

    King, Benedict; Lee, Michael S Y

    2015-05-01

    Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  2. Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures.

    Science.gov (United States)

    Barriuso, Jorge; Martínez, María Jesús

    2017-01-03

    Fungal "Versatile carboxylic ester hydrolases" are enzymes with great biotechnological interest. Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling. Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. The properties of the ancestral candidates are discussed on the basis of their three-dimensional structural models, the hydrophobicity of the lid, and the substrate binding intramolecular tunnel, revealing all of them featured properties of these enzymes. The evolutionary history of the putative lipases revealed an increase on the length and hydrophobicity of the lid region, as well as in the size of the substrate binding pocket, during evolution time. These facts suggest the enzymes' specialization towards certain substrates and their subsequent loss of promiscuity. These results bring to light the presence of different pools of lipases in fungi with different habitats and life styles. Despite the consistency of the data gathered from reconstruction of ancestral sequences, the heterologous expression of some of these candidates would be essential to corroborate enzymes' activities.

  3. Lack of Social Support Raises Stress Vulnerability in Rats with a History of Ancestral Stress.

    Science.gov (United States)

    Faraji, Jamshid; Soltanpour, Nabiollah; Lotfi, Hamid; Moeeini, Reza; Moharreri, Ali-Reza; Roudaki, Shabnam; Hosseini, S Abedin; Olson, David M; Abdollahi, Ali-Akbar; Soltanpour, Nasrin; Mohajerani, Majid H; Metz, Gerlinde A S

    2017-07-13

    Stress is a primary risk factor for psychiatric disorders. However, it is not fully understood why some stressed individuals are more vulnerable to psychiatric disorders than others. Here, we investigated whether multigenerational ancestral stress produces phenotypes that are sensitive to depression-like symptoms in rats. We also examined whether social isolation reveals potentially latent sensitivity to depression-like behaviours. F4 female rats born to a lineage of stressed mothers (F0-F3) received stress in adulthood while housed in pairs or alone. Social isolation during stress induced cognitive and psychomotor retardation only in rats exposed to ancestral stress. Social isolation also hampered the resilience of the hypothalamic-pituitary-adrenal axis to chronic stress and reduced hippocampal volume and brain-derived neurotrophic factor (BDNF) expression. Thus, synergy between social isolation and stress may unmask a latent history of ancestral stress, and raises vulnerability to mental health conditions. The findings support the notion that social support critically promotes stress coping and resilience.

  4. The role of abiotic factors in the Cambrian Substrate Revolution: A review from the benthic community replacements of West Gondwana

    Science.gov (United States)

    Álvaro, J. Javier; Zamora, Samuel; Clausen, Sébastien; Vizcaïno, Daniel; Smith, Andrew B.

    2013-03-01

    The Cambrian Substrate Revolution refers to a substantial and "rapid" change to the nature of marine sedimentary substrates in the early Cambrian and is widely interpreted as a biologically-driven event, a direct response to evolutionary innovations in metazoan burrowing and the development of new shelly faunas. However, abiotic factors such as tectonic and climatic evolution also had the potential to restructure Cambrian substrates, and are here shown to be more plausible drivers of change in the benthic faunas of western Gondwana. The western Mediterranean region underwent a southward drift during Cambrian times, which drove a switch from subtropical carbonates to temperate siliciclastic substrates with short-term episodes of temperate carbonate productivity. As a result, microbial and shelly carbonates disappeared diachronously in a stepwise manner across the lower-middle Cambrian boundary interval. Archaeocyathan-microbial reefs were replaced by chancelloriid-eocrinoid-(spiculate) sponge meadows, in which the stepwise immigration of new echinoderm taxa was primarily controlled by extensional tectonic events, first recorded in rifting settings and later in passive-margin platforms. Availability of new kinds of substrate was thus the primary factor that controlled where and when evolutionary innovations in benthic strategies arose. Examples of this include the early Cambrian colonization of phosphatic hardgrounds and thrombolite crusts by chancelloriids, archaeocyathan and spiculate sponges, and the exploitation by benthos to the increasingly widespread availability of shelly grounds and carbonate firmgrounds by early-diagenetic cementation. A microbial mat/epifaunal antagonistic relationship is demonstrated for echinoderm pelmatozoans based on the non-overlapping palaeogeographic distributions of microbial reefs and mats versus mud-sticker pelmatozoans. Cambrian benthic communities thus evolved in parallel with substrates in response to abiotic factors rather

  5. Rugose corals at the Tournaisian-Viséan transition in the Central Taurides (S Turkey) - Palaeobiogeography and palaeoceanography of the Asian Gondwana margin

    Science.gov (United States)

    Denayer, Julien

    2015-02-01

    This paper gives the first taxonomic description of the Upper Tournaisian-Lower Viséan rugose coral fauna of the Yaricak Formation (Aladag Unit, Central Taurides, South Turkey). Fifteen species belonging to twelve genera were identified, one species is newly described: Eokoninckocarinia gemmina. The corals are stratigraphically distributed in four assemblages. The two typical assemblages of the Upper Tournaisian are composed of widely distributed taxa (Uralinia, Caninia, Proheterelasma, Zaphrentites). The assemblage crossing the Tournaisian-Viséan boundary is characterized by Eurasian and cosmopolitan and widely distributed taxa (Calmiussiphyllum, Siphonophyllia, Bifossularia Amygdalophyllum, Caninophyllum, Keyserlingophyllum) and Asian taxa (Kueichouphyllum). The youngest assemblage, dominated by Eokoninckocarinia gemmina sp. nov., has yielded foraminifers Moliniacian (Lower Viséan) in age. These assemblages form a low diversity level-bottom community which is typical of the South Palaeotethys 'Kueichouphyllum Zone' extending along the Asian margin of Gondwana (Cimmerian Terrane) during Lower Carboniferous times. As in the other Cimmerian blocks, all the corals are solitary and colonial taxa are virtually absent. This absence is tentatively explained by the high palaeolatitude (c. 50°S) position of the Cimmerian Terrane in the southern part of the Palaeotethys Ocean for this time slice. A cold-water palaeo-current running eastward along the Gondwana margin might also be considered as it possibly could explain the wide distribution of the Kueichouphyllum fauna, restricted east of Africa in the southern coast of the Palaeotethys. Palaeoceanography, palaeoclimate and facies issues are discussed as possible causes of the diversity gradient observed between the eastern (Australia, Malaya) and the western (North Africa) margin of the Gondwana.

  6. Tie points for Gondwana reconstructions from a structural interpretation of the Mozambique Basin, East Africa and the Riiser-Larsen Sea, Antarctica

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    J. Klimke

    2018-01-01

    Full Text Available Movements within early East Gondwana dispersal are poorly constrained, and there is debate about conjugate geologic structures and the timing and directions of the rifting and earliest seafloor spreading phases. We present a combined structural interpretation of multichannel reflection seismic profiles from offshore of northern Mozambique (East Africa and the conjugate Riiser-Larsen Sea (Antarctica. We find similar structural styles at the margins of both basins. At certain positions at the foot of the continental slope close to the continent–ocean transition, the basement is intensely deformed and fractured, a structural style very untypical for rifted continental margins. Sediments overlying the fractured basement are deformed and reveal toplap and onlap geometries, indicating a post-breakup deformation phase. We propose this unique deformation zone as a tie point for Gondwana reconstructions. Accordingly, we interpret the western flank of Gunnerus Ridge, Antarctica as a transform margin similar to the Davie Ridge offshore of Madagascar, implying that they are conjugate features. As the continental slope deformation is post-rift, we propose a two-phase opening scenario. A first phase of rifting and early seafloor spreading, likely in NW–SE direction, was subsequently replaced by a N–S-directed transform deformation phase overprinting the continent–ocean transition. From previously identified magnetic chrons and the sediment stratigraphy, this change in the spreading directions from NW–SE to N–S is suggested to have occurred by the late Middle Jurassic. We suggest that the second phase of deformation corresponds to the strike-slip movement of Madagascar and Antarctica and discuss implications for Gondwana breakup.

  7. The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials

    OpenAIRE

    Su?rez-Villota, Elkin Y.; Haro, Ronie E.; Vargas, Rodrigo A.; Gallardo, Milton H.

    2016-01-01

    Background The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials? cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GIS...

  8. Reply to the comments on: ;From source-to-sink: The Late Permian SW gondwana paleogeography and sedimentary dispersion unraveled by a multi-proxy analysis; [journal of South American earth sciences 70 (2016) 368-382] by Vesely & Schemiko

    Science.gov (United States)

    Alessandretti, Luciano; Warren, Lucas Veríssimo; Assine, Mario Luis; Machado, Rômulo; Lana, Cristiano

    2017-07-01

    The publication of the comments by Vesely & Schemiko (Comment on "From source-to-sink: The Late Permian SW Gondwana paleogeography and sedimentary dispersion unraveled by a multi-proxy analysis" by L. Alessandretti, R. Machado, L.V. Warren, M.L. Assine and C. Lana [Journal of South American Earth Sciences 70 (2016) 368-382], Journal of South American Earth Sciences, this issue) on our paper entitled "From source-to-sink: The Late Permian SW Gondwana paleogeography and sedimentary dispersion unraveled by a multi-proxy analysis" (L. Alessandretti, R. Machado, L.V. Warren, M.L. Assine and C. Lana (Journal of South American Earth Sciences 70 (2016) 368-382) provides a worthy opportunity to further clarify our observations and interpretations regarding the provenance of the Late Permian Rio do Rasto Formation and its implications on SW Gondwana paleogeography and sedimentary dispersion.

  9. Phylogeny and biogeography of the amphi-Pacific genus Aphananthe.

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    Mei-Qing Yang

    Full Text Available Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS and two plastid (psbA-trnH & trnL-trnF regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses. Aphananthe was supported to be monophyletic, with the eastern Asian A. aspera resolved as sister to a clade of the remaining four species. Aphananthe was inferred to have originated in the Late Cretaceous (71.5 mya, with 95% HPD: 66.6-81.3 mya, and the crown age of the genus was dated to be in the early Miocene (19.1 mya, with 95% HPD: 12.4-28.9 mya. The fossil record indicates that Aphananthe was present in the high latitude thermophilic forests in the early Tertiary, and experienced extinctions from the middle Tertiary onwards. Aphananthe originated in Europe based on the inference that included fossil and extant species, but eastern Asia was estimated to be the ancestral area of the clade of the extant species of Aphananthe. Both the West Gondwanan vicariance hypothesis and the boreotropics hypothesis could be excluded as explanation for its amphi-Pacific distribution. Long-distance dispersals out of eastern Asia into North America, southern and southeastern Asia and Australia, and Madagascar during the Miocene account for its wide intercontinental disjunct distribution.

  10. Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis

    Directory of Open Access Journals (Sweden)

    Pearson Gareth A

    2011-01-01

    Full Text Available Abstract Background Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated. Results Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence and the Shared Allele (SAD; based on alleles identity distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia. Conclusion These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization

  11. Characterizing genetic diversity of contemporary pacific chickens using mitochondrial DNA analyses.

    Directory of Open Access Journals (Sweden)

    Kelsey Needham Dancause

    Full Text Available BACKGROUND: Mitochondrial DNA (mtDNA hypervariable region (HVR sequences of prehistoric Polynesian chicken samples reflect dispersal of two haplogroups--D and E--by the settlers of the Pacific. The distribution of these chicken haplogroups has been used as an indicator of human movement. Recent analyses suggested similarities between prehistoric Pacific and South American chicken samples, perhaps reflecting prehistoric Polynesian introduction of the chicken into South America. These analyses have been heavily debated. The current distribution of the D and E lineages among contemporary chicken populations in the Western Pacific is unclear, but might ultimately help to inform debates about the movements of humans that carried them. OBJECTIVES: We sought to characterize contemporary mtDNA diversity among chickens in two of the earliest settled archipelagos of Remote Oceania, the Marianas and Vanuatu. METHODS: We generated HVR sequences for 43 chickens from four islands in Vanuatu, and for 5 chickens from Guam in the Marianas. RESULTS: Forty samples from Vanuatu and three from Guam were assigned to haplogroup D, supporting this as a Pacific chicken haplogroup that persists in the Western Pacific. Two haplogroup E lineages were observed in Guam and two in Vanuatu. Of the E lineages in Vanuatu, one was identical to prehistoric Vanuatu and Polynesian samples and the other differed by one polymorphism. Contrary to our expectations, we observed few globally distributed domesticate lineages not associated with Pacific chicken dispersal. This might suggest less European introgression of chickens into Vanuatu than expected. If so, the E lineages might represent lineages maintained from ancient Pacific chicken introductions. The Vanuatu sample might thus provide an opportunity to distinguish between maintained ancestral Pacific chicken lineages and replacement by global domesticates through genomic analyses, which could resolve questions of contemporary

  12. Eastern Pacific Ocean Conference

    Science.gov (United States)

    The promotion of interaction among investigators of all oceanographic disciplines studying the eastern Pacific Ocean was the goal of the 1990 Eastern Pacific Ocean Conference (EPOC), held October 17-19 on the snow-covered slopes of Mt. Hood, Oreg. Thirty oceanographers representing all disciplines attended.Dick Barber, Duke University Marine Lab, Beaufort, N.C., chaired a session on the eastern equatorial Pacific Ocean, emphasizing issues related to biological activity. Steve Ramp of the Naval Postgraduate School in Montery, Calif., chaired a session on recent results from northern and central California experiments. On October 19, following an early morning earthquake, a business meeting and discussions regarding a collaboration in future experiments were held.

  13. Revised model of the East Gondwana Break-up and formation of the Gateway between India and Antarctica

    Science.gov (United States)

    Leitchenkov, German; Guseva, Julia; Ivanov, Sergey; Golynsky, Alexander

    2017-04-01

    The history of break-up and sea-floor spreading between India and Antarctica long remained vague mainly because of the data scarcity off both continents. Geophysical studies carried out recently in the Enderby Basin (Southern Indian Ocean) provided new information and advanced our knowledge on this problem. Magnetic surveys discovered there a prominent linear high-amplitude bipolar magnetic anomaly (HBMA), which stretched more than 1000 km westward from the southern Kerguelen Plateau. This anomaly was interpreted by many as the contact between stretched continental crust and oceanic crust. Gaina et al. (1987) suggested the existence of an abandoned spreading centre in the eastern Enderby Basin and inferred that the Elan Bank (established as a microcontinent) was isolated from the India margin by a ridge jump at about M0 chron (c. 120 Ma). South of an abandoned spreading centre, they identified a series of magnetic anomalies from M2 to M9. New magnetic data collected in the western Enderby Basin and revision of all available geophysical data gives a new notion on the geodynamics of the East Gondwana break-up and separation of India from Antarctica. According to a new model, the HBMA corresponds to M34o chrone and its increased intensity can be explained by the emplacement of the Kerguelen Hotspot and thickening of the oceanic (magmatic) crust at that time. A relationship between hot-spots and appearance of high-amplitude magnetic anomalies is observed elsewhere in the World Ocean. In our model, the continent-ocean boundary is located about 150 km landward of the HBMA, and anomalies from M4 to M0 are identified between these features. The ridge jump (which isolated the Elan Bank) occurred about 110 Ma ago when the Kerguelen Hotspot moved toward the India margin. This model is consistent with the interpretation of sea-floor spreading history off Western Australia. An earlier (around 120 Ma) ridge jump probably occurred in the area of the southern Kerguelen Plateau

  14. Pacific Coastal Salmon Recovery Fund

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Congress established the Pacific Coastal Salmon Recovery Fund (PCSRF) to monitor the restoration and conservation of Pacific salmon and steelhead populations and...

  15. Do Père David's deer lose memories of their ancestral predators?

    Science.gov (United States)

    Li, Chunwang; Yang, Xiaobo; Ding, Yuhua; Zhang, Linyuan; Fang, Hongxia; Tang, Songhua; Jiang, Zhigang

    2011-01-01

    Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound) and domestic dogs (familiar non-predators), of tigers and wolves (ancestral predators), and of lions (potential naïve predator) to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat.

  16. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

    Directory of Open Access Journals (Sweden)

    Azevedo Nathália F

    2012-03-01

    Full Text Available Abstract Background Xenarthra (sloths, armadillos and anteaters represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome. B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4. The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.

  17. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

    Science.gov (United States)

    2012-01-01

    Background Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome). B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4). The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly. PMID:22429690

  18. Contrasting determinants of abundance in ancestral and colonized ranges of an invasive brood parasite

    Science.gov (United States)

    Hahn, D.C.; O'Connor, R.J.; Scott, J. Michael; Heglund, Patricia J.; Morrison, Michael L.; Haufler, Jonathan B.; Wall, William A.

    2002-01-01

    Avian species distributions are typically regarded as constrained by spatially extensive variables such as climate, habitat, spatial patchiness, and microhabitat attributes. We hypothesized that the distribution of a brood parasite depends as strongly on host distribution patterns as on biophysical factors and examined this hypothesis with respect to the national distribution of the Brown-headed Cowbird (Molothrus ater). We applied a classification and regression (CART) analysis to data from the Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) and derived hierarchically organized statistical models of the influence of climate and weather, cropping and land use, and host abundance and distribution on the distribution of the Brown-headed Cowbird within the conterminous United States. The model accounted for 47.2% of the variation in cowbird incidence, and host abundance was the top predictor with an R2 of 18.9%. The other predictors identified by the model (crops 15.7%, weather and climate 14.3%, and region 9.6%) fit the ecological profile of this cowbird. We showed that host abundance was independent of these environmental predictors of cowbird distribution. At the regional scale host abundance played a very strong role in determining cowbird abundance in the cowbird?s colonized range east and west of their ancestral range in the Great Plains (26.6%). Crops were not a major predictor for cowbirds in their ancestral range, although they are the most important predictive factor (33%) for the grassland passerines that are the cowbird?s ancestral hosts. Consequently our findings suggest that the distribution of hosts does indeed take precedence over habitat attributes in shaping the cowbird?s distribution at a national scale, within an envelope of constraint set by biophysical factors.

  19. Analysis of ancestral and functionally relevant CD5 variants in systemic lupus erythematosus patients.

    Directory of Open Access Journals (Sweden)

    Maria Carmen Cenit

    Full Text Available CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively as well as to investigate the potential role of CD5 on the development of SLE and/or SLE nephritis.The CD5 SNPs rs2241002 (C/T; Pro224Leu and rs2229177 (C/T; Ala471Val were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed.T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC haplotype, compared to the more recently derived Pro224-Val471 (CT. The same allelic combination was statistically associated with Lupus nephritis.The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients.

  20. Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification.

    Science.gov (United States)

    Harrington, S; Reeder, T W

    2017-02-01

    The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth-death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time. The HiSSE model also allows researchers to test state-dependent models against appropriate state-independent null models that have the same number of parameters as the state-dependent models being tested. We reanalyse two data sets that originally used BiSSE to reconstruct ancestral states within squamate reptiles and reached surprising conclusions regarding the evolution of toepads within Gekkota and viviparity across Squamata. We used this new method to demonstrate that there are many shifts in diversification rates across squamates. We then fit various HiSSE submodels and null models to the state and phylogenetic data and reconstructed states under these models. We found that there is no single, consistent signal for state-dependent diversification associated with toepads in gekkotans or viviparity across all squamates. Our reconstructions show limited support for the recently proposed hypotheses that toepads evolved multiple times independently in Gekkota and that transitions from viviparity to oviparity are common in Squamata. Our results highlight the importance of considering an adequate pool of models and null models when estimating diversification rate parameters and reconstructing ancestral states. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  1. Ancestral benzo[a]pyrene exposure affects bone integrity in F3 adult fish (Oryzias latipes).

    Science.gov (United States)

    Seemann, Frauke; Jeong, Chang-Bum; Zhang, Ge; Wan, Miles Teng; Guo, Baosheng; Peterson, Drew Ryan; Lee, Jae-Seong; Au, Doris Wai-Ting

    2017-02-01

    Benzo[a]pyrene (BaP) at an environmentally relevant concentration (1μg/L) has previously been shown to affect bone development in a transgenerational manner in F3 medaka (Oryzias latipes) larvae (17dph). Here, we provide novel histomorphometric data demonstrating that the impaired bone formation at an early life stage is not recoverable and can result in a persistent transgenerational impairment of bone metabolism in F3 adult fish. A decrease in bone thickness and the occurrence of microcracks in ancestrally BaP-treated adult male fish (F3) were revealed by MicroCt measurement and histopathological analysis. The expression of twenty conserved bone miRNAs were screened in medaka and their relative expression (in the F3 ancestral BaP treatment vs the F3 control fish) were determined by quantitative real-time PCR. Attempt was made to link bone miRNA expression with the potential target bone mRNA expression in medaka. Five functional pairs of mRNA/miRNA were identified (Osx/miR-214, Col2a1b/miR-29b, Runx2/miR-204, Sox9b/miR-199a-3p, APC/miR-27b). Unique knowledge of bone-related miRNA expression in medaka in response to ancestral BaP-exposure in the F3 generation is presented. From the ecological risk assessment perspective, BaP needs to be regarded as a transgenerational skeletal toxicant which exerts a far-reaching impact on fish survival and fitness. Given that the underlying mechanisms of cartilage/bone formation are conserved between medaka and mammals, the results may also shed light on the potential transgenerational effect of BaP on skeletal disorders in mammals/humans. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Pharo Elizabeth A

    2012-06-01

    Full Text Available Abstract Background The marsupial early lactation protein (ELP gene is expressed in the mammary gland and the protein is secreted into milk during early lactation (Phase 2A. Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine colostrum trypsin inhibitor (CTI protein. Although ELP and CTI both have a single bovine pancreatic trypsin inhibitor (BPTI-Kunitz domain and are secreted only during the early lactation phases, their evolutionary history is yet to be investigated. Results Tammar ELP was isolated from a genomic library and the fat-tailed dunnart and Southern koala ELP genes cloned from genomic DNA. The tammar ELP gene was expressed only in the mammary gland during late pregnancy (Phase 1 and early lactation (Phase 2A. The opossum and fat-tailed dunnart ELP and cow CTI transcripts were cloned from RNA isolated from the mammary gland and dog CTI from cells in colostrum. The putative mature ELP and CTI peptides shared 44.6%-62.2% similarity. In silico analyses identified the ELP and CTI genes in the other species examined and provided compelling evidence that they evolved from a common ancestral gene. In addition, whilst the eutherian CTI gene was conserved in the Laurasiatherian orders Carnivora and Cetartiodactyla, it had become a pseudogene in others. These data suggest that bovine CTI may be the ancestral gene of the Artiodactyla-specific, rapidly evolving chromosome 13 pancreatic trypsin inhibitor (PTI, spleen trypsin inhibitor (STI and the five placenta-specific trophoblast Kunitz domain protein (TKDP1-5 genes. Conclusions Marsupial ELP and eutherian CTI evolved from an ancestral therian mammal gene before the divergence of marsupials and eutherians between 130 and 160 million years ago. The retention of the ELP gene in marsupials suggests that this early lactation-specific milk protein may have an important role in the immunologically naïve young of these species.

  3. Do Père David's deer lose memories of their ancestral predators?

    Directory of Open Access Journals (Sweden)

    Chunwang Li

    Full Text Available Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound and domestic dogs (familiar non-predators, of tigers and wolves (ancestral predators, and of lions (potential naïve predator to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat.

  4. Pb-Nd Isotopes Indicate the Origin of Island Arc Terranes in the Early Paleozoic Pacific.

    Science.gov (United States)

    Münker

    2000-03-01

    The Takaka Terrane in New Zealand is one of the best exposed arc fragments of the early Paleozoic Australian-Antarctic convergent margin and constitutes one of the most outboard terranes of this margin in paleogeographic reconstructions. Pb-Nd isotope compositions of clinopyroxenes from the Cambrian Devil River Volcanics of the Takaka Terrane enable identification of the location of the terrane in the Paleo-Pacific Ocean. The Devil River Volcanics, a suite of primitive arc and back-arc rocks, are interbedded with the partly continent-derived Haupiri Group sediments. Extremely radiogenic Pb and unradiogenic Nd compositions in the arc rocks cannot be explained by assimilation of the Haupiri Group sediments or a continental basement of such a composition. Pb isotope compositions of the Takaka Terrane sediments are much less radiogenic and overlap with crustal compositions of the Lachlan Fold Belt in Australia, suggesting that both units are derived from one source, the Australian-Antarctic Pacific margin. Pb-Nd isotope compositions in the Devil River Volcanics reflect contamination of their mantle sources by subducted sediments derived from Archean provinces in either Antarctica or Laurentia. Both provinces show characteristically high 207Pb/204Pb500 and were located at the Pacific rim in the Cambrian. Mixing between mantle and Proterozoic continental material from present western South America or eastern Laurentia cannot explain the high 207Pb/204Pb500 in the New Zealand rocks. As in New Zealand, extreme spreads in Pb-Nd isotope compositions in other Cambrian volcano-sedimentary sequences in southeast Australia and Tasmania can be explained by the same model, suggesting that all these fragments originated along the Australian-Antarctic Gondwana margin. Pb isotope compositions of arc rocks, therefore, provide a new tool for terrane analysis in the early Paleozoic Pacific ocean.

  5. Allelic Lineages of the Ficolin Genes (FCNs) Are Passed from Ancestral to Descendant Primates

    DEFF Research Database (Denmark)

    Hummelshøj, Tina; Nissen, Janna; Fog, Lea Munthe

    2011-01-01

    The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, res...... serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species....

  6. Allelic lineages of the ficolin genes (FCNs) are passed from ancestral to descendant primates

    DEFF Research Database (Denmark)

    Hummelshøj, Tina; Nissen, Janna; Munthe-Fog, Lea

    2011-01-01

    The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, res...... serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species....

  7. Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

    Directory of Open Access Journals (Sweden)

    Zhebentyayeva Tatyana

    2006-04-01

    Full Text Available Abstract Background Due to the lack of availability of large genomic sequences for peach or other Prunus species, the degree of synteny conservation between the Prunus species and Arabidopsis has not been systematically assessed. Using the recently available peach EST sequences that are anchored to Prunus genetic maps and to peach physical map, we analyzed the extent of conserved synteny between the Prunus and the Arabidopsis genomes. The reconstructed pseudo-ancestral Arabidopsis genome, existed prior to the proposed recent polyploidy event, was also utilized in our analysis to further elucidate the evolutionary relationship. Results We analyzed the synteny conservation between the Prunus and the Arabidopsis genomes by comparing 475 peach ESTs that are anchored to Prunus genetic maps and their Arabidopsis homologs detected by sequence similarity. Microsyntenic regions were detected between all five Arabidopsis chromosomes and seven of the eight linkage groups of the Prunus reference map. An additional 1097 peach ESTs that are anchored to 431 BAC contigs of the peach physical map and their Arabidopsis homologs were also analyzed. Microsyntenic regions were detected in 77 BAC contigs. The syntenic regions from both data sets were short and contained only a couple of conserved gene pairs. The synteny between peach and Arabidopsis was fragmentary; all the Prunus linkage groups containing syntenic regions matched to more than two different Arabidopsis chromosomes, and most BAC contigs with multiple conserved syntenic regions corresponded to multiple Arabidopsis chromosomes. Using the same peach EST datasets and their Arabidopsis homologs, we also detected conserved syntenic regions in the pseudo-ancestral Arabidopsis genome. In many cases, the gene order and content of peach regions was more conserved in the ancestral genome than in the present Arabidopsis region. Statistical significance of each syntenic group was calculated using simulated

  8. Sustainability of ancestral methods of agricultural production in Perú: ¿keep or replace?

    Directory of Open Access Journals (Sweden)

    Dani Eduardo Vargas Huanca

    2016-09-01

    Full Text Available Based on the success of some Andean products such as quinoa, potatoes or maca in international food trade and the growing environmental degradation facing developing countries, resulting from intensive exploitation activities; Our research seeks to show the trend that is assumed from the academic / scientific community and public officials in the food sector in Peru, against the need to maintain sustainable various ancestral modes of agricultural production (case quinoa, for it analyze quantitative and qualitative obtained from public institutions and Peruvian universities.

  9. Fish faunas from the Late Jurassic (Tithonian) Vaca Muerta Formation of Argentina: One of the most important Jurassic marine ichthyofaunas of Gondwana

    Science.gov (United States)

    Gouiric-Cavalli, Soledad; Cione, Alberto Luis

    2015-11-01

    The marine deposits of the Vaca Muerta Formation (Tithonian-Berriasian) houses one of the most diverse Late Jurassic ichthyofaunas of Gondwana. However, most of the specimens remain undescribed. Jurassic fishes have been recovered from several localities at Neuquén Province (i.e., Picún Leufú, Plaza Huincul, Cerro Lotena, Portada Las Lajas, Los Catutos, and Arroyo Covunco) but also from Mendoza Province (i.e., La Valenciana, Los Molles, and Arroyo del Cajón Grande). Presently, the fish fauna of Los Catutos, near Zapala city (Neuquén Province), has yielded the highest number of specimens, which are taxonomically and morphologically diverse. At Los Catutos locality, the Vaca Muerta Formation is represented by the Los Catutos Member, which is considered the only lithographic limestones known in the Southern Hemisphere. Here, we review the Tithonian fish faunas from the Vaca Muerta Formation. During Late Jurassic times, the actual Argentinian territory could have been a morphological diversification center, at least for some actinopterygian groups. The apparently lower species diversity recorded in marine Jurassic ichthyofaunas of Argentina (and some Gondwanan countries) in comparison with Chilean and European fish faunas could be related to the fish paleontological research history in Gondwana and the low number of detailed studies of most of specimens recorded.

  10. Fiji in the South Pacific.

    Science.gov (United States)

    Scott, Rosalind; Semaan, Leslie

    This text introduces Fiji and other island nations located in the Pacific, the world's largest ocean. Cut off from the world by vast expanses of water, these people developed a unique culture. Contents include: Teacher Overview, Geography of the South Pacific Islands, History of the South Pacific, Fiji, Traditional Village Life, Yaquna Ceremony,…

  11. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure

    Science.gov (United States)

    DeGiorgio, Michael; Rosenberg, Noah A.

    2016-01-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R* Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure. PMID:27086043

  12. Pacific Island Pharmacovigilance

    DEFF Research Database (Denmark)

    McEwen, John; Vestergaard, Lasse S.; Sanburg, Amanda L C

    2016-01-01

    Many Pacific Island countries (PICs) are recipients of funding support from the Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund). However, most of these countries cannot be expected to meet Global Fund and World Health Organization (WHO) minimum requirements for a functioning...

  13. Magmatism during Gondwana breakup

    DEFF Research Database (Denmark)

    van der Meer, Quinten; Scott, J.M.; Waight, Tod Earle

    2013-01-01

    Newly determined mid-late Cretaceous 40Ar/39Ar ages on megacrystic kaersutite from lamprophyre dikes in central and north Westland (New Zealand) are presented. These ages (88 Ma, 86 Ma and 68 Ma) indicate that the intrusion of mafic dikes was not necessarily restricted to the previously establish...

  14. Jurassic fishes of Gondwana

    OpenAIRE

    Adriana López-Arbarello; Oliver W. M. Rauhut; Katrin Moser

    2008-01-01

    The Jurassic is an important period for understanding the origin of modern fish faunas, since it saw the first radiation - and in some cases the origin - of most modern groups. In chondrichthyans, neoselachian sharks and rays diversified during this time. In actinopterygians, the neopterygians, and among them the teleosts, experienced an important radiation, which led to the appearance of several of the modern teleosts groups. In the sarcopterygians, dipnoans and actinistians approached their...

  15. Transcripts of Vp-1 homeologues are misspliced in modern wheat and ancestral species.

    Science.gov (United States)

    McKibbin, Rowan S; Wilkinson, Mark D; Bailey, Paul C; Flintham, John E; Andrew, Lucy M; Lazzeri, Paul A; Gale, Mike D; Lenton, John R; Holdsworth, Michael J

    2002-07-23

    The maize (Zea mays) Viviparous 1 (Vp1) transcription factor has been shown previously to be a major regulator of seed development, simultaneously activating embryo maturation and repressing germination. Hexaploid bread wheat (Triticum aestivum) caryopses are characterized by relatively weak embryo dormancy and are susceptible to preharvest sprouting (PHS), a phenomenon that is phenotypically similar to the maize vp1 mutation. Analysis of Vp-1 transcript structure in wheat embryos during grain development showed that each homeologue produces cytoplasmic mRNAs of different sizes. The majority of transcripts are spliced incorrectly, contain insertions of intron sequences or deletions of coding region, and do not have the capacity to encode full-length proteins. Several VP-1-related lower molecular weight protein species were present in wheat embryo nuclei. Embryos of a closely related tetraploid species (Triticum turgidum) and ancestral diploids also contained misspliced Vp-1 transcripts that were structurally similar or identical to those found in modern hexaploid wheat, which suggests that compromised structure and expression of Vp-1 transcripts in modern wheat are inherited from ancestral species. Developing embryos from transgenic wheat grains expressing the Avena fatua Vp1 gene showed enhanced responsiveness to applied abscisic acid compared with the control. In addition, ripening ears of transgenic plants were less susceptible to PHS. Our results suggest that missplicing of wheat Vp-1 genes contributes to susceptibility to PHS in modern hexaploid wheat varieties and identifies a possible route to increase resistance to this environmentally triggered disorder.

  16. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

    Science.gov (United States)

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi. © 2016 by The Mycological Society of America.

  17. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations.

    Science.gov (United States)

    Omberg, Larsson; Salit, Jacqueline; Hackett, Neil; Fuller, Jennifer; Matthew, Rebecca; Chouchane, Lotfi; Rodriguez-Flores, Juan L; Bustamante, Carlos; Crystal, Ronald G; Mezey, Jason G

    2012-06-26

    Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  18. A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.

    Science.gov (United States)

    Lartillot, Nicolas

    2014-02-15

    Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny. Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom. The program is freely available at www.phylobayes.org.

  19. Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures†

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H.; Sharan, Roded; Nussinov, Ruth

    2012-01-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution. PMID:21127809

  20. Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H; Sharan, Roded; Nussinov, Ruth; Przytycka, Teresa M; Panchenko, Anna R

    2011-03-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution.

  1. Evidence for Ancestral Programming of Resilience in a Two-Hit Stress Model

    Directory of Open Access Journals (Sweden)

    Jamshid Faraji

    2017-05-01

    Full Text Available In a continuously stressful environment, the effects of recurrent prenatal stress (PS may accumulate across generations and alter stress vulnerability and resilience. Here, we report in female rats that a family history of recurrent ancestral PS facilitates certain aspects of movement performance, and that these benefits are abolished by the experience of a second hit, induced by a silent ischemia during adulthood. Female F4-generation rats with and without a family history of cumulative multigenerational PS (MPS were tested for skilled motor function before and after the induction of a minor ischemic insult by endothelin-1 infusion into the primary motor cortex. MPS resulted in improved skilled motor abilities and blunted hypothalamic-pituitary-adrenal (HPA axis function compared to non-stressed rats. Deep sequencing revealed downregulation of miR-708 in MPS rats along with upregulation of its predicted target genes Mapk10 and Rasd2. Through miR-708 stress may regulate mitogen-activated protein kinase (MAPK pathway activity. Hair trace elemental analysis revealed an increased Na/K ratio, which suggests a chronic shift in adrenal gland function. The ischemic lesion activated the HPA axis in MPS rats only; the lesion, however, abolished the advantage of MPS in skilled reaching. The findings indicate that MPS generates adaptive flexibility in movement, which is challenged by a second stressor, such as a neuropathological condition. Thus, a second “hit” by a stressor may limit behavioral flexibility and neural plasticity associated with ancestral stress.

  2. Bearing the unbearable: ancestral transmission through dreams and moving metaphors in the analtyic field.

    Science.gov (United States)

    Pickering, Judith

    2012-11-01

    This paper explores how untold and unresolved intergenerational trauma may be transmitted through unconscious channels of communication, manifesting in the dreams of descendants. Unwitting carriers for that which was too horrific for their ancestors to bear, descendants may enter analysis through an unconscious need to uncover past secrets, piece together ancestral histories before the keys to comprehending their terrible inheritance die with their forebears. They seek the relational containment of the analytic relationship to provide psychological conditions to bear the unbearable, know the unknowable, speak the unspeakable and redeem the unredeemable. In the case of 'Rachael', initial dreams gave rise to what Hobson (1984) called 'moving metaphors of self' in the analytic field. Dream imagery, projective and introjective processes in the transference-countertransference dynamics gradually revealed an unknown ancestral history. I clarify the back and forth process from dream to waking dream thoughts to moving metaphors and differentiate the moving metaphor from a living symbol. I argue that the containment of the analytic relationship nested within the security of the analytic space is a necessary precondition for such healing processes to occur. © 2012, The Society of Analytical Psychology.

  3. Long-lasting Cadomian magmatic activity along an active northern Gondwana margin: U-Pb zircon and Sr-Nd isotopic evidence from the Brunovistulian Domain, eastern Bohemian Massif

    Czech Academy of Sciences Publication Activity Database

    Soejono, I.; Janoušek, V.; Žáčková, E.; Sláma, Jiří; Konopásek, J.; Machek, Matěj; Hanžl, P.

    2017-01-01

    Roč. 106, č. 6 (2017), s. 2109-2129 ISSN 1437-3254 Institutional support: RVO:67985530 ; RVO:67985831 Keywords : Cadomian magmatic arc * Brunovistulian Domain * Bohemian Massif * Gondwana margin * U–Pb geochronology * geochemistry Subject RIV: DB - Geology ; Mineralogy; DC - Siesmology, Volcanology, Earth Structure (GFU-E) OBOR OECD: Geology; Volcanology (GFU-E) Impact factor: 2.283, year: 2016

  4. Transition from island-arc to passive setting on the continental margin of Gondwana: U-Pb zircon dating of Neoproterozoic metaconglomerates from the SE margin of the Teplá-Barrandian Unit, Bohemian Massif

    Czech Academy of Sciences Publication Activity Database

    Sláma, Jiří; Dunkley, D. J.; Kachlík, V.; Kusiak, M. A.

    2008-01-01

    Roč. 461, 1-4 (2008), s. 44-59 ISSN 0040-1951 Institutional research plan: CEZ:AV0Z30130516 Keywords : Bohemian Massif * Teplá–Barrandian Unit * Neoproterozoic * Armorican Terrane Assemblage * Gondwana * zircon dating Subject RIV: DB - Geology ; Mineralogy Impact factor: 1.677, year: 2008

  5. A Study on Ground Water Resource Management in Gondwana Formations in Western Part of West Godavari District Andhra Pradesh India

    Science.gov (United States)

    Singara, S.

    2006-05-01

    Groundwater source forms nearly fifty percent of the total irrigation in the country. With green revolution, there has been an increasing demand for water for agricultural and this led to overexploitation of groundwater resources in many parts of the state and the study area is not an exception. With the success of groundwater exploration and development through deep tube wells in the study area, the farmers plunged into hectic activity of tapping groundwater. The present study was taken up to assess to groundwater recharge and draft in the area and to suggest remedial measures to redress overexploitation condition. The study area is underlain by a vide range of geological formations from Archean to Tertiary age. Crystallines consist of two-tier setting of aquifers with weathered and fracture zones. The Gondwana formations with Sandstone, shale and clay zones form unconfined to confined aquifer system. Deccan trap basalt occurs subsurface in some parts. Crystalline aquifers are exploited through borewells with a depth range of 29 to 101.5 m. Static water levels range in depth from 2.5 and 19.27 m bgl. Their yields range from 2.53 to 19.27 m3/hr. Sedimentary aquifers are exploited through tube wells with a depth range of 18 to 293 m and static water levels range from 2.1m agl to 48.0 m bgl. Yields of the wells vary form 1.3 to 67 m3 /hr. Groundwater is lifted by monoblock pumpsets of 5 HP in some places but mostly by submersible pumpsets with 5 to 12.5 HP. The tube wells are subjected to pumping from 5 to 18 hours per day depending on availability of electricity (power supply). They are operated form 90 days to throughout the year in different places. Groundwater development in the study area shows a steady increase since 1960 with number of tube wells uniformly increasing in each decade, from an initial figure of 592 wells in 1960 to 17,173 tube wells in 2002. Crop pattern was shifted from dry crops to paddy and sugar cane as major crops and irrigated dry crops

  6. Chemostratigraphy of the lower Bambuí Group, southwestern São Francisco Craton, Brazil: insights on Gondwana paleoenvironments

    Directory of Open Access Journals (Sweden)

    Matheus Kuchenbecker

    geochemistry of the carbonates is controlled by their terrigenous content (mostly quartz and clay minerals which is concentrated in the lower units. Samples free of terrigenous contamination show Y/Ho ratios ranging from 25 to 50, suggesting a freshwater input during carbonate deposition. It is concluded that the diamictite has a glaciogenic origin and is covered by a cap carbonate. This pair has been identified along the basin and is related to one of the main Neoproterozoic glaciations. Discrepancy between the 86Sr/87Sr values and the global variation curves can be related to freshwater input during the carbonate deposition. Based on the regional tectonic context, the Bambuí Basin may have been a restricted marine basin, totally or partially surrounded by mountain ranges within Gondwana, in the Neoproterozoic/Paleozoic boundary. In its early stages, the sedimentation was influenced by a global glacial event, whose melting phase was responsible by freshwater input in the basin. The gradual rise of the temperature was followed by an increase of the biological activity. Finally, a sudden increase in the biological activity could have been driven by paleogeographic changes caused by the active tectonic.

  7. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

    2011-01-01

    event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus......) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report...

  8. Breadth of T cell responses after immunization with adenovirus vectors encoding ancestral antigens or polyvalent papillomavirus antigens

    DEFF Research Database (Denmark)

    Ragonnaud, Emeline; Pedersen, Anders Gorm; Holst, Peter Johannes

    2017-01-01

    - either by inducing cross-reactive T cells or by administering a polyvalent vaccine. To test these strategies, we designed 3 ancestral and 2 circulating sequences based on the two domains of the E1 and E2 proteins of papillomaviruses (PVs) that exhibit the highest degree of conservation in comparison...... circulating strains and a putative ancestor of oncogenic HPVs, we showed that the ancestral vaccine antigen has to be approximately 90% identical to the circulating PVs before a marked drop of ~90% mean CD8+ T cell responses ensues. Interestingly, the combination of two or three type-specific PV vaccines did...... not induce a significant decrease of the CD8+ T cell response to the individual targeted PV types. Polyvalent HPV vaccine based on the E1 and E2 proteins seem to be capable of triggering responses towards more than one type of PV while the cross-reactivity of ancestral vaccine seems insufficient...

  9. Petrologic, tectonic, and metallogenic evolution of the southern segment of the ancestral Cascades magmatic arc, California and Nevada

    Science.gov (United States)

    du Bray, Edward A.; John, David A.; Cousens, Brian L.

    2013-01-01

    Ongoing arc magmatism along western North America was preceded by ancestral arc magmatism that began ca. 45 Ma and evolved into modern arc volcanism. The southern ancestral arc segment, active from ca. 30 to 3 Ma, adjoins the northern segment in northern California across a proposed subducted slab tear. The east edge of the Walker Lane approximates the east edge of the southern arc whose products, mostly erupted from stratovolcanoes and lava dome complexes arrayed along the crest of the ancestral arc, extend down the west flank of the Sierra Nevada. Southern arc segment rocks include potassic, calc-alkaline intermediate- to silicic-composition lava flows, lava dome complexes, and associated volcaniclastic deposits.

  10. The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis

    Science.gov (United States)

    Fondi, Marco; Brilli, Matteo; Emiliani, Giovanni; Paffetti, Donatella; Fani, Renato

    2007-01-01

    Background It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution. Results The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted. Conclusion The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single

  11. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang

    2005-01-01

    We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable...... in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences. Udgivelsesdato: 2005-Sep...

  12. Effects of ancestral x irradiation followed by random mating on body weight of rats

    International Nuclear Information System (INIS)

    Gianola, D.; Chapman, A.B.; Rutledge, J.J.

    1977-01-01

    Effects of nine generations of 450R per generation of ancestral spermatogonial x irradiation of inbred rats on body weight were examined. After six generations of random mating (avoiding inbreeding) following the termination of irradiation, descendants of irradiated males (R) were significantly lighter than their controls (C) at 3 and 6 weeks, but not at 10 weeks of age. However, differences in growth between R and C populations were small. Among-litter and within-litter variance estimates were generally larger in the R lines than in the C lines, suggesting that selection responses would be greater in R than in C lines. In conjunction with previous evidence--obtained during the irradiation phase of the experiment--this suggested that more rapid response to selection for 6-week body weight, in particular, might accrue in the R lines

  13. A phenol-enriched cuticle is ancestral to lignin evolution in land plants.

    Science.gov (United States)

    Renault, Hugues; Alber, Annette; Horst, Nelly A; Basilio Lopes, Alexandra; Fich, Eric A; Kriegshauser, Lucie; Wiedemann, Gertrud; Ullmann, Pascaline; Herrgott, Laurence; Erhardt, Mathieu; Pineau, Emmanuelle; Ehlting, Jürgen; Schmitt, Martine; Rose, Jocelyn K C; Reski, Ralf; Werck-Reichhart, Danièle

    2017-03-08

    Lignin, one of the most abundant biopolymers on Earth, derives from the plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for plant colonization of land. Early diverging land plants do not form lignin, but already have elements of its biosynthetic machinery. Here we delete in a moss the P450 oxygenase that defines the entry point in angiosperm lignin metabolism, and find that its pre-lignin pathway is essential for development. This pathway does not involve biochemical regulation via shikimate coupling, but instead is coupled with ascorbate catabolism, and controls the synthesis of the moss cuticle, which prevents desiccation and organ fusion. These cuticles share common features with lignin, cutin and suberin, and may represent the extant representative of a common ancestor. Our results demonstrate a critical role for the ancestral phenolic metabolism in moss erect growth and cuticle permeability, consistent with importance in plant adaptation to terrestrial conditions.

  14. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

    Science.gov (United States)

    Baldwin, Maude W.; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J.; Klasing, Kirk C.; Misaka, Takumi; Edwards, Scott V.; Liberles, Stephen D.

    2015-01-01

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. PMID:25146290

  15. Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor.

    Science.gov (United States)

    Baldwin, Maude W; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J; Klasing, Kirk C; Misaka, Takumi; Edwards, Scott V; Liberles, Stephen D

    2014-08-22

    Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. Copyright © 2014, American Association for the Advancement of Science.

  16. Hagfish (cyclostomata, vertebrata): searching for the ancestral developmental plan of vertebrates.

    Science.gov (United States)

    Kuratani, Shigeru; Ota, Kinya G

    2008-02-01

    The phylogenetic position of the hagfish remains enigmatic. In contrast to molecular data that suggest monophyly of the cyclostomes, several morphological features imply a more ancestral state of this animal compared with the lampreys. To resolve this question requires an understanding of the embryology of the hagfish, especially of the neural crest. The early development of the hagfish has long remained a mystery. We collected a shallow-water-dwelling hagfish, Eptatretus burgeri, set up an aquarium tank designed to resemble its habitat, and successfully obtained several embryos. By observing the histology and expression of genes known to play fundamental roles in the neural crest, we found that the hagfish crest develops as delaminating migratory cells, as in other vertebrates. We conclude that the delaminating neural crest is a vertebrate synapomorphy that seems to have appeared from the beginning of their evolutionary history, before the splitting away of the hagfish lineage. (c) 2008 Wiley Periodicals, Inc.

  17. Diachronism in the late Neoproterozoic-Cambrian arc-rift transition of North Gondwana: A comparison of Morocco and the Iberian Ossa-Morena Zone

    Science.gov (United States)

    Álvaro, J. Javier; Bellido, Félix; Gasquet, Dominique; Pereira, M. Francisco; Quesada, Cecilio; Sánchez-García, Teresa

    2014-10-01

    In the northwestern border of the West African craton (North Gondwana), a transition from late Neoproterozoic subduction/collision to Cambrian rift processes was recorded in the Anti-Atlas (Morocco) and in the Ossa-Morena Zone (Iberia). Cambrian rifting affected both Pan-African and Cadomian basements in a stepwise and diachronous way. Subsequently, both areas evolved into a syn-rift margin episodically punctuated by uplift and tilting that precluded Furongian sedimentation. A comparison of sedimentary, volcanic and geodynamic evolution is made in the late Neoproterozoic (Pan-African and Cadomian) belts and Cambrian rifts trying to solve the apparent diachronous (SW-NE-trending) propagation of an early Palaeozoic rifting regime that finally led to the opening of the Rheic Ocean.

  18. Evolução tectónica do Gondwana durante o Paleozóico; um processo crucial na evolução da Terra

    OpenAIRE

    Dias, Rui; Schmitt, Renata

    2013-01-01

    Durante o Paleozóico a actuação de diversos ciclos de Wilson levaram, não só à unificação da Gondwana mas também da própria Pangeia. Se alguns destes ciclos são exclusivamente paleozóicos (é o caso do orógeno Varisco nos sectores setentrionais), outros resultam de processos extensivos iniciados no final do Neoproterozóico e cujas fases colisionais só ocorreram no Paleozóico inferior (e.g. orogenia Búzios - SE do Brasil). Neste simpósio serão abordados os processos e mecanismos associados à ev...

  19. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    Science.gov (United States)

    Lehmann, Tobias; Hess, Martin; Melzer, Roland R

    2012-01-01

    The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes.

  20. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    Directory of Open Access Journals (Sweden)

    Tobias Lehmann

    Full Text Available The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora and Limulus polyphemus (Xiphosura. This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes.

  1. Wiring a Periscope – Ocelli, Retinula Axons, Visual Neuropils and the Ancestrality of Sea Spiders

    Science.gov (United States)

    Lehmann, Tobias; Heß, Martin; Melzer, Roland R.

    2012-01-01

    The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a ‘periscope’ or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon “pseudoinverted” retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have ‘looked’ like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes. PMID:22279594

  2. Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family

    Directory of Open Access Journals (Sweden)

    Teesta Naskar

    2018-02-01

    Full Text Available Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9 Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A > C [p.Ile154Leu], c.541G > A [p.Ala181Thr], c.2036G > C [p.Arg679Pro] and c.2059A > G [p.Lys687Glu] result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading.

  3. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  4. Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family.

    Science.gov (United States)

    Naskar, Teesta; Faruq, Mohammed; Banerjee, Priyajit; Khan, Massarat; Midha, Rashi; Kumari, Renu; Devasenapathy, Subhashree; Prajapati, Bharat; Sengupta, Sanghamitra; Jain, Deepti; Mukerji, Mitali; Singh, Nandini Chatterjee; Sinha, Subrata

    2018-02-01

    Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A>C [p.Ile154Leu], c.541G>A [p.Ala181Thr], c.2036G>C [p.Arg679Pro] and c.2059A>G [p.Lys687Glu]) result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Evolutionary History of Assassin Bugs (Insecta: Hemiptera: Reduviidae): Insights from Divergence Dating and Ancestral State Reconstruction

    Science.gov (United States)

    Hwang, Wei Song; Weirauch, Christiane

    2012-01-01

    Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp.) and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies) to date based on molecular data (5 markers). This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11–14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma), but significant lineage diversification only began in the Late Cretaceous (97 Ma). The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of reduviids and clears

  6. Age and kinematics of ductile deformation in the Cerro Durazno area, NW Argentina: Significance for orogenic processes operating at the western margin of Gondwana during Ordovician - Silurian times

    Science.gov (United States)

    Wegmann, Maja I.; Riller, Ulrich; Hongn, Fernando D.; Glodny, Johannes; Oncken, Onno

    2008-07-01

    The Cerro Durazno Pluton belongs to a suite of Paleozoic granitoid intrusions in NW-Argentina, that are central for understanding the tectonic setting of the western margin of Gondwana in Ordovician and Silurian times. The pluton and its host rocks were tectonically overprinted by metamorphic mineral shape fabrics formed under middle greenschist-facies metamorphic conditions and associated with the nearby Agua Rosada Shear Zone. Kinematic analysis of the shear zone based on the geometric relationship between individual segments of the shear plane and principal axes of mineral fabric ellipsoids indicates reverse-sense of shear with a minor component of left-lateral displacement. This is compatible with the kinematics of other ductile deformation zones in this area, collectively forming a network, which accomplished orogen-parallel extension in addition to vertical thickening. Using the Rb-Sr isotopic system, an undeformed pegmatite dike of the Cerro Durazno Pluton was dated at 455.8 ± 3.6 Ma and mineral fabrics of the Agua Rosada Shear Zone formed at middle greenschist-facies metamorphism gave deformation ages of 437.0 ± 3.8 Ma and ⩽428.4 ± 4.5 Ma. Thus, tectonic overprint at low metamorphic grade occurred about 20-30 Ma after terminal magmatism in the Cerro Durazno area. Our data from the Cerro Durazno area and regional considerations suggest that the western margin of Gondwana was characterized by orogen-parallel extension in addition to crustal thickening as well as episodes of magmatism and ductile deformation that varied greatly in time and space.

  7. New age constraints on the palaeoenvironmental evolution of the late Paleozoic back-arc basin along the western Gondwana margin of southern Peru

    Science.gov (United States)

    Boekhout, F.; Reitsma, M. J.; Spikings, R.; Rodriguez, R.; Ulianov, A.; Gerdes, A.; Schaltegger, U.

    2018-03-01

    The tectonic evolution of the western Gondwana margin during Pangaea amalgation is recorded in variations in the Permo-Carboniferous back-arc basin sedimentation of Peru. This study provides the first radiometric age constraints on the volcanic and sedimentary sequences of south-central eastern Peru up to the western-most tip of Bolivia, and now permits the correlation of lateral facies variations to the late Paleozoic pre-Andean orogenic cycle. The two phases of Gondwanide magmatism and metamorphism at c. 315 Ma and c. 260 Ma are reflected in two major changes in this sedimentary environment. Our detrital U-Pb zircon ages demonstrate that the timing of Ambo Formation deposition corroborates the Late Mississipian age estimates. The transition from the Ambo to the Tarma Formation around the Middle Pennsylvanian Early Gondwanide Orogeny (c. 315 Ma) represents a relative deepening of the basin. Throughout the shallow marine deposits of the Tarma Formation evidence for contemporaneous volcanism becomes gradually more pronounced and culminates around 312 - 309 Ma. Continuous basin subsidence resulted in a buildup of platform carbonates of the Copacabana Formation. Our data highlights the presence of a previously unrecognized phase of deposition of mainly fluvial sandstones and localized volcanism (281-270 Ma), which we named ´Oqoruro Formation'. This sedimentary succession was previously miss-assigned to the so-called Mitu Group, which has recently been dated to start deposition in the Middle Triassic (∼245-240 Ma). The emersion of this marine basin coincides with the onset of a major plutonic pulse related to the Late Gondwanide Orogeny (c. 260). Exhumation lead to the consequent retreat of the epeiric sea to the present-day sub-Andean region, and the coeval accumulation of the fluvial Oqoruro Formation in south eastern Peru. These late Paleozoic palaeoenvironmental changes in the back-arc basins along the western Gondwana margin of southern reflect changes in

  8. Timing of the Late Paleozoic Ice Age: A Review of the Status Quo and New U-Pb Zircon Ages From Southern Gondwana

    Science.gov (United States)

    Mundil, R.; Griffis, N. P.; Keller, C. B.; Fedorchuk, N.; Montanez, I. P.; Isbell, J.; Vesely, F.; Iannuzzi, R.

    2017-12-01

    Throughout the Carboniferous and Permian Late Paleozoic Ice Age (LPIA), glaciations in southern Gondwana exerted a profound influence on global climate and environment, ocean chemistry, and the nature of sedimentary processes. The LPIA is widely regarded as an analogue for Pleistocene glaciations. Our understanding of the latter, as well as the validity of predictions for the future global climate and environment, depends therefore on our ability to reconstruct the LPIA. A robust chronostratigraphic framework built on high precision/high accuracy geochronology is crucial for the reconstruction of events and processes that occurred during the LPIA, particularly in the absence of high-resolution terrestrial biostratigraphic constraints that apply to both near- and far-field proxy records. The occurrence of volcaniclastic layers containing primary volcanic zircon at many levels throughout southern Gondwana makes such a reconstruction feasible, but complications inevitably arise due to the mixing of older age components with primary volcanic crystals, as well as the potential of unrecognized open system behavior to produce spurious younger ages. These pitfalls cause age dispersion that may be difficult to interpret, or is unrecognized if low precision geochronological techniques are used, resulting in inaccurate radioisotopic ages. Our current efforts in the Parana Basin (Southern Brazil) and the Karoo Basin (South Africa/Namibia) concentrate on building a robust and exportable chronostratigraphic framework based on U-Pb zircon CA-TIMS ages with sub-permil level precision combined with Bayesian approaches for resolving the eruption age of dispersed age spectra to facilitate the reconstruction of glaciogenic processes through the Carboniferous-Permian transition, as well as their implications for global sea level, atmospheric pCO2 and ocean chemistry. We will also review currently available geochronological data from contemporaneous Australian successions and their

  9. Provenance of detrital zircons from the Ribeira and Dom Feliciano Belts, comparison with African equivalents and implications on Western Gondwana amalgamation

    International Nuclear Information System (INIS)

    Basei, M.; Frimmel, H.E.; Nutman, A.P.; Preciozzi, F.

    2008-01-01

    The geologic make-up of southern Brazil has been defined by processes related to the Brasiliano orogenic cycle and, in particular, to con tractional tectonic events that led to the amalgamation of different terranes, which culminated in the formation of Western Gondwana (Campos Neto and Figueiredo, 1995; Brito Neves and Cordani, 1991; Brito Neves et al, 1999, Campos Neto, 2000). Polycyclic deformation and metamorphism that masked the characteristics, including the age records, of the protoliths were associated with the juxtaposition of these different terranes. Ophiolitic remains and magmatic arc roots signal the existence of fossil subduction and collision zones, whereas intense post-tectonic to an orogenic granitic magmatism marks the end of the orogenic cycle towards the end of the Neoproterozoic Era. U-Pb dating of domains within single zircon grains has proven to be a very powerful tool for the unraveling of the complex tecto no-thermal evolution as well as in characterizing the provenance of the original sediments. This is due to the high resistance to weathering and to high closure temperatures with respect to the U-Pb isotope system in zircon. Over the past decade, the standard technique for this analytical approach has become the analyses of U-Pb isotope ratios by SHRIMP, preceded by cathodoluminescence analysis (McClaren et al 1994). In this study, a set of 11 new SHRIMP analyses on detrital zircon grains from the major metasedimentary units of the Ribeira and Dom Feliciano Belts of the southeastern portion of South America is presented and the data are compared with available analyses for the Gariep Belt (Basei et al. 2005) and a new analysis for the Damara Belt. Combined with available Sm-Nd bulk rock isotope data, the results will form the basis for a revised tectonic model for the formation of Western Gondwana

  10. Provenance of detrital zircons from the Ribeira and Dom Feliciano Belts, comparison with African equivalents and implications on western Gondwana amalgamation. Geological Society of London-2008

    International Nuclear Information System (INIS)

    Basei, M.; Frimmel, H.E.; Nutman, A.P.; Preciozzi, F.

    2005-01-01

    The geologic make-up of southern Brazil has been defined by processes related to the Brasiliano orogenic cycle and, in particular, to con tractional tectonic events that led to the amalgamation of different terranes, which culminated in the formation of Western Gondwana (Campos Neto and Figueiredo, 1995; Brito Neves and Cordani,1991; Brito Neves et al, 1999, Campos Neto, 2000). Polycyclic deformation and metamorphism that masked the characteristics, including the age records, of the protoliths were associated with the juxtaposition of these different terranes. Ophiolitic remains and magmatic arc roots signal the existence of fossil subduction and collision zones, whereas intense post-tectonic to an orogenic granitic magmatism marks the end of the orogenic cycle towards the end of the Neoproterozoic Era. U-Pb dating of domains within single zircon grains has proven to be a very powerful tool for the unraveling of the complex tecto no-thermal evolution as well as in characterizing the provenance of the original sediments. This is due to the high resistance to weathering and to high closure temperatures with respect to the U-Pb isotope system in zircon. Over the past decade, the standard technique for this analytical approach has become the analyses of U-Pb isotope ratios by SHRIMP,preceded by cathodoluminescence analysis (McClaren et al 1994). In this study, a set of 11 new SHRIMP analyses on detrital zircon grains from the major metasedimentary units of the Ribeira and Dom Feliciano Belts of the southeastern portion of South America is presented and the data are compared with available analyses for the Gariep Belt (Basei et al. 2005) and a new analysis for the Damara Belt. Combined with available Sm-Nd bulk rock isotope data, the results will form the basis for a revised tectonic model for the formation of Western Gondwana

  11. Magmatism and Epithermal Gold-Silver Deposits of the Southern Ancestral Cascade Arc, Western Nevada and Eastern California

    Science.gov (United States)

    John, David A.; du Bray, Edward A.; Henry, Christopher D.; Vikre, Peter

    2015-01-01

    Many epithermal gold-silver deposits are temporally and spatially associated with late Oligocene to Pliocene magmatism of the southern ancestral Cascade arc in western Nevada and eastern California. These deposits, which include both quartz-adularia (low- and intermediate-sulfidation; Comstock Lode, Tonopah, Bodie) and quartz-alunite (high-sulfidation; Goldfield, Paradise Peak) types, were major producers of gold and silver. Ancestral Cascade arc magmatism preceded that of the modern High Cascades arc and reflects subduction of the Farallon plate beneath North America. Ancestral arc magmatism began about 45 Ma, continued until about 3 Ma, and extended from near the Canada-United States border in Washington southward to about 250 km southeast of Reno, Nevada. The ancestral arc was split into northern and southern segments across an inferred tear in the subducting slab between Mount Shasta and Lassen Peak in northern California. The southern segment extends between 42°N in northern California and 37°N in western Nevada and was active from about 30 to 3 Ma. It is bounded on the east by the northeast edge of the Walker Lane. Ancestral arc volcanism represents an abrupt change in composition and style of magmatism relative to that in central Nevada. Large volume, caldera-forming, silicic ignimbrites associated with the 37 to 19 Ma ignimbrite flareup are dominant in central Nevada, whereas volcanic centers of the ancestral arc in western Nevada consist of andesitic stratovolcanoes and dacitic to rhyolitic lava domes that mostly formed between 25 and 4 Ma. Both ancestral arc and ignimbrite flareup magmatism resulted from rollback of the shallowly dipping slab that began about 45 Ma in northeast Nevada and migrated south-southwest with time. Most southern segment ancestral arc rocks have oxidized, high potassium, calc-alkaline compositions with silica contents ranging continuously from about 55 to 77 wt%. Most lavas are porphyritic and contain coarse plagioclase

  12. The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

    DEFF Research Database (Denmark)

    Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki

    2016-01-01

    the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

  13. microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

    OpenAIRE

    Heimberg, Alysha M.; Cowper-Sallari, Richard; Semon, Marie; Donoghue, Philip C. J.; Peterson, Kevin J.

    2010-01-01

    Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclosto...

  14. Stroke and Native Hawaiians/Pacific Islanders

    Science.gov (United States)

    ... Hawaiians/Pacific Islanders Native Hawaiians/Pacific Islanders were four times more likely than non-Hispanic white adults to die from a stroke in 2010. In general, Native Hawaiian/Pacific Islander ...

  15. Intersection of opposing pedagogical frameworks: Native Hawaiian ancestral stories and scientific inquiry in a high school science class

    Science.gov (United States)

    Kanahele-Mossman, Huihui

    Inquiry is defined as "an examination into facts and principles." In science education science inquiry is a process through which important discoveries are made by students through scientific methodology. The most important step in this process is forming the right question. The questions formed by students are usually the wrong questions which deem the remainder of the inquiry process impotent. This research will look at the pedagogy of ancestral stories for a solution. For the researcher, ancestral stories were a source of wonderment and learning not only from the lessons the stories revealed but mainly from the questions that still remained after the stories were told. Questions such as "why does the eel only swim near that part?", or "why does the story only talk about the uhu?" are examples of questions that remained after experiencing an ancestral narrative. The research questions were composed for the purpose of finding compatibility between the two pedagogies. The first research question which reads "how can Native Hawaiian ancestral stories encourage an increased level of student driven interactions at all levels of feedback from Native Hawaiian students in science classroom" focuses the research on the level of student feedback that initiate questions. Question two which reads "how can teachers of Native Hawaiian students facilitate the construction of science inquiry projects from ancestral stories" addresses the skill of the teacher and imbeds the concept of pedagogical knowledge into the literature. The last research question "how do analysis and discussion of the stories connect Native Hawaiian students to their ancestral intelligence" examines the role of identity and identity to ancestral intelligence. The method intended for this research was Grounded theory which allows the researcher to develop principles, concepts and theories based on the data presented. Another method utilized in this research is an undocumented but culturally imbedded method

  16. Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype.

    Science.gov (United States)

    O'Neill, R J; Eldridge, M D; Toder, R; Ferguson-Smith, M A; O'Brien, P C; Graves, J A

    1999-06-01

    Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

  17. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin

    2015-01-01

    necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones. Viruses rescued from...... the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral...... evolution. Importantly, ancestral reconstruction can be done even on the basis of a set of sequences that all correspond to non-functional variants....

  18. Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4.

    Directory of Open Access Journals (Sweden)

    Harinder Manku

    Full Text Available We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls, African-Americans (AA (1529, 2048 and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122. The best evidence of association comes from two adjacent markers: rs2205960-T (P=1.71 × 10(-34 , OR=1.43[1.26-1.60] and rs1234317-T (P=1.16 × 10(-28 , OR=1.38[1.24-1.54]. Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5' region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3 imputation. Conditional regression analyses delineate the 5' risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data

  19. Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

    2013-09-01

    A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene

  20. Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

    Directory of Open Access Journals (Sweden)

    Grünewald Stefan

    2011-01-01

    Full Text Available Abstract Background As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states. Results In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested. Conclusions In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction

  1. Phylogenetic evidence for an ancestral coevolution between a major clade of coccidian parasites and elasmobranch hosts.

    Science.gov (United States)

    Xavier, Raquel; Santos, Joana L; Veríssimo, Ana

    2018-03-16

    Cartilaginous fishes are the oldest jawed vertebrates and are also reported to be the hosts of some of the most basal lineages of Cestoda and Aporocotylidae (Digenea) parasites. Recently a phylogenetic analysis of the coccidia (Apicomplexa) infecting marine vertebrates revealed that the lesser spotted dogfish harbours parasite lineages basal to Eimeria Schneider, 1875 and the group formed by Schellackia Reichenow, 1919, Lankesterella Ames, 1923, Caryospora Leger, 1904 and Isospora Schneider, 1881. In the present study we have found additional lineages of coccidian parasites infecting the cownose ray Rhinoptera bonasus Mitchill and the blue shark Prionace glauca Linnaeus. These lineages were also found as basal to species from the genera Lankesterella, Schellackia, Caryospora and Isospora infecting higher vertebrates. These results confirm previous phylogenetic assessments and suggest that these parasitic lineages first evolved in basal vertebrate hosts (i.e. Chondrichthyes), and that the more derived lineages infect higher vertebrates (e.g. birds and mammals) conforming to the evolution of their hosts. We hypothesise that elasmobranchs might host further ancestral parasite lineages harbouring unknown links of parasite evolution.

  2. Ancestral state reconstruction of ontogeny supports a bilaterian affinity for Dickinsonia.

    Science.gov (United States)

    Gold, David A; Runnegar, Bruce; Gehling, James G; Jacobs, David K

    2015-01-01

    Despite numerous attempts, classification of the Precambrian fossil Dickinsonia has eluded scientific consensus. This is largely because Dickinsonia and its relatives are structurally simple, lacking morphological synapomorphies to clarify their relationship to modern taxa. However, there is increasing precedence for using ontogeny to constrain enigmatic fossils, and growth of the type species Dickinsonia costata is well understood. This study formalizes the connection between ontogeny in Dickinsonia-which grows by the addition of metameric units onto one end of its primary axis-with terminal addition, defined as growth and patterning from a posterior, subtermial growth zone. We employ ancestral state reconstruction and stochastic character mapping to conclude that terminal addition is a synapomorphy of bilaterian animals. Thus, terminal addition allies Dickinsonia with the bilaterians, providing evidence that large stem- or crown-group bilaterians made up a significant proportion of the Precambrian biota. This study also illustrates the potential for combining developmental and phylogenetic data in constraining the placement of ancient problematic fossil taxa on the evolutionary tree. © 2015 Wiley Periodicals, Inc.

  3. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

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    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  4. Determination of ancestral proportions in synthetic bovine breeds using commonly employed microsatellite markers.

    Science.gov (United States)

    Bicalho, H M S; Pimenta, C G; Mendes, I K P; Pena, H B; Queiroz, E M; Pena, S D J

    2006-07-31

    The International Society of Animal Genetics (ISAG) has chosen nine microsatellites (international marker set) as a standard that should be included in all cattle parentage studies. They are BM1824, BM2113, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH10, and ETH225. We decided to ascertain whether this microsatellite set could be used to determine ancestral proportions in individual animals of synthetic breeds produced by crossing zebu and taurine cattle. Since the genotypes of these markers are routinely available, this would constitute a practical and cost-free method to estimate the ancestry of synthetic breed animals. Genotypes of 100 Gir and 100 Holstein animals were examined for this ISAG marker set. As expected, there were very significant allele frequency differences between the two breeds at most loci. We also typed 20 Girolando animals for which there was complete genealogical information. "Structure" software easily distinguished Holstein and Gir animals based on their microsatellite genotypes; it also attributed the genomic proportion of zebu and taurine of each of the 20 Girolando animals. The proportion of Holstein ancestry was then regressed on the genealogical data; there was a highly significant correlation (r = 0.84, P Girolando animals within narrow confidence limits. This microsatellite set might also be useful for estimating the proportions of taurine and zebu origins in commercial meat products.

  5. Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia.

    Science.gov (United States)

    Hoang, Phuong T N; Schubert, Ingo

    2017-12-01

    The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.

  6. Origins and Spread of Machado-Joseph Disease Ancestral Mutations Events.

    Science.gov (United States)

    Martins, Sandra; Sequeiros, Jorge

    2018-01-01

    Machado-Joseph disease (MJD) is the most common autosomal dominant spinocerebellar ataxia reported worldwide, but it shows marked geographic differences in prevalence. The study of ancestral origins and spreading routes of MJD mutational events has contributed to explain such differences. During human evolution, at least two independent de novo MJD expansions occurred in distinct haplotype backgrounds: TTACAC and GTGGCA (named Joseph and Machado lineages). The most ancient Joseph lineage, probably of Asian origin, has been introduced recently in Europe, where founder effects are responsible for the high MJD prevalence, as occurs in the Portuguese/Azorean island of Flores and Northeastern mainland. The Machado lineage is geographically more restricted, with most known families in Portugal (island of São Miguel and along the Tagus valley). The hypothesis of other mutational origins has been raised, namely to explain the disease among Australian aborigines; however, a comprehensive haplotype study suggested the introduction of the Joseph lineage in that community via Asia. Also, additional SNP-based haplotypes (TTAGAC, TTGGAC and GTGCCA) were observed in other MJD families, but phylogenetic analysis with more polymorphic flanking markers did not point to independent mutational events, reinforcing the hypothesis of a very low mutation rate underlying this repeat expansion locus.

  7. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Directory of Open Access Journals (Sweden)

    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  8. The evolution of brachiation in ateline primates, ancestral character states and history.

    Science.gov (United States)

    Jones, Andrea L

    2008-10-01

    This study examines how brachiation locomotion evolved in ateline primates using recently-developed molecular phylogenies and character reconstruction algorithms, and a newly-collected dataset including the fossils Protopithecus, Caipora, and Cebupithecia. Fossils are added to two platyrrhine molecular phylogenies to create several phylogenetic scenarios. A generalized least squares algorithm reconstructs ateline and atelin ancestral character states for 17 characters that differentiate between ateline brachiators and nonbrachiators. Histories of these characters are mapped out on these phylogenies, producing two scenarios of ateline brachiation evolution that have four commonalities: First, many characters change towards the Ateles condition on the ateline stem lineage before Alouatta splits off from the atelins, suggesting that an ateline energy-maximizing strategy began before the atelines diversified. Second, the ateline last common ancestor is always reconstructed as an agile quadruped, usually with suspensory abilities. It is never exactly like Alouatta and many characters reverse and change towards the Alouatta condition after Alouatta separates from the atelins. Third, most characters undergo homoplastic change in all ateline lineages, especially on the Ateles and Brachyteles terminal branches. Fourth, ateline character evolution probably went through a hindlimb suspension with tail-bracing phase. The atelines most likely diversified via a quick adaptive radiation, with bursts of punctuated change occurring in their postcranial skeletons, due to changing climatic conditions, which may have caused competition among the atelines and between atelines and pitheciines.

  9. Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds

    Science.gov (United States)

    Griffin, Christopher T.; Nesbitt, Sterling J.

    2016-12-01

    Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.

  10. Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

    Science.gov (United States)

    Duchêne, Sebastian; Lanfear, Robert

    2015-09-01

    Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. © 2015 Wiley Periodicals, Inc.

  11. Counting all possible ancestral configurations of sample sequences in population genetics.

    Science.gov (United States)

    Song, Yun S; Lyngsø, Rune; Hein, Jotun

    2006-01-01

    Given a set D of input sequences, a genealogy for D can be constructed backward in time using such evolutionary events as mutation, coalescent, and recombination. An ancestral configuration (AC) can be regarded as the multiset of all sequences present at a particular point in time in a possible genealogy for D. The complexity of computing the likelihood of observing D depends heavily on the total number of distinct ACs of D and, therefore, it is of interest to estimate that number. For D consisting of binary sequences of finite length, we consider the problem of enumerating exactly all distinct ACs. We assume that the root sequence type is known and that the mutation process is governed by the infinite-sites model. When there is no recombination, we construct a general method of obtaining closed-form formulas for the total number of ACs. The enumeration problem becomes much more complicated when recombination is involved. In that case, we devise a method of enumeration based on counting contingency tables and construct a dynamic programming algorithm for the approach. Last, we describe a method of counting the number of ACs that can appear in genealogies with less than or equal to a given number R of recombinations. Of particular interest is the case in which R is close to the minimum number of recombinations for D.

  12. Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula.

    Science.gov (United States)

    Smith, Martin R

    2012-10-22

    The Middle Cambrian lophotrochozoans Odontogriphus omalus and Wiwaxia corrugata have been interpreted as stem-group members of either the Mollusca, the Annelida, or a group containing Mollusca + Annelida. The case for each classification rests on the organisms' unusual mouthparts, whose two to three tooth-rows resemble both the molluscan radula and the jaws of certain annelid worms. Despite their potential significance, these mouthparts have not previously been described in detail. This study examined the feeding apparatuses of over 300 specimens from the 505-million-year-old Burgess Shale, many of which were studied for the first time. Rather than denticulate plates, each tooth row comprises a single axial tooth that is flanked on each side by eight to 16 separate shoehorn-shaped teeth. Tooth rows sat on a grooved basal tongue, and two large lobes flanked the apparatus. New observations--the shape, distribution and articulation of the individual teeth, and the mouthparts' mode of growth--are incompatible with an annelid interpretation, instead supporting a classification in Mollusca. The ancestral molluscan radula is best reconstructed as unipartite with a symmetrical medial tooth, and Odontogriphus and Wiwaxia as grazing deposit-feeders.

  13. Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan.

    Science.gov (United States)

    Webster, Bonnie L; Copley, Richard R; Jenner, Ronald A; Mackenzie-Dodds, Jacqueline A; Bourlat, Sarah J; Rota-Stabelli, Omar; Littlewood, D T J; Telford, Maximilian J

    2006-01-01

    Research into arthropod evolution is hampered by the derived nature and rapid evolution of the best-studied out-group: the nematodes. We consider priapulids as an alternative out-group. Priapulids are a small phylum of bottom-dwelling marine worms; their tubular body with spiny proboscis or introvert has changed little over 520 million years and recognizable priapulids are common among exceptionally preserved Cambrian fossils. Using the complete mitochondrial genome and 42 nuclear genes from Priapulus caudatus, we show that priapulids are slowly evolving ecdysozoans; almost all these priapulid genes have evolved more slowly than nematode orthologs and the priapulid mitochondrial gene order may be unchanged since the Cambrian. Considering their primitive bodyplan and embryology and the great conservation of both nuclear and mitochondrial genomes, priapulids may deserve the popular epithet of "living fossil." Their study is likely to yield significant new insights into the early evolution of the Ecdysozoa and the origins of the arthropods and their kin as well as aiding inference of the morphology of ancestral Ecdysozoa and Bilateria and their genomes.

  14. Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.

    Science.gov (United States)

    Manikkam, Mohan; Guerrero-Bosagna, Carlos; Tracey, Rebecca; Haque, Md M; Skinner, Michael K

    2012-01-01

    Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm) that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET), a plastic mixture (bisphenol A and phthalates), dioxin (TCDD) and a hydrocarbon mixture (jet fuel, JP8). After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation). Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR) were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.

  15. Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.

    Directory of Open Access Journals (Sweden)

    Mohan Manikkam

    Full Text Available Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET, a plastic mixture (bisphenol A and phthalates, dioxin (TCDD and a hydrocarbon mixture (jet fuel, JP8. After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation. Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.

  16. Bacterial community composition and diversity in an ancestral ant fungus symbiosis.

    Science.gov (United States)

    Kellner, Katrin; Ishak, Heather D; Linksvayer, Timothy A; Mueller, Ulrich G

    2015-07-01

    Fungus-farming ants (Hymenoptera: Formicidae, Attini) exhibit some of the most complex microbial symbioses because both macroscopic partners (ants and fungus) are associated with a rich community of microorganisms. The ant and fungal microbiomes are thought to serve important beneficial nutritional and defensive roles in these symbioses. While most recent research has investigated the bacterial communities in the higher attines (e.g. the leaf-cutter ant genera Atta and Acromyrmex), which are often associated with antibiotic-producing Actinobacteria, very little is known about the microbial communities in basal lineages, labeled as 'lower attines', which retain the ancestral traits of smaller and more simple societies. In this study, we used 16S amplicon pyrosequencing to characterize bacterial communities of the lower attine ant Mycocepurus smithii among seven sampling sites in central Panama. We discovered that ant and fungus garden-associated microbiota were distinct from surrounding soil, but unlike the situation in the derived fungus-gardening ants, which show distinct ant and fungal microbiomes, microbial community structure of the ants and their fungi were similar. Another surprising finding was that the abundance of actinomycete bacteria was low and instead, these symbioses were characterized by an abundance of Lactobacillus and Pantoea bacteria. Furthermore, our data indicate that Lactobacillus strains are acquired from the environment rather than acquired vertically. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Cranial morphological variation among contemporary Mexicans: Regional trends, ancestral affinities, and genetic comparisons.

    Science.gov (United States)

    Hughes, Cris E; Tise, Meredith L; Trammell, Lindsay H; Anderson, Bruce E

    2013-08-01

    Genetic research has documented geographical variation within Mexico that corresponds to trends in ancestry admixture from postcolonial times on. The purpose of this study is to determine whether craniometric variation among contemporary Mexicans is comparable to that reported in genetic studies. Standard osteometric measurements were taken on 82 male crania derived from forensic cases, with geographic origins of the specimens spanning over two-thirds of Mexico's states. To study similarities in regional clustering patterns with genetic data, k-means clustering analyses were performed, followed by chi-square tests of association between cluster assignments and geographic region of origin. Normal mixtures analyses were performed, centered on three "ancestral" sample proxies to estimate classification probability to each ancestry. The results demonstrate that the cranial morphological sample data cluster similarly to the regional groupings inferred from the genetic data. Additionally, the results indicate a gradient trend in population structure for contemporary Mexicans, with the proportion of Amerindian ancestry increasing from North to South while, conversely, European ancestry proportion estimates increase from South to North. Furthermore, the probabilities for classification of African ancestry remained low across the regions, again reflecting the results for the genetic data. Cranial morphological variation is well aligned with the genetic data for describing broad trends among Mexican populations, as well as yielding comparable estimates of general ancestry affiliations that reflect Mexico's history of Spanish contact and colonialism. Copyright © 2013 Wiley Periodicals, Inc.

  18. A Skull Might Lie: Modeling Ancestral Ranges and Diet from Genes and Shape of Tree Squirrels.

    Science.gov (United States)

    Pečnerová, Patrícia; Moravec, Jiří C; Martínková, Natália

    2015-11-01

    Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they have diversified rapidly. Here, we compare signals from DNA sequences with morphological signals using pictures of skulls and computational simulations. Phylogenetic analyses reveal step-wise geographic divergence across the Northern Hemisphere. In Central and South America, tree squirrels form two separate clades, which split from a common ancestor. Simulations of ancestral distributions show western Amazonia as the epicenter of speciation in South America. This finding suggests that wet tropical forests on the foothills of Andes possibly served as refugia of squirrel diversification during Pleistocene climatic oscillations. Comparison of phylogeny and morphology reveals one major discrepancy: Microsciurus species are a single clade morphologically but are polyphyletic genetically. Modeling of morphology-diet relationships shows that the only group of species with a direct link between skull shape and diet are the bark-gleaning insectivorous species of Microsciurus. This finding suggests that the current designation of Microsciurus as a genus is based on convergent ecologically driven changes in morphology. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes.

    Directory of Open Access Journals (Sweden)

    Vincent J Lynch

    2009-01-01

    Full Text Available While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion--such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these--is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox "paralogon" and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.

  20. Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication.

    Directory of Open Access Journals (Sweden)

    Karin Voordeckers

    Full Text Available Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

  1. Ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects (Phasmatodea).

    Science.gov (United States)

    Shelomi, Matan; Heckel, David G; Pauchet, Yannick

    2016-04-01

    The Phasmatodea (stick insects) have multiple, endogenous, highly expressed copies of glycoside hydrolase family 9 (GH9) genes. The purpose for retaining so many was unknown. We cloned and expressed the enzymes in transfected insect cell lines, and tested the individual proteins against different plant cell wall component poly- and oligosaccharides. Nearly all isolated enzymes were active against carboxymethylcellulose, however most could also degrade glucomannan, and some also either xylan or xyloglucan. The latter two enzyme groups were each monophyletic, suggesting the evolution of these novel substrate specificities in an early ancestor of the order. Such enzymes are highly unusual for Metazoa, for which no xyloglucanases had been reported. Phasmatodea gut extracts could degrade multiple plant cell wall components fully into sugar monomers, suggesting that enzymatic breakdown of plant cell walls by the entire Phasmatodea digestome may contribute to the Phasmatodea nutritional budget. The duplication and neofunctionalization of GH9s in the ancestral Phasmatodea may have enabled them to specialize as folivores and diverge from their omnivorous ancestors. The structural changes enabling these unprecedented activities in the cellulases require further study. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton

    Directory of Open Access Journals (Sweden)

    Richards Thomas A

    2010-04-01

    Full Text Available Abstract Background The genesis of the eukaryotes was a pivotal event in evolution and was accompanied by the acquisition of numerous new cellular features including compartmentalization by cytoplasmic organelles, mitosis and meiosis, and ciliary motility. Essential for the development of these features was the tubulin cytoskeleton and associated motors. It is therefore possible to map ancient cell evolution by reconstructing the evolutionary history of motor proteins. Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA. Results We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. These data enabled us to define 51 anciently-derived kinesin paralogs (including three new kinesin families and 105 domain architectures. We then mapped these characters across eukaryotes, accounting for secondary loss within established eukaryotic groupings, and alternative tree topologies. Conclusions We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell.

  3. Palaeoenvironmental and geochemical approach of Archaeocyath-rich facies from Lower Cambrian of Western Gondwana margin at Central Iberian Zone (Urda, Toledo Mountains, Spain)

    Science.gov (United States)

    Menéndez, Silvia; Rodríguez-Martínez, Marta; Moreno-Eris, Elena; Perejón, Antonio; Reitner, Joachim

    2010-05-01

    in Western Gondwana margin. Powdered microsamples have been analysed for their elemental and isotopic composition (δ13C values range from + 0.41 to + 3.05). Sulphur minerals and silicates where analyzed with XRD and wavelength-dispersive electron microprobe. Major elements were measured with ICP-OES and minor and trace elements were analyzed with ICP-MS. These are the first palaeontological, sedimetological, geochemical and isotopical data provided to reconstruct the depositional environment of these Archaeocyath-rich facies at the Western Gondwana margin. References Julivert, M., Fontboté, J.M., Ribeiro, A., Nabais Conde L.E. 1972. Mapa tectónico de la Península Ibérica y Baleares, Escala 1: 1.000.000, Memoria Explicativa [1974], 113 pp. Instituto Geológico y Minero de España. Perejón, A., Moreno-Eiris, E. 2006. Biostratigraphy and palaeobiography of the archaeocyaths on the south-western margin of Gondwana. Zeitschrift der Deutschen Gesellschaft für Geowissenschaften 157 (4): 611-627.

  4. Paleoproterozoic (ca. 1.8 Ga) arc magmatism in the Lützow-Holm Complex, East Antarctica: Implications for crustal growth and terrane assembly in erstwhile Gondwana fragments

    Science.gov (United States)

    Takahashi, Kazuki; Tsunogae, Toshiaki; Santosh, M.; Takamura, Yusuke; Tsutsumi, Yukiyasu

    2018-05-01

    lithological data from the region, suggest that the LHC can be divided into three units: Neoarchean (ca. 2.5 Ga) unit in the southern LHC (Shirase Orthogneiss or "Shirase microcontinent"), Neoproterozoic (ca. 1.0 Ga) unit in the northern LHC, and supracrustal unit in the central LHC with fragments of Paleoproterozoic (ca. 1.8 Ga) and minor Neoarchean (ca. 2.5 Ga) and Neoproterozoic (ca. 1.0 Ga) magmatic arcs. The 1.8 Ga arc magmatism inferred in this study has also been reported from adjacent Gondwana fragments such as the Highland Complex in Sri Lanka, and the Trivandrum and Nagercoil Blocks in southern India. Although the ca. 1.8 Ga arc-magmatic event is coeval in these regions, the Paleoproterozoic supracrustal unit in the central LHC may not be contiguous with those in the Highland Complex of Sri Lanka because recent studies have shown that the Vijayan Complex in Sri Lanka and the ca. 1.0 Ga northern LHC possibly were part of a single crustal unit (northern Lützow-Holm-Vijayan Complex) within the Kalahari Block. The supracrustal unit possibly marks part of a discrete suture formed by the collision of the ca. 2.5 Ga southern LHC (Shirase microcontinent) and the ca. 1.0 Ga northern Lützow-Holm-Vijayan Complex during the latest Neoproterozoic-Cambrian Gondwana amalgamation, which might be coeval with the collision of the Vijayan and Wanni Complexes and the formation of the Highland Complex in Sri Lanka. Our study provides new insights on crustal growth and terrane assembly in the ancient continental blocks of Gondwana.

  5. Thermal evolution of the Sisters shear zone, southern New Zealand; Formation of the Great South Basin and onset of Pacific-Antarctic spreading

    Science.gov (United States)

    Kula, Joseph; Tulloch, Andy J.; Spell, Terry L.; Wells, Michael L.; Zanetti, Kathleen A.

    2009-10-01

    The separation of Zealandia from West Antarctica was the final stage in the Cretaceous breakup of the Gondwana Pacific margin. Continental extension resulting in formation of the Great South Basin and thinning of the Campbell Plateau leading to development of the Pacific-Antarctic spreading ridge was partially accommodated along the Sisters shear zone. This east-northeast striking brittle-ductile structure exposed along the southeast coast of Stewart Island, New Zealand, is a greenschist facies extensional shear zone that separates a hanging wall of chloritic, brecciated granites, and undeformed conglomerate from a footwall of mylonitic Carboniferous and Early Cretaceous granites. This complex structure exhibits bivergent kinematics and can be subdivided into a northern and southern segment. The 40Ar/39Ar thermochronology indicates that cooling of the shear zone footwall began at ˜94 Ma with accelerated cooling over the interval ˜89-82 Ma. Structural and thermochronological data indicate a spatial and temporal link between the Sisters shear zone, initial sedimentation within the offshore Great South Basin, extension of the Campbell Plateau, and initiation of the Pacific-Antarctic spreading ridge.

  6. Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

    Science.gov (United States)

    Schopp, Pascal; Müller, Dominik; Technow, Frank; Melchinger, Albrecht E

    2017-01-01

    Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ([Formula: see text] and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from [Formula: see text]2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios differing in relatedness of the training and prediction sets and in the types of data used to calculate the relationship matrix (QTL, SNPs, tag markers, and pedigree), we investigated the prediction accuracy (PA) of Genomic best linear unbiased prediction (GBLUP) and analyzed contributions from pedigree relationships captured by SNP markers, as well as from cosegregation and ancestral LD between QTL and SNPs. The effects of training set size [Formula: see text] and marker density were also studied. Sampling few parents ([Formula: see text]) generates substantial sample LD that carries over into synthetics through cosegregation of alleles at linked loci. For fixed [Formula: see text], [Formula: see text] influences PA most strongly. If the training and prediction set are related, using [Formula: see text] parents yields high PA regardless of ancestral LD because SNPs capture pedigree relationships and Mendelian sampling through cosegregation. As [Formula: see text] increases, ancestral LD contributes more information, while other factors contribute less due to lower frequencies of closely related individuals. For unrelated prediction sets, only ancestral LD contributes information and accuracies were poor and highly variable for [Formula: see text] due to large sample LD. For large [Formula: see text], achieving moderate accuracy requires

  7. Age and kinematics of ductile deformation in the Cerro Durazno area, NW Argentina: Significance for orogenic processes operating at the western margin of Gondwana during Ordovician-Silurian times

    OpenAIRE

    M. I. Wegmann; U. Riller; F. D. Hongn; Johannes Glodny; Onno Oncken

    2008-01-01

    The Cerro Durazno Pluton belongs to a suite of Paleozoic granitoid intrusions in NWArgentina, that are central for understanding the tectonic setting of the western margin of Gondwana in Ordovician and Silurian times. The pluton and its host rocks were tectonically overprinted by metamorphic mineral shape fabrics formed under middle greenschist-facies metamorphic conditions and associated with the nearby Agua Rosada Shear Zone. Kinematic analysis of the shear zone based on the geometric relat...

  8. Effectiveness of ancestral irradiation on the direct and correlated responses to selection for body weight in rats

    International Nuclear Information System (INIS)

    Gianola, D.

    1975-01-01

    The effects of ancestral irradiation of rat spermatogonia (a cumulative total of 4050 r of x-rays) were studied in a highly inbred line of rats to explore the feasibility of using irradiation to enhance the effectiveness of selection. Six generations after irradiation was terminated, a selection experiment for body weight at six weeks of age was started in both ancestrally irradiated and non-irradiated populations. There were two non-contemporaneous replicates in each of the populations. Within each of the ancestral treatment-replicate combinations one line was selected for high, one for low body weight at six weeks of age, and a third line was maintained by random selection. In each line, avoidance of mating of animals with grandparents in common was attempted. Data on the first ten progeny generations of selection were included in this study. Five types of covariances among relatives were used to estimate causal components of variance for five different genetic models within the ''non-irradiated'' and ''irradiated'' randomly selected models. The parameters in the genetic models were estimated by generalized least-squares. This analysis suggested that a genetic model including direct genetic and maternal genetic effects was adequate to describe the body weights at 3, 6 and 10 weeks of age and the weight gains between these ages. Ancestral irradiation seemed to have enhanced the maternal genetic variance and the covariance between the direct genetic and the maternal genetic effects. On the basis of the above analysis, it was deduced that mass selection should have been more effective in the descendants of irradiated males than in those of the non-irradiated males as a consequence of greater phenotypic variability in their progeny and an enhancement in the regression of the genetic value on the selection criterion

  9. Genotype-based ancestral background consistently predicts efficacy and side effects across treatments in CATIE and STAR*D.

    Directory of Open Access Journals (Sweden)

    Daniel E Adkins

    Full Text Available Only a subset of patients will typically respond to any given prescribed drug. The time it takes clinicians to declare a treatment ineffective leaves the patient in an impaired state and at unnecessary risk for adverse drug effects. Thus, diagnostic tests robustly predicting the most effective and safe medication for each patient prior to starting pharmacotherapy would have tremendous clinical value. In this article, we evaluated the use of genetic markers to estimate ancestry as a predictive component of such diagnostic tests. We first estimated each patient's unique mosaic of ancestral backgrounds using genome-wide SNP data collected in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE (n = 765 and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D (n = 1892. Next, we performed multiple regression analyses to estimate the predictive power of these ancestral dimensions. For 136/89 treatment-outcome combinations tested in CATIE/STAR*D, results indicated 1.67/1.84 times higher median test statistics than expected under the null hypothesis assuming no predictive power (p<0.01, both samples. Thus, ancestry showed robust and pervasive correlations with drug efficacy and side effects in both CATIE and STAR*D. Comparison of the marginal predictive power of MDS ancestral dimensions and self-reported race indicated significant improvements to model fit with the inclusion of MDS dimensions, but mixed evidence for self-reported race. Knowledge of each patient's unique mosaic of ancestral backgrounds provides a potent immediate starting point for developing algorithms identifying the most effective and safe medication for a wide variety of drug-treatment response combinations. As relatively few new psychiatric drugs are currently under development, such personalized medicine offers a promising approach toward optimizing pharmacotherapy for psychiatric conditions.

  10. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  11. The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials.

    Science.gov (United States)

    Suárez-Villota, Elkin Y; Haro, Ronie E; Vargas, Rodrigo A; Gallardo, Milton H

    2016-01-01

    The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials' cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GISH) were used to detect telomeric and repetitive sequences, respectively. These were complemented with C-, fluorescent banding, and centromere immunodetection over mitotic spreads. The presence of interstitial telomeric sequences (ITS) and diploid numbers were reconstructed and mapped onto the marsupial phylogenetic tree. No interstitial, fluorescent signals, but clearly stained telomeric regions were detected by FISH and self-GISH. Heterochromatin distribution was sparse in the telomeric/subtelomeric regions of large submetacentric chromosomes. Large AT-rich blocks were detected in the long arm of four submetacentrics and CG-rich block in the telomeric regions of all chromosomes. The ancestral reconstructions both ITS presence and diploid numbers suggested that ITS are unrelated to fusion events. Although the lack of interstitial signals in D. gliroides' karyotype does not prove absence of past fusions, our data suggests its non-rearranged plesiomorphic condition.

  12. Unexpectedly High Proportion of Ancestral Manu Genotype Mycobacterium tuberculosis Strains Cultured from Tuberculosis Patients in Egypt ▿

    Science.gov (United States)

    Helal, Zeinab H.; El-Din Ashour, Mohamed Seif; Eissa, Somaia A.; Abd-Elatef, Ghanem; Zozio, Thierry; Babapoor, Sankhiros; Rastogi, Nalin; Khan, Mazhar I.

    2009-01-01

    Tuberculosis is one of the important public health problems in Egypt. However, limited information on the Mycobacterium tuberculosis genotypes circulating in Egypt is available. A total of 151 M. tuberculosis strains were characterized by spoligotyping. The results revealed that 74.8% of M. tuberculosis isolates grouped into 13 different clusters, while 25.2% had unique spoligotype patterns. Comparison with an international spoligotyping database (the SITVIT2 database) showed that types SIT53 (T1 variant) and SIT54 (Manu2 variant) were the most common types between cluster groups. In addition, new shared types SIT2977, SIT2978, and SIT2979 were observed. The results identified for the first time an unusually high proportion of ancestral Manu strains of M. tuberculosis from patients in Egypt. The percentage of the Manu clade in this study (27.15%) was significantly higher than its overall representation of 0.4% in the SITVIT2 database. We show that in Egypt tuberculosis is caused by a predominant M. tuberculosis genotype belonging to the ancestral Manu lineage which could be a missing link in the split between ancestral and modern tubercle bacilli during the evolution of M. tuberculosis. PMID:19553569

  13. When ancestral heritage is a source of discomfort: culture, pre-object relatedness, and self-alienation.

    Science.gov (United States)

    Kradin, Richard L

    2012-04-01

    The ancestral claims on an individual can evoke mental conflict when they involve separating from an ethnic group whose beliefs and customs are devalued by the dominant culture. However, these claims are engraved on the psyche early in development by caretakers to the level of pre-object relatedness, where contents and affect tones are implicit and may be unavailable for later psychoanalytical interventions. In addition, as the anthropologist Clifford Geertz notes, one's culture of origin precedes the development of psyche and creates its own set of claims that must be renegotiated when one encounters a different domain of cultural symbols, a confrontation that can produce psychological dissonance and self-alienation. In this paper, three cases are examined in which mental conflicts were evoked by attempts at divesting ancestral claims in response to conscious efforts to assimilate into the dominant culture. These patients suffered from separation guilt and unstable self-esteem and reported dream imagery suggesting psychological imbalance. The requirement to carefully delineate the ancestral claims on psyche as well as those contents and affects that may not be accessible to therapeutic intervention is emphasized, and the importance of compromise and acceptance with respect to the psychological demands of the unconscious are considered. 2012, The Society of Analytical Psychology.

  14. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  15. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    International Nuclear Information System (INIS)

    Inui, Ken; Sagane, Yoshimasa; Miyata, Keita; Miyashita, Shin-Ichiro; Suzuki, Tomonori; Shikamori, Yasuyuki; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro

    2012-01-01

    Highlights: ► BoNT and NTNHA proteins share a similar protein architecture. ► NTNHA and BoNT were both identified as zinc-binding proteins. ► NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. ► Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X 35 -D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  16. Allelic lineages of the ficolin genes (FCNs are passed from ancestral to descendant primates.

    Directory of Open Access Journals (Sweden)

    Tina Hummelshøj

    Full Text Available The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.

  17. Does body posture influence hand preference in an ancestral primate model?

    Directory of Open Access Journals (Sweden)

    Leliveld Lisette

    2011-02-01

    Full Text Available Abstract Background The origin of human handedness and its evolution in primates is presently under debate. Current hypotheses suggest that body posture (postural origin hypothesis and bipedalism hypothesis have an important impact on the evolution of handedness in primates. To gain insight into the origin of manual lateralization in primates, we studied gray mouse lemurs, suggested to represent the most ancestral primate condition. First, we investigated hand preference in a simple food grasping task to explore the importance of hand usage in a natural foraging situation. Second, we explored the influence of body posture by applying a forced food grasping task with varying postural demands (sit, biped, cling, triped. Results The tested mouse lemur population did not prefer to use their hands alone to grasp for food items. Instead, they preferred to pick them up using a mouth-hand combination or the mouth alone. If mouth usage was inhibited, they showed an individual but no population level handedness for all four postural forced food grasping tasks. Additionally, we found no influence of body posture on hand preference in gray mouse lemurs. Conclusion Our results do not support the current theories of primate handedness. Rather, they propose that ecological adaptation indicated by postural habit and body size of a given species has an important impact on hand preference in primates. Our findings suggest that small-bodied, quadrupedal primates, adapted to the fine branch niche of dense forests, prefer mouth retrieval of food and are less manually lateralized than large-bodied species which consume food in a more upright, and less stable body posture.

  18. Evolutionary history of Lissotriton helveticus: multilocus assessment of ancestral vs. recent colonization of the Iberian Peninsula.

    Science.gov (United States)

    Recuero, Ernesto; García-París, Mario

    2011-07-01

    The Pleistocene was characterized by climatic changes that greatly altered the distribution of organisms. Population extinctions, bottlenecks, isolation, range expansions and contractions were often associated with glaciations, leaving signatures in the spatial patterns of genetic diversity across species. Lissotriton helveticus belongs to a Pan-European lineage of newts that were strongly affected by glaciations and represent an excellent model to analyse the effect of generalized climatic changes in phylogeographic patterns. We studied the genetic diversity of the species using data from two mitochondrial and three nuclear genes analyzed in a Bayesian phylogenetic framework to investigate the historical processes shaping spatial patterns of genetic diversity. Mitochondrial haplotypes cluster in four different groups present in the Iberian Peninsula and of Pleistocene origin, probably by allopatric fragmentation. Nuclear genes present no obvious geographic structure patterns, suggesting gene flow and generalized incomplete lineage sorting. Populations north of the Pyrenees are closely related to those from northeastern Iberia, suggesting recent range expansion from this region. Historical demographic analyses indicate a demographic expansion starting about 100,000years ago and more recent population declines. Compared to other Lissotriton species, L. helveticus includes only relatively young genetic lineages, suggesting a Central European pre-Pleistocene distribution followed by complete extirpation of the species during glaciations in that area. Historical demographic trends in the Iberian Peninsula are reversed with respect to the more Mediterranean species Lissotriton boscai, indicating different responses of both species to climate changes. Diversity patterns among Lissotriton species seem to be defined by four main factors: ancestral distributions, colonization capabilities, interactions with other species and effective population sizes. Differences in these

  19. Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms.

    Science.gov (United States)

    Chiang, Yu-Chung; Hung, Kuo-Hsiang; Moore, Shann-Jye; Ge, Xue-Jun; Huang, Shong; Hsu, Tsai-Wen; Schaal, Barbara A; Chiang, Ty

    2009-07-10

    This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic. Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

  20. Regionalization of the Shark Hindbrain: A Survey of an Ancestral Organization

    Science.gov (United States)

    Rodríguez-Moldes, Isabel; Carrera, Ivan; Pose-Méndez, Sol; Quintana-Urzainqui, Idoia; Candal, Eva; Anadón, Ramón; Mazan, Sylvie; Ferreiro-Galve, Susana

    2011-01-01

    Cartilaginous fishes (chondrichthyans) represent an ancient radiation of vertebrates currently considered the sister group of the group of gnathostomes with a bony skeleton that gave rise to land vertebrates. This out-group position makes chondrichthyans essential in assessing the ancestral organization of the brain of jawed vertebrates. To gain knowledge about hindbrain evolution we have studied its development in a shark, the lesser spotted dogfish Scyliorhinus canicula by analyzing the expression of some developmental genes and the origin and distribution of specific neuronal populations, which may help to identify hindbrain subdivisions and boundaries and the topology of specific cell groups. We have characterized three developmental periods that will serve as a framework to compare the development of different neuronal systems and may represent a suitable tool for comparing the absolute chronology of development among vertebrates. The expression patterns of Pax6, Wnt8, and HoxA2 genes in early embryos of S. canicula showed close correspondence to what has been described in other vertebrates and helped to identify the anterior rhombomeres. Also in these early embryos, the combination of Pax6 with protein markers of migrating neuroblasts (DCX) and early differentiating neurons (general: HuC/D; neuron type specific: GAD, the GABA synthesizing enzyme) revealed the organization of S. canicula hindbrain in both transverse segmental units corresponding to visible rhombomeres and longitudinal columns. Later in development, when the interrhombomeric boundaries fade away, accurate information about S. canicula hindbrain subdivisions was achieved by comparing the expression patterns of Pax6 and GAD, serotonin (serotoninergic neurons), tyrosine hydroxylase (catecholaminergic neurons), choline acetyltransferase (cholinergic neurons), and calretinin (a calcium-binding protein). The patterns observed revealed many topological correspondences with other vertebrates and led to

  1. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    Energy Technology Data Exchange (ETDEWEB)

    Inui, Ken [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Sagane, Yoshimasa [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Miyata, Keita [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Miyashita, Shin-Ichiro [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Suzuki, Tomonori [Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558 (Japan); Shikamori, Yasuyuki [Agilent Technologies International Japan, Ltd. Takaura-cho 9-1, Hachioji-shi, Tokyo 192-0033 (Japan); Ohyama, Tohru; Niwa, Koichi [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Watanabe, Toshihiro, E-mail: t-watana@bioindustry.nodai.ac.jp [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer BoNT and NTNHA proteins share a similar protein architecture. Black-Right-Pointing-Pointer NTNHA and BoNT were both identified as zinc-binding proteins. Black-Right-Pointing-Pointer NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. Black-Right-Pointing-Pointer Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X{sub 35}-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  2. The vomeronasal complex of nocturnal strepsirhines and implications for the ancestral condition in primates.

    Science.gov (United States)

    Garrett, Eva C; Dennis, John C; Bhatnagar, Kunwar P; Durham, Emily L; Burrows, Anne M; Bonar, Christopher J; Steckler, Natalie K; Morrison, Edward E; Smith, Timothy D

    2013-12-01

    This study investigates the vomeronasal organ in extant nocturnal strepsirhines as a model for ancestral primates. Cadaveric samples from 10 strepsirhine species, ranging from fetal to adult ages, were studied histologically. Dimensions of structures in the vomeronasal complex, such as the vomeronasal neuroepithelium (VNNE) and vomeronasal cartilage (VNC) were measured in serial sections and selected specimens were studied immunohistochemically to determine physiological aspects of the vomeronasal sensory neurons (VSNs). Osteological features corresponding to vomeronasal structures were studied histologically and related to 3-D CT reconstructions. The VNC consistently rests in a depression on the palatal portion of the maxilla, which we refer to as the vomeronasal groove (VNG). Most age comparisons indicate that in adults VNNE is about twice the length compared with perinatal animals. In VNNE volume, adults are 2- to 3-fold larger compared with perinatal specimens. Across ages, a strong linear relationship exists between VNNE dimensions and body length, mass, and midfacial length. Results indicate that the VNNE of nocturnal strepsirhines is neurogenic postnatally based on GAP43 expression. In addition, based on Olfactory Marker Protein expression, terminally differentiated VSNs are present in the VNNE. Therefore, nocturnal strepsirhines have basic similarities to rodents in growth and maturational characteristics of VSNs. These results indicate that a functional vomeronasal system is likely present in all nocturnal strepsirhines. Finally, given that osteological features such as the VNG are visible on midfacial bones, primate fossils can be assessed to determine whether primate ancestors possessed a vomeronasal complex morphologically similar to that of modern nocturnal strepsirhines. Copyright © 2013 Wiley Periodicals, Inc.

  3. Ancestral morphology of crown-group molluscs revealed by a new Ordovician stem aculiferan.

    Science.gov (United States)

    Vinther, Jakob; Parry, Luke; Briggs, Derek E G; Van Roy, Peter

    2017-02-23

    Exceptionally preserved fossils provide crucial insights into extinct body plans and organismal evolution. Molluscs, one of the most disparate animal phyla, radiated rapidly during the early Cambrian period (approximately 535-520 million years ago (Ma)). The problematic fossil taxa Halkieria and Orthrozanclus (grouped in Sachitida) have been assigned variously to stem-group annelids, brachiopods, stem-group molluscs or stem-group aculiferans (Polyplacophora and Aplacophora), but their affinities have remained controversial owing to a lack of preserved diagnostic characters. Here we describe a new early sachitid, Calvapilosa kroegeri gen. et sp. nov. from the Fezouata biota of Morocco (Early Ordovician epoch, around 478 Ma). The new taxon is characterized by the presence of a single large anterior shell plate and polystichous radula bearing a median tooth and several lateral and uncinal teeth in more than 125 rows. Its flattened body is covered by hollow spinose sclerites, and a smooth, ventral girdle flanks an extensive mantle cavity. Phylogenetic analyses resolve C. kroegeri as a stem-group aculiferan together with other single-plated forms such as Maikhanella (Siphogonuchites) and Orthrozanclus; Halkieria is recovered closer to the aculiferan crown. These genera document the stepwise evolution of the aculiferan body plan from forms with a single, almost conchiferan-like shell through two-plated taxa such as Halkieria, to the eight-plated crown-group aculiferans. C. kroegeri therefore provides key evidence concerning the long debate about the crown molluscan affinities of sachitids. This new discovery strongly suggests that the possession of only a single calcareous shell plate and the presence of unmineralised sclerites are plesiomorphic (an ancestral trait) for the molluscan crown.

  4. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

    Science.gov (United States)

    van Baren, Marijke J; Bachy, Charles; Reistetter, Emily Nahas; Purvine, Samuel O; Grimwood, Jane; Sudek, Sebastian; Yu, Hang; Poirier, Camille; Deerinck, Thomas J; Kuo, Alan; Grigoriev, Igor V; Wong, Chee-Hong; Smith, Richard D; Callister, Stephen J; Wei, Chia-Lin; Schmutz, Jeremy; Worden, Alexandra Z

    2016-03-31

    Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Extensive differences in gene loss and architecture between related prasinophytes underscore

  5. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria.

    Directory of Open Access Journals (Sweden)

    Roxane Chiori

    Full Text Available BACKGROUND: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

  6. CHAAJ (JUEGO DE PELOTA MESOAMERICANO: UN jUEGO ANCESTRAL ENTRE EMERGENCIAS CULTURALES

    Directory of Open Access Journals (Sweden)

    Jairzinho Francisco Panqueba Cifuentes

    2012-06-01

    Full Text Available Los juegos de pelota mesoamericanos son manifestaciones corporales que han sido exploradasprincipalmente desde perspectivas arqueológicas e históricas, pero también han sido retomadosdesde distintas iniciativas para ponerlos en práctica. Desde la frontera entre Estados Unidos conMéxico, pasando por distintos Estados del país “azteca”, son practicadas diferentes modalidades deeste juego. Sin embargo, decir que el chaaj en Mesoamérica es hoy en día una alternativa recreativay deportiva, es quedarse corto respecto a su ya demostrado potencial. La sacralidad manifestada através de los movimientos corporales está ofreciendo opciones de innovación en varios espacios de lassociedades actuales. En su dimensión ceremonial, revela una comunicación ancestral muy actual. Allíse ponen en juego los códices, las interpretaciones arqueológicas y los conocimientos territoriales depersonas sabedoras de las comunidades. En su dimensión lúdica, el juego reúne elementos culturales,deportivos y pedagógicos. Ha sido una práctica corporal, técnica y motora ejecutada constantementeen algunas regiones mexicanas y guatemaltecas. No obstante su antigüedad, en los últimos años seviene registrando una promoción inusitada, en medio de los actuales tiempos de cambio que fueronanunciados desde tiempos inmemoriales por los sabedores y las sabedoras mayas.

  7. Common ancestral origin of pemphigus vulgaris in Jews and Spaniards: a study using microsatellite markers.

    Science.gov (United States)

    Loewenthal, R; Slomov, Y; Gonzalez-Escribano, M F; Goldberg, I; Korostishevsky, M; Brenner, S; Nunez-Roldan, A; Conejo-Mir, J S; Gazit, E

    2004-04-01

    Pemphigus is a group of autoimmune blistering diseases of the skin and mucous membranes. The association of pemphigus with human leukocyte antigen (HLA) is widely accepted. It was described in many ethnic groups and in most countries of the world. Studies showed that the associated HLA haplotype in Jewish pemphigus vulgaris (PV) patients is HLA-B38, DRB1*0402, and DQB1*0302; or HLA-B35, DRB1*0402, and DQB1*0302. Similar associations with class II genes were found in Spanish non-Jewish PV patients. As Jews lived in Spain for hundreds of years and many converted to Christianity, the presence of the same HLA haplotype in the Jewish and Spanish PV suggests that they may share the same founder. Microsatellite markers which span the entire major histocompatibility complex (MHC) locus were used as genetic probes. They were utilized to dissect the MHC region in the search for possible common haplotypes, besides HLA, which may provide an answer to this question. It was found that in both cohorts, in addition to HLA class II genes, there are probably genes in the class I region which are associated with PV. Alleles belonging to the associated markers were used to construct haplotypes and to estimate genetic distances. The distance between the two PV cohorts is relatively short, but the distance between the Jewish patients and the Jewish controls is greater compared to the distance between Spanish patients and Spanish controls. In both PV populations, the same microsatellite haplotypes in addition to a common class II haplotype were found, suggesting that both patient populations originated from the same genetic stock and, therefore, share the same ancestral disease gene.

  8. The 8.1 ancestral MHC haplotype is strongly associated with colorectal cancer risk.

    Science.gov (United States)

    Tóth, Eva Katalin; Kocsis, Judit; Madaras, Balázs; Bíró, Adrienn; Pocsai, Zsuzsa; Fust, George; Blaskó, Bernadett; Karádi, István; Adány, Róza; Laki, Judit

    2007-10-15

    Many recent data indicate that some alleles encoded in the central major histocompatibility complex (MHC) region (Class III) of short arm of chromosome 6 may modify the risk of cancer development. Therefore we determined 4 single nucleotide polymorphisms (SNPs) of this region (TNF-alpha -308 G > A, RAGE -429 T > C, HSP70-2 -1267 A > G, LTA 252 A > G) in genomic DNA samples from 183 Hungarian patients with colorectal cancer and 141 age matched control subjects representing the Hungarian population of the same age and gender. No significant differences were found in either SNP tested. When, however, three- or four-locus haplotypes consisting of known constituents of the so-called 8.1 ancestral haplotype (8.1AH) were considered, marked differences were observed. Frequency of TNF-alpha -308A, RAGE -429C, HSP70-2 -1267G, LTA 252G (8.1AH) haplotype was significantly (p = 0.006) more frequent (19.1%) among patients than in the controls (7.7%). Age- and gender-adjusted ratio of the 8.1AH carriers vs. non-carriers to have colorectal cancer was 2.514 (1.130-5.594). This risk was higher in cancer-indicate that carriers of the 8.1AH, encoding for an altered immune response and known to be associated with alterations of several immune functions and autoimmune diseases have an increased risk for some cancer types. These findings may contribute to better understanding how the defense mechanisms against tumors could be enhanced/strengthened. (c) 2007 Wiley-Liss, Inc.

  9. The application of the 'Alpern scientific classification of solid fuels' to qualify Gondwana coals from different basins

    Energy Technology Data Exchange (ETDEWEB)

    Alpern, B.; Nahuys, J.; Lemos de Sousa, M.J.; Pinheiro, H.J.; Marques, M.M.; Flores, D.; Moreira, V.; Jorge, A.

    1988-01-01

    Coals are classified according to three main parameters, namely rank, type and facies (grade). The rank and type parameters are essentially based on petrographic analyses: reflectance and maceral composition, respectively. Complementary rank parameters based on chemical analyses have also been considered. The facies (grade) parameter is defined by the ash content. The rank categories are lignite, bituminous and anthracite, each one subdivided into hypo, meso and meta. Type is sub-divided into three genetic categories: vitric, liptic and fusic; however, a combination of the three permits the inclusion of a further, intermediate category. Facies is sub-divided into three major categories: coal, mixte and shale. The system can be expressed graphically by standardized charts in which, besides the three main parameters referred to, the beneficiation characteristics of a run-of-mine coal in terms of its washability potential can be included. The classification system is concerned not only with geological purposes, such as basin characterization, reserve calculation and in situ evaluation, but also with practical applications like beneficiation and carbonization. The application of the classification to Gondwana coals from Brazil, Mozambique and South Africa is discussed. The system has also been computerized. 4 refs., 19 figs., 2 tabs.

  10. Sedimentological characteristics and depositional environment of Upper Gondwana rocks in the Chintalapudi sub-basin of the Godavari valley, Andhra Pradesh, India

    Science.gov (United States)

    Ramamohanarao, T.; Sairam, K.; Venkateswararao, Y.; Nagamalleswararao, B.; Viswanath, K.

    2003-03-01

    The Kota (Early to Middle Jurassic) and Gangapur (Early Cretaceous) rocks of the Chintalapudi sub-basin of Gondwana are poorly to very poorly sorted, positively to very positively skewed, and leptokurtic to very leptokurtic. The Kota rocks show a single prominent truncation line at the inflection of saltation/suspension at 2.0 φ of the river mode of transportation. The Gangapur rocks show two truncation lines of saltation/suspension, one at 0.5-1.7 φ and the other at 2.4-4.0 φ. These are inferred to be due to a high turbulent phase of the river. On the multigroup multivariant discriminant functions V1- V2 diagram, the bulk of the samples from Kota and Gangapur fall in the field of turbidite deposition. This study supports the view that the discrimination of river from turbidite deposits on this diagram is poor since both deposits are identical in terms of settling velocity distribution. On the C- M diagram, the Kota and Gangapur rocks show segments of rolling, bottom suspension, and graded suspension during river transport of sediment. The Q-R segments of graded suspension for these rocks have a C/ M ratio of 2.5, which is close to the ratio of the turbidites. The Kota and Gangapur rocks have nearly the same assemblage of heavy minerals. The provenance is inferred to consist of basic igneous rocks, acid igneous rocks, high-grade metamorphic rocks and sedimentary rocks.

  11. Two-stage terrane assembly in Western Gondwana: Insights from structural geology and geophysical data of central Borborema Province, NE Brazil

    Science.gov (United States)

    Santos, Lauro Cézar M. de Lira; Dantas, Elton L.; Vidotti, Roberta M.; Cawood, Peter A.; dos Santos, Edilton J.; Fuck, Reinhadt A.; Lima, Haroldo M.

    2017-10-01

    Combined geophysical and structural data from the Transversal Subprovince of the Borborema Province (NE Brazil) highlight the internal structure of, and interrelationships between, the constituent terranes. Radiometric and magnetic maps show distinctive signatures for the Archean-Paleoproterozoic Alto Moxotó and Meso-to Neoproterozoic Alto Pajeú and Pernambuco-Alagoas terranes. Mapped radiometric and first and second order magnetic lineaments, associated with Euler deconvolution, enable correlation between geophysical data and major structures. In addition to early related deformation of the Alto Moxotó Terrane, combined analysis of late transposition foliations, lineations and kinematic criteria reveal a complex structural evolution marked by two distinct assembly stages. The first phase is characterized by thrust tectonics with top-to-the-south vergence, resulting in the juxtaposition of the allochtonous Alto Pajeú Terrane with the structurally underlying Alto Moxotó Terrane. The terrane boundary is delineated by the Serra de Jabitacá Shear Zone, which is associated with low dipping collisional granitic sheets and ca. 1.0 Ga mafic-ultramafic rocks interpreted as obtudcted ophiolite remnants. Later strike-slip movements strongly folded and obliterated thrust-related markers, and the continental scale E-W Pernambuco Lineament is interpreted as the result of lateral assembly between the composite Alto Pajeú-Alto Moxotó terranes and the Pernambuco-Alagoas Terrane during the metamorphic peak of the Brasiliano orogeny. Evolution of the Borborema Province reflects accretionary processes during the assembly of Western Gondwana.

  12. Late-Proterozoic to Paleozoic history of the peri-Gondwana Calabria-Peloritani Terrane inferred from a review of zircon chronology.

    Science.gov (United States)

    Fornelli, Annamaria; Micheletti, Francesca; Piccarreta, Giuseppe

    2016-01-01

    U-Pb analyses of zircon from ten samples of augen gneisses, eight mafic and intermediate metaigneous rocks and six metasediments from some tectonic domains along the Calabria-Peloritani Terrane (Southern Italy) contribute to knowledge of peri-Gondwanan evolution from Late-Proterozoic to Paleozoic times. All samples were equilibrated under amphibolite to granulite facies metamorphism during the Variscan orogeny. The zircon grains of all considered samples preserve a Proterozoic memory suggestive of detrital, metamorphic and igneous origin. The available data fit a frame involving: (1) Neoproterozoic detrital input from cratonic areas of Gondwana; (2) Pan-African/Cadomian assemblage of blocks derived from East and West African Craton; (3) metamorphism and bimodal magmatism between 535 and 579 Ma, within an active margin setting; (4) rifting and opening of Ordovician basins fed by detrital input from the assembled Cadomian blocks. The Paleozoic basins evolved through sedimentation, metamorphism and magmatism during the Variscan orogeny involving Palaeozoic and pre-Paleozoic blocks. The Proterozoic zircon records decidedly decrease in the high grade metamorphic rocks affected by Variscan pervasive partial melting.

  13. Geophysical perspective on the structural interference zone along the Neoproterozoic Brasília and Ribeira fold belts in West Gondwana

    Directory of Open Access Journals (Sweden)

    João Gabriel Motta

    Full Text Available ABSTRACT: The Brasília and Ribeira fold belts have been established in south-southwestern São Francisco Craton during the Brasiliano-Pan African orogeny (0.9-0.5 Ga - Tonian to Cambrian, and played an important role in West Gondwana continent assembly. The region is given by a complex regional fold and thrust belt superposed by shearing during the orogeny late times, with superposing stress fields forming a structural interference zone. These thrust sheets encompasses assemblies from lower- to upper-crust from different major tectonic blocks (Paranapanema, São Francisco, and newly created metamorphic rocks. Re-evaluation of ground gravity datasets in a geologically constrained approach including seismology (CRUST1 model and magnetic data (EMAG2 model unveiled details on the deep- crust settings, and the overall geometry of the structural interference zone. The Simple Bouguer Anomaly map shows heterogeneous density distribution in the area, highlighting the presence of high-density, high metamorphic grade rocks along the Alterosa suture zone in the Socorro-Guaxupé Nappe, lying amid a series of metasedimentary thrust scales in a regional nappe system with important verticalization along regional shear zones. Forward gravity modeling favors interpretations of structural interference up North into Guaxupé Nappe. Comparison to geotectonic models shows similarities with modern accretionary belts, renewing the discussion.

  14. Western Pacific Typhoon Aircraft Fixes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Western Pacific typhoon aircraft reconnaissance data from the years 1946 - 1965 and 1978, excluding 1952, were transcribed from original documents, or copy of...

  15. 78 FR 41033 - Fisheries of the Northeast Region, Southeast Region, North Pacific Region, Pacific Region...

    Science.gov (United States)

    2013-07-09

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XC399 Fisheries of the Northeast Region, Southeast Region, North Pacific Region, Pacific Region; Western Pacific Region AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA...

  16. Pacific Studies: Quo Vadis?

    Directory of Open Access Journals (Sweden)

    Anne Holden Rønning

    2014-02-01

    Full Text Available Looking back to the past this paper discusses why Pacific studies and in particular Australasian studies became an area of interest in tertiary education in Europe. What subject areas initiated these studies, and how do past legacies shape the present? With cutbacks in higher education over the past two decades the future of interdisciplinary studies and the humanities looks bleak. At the same time due to global business and increased political communication across borders there is a vibrant interest in and need for such studies among businesses and students. For most Europeans the literature of settler countries, with their European legacy, makes access to ways of thought and culture easier than studies of countries with other mythological backgrounds. In today’s multicultural environment such studies can provide knowledge for an understanding of other cultures and increase tolerance of the ‘other’. Area studies have relevance to our situation in Europe with increased migrancy, not least as a result of Schengen and EU regulations.

  17. Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

    DEFF Research Database (Denmark)

    Kutty, Sujatha Narayanan; Pont, Adrian C.; Meier, Rudolf

    2014-01-01

    split within this family. The ancestral larval feeding habit is reconstructed to be saprophagy with more specialised coprophagous saprophagy, phytophagy, and carnivory evolving multiple times from saprophagous ancestors. The origins of carnivory in larvae are significantly correlated with a reduction...

  18. Ancestral role of Pax2/5/8 in molluscan brain and multimodal sensory system development.

    Science.gov (United States)

    Wollesen, Tim; Rodríguez Monje, Sonia Victoria; Todt, Christiane; Degnan, Bernard M; Wanninger, Andreas

    2015-10-28

    esthetes and the ampullary system of polyplacophorans as well as the eyes of cephalopods. Pax2/5/8-expressing cells are present in regions where the future sensory cells such as the polyplacophoran esthetes are situated and hence Pax2/5/8 expression probably predates sensory cell development during ontogeny. In mollusks, Pax2/5/8 is only expressed in derivatives of the ectoderm and hence an ancestral role in molluscan ectoderm differentiation is inferred.

  19. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

    Directory of Open Access Journals (Sweden)

    Nicholas C Butzin

    Full Text Available The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS. These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

  20. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

    Science.gov (United States)

    Butzin, Nicholas C; Lapierre, Pascal; Green, Anna G; Swithers, Kristen S; Gogarten, J Peter; Noll, Kenneth M

    2013-01-01

    The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

  1. Phanerozoic tectonic evolution of the Circum-North Pacific

    Science.gov (United States)

    Nokleberg, Warren J.; Parfenov, Leonid M.; Monger, James W.H.; Norton, Ian O.; Khanchuk, Alexander I.; Stone, David B.; Scotese, Christopher R.; Scholl, David W.; Fujita, Kazuya

    2000-01-01

    the ancestral margins of present-day Northeast Asia and northwestern North America. The rifting resulted in the fragmentation of each continent and the formation of cratonal and passive continental-margin terranes that eventually migrated and accreted to other sites along the evolving margins of the original or adjacent continents. (2) From about the Late Triassic through the mid-Cretaceous, a succession of island arcs and tectonically paired subduction zones formed near the continental margins. (3) From about mainly the mid-Cretaceous through the present, a succession of igneous arcs and tectonically paired subduction zones formed along the continental margins. (4) From about the Jurassic to the present, oblique convergence and rotations caused orogenparallel sinistral and then dextral displacements within the upper-plate margins of cratons that have become Northeast Asia and North America. The oblique convergences and rotations resulted in the fragmentation, displacement, and duplication of formerly more nearly continuous arcs, subduction zones, and passive continental margins. These fragments were subsequently accreted along the expanding continental margins. (5) From the Early Jurassic through Tertiary, movement of the upper continental plates toward subduction zones resulted in strong plate coupling and accretion of the former island arcs and subduction zones to the continental margins. Accretions were accompanied and followed by crustal thickening, anatexis, metamorphism, and uplift. The accretions resulted in substantial growth of the North Asian and North American Continents. (6) During the middle and late Cenozoic, oblique to orthogonal convergence of the Pacifi c plate with present-day Alaska and Northeast Asia resulted in formation of the modern-day ring of volcanoes around the Circum-North Pacific. Oblique convergence between the Pacific plate and Alaska also resulted in major dextral-slip faulting in interior and southern Alaska and along the western p

  2. Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes.

    Directory of Open Access Journals (Sweden)

    Sébastien Lavoué

    Full Text Available The clupeoid fishes are distributed worldwide, with marine, freshwater and euryhaline species living in either tropical or temperate environments. Regional endemism is important at the species and genus levels, and the highest species diversity is found in the tropical marine Indo-West Pacific region. The clupeoid distribution follows two general pattern of species richness, the longitudinal and latitudinal gradients. To test historical hypotheses explaining the formation of these two gradients, we have examined the early biogeography of the Clupeoidei in reconstructing the evolution of their habitat preferences along with their ancestral range distributions on a time-calibrated mitogenomic phylogeny. The phylogenetic results support the distinction of nine main lineages within the Clupeoidei, five of them new. We infer several independent transitions from a marine to freshwater environment and from a tropical to temperate environment that occurred after the initial diversification period of the Clupeoidei. These results combined with our ancestral range reconstruction hypothesis suggest that the probable region of origin and diversification of the Clupeoidei during the Cretaceous period was the tropical marine precursor to the present Indo-West Pacific region. Thus, our study favors the hypotheses of "Region of origin" and "Tropical conservatism" to explain the origins of the longitudinal and latitudinal gradients of clupeoid species richness, respectively. Additional geological and paleontological evidence further define the tropical marine paleo-region of origin as the eastern Tethys Sea region. The Cretaceous fossil record of the Clupeoidei is partially incongruent with the results here as it contains taxa found outside this region. We discuss three possible causes of conflict between our biogeographical hypothesis and the distributions of the Cretaceous clupeoid fossils: regional extinction, incomplete taxonomic sampling and incorrect

  3. Reinterpretation of adcoh and cocorp seismic reflection data with constraints from detailed forward modeling of potential field data - Implications for Laurentia-Peri-Gondwana suture

    Science.gov (United States)

    Duff, Patrick D.; Kellogg, James N.

    2017-08-01

    To better constrain the structure of the Laurentian - Peri-Gondwana suture zone, maps and a 2-dimensional regional cross-section model constrained by seismic data and surface geology have been developed by forward and inverse modeling the aeromagnetic and gravity fields. The Central Piedmont Suture (CPS), the boundary between the Laurentian Inner Piedmont and the Peri-Gondwanan Carolina terrane is a low-angle thrust fault ( 30°) ramping up from an Alleghanian mid-crustal detachment at depths of about 12 km. ADCOH and COCORP seismic data image anticlinal structures in the footwalls of the Hayesville thrust and the CPS, above the Alleghanian decollement. The footwall rocks have previously been interpreted as Paleozoic shelf strata on the basis of sub-horizontal seismic reflectors; however, the high densities required to fit the observed gravity anomaly suggest that the folded footwall reflectors may need to be reinterpreted as horse blocks or duplex structures of Grenvillian basement. The Appalachian paired gravity anomaly can be explained by an increase in crustal thickness and a decrease in upper crustal density moving northwestward from the Carolina Terrane toward the Appalachian core. A change in lower crustal density is not required, so that Grenville basement rocks may extend farther to the southeast than previously thought. The 5 to 10 km of Alleghanian uplift and exhumation predicted by P-T crystallization data compiled in this paper can be easily accommodated by thrusting on four major low-angle thrust systems: Great Smoky Mountain Thrust (GSMT), Hayesville, Brevard, and CPS. Unroofing of metamorphic core complexes by normal faulting may therefore not be required to explain the observed exhumation. Alleghanian collision along the southeastern Appalachian margin was predominately orthogonal to strike consistent with the previous reconstructions that call for the counter-clockwise rotation of Gondwanan West Africa, creating head-on collision in the southern

  4. An early bird from Gondwana: Paleomagnetism of Lower Permian lavas from northern Qiangtang (Tibet) and the geography of the Paleo-Tethys

    Science.gov (United States)

    Song, Peiping; Ding, Lin; Li, Zhenyu; Lippert, Peter C.; Yue, Yahui

    2017-10-01

    The origin of the northern Qiangtang block and its Late Paleozoic-Early Mesozoic drift history remain controversial, largely because paleomagnetic constraints from pre-Mesozoic units are sparse and of poor quality. In this paper, we provide a robust and well-dated paleomagnetic pole from the Lower Permian Kaixinling Group lavas on the northern Qiangtang block. This pole suggests that the northern Qiangtang block had a paleolatitude of 21.9 ± 4.7 °S at ca. 296.9 ± 1.9 Ma. These are the first volcanic-based paleomagnetic results from pre-Mesozoic rocks of the Qiangtang block that appear to average secular variation accurately enough to yield a well-determined paleolatitude estimate. This new pole corroborates the hypothesis, first noted on the basis of less rigorous paleomagnetic data, the presence of diamictites, detrital zircon provenance records, and faunal assemblages, that the northern Qiangtang block rifted away from Gondwana prior to the Permian. Previous studies have documented that the northern Qiangtang block accreted to the Tarim-North China continent by Norian time. We calculate a total northward drift of ca. 7000 km over ca. 100 myr, which corresponds to an average south-north plate velocities of ∼7.0 cm/yr. Our results do not support the conclusion that northern Qiangtang has a Laurasian affinity, nor that the central Qiangtang metamorphic belt is an in situ Paleo-Tethys suture. Our analysis, however, does not preclude paleogeographies that interpret the central Qiangtang metamorphic belt as an intra-Qiangtang suture that developed at southernly latitudes outboard of the Gondwanan margin. We emphasize that rigorous paleomagnetic data from Carboniferous units of northern Qiangtang and especially upper Paleozoic units from southern Qiangtang can test and further refine these paleogeographic interpretations.

  5. Middle to late Cambrian shallow marine trace fossils from the Imfout Syncline (Western Meseta, Morocco): Palaeoecological and palaeoenvironmental significance in NW-Gondwana

    Science.gov (United States)

    Oukassou, Mostafa; Lagnaoui, Abdelouahed; Raji, Mohammed; Michard, André; Saddiqi, Omar

    2017-05-01

    The present research provides the first evidence of invertebrate activity assigned to the ichnogenus Selenichnites occurring together with moderately diverse ichnofossils from the middle to late Cambrian of the Moroccan Meseta. The invertebrate traces occur in sandstone strata of the El Hank Formation within the Imfout Syncline, in the northern part of the Rehamna Massif (Coastal Block, western Moroccan Meseta). Bedding surfaces from the top of the El Hank Formation near the Imfout Dam show diverse forms of current ripples and distincts crescentic ichnofossils in concave epirelief scattered on the surface. In this section, the traces provide evidence of the ethology of an organism inhabiting the relatively shallow waters of the area during this time. Selenichnites co-occurs with the ichnogenera Arenicolites, Diplocraterion, Lingulichnus, Monocraterion, Skolithos and unidentified burrows, and the ichnoassemblage is referred to the Skolithos ichnofacies. These traces can be referred to arthropods (e.g. polychaete worms and amphipod crustaceans), lingulid brachiopods, annelids and/or phoronids. The Imfout Selenichnites represents the first occurrence of this ichnogenus from the Cambrian of the Moroccan Meseta, and the second from the Cambrian deposits of Morocco. The potential tracemakers are still questionable, but were most likely xiphosurans, trilobites, euthycarcinoids or crustaceans. If so, the Imfout traces could be among the oldest pieces of evidence for the presence of horseshoe crabs during the Cambrian. The combination of sedimentological and ichnological data indicates that the El Hank Formation was deposited in a sublittoral soft ground environment next to a sandy shore. It was originally part of an early Palaeozoic shallow marine epicontinental platform in west-central Morocco. In addition to the equivalent Cambrian deposits from the Anti-Atlas, the El Hank Formation constituted a part of the northern Gondwana platform domain during the transgression

  6. Evidence of early Archean crust in northwest Gondwana, from U-Pb and Hf isotope analysis of detrital zircon, in Ediacaran surpacrustal rocks of northern Spain

    Science.gov (United States)

    Naidoo, Thanusha; Zimmermann, Udo; Vervoort, Jeff; Tait, Jenny

    2018-03-01

    The Mora Formation (Narcea Group) is one of the oldest Precambrian supracrustal successions in northern Spain. Here, we use U-Pb and in situ Hf isotope analysis on detrital zircon to determine its age and provenance. The youngest U-Pb dates constrain the maximum depositional age of the Mora Formation at 565 ± 11 Ma. Results indicate: (1) a dominant Ediacaran zircon population (33%; 565-633 Ma, Cadomian) within a spectrum of Neoproterozoic ages (40%; 636-996 Ma); and (2) smaller Mesoproterozoic (5%; 1004-1240 Ma), Palaeoproterozoic (11%; 1890-2476 Ma) and Archean (11%; 2519-3550 Ma) populations. Results here do not point to one specific cratonic source area; instead, detritus may have been derived from the West African craton and Amazonia, or even the concealed Iberian basement. The lack of 1.3-1.8 Ga grains suggests exclusion of the Sahara Craton as a major source, but this is not certain. This mixed composition favours a complex source history with reworking of detritus across terrane/craton boundaries. Hafnium isotope compositions indicate a range of crustal and juvenile sources, with initial ɛHf values between -15.8 and 11.1, and Hf model ages from 0.8 to 3.7 Ga. For Neoproterozoic zircons (80%), juvenile components (ɛHf(i) +10) may be related to Rodinia fragmentation and the onset of an active margin setting leading to the Cadomian orogeny. Palaeoproterozoic to Paleoarchean grains (20%) all have negative ɛHf values and Meso- to Eoarchean Hf model ages. This indicates an early (Archean) sialic crustal component for northwestern Gondwana.

  7. New U-Pb ages in the Diablillos Intrusive Complex, Southern Puna, Argentina: A long magmatic event in the Paleozoic Arc, SW Gondwana

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz, Agustin; Hauser, Natalia [Universidade de Brasilia (UnB), DF (Brazil). Instituto de Geociencias. Lab. de Geocronologia; Becchio, Raul; Nieves, Alexis; Suzano, Nestor [Universidad Nacional de Salta (UNSa)-CONICET, Salta (Argentina)

    2015-07-01

    The Puna geological region comprises Salta, Jujuy and Catamarca provinces, northwestern Argentina. This 4000 meter above sea level high-plateau region lies between the Central Argentinian Andes. The Puna basement in the central Andes consists of Proterozoic–Paleozoic metamorphic rocks and granitoids. Diverse authors, proposed different models to explain the origin of the basement, where two orogenic events are recognized: the Pampean (Upper Precambrian–Lower Cambrian) and Famatinian (Upper Cambrian–Lower Silurian) (e.g. Ramos et al., 1986; Ramos, 1988; Loewy et al., 2004; for opposite points of view see Becchio et al., 1999; Bock et al., 2000; Buttner et al., 2005). Hence, Lucassen et al. (2000) proposed for the Central Andean basement, an evolution in a mobile belt, where the Pampean and Famatinian cycles are not distinct events but, they are one single, non-differentiable event from 600 to 400 Ma. The mobile belt culminated in low-P/ high-T metamorphism at approximately 525-500 Ma. Then, these were followed by a long-lasting high-thermal gradient regime in the mid-crust until Silurian times. Becchio et al., (2011) defined the Diablillos Intrusive Complex (CID, by its Spanish name), emplaced in the Inca Viejo Range. This range splits the Salares Ratones-Centenario with the Salar Diablillos (Fig.1). This Complex is located in the Eastern Magmatic Belt, Southern Puna, Argentina. Here we present new zircons U-Pb ages by LA-MC-ICPMS in the Diablillos Intrusive Complex, contributing to understanding the magmatic event in the lower Paleozoic arc, SW Gondwana. (author)

  8. Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.

    Science.gov (United States)

    Karlin, Eric F; Smouse, Peter E

    2017-08-01

    Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation

  9. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

    Directory of Open Access Journals (Sweden)

    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  10. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population.

    Directory of Open Access Journals (Sweden)

    Nora Cardona-Castro

    Full Text Available Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers, Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations.

  11. High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

    Science.gov (United States)

    Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

    2016-11-01

    Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

  12. Saccharomyces cerevisiae Bat1 and Bat2 Aminotransferases Have Functionally Diverged from the Ancestral-Like Kluyveromyces lactis Orthologous Enzyme

    Science.gov (United States)

    Colón, Maritrini; Hernández, Fabiola; López, Karla; Quezada, Héctor; González, James; López, Geovani; Aranda, Cristina; González, Alicia

    2011-01-01

    Background Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. Principal Findings Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs). This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1), while catabolic substrates are accumulated in the cytosol (Bat2). Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. Conclusions Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the biosynthetic and catabolic

  13. Ancestral polymorphism at the major histocompatibility complex (MHCIIß in the Nesospiza bunting species complex and its sister species (Rowettia goughensis

    Directory of Open Access Journals (Sweden)

    van Rensburg Alexandra

    2012-08-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIß variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR. Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIß alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIß among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective

  14. Pacific Northwest Salmon Habitat Project Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In the Pacific Northwest Salmon Habitat Project Database Across the Pacific Northwest, both public and private agents are working to improve riverine habitat for a...

  15. Infant Mortality and Asians and Pacific Islanders

    Science.gov (United States)

    ... Population Profiles > Asian American > Infant Health & Mortality Infant Mortality and Asians and Pacific Islanders Among Asian/Pacific ... as compared to non-Hispanic white mothers. Infant Mortality Rate Infant mortality rate per 1,000 live ...

  16. 76 FR 38370 - Western Pacific Fisheries; Approval of a Marine Conservation Plan for Pacific Insular Areas...

    Science.gov (United States)

    2011-06-30

    ... is, in the EEZ around the Pacific remote island areas (PRIA). The PRIA are Baker Island, Howland... National Oceanic and Atmospheric Administration RIN 0648-XA517 Western Pacific Fisheries; Approval of a Marine Conservation Plan for Pacific Insular Areas; Western Pacific Sustainable Fisheries Fund AGENCY...

  17. Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.

    Science.gov (United States)

    Corman, Victor Max; Baldwin, Heather J; Tateno, Adriana Fumie; Zerbinati, Rodrigo Melim; Annan, Augustina; Owusu, Michael; Nkrumah, Evans Ewald; Maganga, Gael Darren; Oppong, Samuel; Adu-Sarkodie, Yaw; Vallo, Peter; da Silva Filho, Luiz Vicente Ribeiro Ferreira; Leroy, Eric M; Thiel, Volker; van der Hoek, Lia; Poon, Leo L M; Tschapka, Marco; Drosten, Christian; Drexler, Jan Felix

    2015-12-01

    We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a

  18. The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

    Science.gov (United States)

    Desroches, M; Royer, G; Roche, D; Mercier-Darty, M; Vallenet, D; Médigue, C; Bastard, K; Rodriguez, C; Clermont, O; Denamur, E; Decousser, J-W

    2018-01-01

    More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli , one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS . These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to

  19. Geochronology, stratigraphy and geochemistry of Cambro-Ordovician, Silurian and Devonian volcanic rocks of the Saxothuringian Zone in NE Bavaria (Germany)—new constraints for Gondwana break up and ocean-island magmatism

    Science.gov (United States)

    Höhn, Stefan; Koglin, Nikola; Klopf, Lisa; Schüssler, Ulrich; Tragelehn, Harald; Frimmel, Hartwig E.; Zeh, Armin; Brätz, Helene

    2018-01-01

    Stratigraphically well-defined volcanic rocks in Palaeozoic volcano-sedimentary units of the Frankenwald area (Saxothuringian Zone, Variscan Orogen) were sampled for geochemical characterisation and U-Pb zircon dating. The oldest rock suite comprises quartz keratophyre, brecciated keratophyre, quartz keratophyre tuff and basalt, formed in Upper Cambrian to Tremadocian time (c. 497-478 Ma). Basaltic volcanism continued until the Silurian. Quartz keratophyre shows post-collisional calc-alkaline signature, the Ordovician-Silurian basalt has alkaline signature typical of continental rift environments. The combined datasets provide evidence of Cambro-Ordovician bimodal volcanism and successive rifting until the Silurian. This evolution very likely resulted from break-up of the northern Gondwana margin, as recorded in many terranes throughout Europe. The position at the northern Gondwana margin is supported by detrital zircon grains in some tuffs, with typical Gondwana-derived age spectra mostly recording ages of 550-750 Ma and minor age populations of 950-1100 and 1700-2700 Ma. The absence of N-MORB basalt in the Frankenwald area points to a retarded break-off of the Saxothuringian terrane along a continental rift system from Uppermost Cambrian to Middle Silurian time. Geochemical data for a second suite of Upper Devonian basalt provide evidence of emplacement in a hot spot-related ocean-island setting south of the Rheic Ocean. Our results also require partial revision of the lithostratigraphy of the Frankenwald area. The basal volcanic unit of the Randschiefer Formation yielded a Tremadocian age and, therefore, should be attributed to the Vogtendorf Formation. Keratophyre of the Vogtendorf Formation, previously assigned to the Tremadoc, is most likely of Upper Devonian age.

  20. South Pacific Nuclear Free Zone Treaty

    International Nuclear Information System (INIS)

    1986-02-01

    The full text of the South Pacific Nuclear Free Zone Treaty with its Annexes endorsed on 6 August 1985 by the South Pacific Forum (a body comprising the independent and self-governing countries of the South Pacific, namely Australia, the Cook Islands, Fiji, Kiribati, Nauru, New Zealand, Nive, Papua New Guinea, the Solomon Islands, Tonga, Tuvalu, Vanuatu and Western Samoa) is presented

  1. South Pacific Nuclear Free Zone Treaty

    International Nuclear Information System (INIS)

    1986-02-01

    On 6 August 1985 the South Pacific Forum, a body comprising the independent and self-governing countries of the South Pacific (Australia, the Cook Islands, Fiji, Kiribati, Nauru, New Zealand, Niue, Papua New Guinea, the Solomon Islands, Tonga, Tuvalu, Vanuatu and Western Samoa), endorsed the text of the South Pacific Nuclear Free Zone Treaty and opened it for signature [es

  2. South Pacific Nuclear Free Zone Treaty

    International Nuclear Information System (INIS)

    1986-02-01

    On 6 August 1985 the South Pacific Forum, a body comprising the independent and self-governing countries of the South Pacific (Australia, the Cook Islands, Fiji, Kiribati, Nauru, New Zealand, Niue, Papua New Guinea, the Solomon Islands, Tonga, Tuvalu, Vanuatu and Western Samoa), endorsed the text of the South Pacific Nuclear Free Zone Treaty and opened it for signature [ru

  3. Amplification of an ancestral mammalian L1 family of long interspersed repeated DNA occurred just before the murine radiation

    International Nuclear Information System (INIS)

    Pascale, E.; Valle, E.; Furano, A.V.

    1990-01-01

    Each mammalian genus examined so far contains 50,000-100,000 members of an L1 (LINE 1) family of long interspersed repeated DNA elements. Current knowledge on the evolution of L1 families presents a paradox because, although L1 families have been in mammalian genomes since before the mammalian radiation ∼80 million years ago, most members of the L1 families are only a few million years old. Accordingly it has been suggested either that the extensive amplification that characterizes present-day L1 families did not occur in the past or that old members were removed as new one were generated. However, the authors show here that an ancestral rodent L1 family was extensively amplified ∼10 million years ago and that the relics of this amplification have persisted in modern murine genomes. This amplification occurred just before the divergence of modern murine genera from their common ancestor and identifies the murine node in the lineage of modern muroid rodents The results suggest that repeated amplification of L1 elements is a feature of the evaluation of mammalian genomes and that ancestral amplification events could provide a useful tool for determining mammalian lineages

  4. Topologies of the conditional ancestral trees and full-likelihood-based inference in the general coalescent tree framework.

    Science.gov (United States)

    Sargsyan, Ori

    2010-08-01

    The general coalescent tree framework is a family of models for determining ancestries among random samples of DNA sequences at a nonrecombining locus. The ancestral models included in this framework can be derived under various evolutionary scenarios. Here, a computationally tractable full-likelihood-based inference method for neutral polymorphisms is presented, using the general coalescent tree framework and the infinite-sites model for mutations in DNA sequences. First, an exact sampling scheme is developed to determine the topologies of conditional ancestral trees. However, this scheme has some computational limitations and to overcome these limitations a second scheme based on importance sampling is provided. Next, these schemes are combined with Monte Carlo integrations to estimate the likelihood of full polymorphism data, the ages of mutations in the sample, and the time of the most recent common ancestor. In addition, this article shows how to apply this method for estimating the likelihood of neutral polymorphism data in a sample of DNA sequences completely linked to a mutant allele of interest. This method is illustrated using the data in a sample of DNA sequences at the APOE gene locus.

  5. Chromosome Painting in Callicebus nigrifrons Provides Insights into the Genome Evolution of Titi Monkeys and the Ancestral Callicebinae Karyotype.

    Science.gov (United States)

    Pereira Araújo, Naiara; Alves do Espírito Santo, Alice; do Socorro Pereira, Valéria; Stanyon, Roscoe; Svartman, Marta

    2017-01-01

    We studied the chromosomes of Callicebus nigrifrons with conventional and molecular cytogenetic methods. Our chromosome painting analysis in C. nigrifrons together with previous reports allowed us to hypothesize an ancestral Callicebinae karyotype with 2n = 48. The associations of human chromosomes (HSA) 2/22, 7/15, 10/11, and the inverted HSA2/16 would link Callicebus, Cheracebus, and Plecturocebus and would thus be present in the ancestral Callicebinae karyotype. Four fusions (HSA1b/1c, 3c/8b, 13/20, and 14/15/3/21) and 1 fission (HSA2/22) are synapomorphies of Callicebus. The associations HSA3/15 and HSA3/9 are chromosome features linking Callicebus and Cheracebus, whereas the association HSA13/17 would represent a link between Callicebus and the moloch group (Plecturocebus). Only 6 of the 33 recognized titi monkey species have now been painted with human chromosome-specific probes. Further analyses are needed to clarify the phylogenomic relationships in this species-rich group. © 2017 S. Karger AG, Basel.

  6. Cortisol mobilizes mineral stores from vertebral skeleton in the European eel: an ancestral origin for glucocorticoid-induced osteoporosis?

    Science.gov (United States)

    Sbaihi, Miskal; Rousseau, Karine; Baloche, Sylvie; Meunier, François; Fouchereau-Peron, Martine; Dufour, Sylvie

    2009-05-01

    Endogenous excess cortisol and glucocorticoid (GC) therapy are a major cause of secondary osteoporosis in humans. Intense bone resorption can also be observed in other vertebrates such as migratory teleost fish at the time of reproductive migration and during fasting when large amounts of calcium and phosphate are required. Using a primitive teleost, the European eel, as a model, we investigated whether cortisol could play an ancestral role in the induction of vertebral skeleton demineralization. Different histological and histomorphometric methods were performed on vertebral samples of control and cortisol-treated eels. We demonstrated that cortisol induced a significant bone demineralization of eel vertebrae, as shown by significant decreases of the mineral ratio measured by incineration, and the degree of mineralization measured by quantitative microradiography of vertebral sections. Histology and image analysis of ultrathin microradiographs showed the induction by cortisol of different mechanisms of bone resorption, including periosteocytic osteolysis and osteoclastic resorption. Specificity of cortisol action was investigated by comparison with the effects of sex steroids. Whereas, testosterone had no effect, estradiol induced vertebral skeleton demineralization, an effect related to the stimulated synthesis of vitellogenin (Vg), an oviparous specific phospho-calcio-lipoprotein. By contrast, the cortisol demineralization effect was not related to any stimulation of Vg. This study demonstrates GC-induced bone demineralization in an adult non-mammalian vertebrate, which undergoes natural bone resorption during its life cycle. Our data suggest that the stimulatory action of cortisol on bone loss may represent an ancestral and conserved endocrine regulation in vertebrates.

  7. A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions.

    Science.gov (United States)

    Blank, Matthew L; Parker, Michelle L; Ramaswamy, Raghavendran; Powell, Cameron J; English, Elizabeth D; Adomako-Ankomah, Yaw; Pernas, Lena F; Workman, Sean D; Boothroyd, John C; Boulanger, Martin J; Boyle, Jon P

    2018-03-05

    The Toxoplasma gondii locus mitochondrial association factor 1 (MAF1) encodes multiple paralogs, some of which mediate host mitochondrial association (HMA). Previous work showed that HMA was a trait that arose in T. gondii through neofunctionalization of an ancestral MAF1 ortholog. Structural analysis of HMA-competent and incompetent MAF1 paralogs (MAF1b and MAF1a, respectively) revealed that both paralogs harbor an ADP ribose binding macro domain, with comparatively low (micromolar) affinity for ADP ribose. Replacing the 16 C-terminal residues of MAF1b with those of MAF1a abrogated HMA, and we also show that only three residues in the C-terminal helix are required for MAF1-mediated HMA. Importantly these same three residues are also required for the in vivo growth advantage conferred by MAF1b, providing a definitive link between in vivo proliferation and manipulation of host mitochondria. Co-immunoprecipitation assays reveal that the ability to interact with the mitochondrial MICOS complex is shared by HMA-competent and incompetent MAF1 paralogs and mutants. The weak ADPr coordination and ability to interact with the MICOS complex shared between divergent paralogs may represent modular ancestral functions for this tandemly expanded and diversified T. gondii locus. This article is protected by copyright. All rights reserved. © 2018 John Wiley & Sons Ltd.

  8. The ghost of Afrikaner identity in Ancestral voices, Leap year and The long silence of Mario Salviati (Etienne van Heerden

    Directory of Open Access Journals (Sweden)

    Mariëtte van Graan

    2017-04-01

    Full Text Available Ghost characters are a characteristic of the novels of Etienne van Heerden, but little research has been done concerning the nature and function of these ghost characters. In this article I discuss Van Heerden’s use of ghost characters diachronically with reference to the novels Ancestral voices (1986, Leap year (1993 and The long silence of Mario Salviati (2000. In order to clarify the nature of these ghosts, I use the so-called science of the paranormal as a framework. The ghosts in the three novels will be classified accordingly, and then discussed within the context of the novels in which they appear. In this way, I shall show how the ghost characters in these novels can be read as a constantly changing embodiment of Afrikaner identity (a central theme in Van Heerden’s oeuvre. Van Heerden’s Afrikaner changes with the times: in Ancestral voices the ghost characters form a collective that represents a fragmented image of the stereotypical, archaic male Afrikaner identity; in Leap year a liminal character is written in a liminal time to embody a liminal Afrikaner identity; and in The long silence of Mario Salviati Van Heerden moves away from the exclusive Afrikaner identity to a broader South African identity by using ghost characters from very different backgrounds and origins. In conclusion I shall compare these identities and the historical contexts of these novels in order to show the function of Van Heerden’s ghost characters as constant rewritings of South African identities.

  9. Code breaking in the pacific

    CERN Document Server

    Donovan, Peter

    2014-01-01

    Covers the historical context and the evolution of the technically complex Allied Signals Intelligence (Sigint) activity against Japan from 1920 to 1945 Describes, explains and analyzes the code breaking techniques developed during the war in the Pacific Exposes the blunders (in code construction and use) made by the Japanese Navy that led to significant US Naval victories

  10. The Stylasterina of the Pacific

    NARCIS (Netherlands)

    Boschma, H.

    1953-01-01

    In 1857 and 1860, Milne Edwards and Haime listed 9 species of Stylasterlna known to occur in the Pacific region, including "Allopora (Stylaster) infundibulifera", a species which later, as Amphelia infundibulifera (Lamarck), was to be classified in the Madreporaria (Scleractinia). Moseley (1880),

  11. Sustainable fisheries management: Pacific salmon

    Science.gov (United States)

    Knudsen, E. Eric; Steward, Cleveland R.; MacDonald, Donald; Williams, Jack E.; Reiser, Dudley W.

    1999-01-01

    What has happened to the salmon resource in the Pacific Northwest? Who is responsible and what can be done to reverse the decline in salmon populations? The responsibly falls on everyone involved - fishermen, resource managers and concerned citizens alike - to take the steps necessary to ensure that salmon populations make a full recovery.This collection of papers examines the state of the salmon fisheries in the Pacific Northwest. They cover existing methods and supply model approaches for alternative solutions. The editors stress the importance of input from and cooperation with all parties involved to create a viable solution. Grass roots education and participation is the key to public support - and ultimately the success - of whatever management solutions are developed.A unique and valuable scientific publication, Sustainable Fisheries Management: Pacific Salmon clearly articulates the current state of the Pacific salmon resource, describes the key features of its management, and provides important guidance on how we can make the transition towards sustainable fisheries. The solutions presented in this book provide the basis of a strategy for sustainable fisheries, requiring society and governmental agencies to establish a shared vision, common policies, and a process for collaborative management.

  12. Trade in the Pacific Rim.

    Science.gov (United States)

    Dollar, David

    1988-01-01

    States that international trade is a prime factor linking the Pacific Rim nations. Discusses the differences in each nation's productive factors (land, labor, capital) and examines the emerging technological competition. Concludes that if U.S. firms cannot meet the challenge of foreign competition, then protectionism might limit further economic…

  13. Indian Ocean warming modulates Pacific climate change.

    Science.gov (United States)

    Luo, Jing-Jia; Sasaki, Wataru; Masumoto, Yukio

    2012-11-13

    It has been widely believed that the tropical Pacific trade winds weakened in the last century and would further decrease under a warmer climate in the 21st century. Recent high-quality observations, however, suggest that the tropical Pacific winds have actually strengthened in the past two decades. Precise causes of the recent Pacific climate shift are uncertain. Here we explore how the enhanced tropical Indian Ocean warming in recent decades favors stronger trade winds in the western Pacific via the atmosphere and hence is likely to have contributed to the La Niña-like state (with enhanced east-west Walker circulation) through the Pacific ocean-atmosphere interactions. Further analysis, based on 163 climate model simulations with centennial historical and projected external radiative forcing, suggests that the Indian Ocean warming relative to the Pacific's could play an important role in modulating the Pacific climate changes in the 20th and 21st centuries.

  14. New glacial evidences at the Talacasto paleofjord (Paganzo basin, W-Argentina) and its implications for the paleogeography of the Gondwana margin

    Science.gov (United States)

    Aquino, Carolina Danielski; Milana, Juan Pablo; Faccini, Ubiratan Ferrucio

    2014-12-01

    The Talacasto paleovalley is situated in the Central Precordillera of San Juan, Argentina, where upper Carboniferous-Permian rocks (Paganzo Group) rest on Devonian sandstones of the Punta Negra Formation. This outcrop is an excellent example of a glacial valley-fill sequence that records at least two high-frequency cycles of the advance and retreat of a glacier into the valley. The paleocurrent analysis shows transport predominantly to the south, indicating that at this site the ice flow differs from the other nearby paleovalleys. Evidence of the glacial origin of this valley can be seen in the glacial striae on the valley's sides, as well as the U-shape of the valley, indicated by very steep locally overhanging valley walls. Deglaciation is indicated by a set of retransported conglomerates deposited in a shallow-water environment followed by a transgressive succession, which suggests eustatic rise due to meltwater input to the paleofjord. The complete sedimentary succession records distinct stages in the evolution of the valley-fill, represented by seven stratigraphical units. These units are identified based on facies associations and their interpreted depositional setting. Units 1 to 5 show one cycle of deglaciation and unit 6 marks the beginning of a new cycle of glacier advance which is characterized by different types of glacial deposits. All units show evidence of glacial influence such as dropstones and striated clasts, which indicates that the glaciers were always present in the valley or in adjacent areas during sedimentation. The Talacasto paleofjord provides good evidence of the Late Paleozoic Gondwana glaciation in western Argentina and examples of sedimentary successions which have been interpreted as being deposited by a confined wet-based glacier in advance and retreat cycles, with eventual release of icebergs into the basin. The outcrop is also a key for reconstructing the local glacial paleogeography, and it suggests a new interpretation that is

  15. Late Mesoproterozoic to Early Paleozoic history of metamorphic basement from the southeastern Chiapas Massif Complex, Mexico, and implications for the evolution of NW Gondwana

    Science.gov (United States)

    Weber, Bodo; González-Guzmán, Reneé; Manjarrez-Juárez, Román; Cisneros de León, Alejandro; Martens, Uwe; Solari, Luigi; Hecht, Lutz; Valencia, Victor

    2018-02-01

    the amphibolite have E-MORB characteristics and were derived from a depleted mantle source younger than the Rodinia-type basement. Inasmuch as similar amphibolites also occur in the Ediacaran metasedimentary rocks as dykes or lenses, Late Neoproterozoic magmatism in a rift setting is suggested. Hence, the geologic record of the El Triunfo Complex includes evidences for Rodinia assemblage, Tonian circum-Rodinia subduction, and breakup during the Late Neoproterozoic. Metamorphism, and partial melting are interpreted in terms of a convergent margin setting during the Ordovician. The results place the southern Chiapas Massif along with Oaxaquia and similar Northern Andes terranes on the NW margin of Gondwana interpreted as the extension of the Famatinian orogen that evolved during the closure of the Iapetus Ocean.

  16. Compositional variations of zirconolite from the Evate apatite deposit (Mozambique) as an indicator of magmatic-hydrothermal conditions during post-orogenic collapse of Gondwana

    Science.gov (United States)

    Hurai, Vratislav; Huraiová, Monika; Gajdošová, Michaela; Konečný, Patrik; Slobodník, Marek; Siegfried, Pete R.

    2017-11-01

    substitution trends of the REE-zirconolite overlaps that genetically linked with carbonatites, syenites and mafic igneous rocks, whereas the U,Th-zirconolite is reminiscent of hydrothermal-metasomatic deposits. The predominance of trivalent iron in zirconolite most likely reflects strongly oxidizing parental fluids that percolated during episodic Late Ordovician to Late Cambrian rifting of Gondwana.

  17. Comparative Study on the Electrical Properties of the Oceanic Mantle Beneath the Northwest Pacific Ocean

    Science.gov (United States)

    Toh, H.

    2013-12-01

    responses as well. It, however, should be also noted here that the penetration depth beneath Site WPB is significantly smaller than that beneath Site NWP because the solar activity has been very low since 2006. References Ichiki, M., K. Baba, H. Toh and K. Fuji-ta, An overview of electrical conductivity structures of the crust and upper mantle beneath the northwestern Pacific, the Japanese Islands, and continental East Asia, Gondwana Research, 16, 545?562, doi:10.1016/j.gr.2009.04.007, 2009. Salisbury MH et al (2006) 2. Leg 195 Synthesis: Site 1201?A geological and geophysical section in the West Philippine Basin from the 660-km discontinuity to the mudline. Proc. Ocean Drilling Program, Scientific Reports 195:27. Shipboard Scientific Party of ODP Leg 191 (2000) Northwest Pacific seismic observatory and hammer drill tests, Proc. Ocean Drilling Program, Initial Reports 191. Toh, H., Y. Hamano and M. Ichiki, Long-term seafloor geomagnetic station in the northwest Pacific: A possible candidate for a seafloor geomagnetic observatory, Earth Planets Space, 58, 697-705, 2006. Toh, H., Y. Hamano, M. Ichiki and H. Utada, Geomagnetic observatory operates at the seafloor in the Northwest Pacific Ocean, Eos, Trans. Am. Geophys. Union, 85, 467/473, DOI: 10.1029/2004EO450003, 2004.

  18. The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera.

    Science.gov (United States)

    Cao, Yong-Qiang; Ma, Chuan; Chen, Ji-Yue; Yang, Da-Rong

    2012-06-22

    Lepidoptera encompasses more than 160,000 described species that have been classified into 45-48 superfamilies. The previously determined Lepidoptera mitochondrial genomes (mitogenomes) are limited to six superfamilies of the lineage Ditrysia. Compared with the ancestral insect gene order, these mitogenomes all contain a tRNA rearrangement. To gain new insights into Lepidoptera mitogenome evolution, we sequenced the mitogenomes of two ghost moths that belong to the non-ditrysian lineage Hepialoidea and conducted a comparative mitogenomic analysis across Lepidoptera. The mitogenomes of Thitarodes renzhiensis and T. yunnanensis are 16,173 bp and 15,816 bp long with an A + T content of 81.28 % and 82.34 %, respectively. Both mitogenomes include 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the A + T-rich region. Different tandem repeats in the A + T-rich region mainly account for the size difference between the two mitogenomes. All the protein-coding genes start with typical mitochondrial initiation codons, except for cox1 (CGA) and nad1 (TTG) in both mitogenomes. The anticodon of trnS(AGN) in T. renzhiensis and T. yunnanensis is UCU instead of the mostly used GCU in other sequenced Lepidoptera mitogenomes. The 1,584-bp sequence from rrnS to nad2 was also determined for an unspecified ghost moth (Thitarodes sp.), which has no repetitive sequence in the A + T-rich region. All three Thitarodes species possess the ancestral gene order with trnI-trnQ-trnM located between the A + T-rich region and nad2, which is different from the gene order trnM-trnI-trnQ in all previously sequenced Lepidoptera species. The formerly identified conserved elements of Lepidoptera mitogenomes (i.e. the motif 'ATAGA' and poly-T stretch in the A + T-rich region and the long intergenic spacer upstream of nad2) are absent in the Thitarodes mitogenomes. The mitogenomes of T. renzhiensis and T. yunnanensis exhibit unusual features compared with the previously determined

  19. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.

    Science.gov (United States)

    Gramzow, Lydia; Weilandt, Lisa; Theißen, Günter

    2014-11-01

    MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is

  20. Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

    DEFF Research Database (Denmark)

    Henryon, M; Berg, P; Sørensen, A C

    2009-01-01

    We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stoch......We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis...

  1. EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution

    Directory of Open Access Journals (Sweden)

    Liran Carmel

    2010-01-01

    Full Text Available Evolutionary binary characters are features of species or genes, indicating the absence (value zero or presence (value one of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus, gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes and events (gain and loss events along branches.

  2. EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.

    Science.gov (United States)

    Carmel, Liran; Wolf, Yuri I; Rogozin, Igor B; Koonin, Eugene V

    2010-01-01

    Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).

  3. Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate-binding protein

    Directory of Open Access Journals (Sweden)

    Daniel Gonzalez

    2014-01-01

    Full Text Available Stable and soluble proteins are ideal candidates for functional and structural studies. Unfortunately, some proteins or enzymes can be difficult to isolate, being sometimes poorly expressed in heterologous systems, insoluble and/or unstable. Numerous methods have been developed to address these issues, from the screening of various expression systems to the modification of the target protein itself. Here we use a hydrophobic, aggregation-prone, phosphate-binding protein (HPBP as a case study. We describe a simple and fast method that selectively uses ancestral mutations to generate a soluble, stable and functional variant of the target protein, here named sHPBP. This variant is highly expressed in Escherichia coli, is easily purified and its structure was solved at much higher resolution than its wild-type progenitor (1.3 versus 1.9 Å, respectively.

  4. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

    Directory of Open Access Journals (Sweden)

    Victor Hanson-Smith

    2016-07-01

    Full Text Available The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1 reconstruct and "resurrect" (that is, synthesize in vivo or in vitro extinct proteins to study how they differ from modern proteins, (2 identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3 order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above, or use our open-source code to launch their own PhyloBot server.

  5. Cis-by-Trans regulatory divergence causes the asymmetric lethal effects of an ancestral hybrid incompatibility gene.

    Directory of Open Access Journals (Sweden)

    Shamoni Maheshwari

    Full Text Available The Dobzhansky and Muller (D-M model explains the evolution of hybrid incompatibility (HI through the interaction between lineage-specific derived alleles at two or more loci. In agreement with the expectation that HI results from functional divergence, many protein-coding genes that contribute to incompatibilities between species show signatures of adaptive evolution, including Lhr, which encodes a heterochromatin protein whose amino acid sequence has diverged extensively between Drosophila melanogaster and D. simulans by natural selection. The lethality of D. melanogaster/D. simulans F1 hybrid sons is rescued by removing D. simulans Lhr, but not D. melanogaster Lhr, suggesting that the lethal effect results from adaptive evolution in the D. simulans lineage. It has been proposed that adaptive protein divergence in Lhr reflects antagonistic coevolution with species-specific heterochromatin sequences and that defects in LHR protein localization cause hybrid lethality. Here we present surprising results that are inconsistent with this coding-sequence-based model. Using Lhr transgenes expressed under native conditions, we find no evidence that LHR localization differs between D. melanogaster and D. simulans, nor do we find evidence that it mislocalizes in their interspecific hybrids. Rather, we demonstrate that Lhr orthologs are differentially expressed in the hybrid background, with the levels of D. simulans Lhr double that of D. melanogaster Lhr. We further show that this asymmetric expression is caused by cis-by-trans regulatory divergence of Lhr. Therefore, the non-equivalent hybrid lethal effects of Lhr orthologs can be explained by asymmetric expression of a molecular function that is shared by both orthologs and thus was presumably inherited from the ancestral allele of Lhr. We present a model whereby hybrid lethality occurs by the interaction between evolutionarily ancestral and derived alleles.

  6. ¿Con o sin ancestros? Vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-07-01

    Full Text Available The existence —or not— of the concept of ancestors in the indigenous Amazon has been the subject of much debate. However, regional leaders do not hesitate to call upon ‘ancestral’ knowledge, customs, or territories in the sense that, from an academic point of view, could appear enigmatic. «Ancestral, but… with or without ancestors?» is the question a confused anthropologist might ask. In this article, I propose to offer elements of a response to this question,based on a case study in Peru. First I analyze how Amazonian indigenous leaders, following international law, have adopted the legal notion of ‘ancestral possession’ of their territory to adapt it to the political sphere. This approach accounts for the recent generalization and uniformization of the term ‘ancestral’, but poses the problem of how it articulates with the indigenous cosmologies that it supposes to reflect. For this reason, I explore in the second section the pertinence of the category of ‘ancestor’ in the indigenous Amazon, briefly drawing upon the academic debate in order to define inwhat way this category takes on meaning. Based on testimony from an experienced Awajún leader, we thus return in the third section more explicitly to the different meanings and planes of reference that unfold when one uses the term ‘ancestral’, showing how Amazonian indigenous people not only adopt external conceptual elements and arguments, but also transform them based on their own cosmological singularities and political perspectives.

  7. Spodoptera frugiperda X-tox protein, an immune related defensin rosary, has lost the function of ancestral defensins.

    Directory of Open Access Journals (Sweden)

    Delphine Destoumieux-Garzón

    Full Text Available BACKGROUND: X-tox proteins are a family of immune-related proteins only found in Lepidoptera and characterized by imperfectly conserved tandem repeats of several defensin-like motifs. Previous phylogenetic analysis of X-tox genes supported the hypothesis that X-tox have evolved from defensins in a lineage-specific gene evolution restricted to Lepidoptera. In this paper, we performed a protein study in which we asked whether X-tox proteins have conserved the antimicrobial functions of their ancestral defensins and have evolved as defensin reservoirs. METHODOLOGY/PRINCIPAL FINDINGS: We followed the outcome of Spod-11-tox, an X-tox protein characterized in Spodoptera frugiperda, in bacteria-challenged larvae using both immunochemistry and antimicrobial assays. Three hours post infection, the Spod-11-tox protein was expressed in 80% of the two main classes of circulating hemocytes (granulocytes and plasmatocytes. Located in secretory granules of hemocytes, Spod-11-tox was never observed in contact with microorganisms entrapped within phagolyzosomes showing that Spod-11-tox is not involved in intracellular pathogen killing. In fact, the Spod-11-tox protein was found to be secreted into the hemolymph of experimentally challenged larvae. In order to determine antimicrobial properties of the Spod-11-tox protein, it was consequently fractionated according to a protocol frequently used for antimicrobial peptide purification. Over the course of purification, the anti-Spod-11-tox immunoreactivity was found to be dissociated from the antimicrobial activity. This indicates that Spod-11-tox is not processed into bioactive defensins in response to a microbial challenge. CONCLUSIONS/SIGNIFICANCE: Altogether, our results show that X-tox proteins have not evolved as defensin reservoirs and have lost the antimicrobial properties of the ancestral insect defensins. The lepidopteran X-tox protein family will provide a valuable and tractable model to improve our

  8. Spodoptera frugiperda X-tox protein, an immune related defensin rosary, has lost the function of ancestral defensins.

    Science.gov (United States)

    Destoumieux-Garzón, Delphine; Brehelin, Michel; Bulet, Philippe; Boublik, Yvan; Girard, Pierre-Alain; Baghdiguian, Stephen; Zumbihl, Robert; Escoubas, Jean-Michel

    2009-08-27

    X-tox proteins are a family of immune-related proteins only found in Lepidoptera and characterized by imperfectly conserved tandem repeats of several defensin-like motifs. Previous phylogenetic analysis of X-tox genes supported the hypothesis that X-tox have evolved from defensins in a lineage-specific gene evolution restricted to Lepidoptera. In this paper, we performed a protein study in which we asked whether X-tox proteins have conserved the antimicrobial functions of their ancestral defensins and have evolved as defensin reservoirs. We followed the outcome of Spod-11-tox, an X-tox protein characterized in Spodoptera frugiperda, in bacteria-challenged larvae using both immunochemistry and antimicrobial assays. Three hours post infection, the Spod-11-tox protein was expressed in 80% of the two main classes of circulating hemocytes (granulocytes and plasmatocytes). Located in secretory granules of hemocytes, Spod-11-tox was never observed in contact with microorganisms entrapped within phagolyzosomes showing that Spod-11-tox is not involved in intracellular pathogen killing. In fact, the Spod-11-tox protein was found to be secreted into the hemolymph of experimentally challenged larvae. In order to determine antimicrobial properties of the Spod-11-tox protein, it was consequently fractionated according to a protocol frequently used for antimicrobial peptide purification. Over the course of purification, the anti-Spod-11-tox immunoreactivity was found to be dissociated from the antimicrobial activity. This indicates that Spod-11-tox is not processed into bioactive defensins in response to a microbial challenge. Altogether, our results show that X-tox proteins have not evolved as defensin reservoirs and have lost the antimicrobial properties of the ancestral insect defensins. The lepidopteran X-tox protein family will provide a valuable and tractable model to improve our knowledge on the molecular evolution of defensins, a class of innate immune effectors largely

  9. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens.

    Science.gov (United States)

    Merda, Déborah; Briand, Martial; Bosis, Eran; Rousseau, Céline; Portier, Perrine; Barret, Matthieu; Jacques, Marie-Agnès; Fischer-Le Saux, Marion

    2017-11-01

    Deciphering the evolutionary history and transmission patterns of virulence determinants is necessary to understand the emergence of novel pathogens. The main virulence determinant of most pathogenic proteobacteria is the type three secretion system (T3SS). The Xanthomonas genus includes bacteria responsible for numerous epidemics in agroecosystems worldwide and represents a major threat to plant health. The main virulence factor of Xanthomonas is the Hrp2 family T3SS; however, this system is not conserved in all strains and it has not been previously determined whether the distribution of T3SS in this bacterial genus has resulted from losses or independent acquisitions. Based on comparative genomics of 82 genome sequences representing the diversity of the genus, we have inferred three ancestral acquisitions of the Hrp2 cluster during Xanthomonas evolution followed by subsequent losses in some commensal strains and re-acquisition in some species. While mutation was the main force driving polymorphism at the gene level, interspecies homologous recombination of large fragments expanding through several genes shaped Hrp2 cluster polymorphism. Horizontal gene transfer of the entire Hrp2 cluster also occurred. A reduced core effectome composed of xopF1, xopM, avrBs2 and xopR was identified that may allow commensal strains overcoming plant basal immunity. In contrast, stepwise accumulation of numerous type 3 effector genes was shown in successful pathogens responsible for epidemics. Our data suggest that capacity to intimately interact with plants through T3SS would be an ancestral trait of xanthomonads. Since its acquisition, T3SS has experienced a highly dynamic evolutionary history characterized by intense gene flux between species that may reflect its role in host adaptation. © 2017 John Wiley & Sons Ltd.

  10. Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region.

    Science.gov (United States)

    Chiatante, Giorgia; Giannuzzi, Giuliana; Calabrese, Francesco Maria; Eichler, Evan E; Ventura, Mario

    2017-07-01

    Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Stem cell-specific activation of an ancestral myc protooncogene with conserved basic functions in the early metazoan Hydra.

    Science.gov (United States)

    Hartl, Markus; Mitterstiller, Anna-Maria; Valovka, Taras; Breuker, Kathrin; Hobmayer, Bert; Bister, Klaus

    2010-03-02

    The c-myc protooncogene encodes a transcription factor (Myc) with oncogenic potential. Myc and its dimerization partner Max are bHLH-Zip DNA binding proteins controlling fundamental cellular processes. Deregulation of c-myc leads to tumorigenesis and is a hallmark of many human cancers. We have identified and extensively characterized ancestral forms of myc and max genes from the early diploblastic cnidarian Hydra, the most primitive metazoan organism employed so far for the structural, functional, and evolutionary analysis of these genes. Hydra myc is specifically activated in all stem cells and nematoblast nests which represent the rapidly proliferating cell types of the interstitial stem cell system and in proliferating gland cells. In terminally differentiated nerve cells, nematocytes, or epithelial cells, myc expression is not detectable by in situ hybridization. Hydra max exhibits a similar expression pattern in interstitial cell clusters. The ancestral Hydra Myc and Max proteins display the principal design of their vertebrate derivatives, with the highest degree of sequence identities confined to the bHLH-Zip domains. Furthermore, the 314-amino acid Hydra Myc protein contains basic forms of the essential Myc boxes I through III. A recombinant Hydra Myc/Max complex binds to the consensus DNA sequence CACGTG with high affinity. Hybrid proteins composed of segments from the retroviral v-Myc oncoprotein and the Hydra Myc protein display oncogenic potential in cell transformation assays. Our results suggest that the principal functions of the Myc master regulator arose very early in metazoan evolution, allowing their dissection in a simple model organism showing regenerative ability but no senescence.

  12. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

    Science.gov (United States)

    Hanson-Smith, Victor; Johnson, Alexander

    2016-07-01

    The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

  13. Central Equatorial Pacific Experiment (CEPEX)

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The Earth's climate has varied significantly in the past, yet climate records reveal that in the tropics, sea surface temperatures seem to have been remarkably stable, varying by less than a few degrees Celsius over geologic time. Today, the large warm pool of the western Pacific shows similar characteristics. Its surface temperature always exceeds 27[degree]C, but never 31[degree]C. Heightened interest in this observation has been stimulated by questions of global climate change and the exploration of stabilizing climate feedback processes. Efforts to understand the observed weak sensitivity of tropical sea surface temperatures to climate forcing has led to a number of competing ideas about the nature of this apparent thermostat. Although there remains disagreement on the processes that regulate tropical sea surface temperature, most agree that further progress in resolving these differences requires comprehensive field observations of three-dimensional water vapor concentrations, solar and infrared radiative fluxes, surface fluxes of heat and water vapor, and cloud microphysical properties. This document describes the Central Equatorial Pacific Experiment (CEPEX) plan to collect such observations over the central equatorial Pacific Ocean during March of 1993.

  14. Pacific Northwest regional assessment program

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    The Pacific Northwest (comprised of the states of Alaska, Idaho, Montana, Oregon, Washington and Wyoming) can by several measures be regarded as a national warehouse of fossil energy resources. This condition coupled with an evolving national policy stressing utilization of fossil fuels in the near term prior to development of more advanced technologies for energy supply, could result in the imposition of major changes in the region's environmental, socioeconomic and possibly health status. The objective of the Pacific Northwest Regional Assessment Program is to establish and exercise an integrated analytical assessment program for evaluation of these potential changes that may result from various energy development or conservation scenarios. After consideration of a variety of approaches to integrated assessment at a regional level, Pacific Northwest Laboratories (PNL) has concluded that dynamic simulation techniques provide the best available approach to evaluating the issues pertinent to the Northwest. As a result, the PNW Regional Assessment Program has been structured in a framework involving ten sectors. Each of these sectors involve their own submodels that receive information either from outside the model as exogenous inputs or from other sector submodels

  15. Paleoceanography of the tropical eastern pacific ocean.

    Science.gov (United States)

    Grigg, R W; Hey, R

    1992-01-10

    The East Pacific Barrier (EPB) is the most effective marine barrier to dispersal of tropical shallow-water fauna in the world today. The fossil record of corals in the eastern Pacific suggests this has been true throughout the Cenozoic. In the Cretaceous, the EPB was apparently less effective in limiting dispersal. Equatorial circulation in the Pacific then appears to have been primarily east to west and the existence of oceanic atolls (now drowned guyots) in the eastern Pacific probably aided dispersal. Similarly, in the middle and early Mesozoic and late Paleozoic, terranes in the central tropical Pacific likely served as stepping stones to dispersal of tropical shelf faunas, reducing the isolating effect of an otherwise wider Pacific Ocean (Panthalassa).

  16. Indian Ocean warming modulates Pacific climate change

    Science.gov (United States)

    Luo, Jing-Jia; Sasaki, Wataru; Masumoto, Yukio

    2012-01-01

    It has been widely believed that the tropical Pacific trade winds weakened in the last century and would further decrease under a warmer climate in the 21st century. Recent high-quality observations, however, suggest that the tropical Pacific winds have actually strengthened in the past two decades. Precise causes of the recent Pacific climate shift are uncertain. Here we explore how the enhanced tropical Indian Ocean warming in recent decades favors stronger trade winds in the western Pacific via the atmosphere and hence is likely to have contributed to the La Niña-like state (with enhanced east–west Walker circulation) through the Pacific ocean–atmosphere interactions. Further analysis, based on 163 climate model simulations with centennial historical and projected external radiative forcing, suggests that the Indian Ocean warming relative to the Pacific’s could play an important role in modulating the Pacific climate changes in the 20th and 21st centuries. PMID:23112174

  17. 78 FR 61840 - Pacific Fishery Management Council (Pacific Council); Public Meetings

    Science.gov (United States)

    2013-10-04

    ... Proposals to Modify EFH 7. Electronic Monitoring Alternatives 8. Consideration of Inseason Adjustments 9... Fishery Management Council (Pacific Council); Public Meetings AGENCY: National Marine Fisheries Service... broadcast are given under SUPPLEMENTARY INFORMATION below. Council address: Pacific Fishery Management...

  18. Gridded multibeam bathymetry of Howland Island, Pacific Remote Island Areas, Central Pacific

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded bathymetry at 40m resolution surrounding Howland Island, within the Pacific Remote Island Areas - Central Pacific Ocean. Bottom coverage was achieved in...

  19. Biological data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

  20. Oceanographic data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

  1. Climate Prediction Center (CPC) East Pacific/ North Pacific Teleconnection Pattern Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Monthly tabulated index of the East Pacific/ North Pacific teleconnection pattern. The data spans the period 1950 to present. The index is derived from a rotated...

  2. Pacific Hake - Growth and natal origin of Pacific hake from the Georgia Basin DPS

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Pacific hake (Merluccius productus) is an abundant species residing along the Pacific coast from the Gulf of California to the Strait of Georgia. It is the most...

  3. Acoustic data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

  4. 76 FR 28422 - Fisheries of the Pacific Region; Western Pacific Region

    Science.gov (United States)

    2011-05-17

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration RIN 0648-XX57 Fisheries of the Pacific Region; Western Pacific Region AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notification of determination of...

  5. Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii).

    Science.gov (United States)

    Liu, Jin-Xian; Tatarenkov, Andrey; Beacham, Terry D; Gorbachev, Victor; Wildes, Sharon; Avise, John C

    2011-09-01

    We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more. © 2011 Blackwell Publishing Ltd.

  6. Panoramic view of the Mexican Pacific Coastline

    Science.gov (United States)

    1993-01-01

    In this scenic panoramic view, the orbiter tail points toward the Mexican Pacific coastline (18.0N, 103.0W) near the international resort of Acapulco on the nearly cloud free eastern Pacific Ocean. Almost all of southern Mexico can be seen from Puerto Vallarta in the north to the Isthmus of Tehuantepec in the south. The cloud covered Gulf of Mexico at the horizon contrasts sharply with the blue Pacific.

  7. Bathymetric Atlas of the North Pacific Ocean.

    Science.gov (United States)

    1978-01-01

    of volcanic ash layers and turbidito% ini 1956. Clipperton fracture zone in the northeastern equa- the north Pacific, Gal. Soc. Amer. Bull., v. 80, p...1964. Galapagos Rise in the southeastern Pacific, Deep- 1961. Geology of the sea floor east of Guadalupe Island, Sea Research, v. 11, p. 233.242.I...charts. 52 p. Richards, A.F. Monard, H.W. 1959. Geology of the Islas Revillagigedo, Mexico, Volcan . 1955. Deformation of the northeastern Pacific

  8. South Pacific Nuclear Free Zone Treaty

    International Nuclear Information System (INIS)

    1987-03-01

    On 8 August 1986 the Protocols to the South Pacific Nuclear Free Zone Treaty were adopted by the South Pacific Forum at its 17 th session, in Suva. The attached texts of the Protocols were formally communicated to the Director General by the Director of the South Pacific Bureau for Economic Co-operation (SPEC) and are herewith being circulated to all Member States for their information pursuant to a request made by the Director of SPEC. Following the deposit of the eighth instrument of ratification, the South Pacific Nuclear Free Zone Treaty entered into force on 11 December 1986 [es

  9. 76 FR 54739 - Pacific Halibut Fishery; Guideline Harvest Levels for the Guided Sport Fishery for Pacific...

    Science.gov (United States)

    2011-09-02

    ... Levels for the Guided Sport Fishery for Pacific Halibut in International Pacific Halibut Commission... 2011 Pacific halibut guideline harvest levels (GHLs) for the guided sport fishery in International... to inform the public about the 2011 GHLs for the guided sport fishery for halibut. The GHLs are...

  10. 78 FR 18323 - Pacific Halibut Fishery; Guideline Harvest Levels for the Guided Sport Fishery for Pacific...

    Science.gov (United States)

    2013-03-26

    ... Levels for the Guided Sport Fishery for Pacific Halibut in International Pacific Halibut Commission... 2013 Pacific halibut guideline harvest levels (GHLs) for the guided sport fishery in International... to inform the public about the 2013 GHLs for the guided sport fishery for halibut. The GHLs are...

  11. 78 FR 48861 - Western Pacific Fisheries; Approval of a Marine Conservation Plan for Pacific Insular Areas...

    Science.gov (United States)

    2013-08-12

    ....S. Exclusive Economic Zone (EEZ) adjacent to any Pacific Insular Area other than American Samoa, Guam, or the Northern Mariana Islands, that is, in the EEZ around the Pacific remote island areas (PRIA... National Oceanic and Atmospheric Administration RIN 0648-XC792 Western Pacific Fisheries; Approval of a...

  12. Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states.

    Science.gov (United States)

    Pedersen, Niklas; Holyoak, David T; Newton, Angela E

    2007-06-01

    The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.

  13. Blood types in Pacific salmon

    Science.gov (United States)

    Ridgway, G.L.; Klontz, G.W.

    1961-01-01

    Intraspecific differences in erythrocyte antigens (blood types) were shown to occur in four species of Pacific salmon, the sockeye or red salmon (Oncorhynchus nerka), the chinook or king salmon (0. tshawytscha), the chum salmon (O. keta), and the pink salmon (O. gorbuscha). Antisalmon-erythrocyte sera prepared in rabbits and chickens were used after absorption of species-specific antibodies. Some of these blood types were shown to differ in their frequency of occurrence between different geographic races. In addition, isoimmunizations were conducted on one race of sockeye salmon. Antisera of seven different specificities were prepared and at least eight different patterns of antigenic composition were displayed by the cells tested.

  14. Asia-Pacific energy database

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    Statistical data is presented in graphic and tabular form on the petroleum market in Asia and Pacific nations. Seven major categories are reported: (1) primary energy production and consumption; (2) historical petroleum product demand and forecasts; (3) crude oil production and exports; (4) import dependence; (5) crude and product pricing assumptions; (6) market share of refined products by suppliers in selected countries; and (7) refining margins. Petroleum demand and forecasts and crude oil production and exports are reported by country. Historical data are presented from 1970 through 1996, and forecasts are made through 2010.

  15. Testing the reliability of software tools in sex and ancestry estimation in a multi-ancestral Brazilian sample.

    Science.gov (United States)

    Urbanová, Petra; Ross, Ann H; Jurda, Mikoláš; Nogueira, Maria-Ines

    2014-09-01

    In the framework of forensic anthropology osteometric techniques are generally preferred over visual examinations due to a higher level of reproducibility and repeatability; qualities that are crucial within a legal context. The use of osteometric methods has been further reinforced by incorporating statistically-based algorithms and large reference samples in a variety of user-friendly software applications. However, the continued increase in admixture of human populations have made the use of osteometric methods for estimation of ancestry much more complex, which confounds one of major requirements of ancestry assessment - intra-population homogeneity. The present paper tests the accuracy of ancestry and sex assessment using four identification software tools, specifically FORDISC 2.0, FORDISC 3.1.293, COLIPR 1.5.2 and 3D-ID 1.0. Software accuracy was tested in a sample of 174 documented human crania of Brazilian origin composed of different ancestral groups (i.e., European Brazilians, Afro-Brazilians, and Japanese Brazilians and of admixed ancestry). The results show that regardless of the software algorithm employed and composition of the reference database, all methods were able to allocate approximately 50% of Brazilian specimens to an appropriate major reference group. Of the three ancestral groups, Afro-Brazilians were especially prone to misclassification. Japanese Brazilians, by contrast, were shown to be relatively easily recognizable as being of Asian descent but at the same time showed a strong affinity towards Hispanic crania, in particularly when the classification based on FDB was carried out in FORDISC. For crania of admixed origin all of the algorithms showed a considerable higher rate of inconsistency with a tendency for misclassification into Asian and American Hispanic groups. Sex assessments revealed an overall modest to poor reliability (60-71% of correctly classified specimens) using the tested software programs with unbalanced individual

  16. Mangroves of the Pacific Islands: research opportunities

    Science.gov (United States)

    Ariel E. Lugo

    1990-01-01

    The perception of mangroves by people in the Pacific islands and throughout all the world has changed in the past decades. Today, the economic, social, ecologic, and esthetic values of mangroves are well recognized. Past research on these ecosystems is responsible for the change in perception. However, a review of eleven subjects relevant to the management of Pacific...

  17. Commonwealth Local Government Forum Pacific Project

    Directory of Open Access Journals (Sweden)

    Terry Parker

    2008-04-01

    Full Text Available The Commonwealth Local Government Forum (CLGF Pacific Project works with local government and other stakeholders in nine Pacific Island countries – Cook Islands, Fiji Islands, Kiribati, Samoa, Papua New Guinea, Solomon Islands, Tonga, Tuvalu and Vanuatu. It seeks to strengthen local democracy and good governance, and to help local governments deal with the increasing challenges of service delivery and urban management in the unique Pacific environment. Human settlement patterns in the region are changing rapidly. The Pacific has traditionally been a rural agricultural/subsistence society, but this is no longer the case. The accelerated pace of urbanisation has impacted significantly on Pacific nations and in the very near future the majority of Pacific Islanders will be found in urban areas. Already over 50% of Fiji’s population are urban dwellers. Rapid urbanisation brings with it unique challenges and opportunities. Local governments are at the forefront of this phenomenon, with the responsibility to manage urban development and the transition from rural areas to cities and towns. Their success or failure to manage urbanisation and provide the required levels of physical and social infrastructure will affect many lives in a new urban Pacific. The project now has three components – the main Pacific Regional Project and two country-specific programmes: the Honiara City Council Institutional Capacity Building Project and the Commonwealth Local Government Good Practice Scheme in Papua New Guinea.

  18. Sponges from Clipperton Island, East Pacific

    NARCIS (Netherlands)

    van Soest, R.W.M.; Kaiser, K.L.; van Syoc, R.

    2011-01-01

    Twenty sponge species (totalling 190 individuals) were collected during the 1938, 1994 and 2004/5 expeditions to the remote island of Clipperton in the East Pacific Ocean. Seven species are widespread Indo-Pacific sponges; nine species comprise sponges new to science; four species were represented

  19. Pacific Northwest regional AGU meeting

    Science.gov (United States)

    Bentley, R.; Hinthome, J.

    The 28th Annual Pacific Northwest Regional American Geophysical Union Meeting, September 13-20, 1981, was hosted by the Department of Geology at Central Washington University, Ellensburg, Washington. A total of 31 papers was presented to the 91 registrants in two general sessions. Topics included seismology, general geophysics, volcanology, hydrology, oceanography, and two special symposia: Tectonics of the Columbia Plateau and Neogene —Quaternary Faults of the Pacific Northwest' and ‘Studies of the Eruption of Mount Saint Helens.’ Before and after the formal meetings, several field conferences were conducted to examine the Neogene tectonics of the Coast Range (Bob Bentley, Al Niem, and Ray Wells, leaders); the Columbia River Gorge (Bob Bentley, Marv Beeson, and Terry Tolan, leaders); the western Columbia Plateau northsouth transect (Bob Bentley and Jim Anderson, leaders); Quaternary structures of the Toppenish Ridge anticline (Don Tahkeal, Newell Campbell, and Bob Bentley, leaders); the Umtanum imbricate fault zone and pre-Saddle Mountains unconformity near Priest Rapids Dam (Ed Price and Bob Bentley, leaders); and the Yakima anticlines in the Cle Elum-Wallula deformed zone between Ellensburg and Yakima (Bob Bentley, leader).

  20. Tsunami scattering provinces in the Pacific Ocean

    Science.gov (United States)

    Mofjeld, H. O.; Titov, V. V.; González, F. I.; Newman, J. C.

    We use a scattering index to identify the regions in the Pacific Ocean where topographic features scatter significant tsunami energy. Based on linear wave theory, the index is computed from the Smith/Sandwell topography. Consistent with numerical simulations, it shows that there is a narrow band of strong scatterers running across the ocean from the northwest (Emperor Seamount Chain) to the southeast (Easter Island Fracture Zone). The eastern Pacific is nearly devoid of scatterers, except for this band and isolated features along the eastern margin. To the west of the band lies a region with moderate scattering; the strongest scattering occurs in the southwestern Pacific. The Pacific is rimmed by island arcs and shallow continental shelves that also trap and scatter tsunamis. These results show that numerical models of trans-Pacific tsunamis must resolve the effects of the small-scale topography in order to accurately simulate their wave patterns and amplitudes.

  1. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    Science.gov (United States)

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-03-10

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.

  2. Research on Non-Destructive Testing Technology in Conservation Repair Project of Ancestral Temple in Mukden Palace

    Science.gov (United States)

    Yang, J.; Fu, M.

    2017-08-01

    Due to the use of wood and other non-permanent materials, traditional Chinese architecture is one of the most fragile constructions in various heritage objects today. With the increasing emphasis on the protection of cultural relics, the repair project of wooden structure has become more and more important. There are various kinds of destructions, which pose a hidden danger to the overall safety of the ancient buildings, caused not only by time and nature, but also by improper repairs in history or nowadays. Today, the use of digital technology is a basic requirement in the conservation of cultural heritage. Detection technology, especially non-destructive testing technology, could provide more accurate records in capturing detailed physical characteristics of structures such as geometric deformation and invisible damage, as well as prevent a man-made destruction in the process of repair project. This paper aims to interpret with a typical example, Ancestral Temple in Mukden Palace, along with a discussion of how to use the non-destructive testing technology with ground penetrating radar, stress wave, resistograph and so on, in addition to find an appropriate protection method in repair project of traditional Chinese wooden architecture.

  3. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants.

    Science.gov (United States)

    Moreau, Corrie S; Bell, Charles D

    2013-08-01

    Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  4. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy.

    Science.gov (United States)

    Chavan, Arun Rajendra; Bhullar, Bhart-Anjan S; Wagner, Günter P

    2016-04-01

    In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears.

    Science.gov (United States)

    Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

    2013-01-01

    Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

  6. Evolution of the human diet: linking our ancestral diet to modern functional foods as a means of chronic disease prevention.

    Science.gov (United States)

    Jew, Stephanie; AbuMweis, Suhad S; Jones, Peter J H

    2009-10-01

    The evolution of the human diet over the past 10,000 years from a Paleolithic diet to our current modern pattern of intake has resulted in profound changes in feeding behavior. Shifts have occurred from diets high in fruits, vegetables, lean meats, and seafood to processed foods high in sodium and hydrogenated fats and low in fiber. These dietary changes have adversely affected dietary parameters known to be related to health, resulting in an increase in obesity and chronic disease, including cardiovascular disease (CVD), diabetes, and cancer. Some intervention trials using Paleolithic dietary patterns have shown promising results with favorable changes in CVD and diabetes risk factors. However, such benefits may be offset by disadvantages of the Paleolithic diet, which is low in vitamin D and calcium and high in fish potentially containing environmental toxins. More advantageous would be promotion of foods and food ingredients from our ancestral era that have been shown to possess health benefits in the form of functional foods. Many studies have investigated the health benefits of various functional food ingredients, including omega-3 fatty acids, polyphenols, fiber, and plant sterols. These bioactive compounds may help to prevent and reduce incidence of chronic diseases, which in turn could lead to health cost savings ranging from $2 to $3 billion per year as estimated by case studies using omega-3 and plant sterols as examples. Thus, public health benefits should result from promotion of the positive components of Paleolithic diets as functional foods.

  7. Reconstruction of the putative cervidae ancestral karyotype by chromosome painting of Siberian roe deer (Capreolus pygargus) with dromedary probes.

    Science.gov (United States)

    Dementyeva, P V; Trifonov, V A; Kulemzina, A I; Graphodatsky, A S

    2010-06-01

    The Siberian roe deer (Capreolus pygargus) is one of a few deer species presumably preserving the ancestral cervid karyotype. The comparative genomic data of the Siberian roe deer are critical for our understanding of the karyotypic relationships within artiodactyls. We have established chromosomal homologies between the Siberian roe deer and the dromedary (Camelus dromedarius) by cross-species chromosome painting with dromedary chromosome-specific painting probes. Dromedary chromosome paints detected 53 autosomal homologies in the genome of the Siberian roe deer. The identification of chromosomal homologies between the Siberian roe deer and cattle resulted from previously detected cattle-dromedary homologies. We have found 8 chromosomal rearrangements (6 fissions in the Siberian roe deer, 1 fission in the cattle and 1 inversion on the CPY11) that have separated the karyotypes of the cattle and the Siberian roe deer. The inversion on CPY11 might be an apomorphic trait of cervids, since we detected its presence in the gray brocket deer (Mazama gouazoubira). Thus our data further prove the scenario of chromosomal rearrangements that was previously proposed and add some new data. 2010 S. Karger AG, Basel.

  8. Total immediate ancestral longevity (TIAL) score as a longevity indicator: an analysis on Einstein and three of his scientist peers.

    Science.gov (United States)

    Sri Kantha, S

    2001-04-01

    The total immediate ancestral longevity (TIAL) score was first introduced by Raymond Pearl as a convenient parameter for quantitating human longevity. TIAL is the summed ages at death of the six immediate ancestors (namely parents and four grandparents) of a propositus. In this communication, I present the calculations of TIAL score for Einstein (1879--1955) and three of his scientist peers, namely Charles Darwin (1809--1882), Irene Joliot Curie (1897--1956) and Aage Bohr (1922--). The TIAL scores for Einstein, Darwin, Irene Curie and Aage Bohr were 390, 378, 372 and 436 respectively. These are markedly lower than 477 reported for Jeanne Calment, the French woman who died in 1997 at the oldest authenticated age of 122 years and 164 days. I conclude that the TIAL score is a convenient and easily quantifiable longevity parameter which anyone interested in determining his or her longevity can use to estimate a tentative number. More light could be shed on the worth of the TIAL score as a longevity indicator, if additional data on the TIAL scores of royalty and celebrities (for whom verified genealogical data are available) are reported. Copyright 2001 Harcourt Publishers Ltd.

  9. Pliocene terrace gravels of the ancestral Yukon River near Circle, Alaska: Palynology, paleobotany, paleoenvironmental reconstruction and regional correlation

    Science.gov (United States)

    Ager, T.A.; Matthews, J.V.; Yeend, W.

    1994-01-01

    Gravels deposited by the ancestral Yukon River are preserved in terrace remnants on the margins of the Yukon River valley near the village of Circle in east-central Alaska. Plant fossils recovered from sandy silt lenses within these gravels include cones and needles of Picea and Larix and a variety of seeds. Seed types include several taxa which no longer grow in Alaska, such as Epipremnum, Prunus and Weigela. Pollen types recovered from these deposits represent tree and shrub taxa that grow in interior Alaska today, such as Picea, Larix, Betula and Alnus, as well as several taxa that no longer grow in interior Alaska today, such as Pinus, Tsuga, Abies and Corylus. Pollen of herb taxa identified include Gramineae, Cyperaceae, Caryophyllaceae, Compositae, Polemonium and Epilobium. The fossil flora from the gravels near Circle are similar and probably age-equivalent to the flora recovered from the Nenana Gravel in the Alaska Range 250 km to the south. Palynological and tectonic evidence summarized in this paper now suggests that the Nenana Gravel was deposited during the early and middle Pliocene. The presence of plant fossils of Tsuga, Abies, Pinus, Weigela and Prunus suggests that the mean annual temperature (MAT) of eastern interior Alaska during the early and middle Pliocene was perhaps 7-9??C warmer and less continental than today's MAT of -6.4??C. ?? 1994.

  10. Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears.

    Directory of Open Access Journals (Sweden)

    Shigeki Nakagome

    Full Text Available Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA and matrilineal mitochondrial DNA (mtDNA. Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA or more than 14 times (mtDNA larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

  11. Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia

    Directory of Open Access Journals (Sweden)

    Libia M Rodriguez

    2015-03-01

    Full Text Available A significant association between HFE gene mutations and the HLA-A*03-B*07 and HLA-A*29-B*44 haplotypes has been reported in the Spanish population. It has been proposed that these mutations are probably connected with Celtic and North African ancestry, respectively. We aimed to find the possible ancestral association between HLA alleles and haplotypes associated with the HFE gene (C282Y and H63D mutations in 214 subjects from Antioquia, Colombia. These were 18 individuals with presumed hereditary hemochromatosis (“HH” and 196 controls. The HLA-B*07 allele was in linkage disequilibrium (LD with C282Y, while HLA-A*23, A*29, HLA-B*44, and B*49 were in LD with H63D. Altogether, our results show that, although the H63D mutation is more common in the Antioquia population, it is not associated with any particular HLA haplotype, whereas the C282Y mutation is associated with HLA-A*03-B*07, this supporting a northern Spaniard ancestry.

  12. Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep.

    Science.gov (United States)

    Demars, Julie; Cano, Margarita; Drouilhet, Laurence; Plisson-Petit, Florence; Bardou, Philippe; Fabre, Stéphane; Servin, Bertrand; Sarry, Julien; Woloszyn, Florent; Mulsant, Philippe; Foulquier, Didier; Carrière, Fabien; Aletru, Mathias; Rodde, Nathalie; Cauet, Stéphane; Bouchez, Olivier; Pirson, Maarten; Tosser-Klopp, Gwenola; Allain, Daniel

    2017-07-01

    The composition and structure of fleece variation observed in mammals is a consequence of a strong selective pressure for fiber production after domestication. In sheep, fleece variation discriminates ancestral species carrying a long and hairy fleece from modern domestic sheep (Ovis aries) owning a short and woolly fleece. Here, we report that the "woolly" allele results from the insertion of an antisense EIF2S2 retrogene (called asEIF2S2) into the 3' UTR of the IRF2BP2 gene leading to an abnormal IRF2BP2 transcript. We provide evidence that this chimeric IRF2BP2/asEIF2S2 messenger 1) targets the genuine sense EIF2S2 RNA and 2) creates a long endogenous double-stranded RNA which alters the expression of both EIF2S2 and IRF2BP2 mRNA. This represents a unique example of a phenotype arising via a RNA-RNA hybrid, itself generated through a retroposition mechanism. Our results bring new insights on the sheep population history thanks to the identification of the molecular origin of an evolutionary phenotypic variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

    Science.gov (United States)

    Heimberg, Alysha M.; Cowper-Sal·lari, Richard; Sémon, Marie; Donoghue, Philip C. J.; Peterson, Kevin J.

    2010-01-01

    Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more primitive microRNA families, and 22 unique substitutions to the mature gene products. Reanalysis of morphological data reveals that support for cyclostome paraphyly was based largely on incorrect character coding, and a revised dataset is not decisive on the mono- vs. paraphyly of cyclostomes. Furthermore, we show fundamental conservation of microRNA expression patterns among lamprey, hagfish, and gnathostome organs, implying that the role of microRNAs within specific organs is coincident with their appearance within the genome and is conserved through time. Together, these data support the monophyly of cyclostomes and suggest that the last common ancestor of all living vertebrates was a more complex organism than conventionally accepted by comparative morphologists and developmental biologists. PMID:20959416

  14. Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira).

    Science.gov (United States)

    Brinkman, Donald; Rabi, Márton; Zhao, Lijun

    2017-07-27

    Pan-trionychids or softshell turtles are a highly specialized and widespread extant group of aquatic taxa with an evolutionary history that goes back to the Early Cretaceous. The earliest pan-trionychids had already fully developed the "classic" softshell turtle morphology and it has been impossible to resolve whether they are stem members of the family or are within the crown. This has hindered our understanding of the evolution of the two basic body plans of crown-trionychids. Thus it remains unclear whether the more heavily ossified shell of the cyclanorbines or the highly reduced trionychine morphotype is the ancestral condition for softshell turtles. A new pan-trionychid from the Early Cretaceous of Zhejiang, China, Perochelys hengshanensis sp. nov., allows a revision of softshell-turtle phylogeny. Equal character weighting resulted in a topology that is fundamentally inconsistent with molecular divergence date estimates of deeply nested extant species. In contrast, implied weighting retrieved Lower Cretaceous Perochelys spp. and Petrochelys kyrgyzensis as stem trionychids, which is fully consistent with their basal stratigraphic occurrence and an Aptian-Santonian molecular age estimate for crown-trionychids. These results indicate that the primitive morphology for soft-shell turtles is a poorly ossified shell like that of crown-trionychines and that shell re-ossification in cyclanorbines (including re-acquisition of peripheral elements) is secondary.

  15. Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon

    Directory of Open Access Journals (Sweden)

    Lubieniecki Krzysztof P

    2008-11-01

    Full Text Available Abstract Background Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD in their ancestry (2R duplication. Salmonids have experienced one additional WGD (4R duplication event compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes. Results Evidence is presented for the retention of large whole-arm affinities between the ancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segments in Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, there is also evidence for the retention of large whole-arm homeologous affinities that are associated with the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regions expressing the highest level of duplicate gene expression in rainbow trout share homologous synteny to the 5 pairs of homeologs with the greatest duplicate gene expression in Atlantic salmon. These regions are derived from proto-Actinopterygian linkage groups B, C, E, J and K. Conclusion Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3R duplication can, in most instances be related to at least 4 whole or partial chromosomal arms in the salmonid species. Multiple arm assignments in the two salmonid species do not clearly support a 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., a separate single chromosome duplication and ancestral fusion/fissions/recombination within the putative G/H/I groupings may have occurred in

  16. Diabetic Retinopathy in the Asia-Pacific.

    Science.gov (United States)

    Chua, Jacqueline; Lim, Claire Xin Ying; Wong, Tien Yin; Sabanayagam, Charumathi

    2018-01-01

    Diabetic retinopathy (DR), the most common complication of diabetes mellitus, is the leading cause of new cases of blindness in middle-aged and elderly in the Asia-Pacific. It has been estimated that 51% of all those with blindness due to DR globally (n = 424,400) and 56% of those with visual impairment due to DR (2.1 million) come from the Asia-Pacific. Prevalence of DR among those with diabetes ranged from 10% in India to 43% in Indonesia within the Asia-Pacific. Awareness of DR among persons with diabetes ranged from 28% to 84%. Most common modifiable risk factors for DR in the Asia-Pacific were hyperglycemia, blood pressure, dyslipidemia, and obesity. Implementation of systematic screening programs for DR and advancement in telemedicine screening methods have increased patient coverage and cost-effectiveness, though there are still numerous factors impeding screening uptake in the low-middle income regions of the Asia-Pacific. Management and treatment of DR in the Asia-Pacific is mainly limited to traditional laser retinopexy, but it is suboptimal despite new clinical approaches such as use of intravitreal anti.vascular endothelial growth factor and steroids due to limited resources. Further research and data are required to structure a more cost-effective public healthcare program and more awareness-building initiatives to increase the effectiveness of DR screening programs. Copyright 2017 Asia-Pacific Academy of Ophthalmology.

  17. Salinity fronts in the tropical Pacific Ocean.

    Science.gov (United States)

    Kao, Hsun-Ying; Lagerloef, Gary S E

    2015-02-01

    This study delineates the salinity fronts (SF) across the tropical Pacific, and describes their variability and regional dynamical significance using Aquarius satellite observations. From the monthly maps of the SF, we find that the SF in the tropical Pacific are (1) usually observed around the boundaries of the fresh pool under the intertropical convergence zone (ITCZ), (2) stronger in boreal autumn than in other seasons, and (3) usually stronger in the eastern Pacific than in the western Pacific. The relationship between the SF and the precipitation and the surface velocity are also discussed. We further present detailed analysis of the SF in three key tropical Pacific regions. Extending zonally around the ITCZ, where the temperature is nearly homogeneous, we find the strong SF of 1.2 psu from 7° to 11°N to be the main contributor of the horizontal density difference of 0.8 kg/m 3 . In the eastern Pacific, we observe a southward extension of the SF in the boreal spring that could be driven by both precipitation and horizontal advection. In the western Pacific, the importance of these newly resolved SF associated with the western Pacific warm/fresh pool and El Niño southern oscillations are also discussed in the context of prior literature. The main conclusions of this study are that (a) Aquarius satellite salinity measurements reveal the heretofore unknown proliferation, structure, and variability of surface salinity fronts, and that (b) the fine-scale structures of the SF in the tropical Pacific yield important new information on the regional air-sea interaction and the upper ocean dynamics.

  18. The presence of the ancestral insect telomeric motif in kissing bugs (Triatominae) rules out the hypothesis of its loss in evolutionarily advanced Heteroptera (Cimicomorpha)

    Science.gov (United States)

    Pita, Sebastián; Panzera, Francisco; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Lorite, Pedro

    2016-01-01

    Abstract Next-generation sequencing data analysis on Triatoma infestans Klug, 1834 (Heteroptera, Cimicomorpha, Reduviidae) revealed the presence of the ancestral insect (TTAGG)n telomeric motif in its genome. Fluorescence in situ hybridization confirms that chromosomes bear this telomeric sequence in their chromosomal ends. Furthermore, motif amount estimation was about 0.03% of the total genome, so that the average telomere length in each chromosomal end is almost 18 kb long. We also detected the presence of (TTAGG)n telomeric repeat in mitotic and meiotic chromosomes in other three species of Triatominae: Triatoma dimidiata Latreille, 1811, Dipetalogaster maxima Uhler, 1894, and Rhodnius prolixus Ståhl, 1859. This is the first report of the (TTAGG)n telomeric repeat in the infraorder Cimicomorpha, contradicting the currently accepted hypothesis that evolutionarily recent heteropterans lack this ancestral insect telomeric sequence. PMID:27830050

  19. Local Government in the South Pacific Islands

    Directory of Open Access Journals (Sweden)

    Graham Hassall

    2008-04-01

    Full Text Available In this paper we seek to answer some basic questions about the condition of local government in the Pacific. Firstly, we examine what is meant by ‘local government’ in the various islands and for that matter how Pacific Island states have perceived and accepted local government institutions in practice; second, we ask basic questions about existing legal and constitutional recognition and powers; and third, we provide initial findings on current per capita expenditure and local government financial viability in a number of Pacific cities and towns. We also make some observations on current moves towards local government reform.

  20. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes.

    Science.gov (United States)

    DiBattista, Joseph D; Whitney, Jonathan; Craig, Matthew T; Hobbs, Jean-Paul A; Rocha, Luiz A; Feldheim, Kevin A; Berumen, Michael L; Bowen, Brian W

    2016-08-01

    Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P<0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mtDNA lineage and

  1. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

    KAUST Repository

    DiBattista, Joseph

    2016-04-30

    Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N = 141) and A. nigricans (N = 412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N = 54) and A. japonicus (N = 49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000 to 2.25 million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr ≈ 0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST = 0.6533, P < 0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mt

  2. The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence.

    OpenAIRE

    Hakim, I; Amariglio, N; Grossman, Z; Simoni-Brok, F; Ohno, S; Rechavi, G

    1994-01-01

    Amplification of rearranged human immunoglobulin heavy-chain genes using the polymerase chain reaction resulted unexpectedly in the amplification of human transposable repetitive element genomes. These were identified as members of the THE I (transposon-like human element I) transposable element family. Analysis of the THE I sequences revealed the presence of several copies of the ancestral building block described > 10 years ago by Ohno and coworkers as the primordial immunoglobulin sequence...

  3. The canonical twin-arginine translocase components are not required for secretion of folded green fluorescent protein from the ancestral strain of Bacillus subtilis.

    Science.gov (United States)

    Snyder, Anthony J; Mukherjee, Sampriti; Glass, J Kyle; Kearns, Daniel B; Mukhopadhyay, Suchetana

    2014-05-01

    Cellular processes, such as the digestion of macromolecules, phosphate acquisition, and cell motility, require bacterial secretion systems. In Bacillus subtilis, the predominant protein export pathways are Sec (generalized secretory pathway) and Tat (twin-arginine translocase). Unlike Sec, which secretes unfolded proteins, the Tat machinery secretes fully folded proteins across the plasma membrane and into the medium. Proteins are directed for Tat-dependent export by N-terminal signal peptides that contain a conserved twin-arginine motif. Thus, utilizing the Tat secretion system by fusing a Tat signal peptide is an attractive strategy for the production and export of heterologous proteins. As a proof of concept, we expressed green fluorescent protein (GFP) fused to the PhoD Tat signal peptide in the laboratory and ancestral strains of B. subtilis. Secretion of the Tat-GFP construct, as well as secretion of proteins in general, was substantially increased in the ancestral strain. Furthermore, our results show that secreted, fluorescent GFP could be purified directly from the extracellular medium. Nonetheless, export was not dependent on the known Tat secretion components or the signal peptide twin-arginine motif. We propose that the ancestral strain contains additional Tat components and/or secretion regulators that were abrogated following domestication.

  4. An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression.

    Directory of Open Access Journals (Sweden)

    Tokiho Akiyama

    Full Text Available Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05. The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P < 0.05, and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.

  5. Light from dark: A relictual troglobite reveals a broader ancestral distribution for kimulid harvestmen (Opiliones: Laniatores: Kimulidae) in South America

    Science.gov (United States)

    Ceccarelli, F. Sara; Monte, Bruno G. O.; Proud, Daniel N.; DaSilva, Márcio Bernardino; Bichuette, Maria E.

    2017-01-01

    A new troglobitic harvestman, Relictopiolus galadriel gen. nov et sp. nov., is described from Olhos d’Água cave, Itacarambi, Minas Gerais State, Brazil. Morphological characters, including male genitalia and exomorphology, suggest that this species belongs to the family Kimulidae, and it appears to share the greatest similarities with Tegipiolus pachypus. Bayesian inference analyses of a molecular dataset strongly support the inclusion of this species in Kimulidae and confirm the hypothesized sister-group relationship between R. galadriel and T. pachypus. A time calibrated phylogeny indicates that these sister-taxa diverged from a common ancestor approximately 40 Mya, during the Paleogene. The current range of Kimulidae illustrates a remarkable disjunct distribution, and leads us to hypothesize that the ancestral distribution of Kimulidae was once much more widespread across eastern Brazil. This may be attributed to the Eocene radiation associated with the warming (and humidifying) events in the Cenozoic when the best conditions for evergreen tropical vegetation in South America were established and followed by the extinction of kimulid epigean populations together with the retraction of rain forests during the Oligocene to Miocene cooling. The discovery of this relictual troglobite indicates that the Olhos d’Água cave was a stable refugium for this ancient lineage of kimulids and acted as a "museum" of biodiversity. Our findings, considered collectively with the diverse troglofauna of the Olhos d’Água cave, highlight it as one of the most important hotspots of troglobite diversity and endemism in the Neotropics. Given the ecological stresses on this habitat, the cavernicolous fauna are at risk of extinction and we emphasize the urgent need for appropriate conservation actions. Finally, we propose the transfer of Acanthominua, Euminua, Euminuoides and Pseudominua from Kimulidae to Zalmoxidae, resulting in two new synonymies and 13 new combinations. PMID

  6. Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera.

    Science.gov (United States)

    Richards, Leigh R; Rambau, Ramugondo V; Lamb, Jennifer M; Taylor, Peter J; Yang, Fengtang; Schoeman, M Corrie; Goodman, Steven M

    2010-09-01

    The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.

  7. Phylogenetic analysis of glycerol 3-phosphate acyltransferases in opisthokonts reveals unexpected ancestral complexity and novel modern biosynthetic components.

    Directory of Open Access Journals (Sweden)

    Heather C Smart

    Full Text Available Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT, have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of 'fungal' orthologs in the basal taxa of the holozoa and 'animal' orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.

  8. Light from dark: A relictual troglobite reveals a broader ancestral distribution for kimulid harvestmen (Opiliones: Laniatores: Kimulidae in South America.

    Directory of Open Access Journals (Sweden)

    Abel Pérez-González

    Full Text Available A new troglobitic harvestman, Relictopiolus galadriel gen. nov et sp. nov., is described from Olhos d'Água cave, Itacarambi, Minas Gerais State, Brazil. Morphological characters, including male genitalia and exomorphology, suggest that this species belongs to the family Kimulidae, and it appears to share the greatest similarities with Tegipiolus pachypus. Bayesian inference analyses of a molecular dataset strongly support the inclusion of this species in Kimulidae and confirm the hypothesized sister-group relationship between R. galadriel and T. pachypus. A time calibrated phylogeny indicates that these sister-taxa diverged from a common ancestor approximately 40 Mya, during the Paleogene. The current range of Kimulidae illustrates a remarkable disjunct distribution, and leads us to hypothesize that the ancestral distribution of Kimulidae was once much more widespread across eastern Brazil. This may be attributed to the Eocene radiation associated with the warming (and humidifying events in the Cenozoic when the best conditions for evergreen tropical vegetation in South America were established and followed by the extinction of kimulid epigean populations together with the retraction of rain forests during the Oligocene to Miocene cooling. The discovery of this relictual troglobite indicates that the Olhos d'Água cave was a stable refugium for this ancient lineage of kimulids and acted as a "museum" of biodiversity. Our findings, considered collectively with the diverse troglofauna of the Olhos d'Água cave, highlight it as one of the most important hotspots of troglobite diversity and endemism in the Neotropics. Given the ecological stresses on this habitat, the cavernicolous fauna are at risk of extinction and we emphasize the urgent need for appropriate conservation actions. Finally, we propose the transfer of Acanthominua, Euminua, Euminuoides and Pseudominua from Kimulidae to Zalmoxidae, resulting in two new synonymies and 13 new

  9. Somatostatin signaling system as an ancestral mechanism: Myoregulatory activity of an Allatostatin-C peptide in Hydra.

    Science.gov (United States)

    Alzugaray, María Eugenia; Hernández-Martínez, Salvador; Ronderos, Jorge Rafael

    2016-08-01

    The coordination of physiological processes requires precise communication between cells. Cellular interactions allow cells to be functionally related, facilitating the maintaining of homeostasis. Neuropeptides functioning as intercellular signals are widely distributed in Metazoa. It is assumed that neuropeptides were the first intercellular transmitters, appearing early during the evolution. In Cnidarians, neuropeptides are mainly involved in neurotransmission, acting directly or indirectly on epithelial muscle cells, and thereby controlling coordinated movements. Allatostatins are a group of chemically unrelated neuropeptides that were originally characterized based on their ability to inhibit juvenil hormone synthesis in insects. Allatostatin-C has pleiotropic functions, acting as myoregulator in several insects. In these studies, we analyzed the myoregulatory effect of Aedes aegypti Allatostatin-C in Hydra sp., a member of the phylum Cnidaria. Allatostatin-C peptide conjugated with Qdots revealed specifically distributed cell populations that respond to the peptide in different regions of hydroids. In vivo physiological assays using Allatostatin-C showed that the peptide induced changes in shape and length in tentacles, peduncle and gastrovascular cavity. The observed changes were dose and time dependent suggesting the physiological nature of the response. Furthermore, at highest doses, Allatostatin-C induced peristaltic movements of the gastrovascular cavity resembling those that occur during feeding. In silico search of putative Allatostatin-C receptors in Cnidaria showed that genomes predict the existence of proteins of the somatostatin/Allatostatin-C receptors family. Altogether, these results suggest that Allatostatin-C has myoregulatory activity in Hydra sp, playing a role in the control of coordinated movements during feeding, indicating that Allatostatin-C/Somatostatin based signaling might be an ancestral mechanism. Copyright © 2016 Elsevier Inc. All

  10. Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background Thrombospondins (TSPs are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. Results We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs. Conclusion A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.

  11. Gastric cancer incidence and mortality is associated with altitude in the mountainous regions of Pacific Latin America.

    Science.gov (United States)

    Torres, Javier; Correa, Pelayo; Ferreccio, Catterina; Hernandez-Suarez, Gustavo; Herrero, Rolando; Cavazza-Porro, Maria; Dominguez, Ricardo; Morgan, Douglas

    2013-02-01

    In Latin America, gastric cancer is a leading cancer, and countries in the region have some of the highest mortality rates worldwide, including Chile, Costa Rica, and Colombia. Geographic variation in mortality rates is observed both between neighboring countries and within nations. We discuss epidemiological observations suggesting an association between altitude and gastric cancer risk in Latin America. In the Americas, the burden of gastric cancer mortality is concentrated in the mountainous areas along the Pacific rim, following the geography of the Andes sierra, from Venezuela to Chile, and the Sierra Madre and Cordillera de Centroamérica, from southern Mexico to Costa Rica. Altitude is probably a surrogate for host genetic, bacterial, dietary, and environmental factors that may cluster in the mountainous regions. For example, H. pylori strains from patients of the Andean Nariño region of Colombia display European ancestral haplotypes, whereas strains from the Pacific coast are predominantly of African origin. The observation of higher gastric cancer rates in the mountainous areas is not universal: the association is absent in Chile, where risk is more strongly associated with the age of H. pylori acquisition and socio-economic determinants. The dramatic global and regional variations in gastric cancer incidence and mortality rates offer the opportunity for scientific discovery and focused prevention programs.

  12. Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia.

    Science.gov (United States)

    Godbout, Julie; Fazekas, Aron; Newton, Craig H; Yeh, Francis C; Bousquet, Jean

    2008-05-01

    The Canadian side of the Pacific Northwest was almost entirely covered by ice during the last glacial maximum, which has induced vicariance and genetic population structure for several plant and animal taxa. Lodgepole pine (Pinus contorta Dougl. ex. Loud.) has a wide latitudinal and longitudinal distribution in the Pacific Northwest. Our main objective was to identify relictual signatures of glacial vicariance in the population structure of the species and search for evidence of distinct glacial refugia in the Pacific Northwest. A maternally inherited mitochondrial DNA minisatellite-like marker was used to decipher haplotype diversity in 91 populations of lodgepole pine located across the natural range. Overall population differentiation was sizeable (G(ST) = 0.365 and R(ST) = 0.568). Four relatively homogeneous groups of populations, possibly representative of as many genetically distinct glacial populations, were identified for the two main subspecies, ssp. latifolia and ssp. contorta. For ssp. contorta, one glacial lineage is suggested to have been located at high latitudes and possibly off the coast of mainland British Columbia (BC), while the other is considered to have been located south of the ice sheet along the Pacific coast. For ssp. latifolia, two genetically distinct glacial populations probably occurred south of the ice sheet: in the area bounded by the Cascades and Rocky Mountains ranges, and on the eastern side of the Rockies. A possible fifth refugium located in the Yukon may have also been present for ssp. latifolia. Zones of contact between these ancestral lineages were also apparent in interior and northern BC. These results indicate the role of the Queen Charlotte Islands and the Alexander Archipelago as a refugial zone for some Pacific Northwest species and the vicariant role played by the Cascades and the American Rocky Mountains during glaciation.

  13. Different hatching strategies in embryos of two species, pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, that belong to the same order Clupeiformes, and their environmental adaptation.

    Science.gov (United States)

    Kawaguchi, Mari; Fujita, Hideaki; Yoshizaki, Norio; Hiroi, Junya; Okouchi, Hiroyuki; Nagakura, Yoshitomo; Noda, Tsutomu; Watanabe, Satoshi; Katayama, Satoshi; Iwamuro, Shawichi; Nishida, Mutsumi; Iuchi, Ichiro; Yasumasu, Shigeki

    2009-03-15

    Pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, which belong to the same order Clupeiformes, spawn different types of eggs: demersal adherent eggs and pelagic eggs, respectively. We cloned three cDNAs for Pacific herring hatching enzyme and five for Japanese anchovy. Each of them was divided into two groups (group A and B) by phylogenetic analysis. They were expressed specifically in hatching gland cells (HGCs), which differentiated from the pillow and migrated to the edge of the head in both species. HGCs of Japanese anchovy stopped migration at that place, whereas those of Pacific herring continued to migrate dorsally and distributed widely all over the head region. During evolution, the program for the HGC migration would be varied to adapt to different hatching timing. Analysis of the gene expression revealed that Pacific herring embryos synthesized a large amount of hatching enzyme when compared with Japanese anchovy. Chorion of Pacific herring embryo was about 7.5 times thicker than that of Japanese anchovy embryo. Thus, the difference in their gene expression levels between two species is correlated with the difference in the thickness of chorion. These results suggest that the hatching system of each fish adapted to its respective hatching environment. Finally, hatching enzyme genes were cloned from each genomic DNA. The exon-intron structure of group B genes basically conserved that of the ancestral gene, whereas group A genes lost one intron. Several gene-specific changes of the exon-intron structure owing to nucleotide insertion and/or duplication were found in Japanese anchovy genes.

  14. 9th Pacific Basin Nuclear Conference. Nuclear energy, science and technology - Pacific partnership. Proceedings Volume 1

    International Nuclear Information System (INIS)

    1994-04-01

    The theme of the 9th Pacific Basin Nuclear conference held in Sydney from 1-6 May 1994, embraced the use of the atom in energy production and in science and technology. The focus was on selected topics of current and ongoing interest to countries around the Pacific Basin. The two-volume proceedings include both invited and contributed papers. They have been indexed separately. This document, Volume 1 covers the following topics: Pacific partnership; perspectives on nuclear energy, science and technology in Pacific Basin countries; nuclear energy and sustainable development; economics of the power reactors; new power reactor projects; power reactor technology; advanced reactors; radioisotope and radiation technology; biomedical applications

  15. Culturally Speaking: Asian Pacific American Heritage Month

    Science.gov (United States)

    York, Sherry

    2004-01-01

    The celebration of the Asian Pacific American heritage month is to be held in May 2004. The librarians are advised to include authentic literature by and about Asian Americans for cross-cultural understanding.

  16. Out of the Pacific and back again

    DEFF Research Database (Denmark)

    Foote, Andrew David; Morin, Phillip A.; Durban, John W.

    2011-01-01

    to partitioned mitochondrial genome sequences to better resolve the pattern of past radiations in this species. Our phylogenetic reconstructions indicate that in the North Pacific, sympatry between the maternal lineages that make up each ecotype arises from secondary contact. Both the phylogenetic...... divergence. Previous phylogeographic analysis using complete mitogenomes yielded a bifurcating tree of clades corresponding to described ecotypes. However, there was low support at two nodes at which two Pacific and two Atlantic clades diverged. Here we apply further phylogenetic and coalescent analyses...... reconstructions and a clinal decrease in diversity suggest a North Pacific to North Atlantic founding event, and the later return of killer whales to the North Pacific. Therefore, ecological divergence could have occurred during the allopatric phase through drift or selection and/or may have either commenced...

  17. 1- HARPs of the Pacific Islands Region

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains information on acoustic recordings of cetaceans collected from areas within the Pacific Islands Region since 2006. In collaboration with...

  18. Pacific Islands Climate Change Virtual Library

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Virtual Library provides access to web based climate variability and climate change information and tools relevant to the Pacific Islands including case studies,...

  19. Food irradiation seminar: Asia and the Pacific

    International Nuclear Information System (INIS)

    Mitchell, G.E.

    1986-01-01

    The report covers the Seminar for Asia and the Pacific on the practical application of food irradiation. The seminar assessed the practical application of food irradiation processes, commercial utilisation and international trade of irradiated food

  20. Asian & Pacific Islanders and Cardiovascular Diseases

    Science.gov (United States)

    ... Fact Sheet 2016 Update Asian & Pacific Islanders and Cardiovascular Diseases Cardiovascular Disease (CVD) (ICD 10 codes I00-I99, Q20- ... of na- tive Hawaiians or oth- A indicates cardiovascular disease plus congenital cardiovascular disease (ICD-10 I00- ...

  1. 1994 Pacific Northwest Loads and Resources Study.

    Energy Technology Data Exchange (ETDEWEB)

    United States. Bonneville Power Administration.

    1994-12-01

    The 1994 Pacific Northwest Loads and Resources Study presented herein establishes a picture of how the agency is positioned today in its loads and resources balance. It is a snapshot of expected resource operation, contractual obligations, and rights. This study does not attempt to present or analyze future conservation or generation resource scenarios. What it does provide are base case assumptions from which scenarios encompassing a wide range of uncertainties about BPA`s future may be evaluated. The Loads and Resources Study is presented in two documents: (1) this summary of Federal system and Pacific Northwest region loads and resources and (2) a technical appendix detailing the loads and resources for each major Pacific Northwest generating utility. This analysis updates the 1993 Pacific Northwest Loads and Resources Study, published in December 1993. In this loads and resources study, resource availability is compared with a range of forecasted electricity consumption. The Federal system and regional analyses for medium load forecast are presented.

  2. Pacific Islands Mass Communications; Selected Information Sources.

    Science.gov (United States)

    Richstad, Jim; McMillan, Michael

    1977-01-01

    Presents a bibliography of materials on such area of mass communications in the Pacific Islands as broadcasting, radio and television, cinema, communication research, mass media in education, Honululu Media Council, newspapers and newspapermen, and printing and satellite communication. (JEG)

  3. PODs cruise - Pacific Orcinus Distrbution Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Orcinus spp. occur in the Pacific Ocean throughout the West Coast of North America. Data concerning their precise locations and abundance are critical to...

  4. Northeast Pacific Regional Climatology (NCEI Accession 0163799)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Northeast Pacific (NEP) new regional climatology is derived from the NCEI World Ocean Database archive of temperature and salinity and covers a time period from...

  5. Eastern Pacific Ocean Purse-seine Fishery

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vessel logbook and landings data sets from U.S.A.-flagged purse-seine vessels fishing in the Eastern Pacific Ocean (EPO). These purse seiners...

  6. Sponges from Clipperton Island, East Pacific

    OpenAIRE

    van Soest, R.W.M.; Kaiser, K.L.; van Syoc, R.

    2011-01-01

    Twenty sponge species (totalling 190 individuals) were collected during the 1938, 1994 and 2004/5 expeditions to the remote island of Clipperton in the East Pacific Ocean. Seven species are widespread Indo-Pacific sponges; nine species comprise sponges new to science; four species were represented only by small thin patches insufficient for proper characterization and could be only determined to genus. The new species may not be necessarily endemic to the island, as several show similarities ...

  7. 1993 Pacific Northwest Loads and Resources Study.

    Energy Technology Data Exchange (ETDEWEB)

    United States. Bonneville Power Administration.

    1993-12-01

    The Loads and Resources Study is presented in three documents: (1) this summary of Federal system and Pacific Northwest region loads and resources; (2) a technical appendix detailing forecasted Pacific Northwest economic trends and loads, and (3) a technical appendix detailing the loads and resources for each major Pacific Northwest generating utility. In this loads and resources study, resource availability is compared with a range of forecasted electricity consumption. The forecasted future electricity demands -- firm loads -- are subtracted from the projected capability of existing and {open_quotes}contracted for{close_quotes} resources to determine whether Bonneville Power Administration (BPA) and the region will be surplus or deficit. If resources are greater than loads in any particular year or month, there is a surplus of energy and/or capacity, which BPA can sell to increase revenues. Conversely, if firm loads exceed available resources, there is a deficit of energy and/or capacity, and additional conservation, contract purchases, or generating resources will be needed to meet load growth. The Pacific Northwest Loads and Resources Study analyzes the Pacific Northwest`s projected loads and available generating resources in two parts: (1) the loads and resources of the Federal system, for which BPA is the marketing agency; and (2) the larger Pacific Northwest regional power system, which includes loads and resource in addition to the Federal system. The loads and resources analysis in this study simulates the operation of the power system under the Pacific Northwest Coordination Agreement (PNCA) produced by the Pacific Northwest Coordinating Group. This study presents the Federal system and regional analyses for five load forecasts: high, medium-high, medium, medium-low, and low. This analysis projects the yearly average energy consumption and resource availability for Operating Years (OY) 1994--95 through 2003--04.

  8. Boundary scavenging in the Pacific Ocean

    International Nuclear Information System (INIS)

    Anderson, R.F.; Lao, Y.; Broecker, W.S.; Trumbore, S.E.; Hofmann, H.J.; Wolfli, W.

    1990-01-01

    Concentrations of U, Th, 231 Pa and 10 Be were measured in Holocene sediments from two cores collected off the west coast of South America, two cores from the East Pacific Rise, two from the equatorial Pacific and one from the south Pacific central gyre. Our results, together with data from 5 cores reported in the literature, show that boundary scavenging plays a major role in the removal of 10 Be from the Pacific Ocean. Deposition rates of 10 Be at three margin sites are more than an order of magnitude greater than at sites of red clay accumulation in the deep central Pacific. Deposition of 231 Pa is 4 to 5-fold greater at the margin sites. The residence time of 10 Be with respect to chemical scavenging, defined as its inventory in the water column divided by its rate of removal to the sediments, varies regionally from >1000 years at the red-clay sites in the deep central Pacific to ∝100 years at the margin sites. Different factors control boundary scavenging of Pa and Be. For example, scavenging of 231 Pa is enhanced by metal-oxide coatings of particles, whereas this seems to have little influence on the scavenging of 10 Be. (orig.)

  9. A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.

    Science.gov (United States)

    Nakano, Hiroaki; Miyazawa, Hideyuki; Maeno, Akiteru; Shiroishi, Toshihiko; Kakui, Keiichi; Koyanagi, Ryo; Kanda, Miyuki; Satoh, Noriyuki; Omori, Akihito; Kohtsuka, Hisanori

    2017-12-18

    Xenoturbella is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure. Here we describe a new Xenoturbella species from the western Pacific Ocean, and report a new xenoturbellid structure - the frontal pore. Non-destructive microCT was used to investigate the internal morphology of this soft-bodied animal. This revealed the presence of a frontal pore that is continuous with the ventral glandular network and which exhibits similarities with the frontal organ in acoelomorphs. Our results suggest that large size, oval mouth, frontal pore and ventral glandular network may be ancestral features for Xenoturbella. Further studies will clarify the evolutionary relationship of the frontal pore and ventral glandular network of xenoturbellids and the acoelomorph frontal organ. One of the habitats of the newly identified species is easily accessible from a marine station and so this species promises to be valuable for research on bilaterian and deuterostome evolution.

  10. North America as an exotic terrane'' and the origin of the Appalachian--Andean Mountain system

    Energy Technology Data Exchange (ETDEWEB)

    Dalziel, I.W.D; Gahagan, L.M. (Univ. of Texas, Austin, TX (United States). Inst. for Geophysics); Dalla Salda, L.H. (Univ. Nacional de La Plata, La Plata (Argentina). Centro de Investigaciones Geologicas)

    1992-01-01

    North America was sutured to Gondwana in the terminal Alleghanian event of Appalachian orogenesis, thus completing the late Paleozoic assembly of Pangea. The suggestion that the Pacific margins of East Antarctica-Australia and Laurentia may have been juxtaposed during the Neoproterozoic prompts reevaluation of the widely held assumptions that the ancestral Appalachian margin rifted from northwestern Africa during the earliest Paleozoic opening of Iapetus, and remained juxtaposed to that margin, even though widely separated from it at times, until the assembly of Pangea. The lower Paleozoic carbonate platform of northwestern Argentina has been known for a long time to contain Olenellid trilobites of the Pacific or Columbian realm. Although normally regarded as some kind of far-travelled terrane that originated along the Appalachian margin of Laurentia, it has recently been interpreted as a fragment detached from the Ouachita embayment of Laurentia following Taconic-Famatinian collision with Gondwana during the Ordovician. The Oaxaca terrane of Mexico, on the other hand, contains a Tremadocian trilobite fauna of Argentine-Bolivian affinities, and appears to have been detached from Gondwana following the same collision. The Wilson cycle'' of Iapetus ocean basin opening and closing along the Appalachian and Andean orogens may have involved more than one such continental collision during clockwise drift of Laurentia around South America following late Neoproterozoic to earliest Cambrian separation. Together with the collisions of baltic and smaller terranes with Laurentia, this could explain the protracted Paleozoic orogenic history of both the Appalachian and proto-Andean orogens.

  11. The Trans-Pacific Partnership

    Directory of Open Access Journals (Sweden)

    Voon Tania

    2016-12-01

    Full Text Available This article provides an overview of the recently concluded Trans-Pacific Partnership Agreement (TPP, a treaty the parties have described as comprehensive and ambitious, yet also representing a balance of competing interests. The article focuses on the TPP’s chapters relating to investment, services, intellectual property and regulatory coherence, each of which provides insight into the motivations that drove the conclusion of the TPP and the negotiating dynamics that determined its final content. In areas such as investment, the TPP takes a more balanced approach than many earlier agreements, providing greater safeguards for the regulatory autonomy of states while still embodying core protections for foreign investors. In relation to intellectual property and services, the TPP goes beyond earlier agreements in several key respects, such as preventing the imposition of local presence requirements for service providers or requiring longer copyright terms than those demanded by other international treaties. The TPP chapter on regulatory coherence is one of the most novel features of the treaty, as regulatory coherence is not frequently included in earlier trade agreements, demonstrating the increased focus of states on addressing regulatory barriers to trade and investment. While all of these elements of the TPP are interesting in their own right, given the number and size of the parties involved in the agreement, they also provide valuable guidance about the direction of other ongoing and future preferential trade agreement negotiations, such as the proposed Transatlantic Trade and Investment Partnership (TTIP and Trade in Services Agreement (TiSA.

  12. The Pacific sea surface temperature

    International Nuclear Information System (INIS)

    Douglass, David H.

    2011-01-01

    The Pacific sea surface temperature data contains two components: N L , a signal that exhibits the familiar El Niño/La Niña phenomenon and N H , a signal of one-year period. Analysis reveals: (1) The existence of an annual solar forcing F S ; (2) N H is phase locked directly to F S while N L is frequently phase locked to the 2nd or 3rd subharmonic of F S . At least ten distinct subharmonic time segments of N L since 1870 are found. The beginning or end dates of these segments have a near one-to-one correspondence with the abrupt climate changes previously reported. Limited predictability is possible. -- Highlights: ► El Niño/La Niña consists of 2 components phase-locked to annual solar cycle. ► The first component N L is the familiar El Niño/La Niña effect. ► The second N H component has a period of 1 cycle/year. ► N L can be phase-locked to 2nd or 3rd subharmonic of annual cycle. ► Ends of phase-locked segments correspond to abrupt previously reported climate changes.

  13. Renewable Energy Country Profiles. Pacific

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-09-15

    The IRENA Renewable Energy Country Profiles take stock of the latest development of renewable energy in two regions where renewable energy can make a significant contribution to combat climate change and bring modern energy services to everyone: Africa and the Pacific. These two regions are presented separately in this volume and its sister publication. The country profiles combine elements of IRENA analysis with the latest information available from a vast array of sources in order to give a brief yet comprehensive and up-to-date picture of the situation of renewable energy that includes energy supply, electrical capacity, energy access, policies, targets, investment climate, projects and endowment in renewable energy resources. Because of the different timelines of these sources, data presented here refer to years between 2008 and 2012. Data availability also differs from country to country, which makes comparison with a wider regional group possible only for the year for which figures are available for all the members of the group; while this may not be the most recent year, the differences between countries, regions and the world remain striking. The current country profiles are just a starting point; they will be extended upon with new indicators to make them more informative, and maintained as a live product on the IRENA website as a key source of information on renewable energy.

  14. Magmatic evolution in the N-Gondwana margin related to the opening of the Rheic Ocean—evidence from the Upper Parautochthon of the Galicia-Trás-os-Montes Zone and from the Central Iberian Zone (NW Iberian Massif)

    Science.gov (United States)

    Dias da Silva, Ícaro; Díez Fernández, Rubén; Díez-Montes, Alejandro; González Clavijo, Emilio; Foster, David A.

    2016-06-01

    LA-MC-ICP-MS U-Pb zircon ages and whole-rock geochemical data obtained from volcanic rocks erupted in the northern margin of Gondwana provide new insights on the polyphase magmatic evolution of the NW Iberian domain during the establishment of passive margin conditions in Lower Paleozoic times. The U-Pb data show crystallization ages of ca. 455 Ma for two calc-alkaline rhyolites sampled in the Upper Parautochthon of the eastern Galicia—Trás-os-Montes Zone (GTMZ) and for an intraplate basalt intruded into Middle Ordovician slates of the autochthonous series of the Central Iberian Zone (CIZ). Together with previous data, the ages obtained reveal a periodic magmatic activity across the northern Gondwana margin during the Lower Paleozoic, which is comparable to that observed in NE Iberia and in other massifs of the Mediterranean realm. Both geochronological and geochemical data reinforce paleontological and stratigraphic evidences for paleogeographic proximity between these domains and contribute to the recognition of extensional-related magmatism along the northern margin of Central Gondwana associated with the opening of the Rheic Ocean.

  15. 78 FR 23539 - National Marine Fisheries Service, Pacific Fishery Management Council (Pacific Council); May 6...

    Science.gov (United States)

    2013-04-19

    ... results, Endangered Species Act transparency, electronic monitoring, allocation review process, Department... Friday, May 10, 2013 9 a.m.-12 p.m. ESA Transparency Electronic Monitoring Allocation Review Process 12-1... Marine Fisheries Service, Pacific Fishery Management Council (Pacific Council); May 6 and 9-10, 2013...

  16. Rare Central Pacific El Niño Events Caused by Interdecadal Tropical Pacific Variability

    Science.gov (United States)

    Zhong, Wenxiu; Zheng, Xiaotong; Cai, Wenju

    2017-04-01

    The frequency of Central Pacific (CP) El Niño events displays strong decadal-variability but the associated dynamics is still not clear. The Inter-decadal Pacific Oscillation (IPO) and the Tropical Pacific Decadal Variability (TPDV) are two dominant modes of the Pacific low-frequency variability that can modify high-frequency behaviors. Using a 500-year control integration of Geophysical Fluid Dynamics Laboratory Earth System Model simulation, we find that the mean state, determined by the two independent modes of tropical Pacific decadal variability, strongly affects CP El Niño frequency and the associated developing processes. A positive TPDV features a shallow thermocline and cool sea surface temperature anomalies (SSTAs) across the central-to-western tropical Pacific, and a negative IPO features cool SSTAs and strong trade winds along the equatorial Pacific. The combination of a positive TPDV and a negative IPO generates a decadal mean state, in which the climatological zonal temperature gradient is reduced, equatorward and westward current anomalies are harder to be generated over the central-to-western tropical Pacific, resulting in the lack of CP El Niño.

  17. 78 FR 66695 - Loveland Area Projects, Colorado River Storage Project, Pacific Northwest-Pacific Southwest...

    Science.gov (United States)

    2013-11-06

    ... DEPARTMENT OF ENERGY Western Area Power Administration Loveland Area Projects, Colorado River Storage Project, Pacific Northwest-Pacific Southwest Intertie Project, Central Arizona Project, and Parker-Davis Project--Rate Order No. WAPA-163 AGENCY: Western Area Power Administration, DOE. ACTION: Notice of...

  18. Whirling in the late Permian: ancestral Gyrinidae show early radiation of beetles before Permian-Triassic mass extinction.

    Science.gov (United States)

    Yan, Evgeny V; Beutel, Rolf G; Lawrence, John F

    2018-03-16

    Gyrinidae are a charismatic group of highly specialized beetles, adapted for a unique lifestyle of swimming on the water surface. They prey on drowning insects and other small arthropods caught in the surface film. Studies based on morphological and molecular data suggest that gyrinids were the first branch splitting off in Adephaga, the second largest suborder of beetles. Despite its basal position within this lineage and a very peculiar morphology, earliest Gyrinidae were recorded not earlier than from the Upper Triassic. Tunguskagyrus. with the single species Tunguskagyrus planus is described from Late Permian deposits of the Anakit area in Middle Siberia. The genus is assigned to the stemgroup of Gyrinidae, thus shifting back the minimum age of this taxon considerably: Tunguskagyrus demonstrates 250 million years of evolutionary stability for a very specialized lifestyle, with a number of key apomorphies characteristic for these epineuston predators and scavengers, but also with some preserved ancestral features not found in extant members of the family. It also implies that major splitting events in this suborder and in crown group Coleoptera had already occurred in the Permian. Gyrinidae and especially aquatic groups of Dytiscoidea flourished in the Mesozoic (for example Coptoclavidae and Dytiscidae) and most survive until the present day, despite the dramatic "Great Dying" - Permian-Triassic mass extinction, which took place shortly (in geological terms) after the time when Tunguskagyrus lived. Tunguskagyrus confirms a Permian origin of Adephaga, which was recently suggested by phylogenetic "tip-dating" analysis including both fossil and Recent gyrinids. This also confirms that main splitting events leading to the "modern" lineages of beetles took place before the Permian-Triassic mass extinction. Tunguskagyrus shows that Gyrinidae became adapted to swimming on the water surface long before Mesozoic invasions of the aquatic environment took place

  19. ¿Con o sin ancestros?: vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-06-01

    Full Text Available La existencia o no de ancestros en la Amazonía indígena ha sido objeto de importantes debates. Sin embargo, los líderes de la región no dudan en llamar ‘ancestrales’ sus saberes, normas o territorios, en un sentido que, desde un punto de vista académico, puede parecer enigmático. «Ancestrales, pero… ¿con o sin ancestros?», preguntaría entonces, confuso, el antropólogo. En este artículo propongo aportar elementos de respuesta a esta pregunta a través del caso peruano. Primero analizo cómo los líderes indígenas amazónicos, conectándose al circuito del derecho internacional, adoptan la noción jurídica de ‘posesión ancestral’ del territorio para adaptarla al ámbito político. Este planteamiento rinde cuenta de la generalización y uniformización reciente del vocablo ‘ancestral’ pero deja pendiente el problema de su eventual articulación con las cosmologías indígenas que pretende reflejar. Por eso, en la segunda parte, intento sondear sobre la pertinencia de la categoría de ‘ancestro’ en la Amazonía indígena, recordando brevemente el debate académico para ir definiendo en qué medida esta categoría puede cobrar sentido. A partir del testimonio de un experimentado líder awajún, la tercera parte permite, entonces, volver más explícitos los diferentes sentidos y planos referenciales que despliega la referencia a lo ancestral, mostrando cómo los indígenas amazónicos no solo adoptan elementos conceptuales y discursivos externos, sino que al mismo tiempo los transforman a partir de sus propias singularidades cosmológicas y perspectivas políticas.

  20. Climate Change in the Pacific Islands

    Science.gov (United States)

    Hamnett, Michael P.

    Climate change have been a major concern among Pacific Islanders since the late 1990s. During that period, Time Magazine featured a cover story that read: Say Goodbye to the Marshall Islands, Kiribati, and Tuvalu from sea level rise. Since that time, the South Pacific Regional Environment Programme, UN and government agencies and academic researchers have been assessing the impacts of long-term climate change and seasonal to inter-annual climate variability on the Pacific Islands. The consensus is that long-term climate change will result in more extreme weather and tidal events including droughts, floods, tropical cyclones, coastal erosion, and salt water inundation. Extreme weather events already occur in the Pacific Islands and they are patterned. El Niño Southern Oscillation (ENSO) events impact rainfall, tropical cyclone and tidal patterns. In 2000, the first National Assessment of the Consequences of Climate Variability and Change concluded that long-term climate change will result in more El Niño events or a more El Niño like climate every year. The bad news is that will mean more natural disasters. The good news is that El Niño events can be predicted and people can prepare for them. The reallly bad news is that some Pacific Islands are already becoming uninhabitable because of erosion of land or the loss of fresh water from droughts and salt water intrusion. Many of the most vulnerable countries already overseas populations in New Zealand, the US, or larger Pacific Island countries. For some Pacific Islander abandoning their home countries will be their only option.

  1. Written Exercises: Ancestral Magic and Emergent Intellectuals in Mia Couto, Lhoussain Azergui and Dorota Masłowska

    Directory of Open Access Journals (Sweden)

    Ewa Łukaszyk

    2016-12-01

    Full Text Available Written Exercises: Ancestral Magic and Emergent Intellectuals in Mia Couto, Lhoussain Azergui and Dorota Masłowska The article consists in a comparative reading of three novels: Um rio chamado tempo by Mia Couto, Le pain des corbeaux by Lhoussain Azergui and Paw królowej by Dorota Masłowska. In spite of the difference of the historical circumstances of Mozambique, Morocco and Poland, these three books meet at an intersecting point: the emergence of an intelligentsia that uses literacy and writing as an instrument to deconstruct the post-colonial concept of nation and to operate a trans-colonial renegotiation of identity. By the notion of trans-colonial, I understand the opposition against new kinds of symbolic violence that emerged after the end of the colonial period; here this new form of oppression is related to the concept of national unity – an artificial construct that leaves no place for a dualism or pluralism of cultural reality (two shores of the Zambezi river, Arab and Berber dualism in Morocco, “small homelands” in Poland. The young heroes of the novels grasp the pen in order to break through the falseness or the taboos created by the fathers, establishing, at the same time, the relation of solidarity with the world of the grandfathers. The act of writing becomes an actualization of the ancestral universe of magic. The settlement of accounts with the parental generation concerns the vision of nation built upon the resistance against the colonizer (it also refers to the Polish cultural formation, based on the tradition of uprisings and resistance against the Russians.   Ćwiczenia pisemne: magia przodków i nowi intelektualiści w powieściach Mii Couto, Lhoussaina Azerguiego i Doroty Masłowskiej Na podstawie powieści Um rio chamado tempo, uma casa chamada terra Mii Couto (2002, Le pain des corbeaux Lhoussaina Azerguiego (2012 oraz Paw królowej Doroty Masłowskiej (2005 dokonano analizy zjawiska wyłonienia się nowej

  2. Evolution of the late Paleozoic accretionary complex and overlying forearc-magmatic arc, south central Chile (38°-41°S): Constraints for the tectonic setting along the southwestern margin of Gondwana

    Science.gov (United States)

    Martin, Mark W.; Kato, Terence T.; Rodriguez, Carolina; Godoy, Estanislao; Duhart, Paul; McDonough, Michael; Campos, Alberto

    1999-08-01

    Stratigraphic, structural, metamorphic, and geochronologic studies of basement rocks in the Andean foothills and Coast Ranges of south central Chile (39°-41°S) suggest a protracted late Paleozoic to middle Mesozoic deformational and metamorphic history that imposes important constraints on the tectonic development of the southwestern Gondwana margin. In the study area the late Paleozoic paired metamorphic belt, coeval magmatic arc, and overlying Triassic sedimentary units preserve a record of Late Carboniferous to Early Permian subduction and arc magmatism, subsequent deep exhumation of the Western Series subduction complex, and diminished uplift and erosion of the Eastern Series arc-forearc region by the Late Triassic. Late Paleozoic structural elements and metamorphic assemblages formed during early subduction and arc magmatism, collectively referred to as Dl, are largely erased in the Western Series by the dominant D2 schistosity and lower greenschist grade metamorphism. D1 structural features, as well as original sedimentary textures, are relatively well preserved in the less penetratively deformed Eastern Series. The regional distribution of late Paleozoic arc magmatism suggests that the late Paleozoic convergent margin deviated from a N-S trend north of this area to a NW-SE trend near this latitude and faced an open marine environment to the southwest. A transition from F2 isoclinal folding to more open, larger-scale F3 folds, interpreted as change in ductility during differential uplift of the Western Series, is not apparent in the Eastern Series. Despite a lesser degree of uplift during the main exhumational D2 event, delineation of unconformities and U-Pb dating of detrital zircons and intrusions into the Eastern Series allow tighter constraints to be placed on timing of uplift and denudation of the Eastern Series than on that in the Western Series. A regional unconformity exposed in the Lake District that separates more highly deformed Eastern Series

  3. The Pacific Island Health Care Project

    Directory of Open Access Journals (Sweden)

    Donald Ames Person

    2014-10-01

    Full Text Available Introduction/BackgroundUS Associated/Affiliated Pacific Islands (USAPI include 3 Freely Associated States: Marshall Islands, Federated States of Micronesia, Palau and 3 Territories: American Samoa, Guam, and Commonwealth of the Northern Mariana Islands. ObjectiveThe Pacific Island Health Care Project (PIHCP provides humanitarian medical referral/consultation/care to >500,000 indigenous people of these remote islands. Methods In the mid-1990s, we developed a simple store-and-forward program to link the USAPI with Tripler Army Medical Center (TAMC. This application allowed image attachment to email consultations. ResultsMore than 8000 Pacific Islanders have benefited from the program. 3000 Pacific Islanders prior to telemedicine (1990-1997 and since store-and-forward telemedicine (1997-present, the PIHCP has helped an additional 5000. Records post dynamically and are stored in an archival database. Conclusion The PIHCP is the longest running telemedicine program in the world delivering humanitarian medical care. It has bridged the Developing World of the remote Pacific islands with advanced medical and surgical care available at a major US military teaching hospital.(The opinions expressed here are those of the author and not that of the Army, Department of Defense, or the US Government.

  4. Asia-Pacific lube oil markets

    International Nuclear Information System (INIS)

    Yamaguchi, N.

    2001-01-01

    An overview of the Asia-Pacific (AP) lubricating oils market, its special characteristics, and its role in the global economy are presented. In the 'boom and bust' years of 1997-1999, the Asia-Pacific market was even bigger then the US market. For the short-term, the scenario is surplus capacity and poor margins, but in the long term there is enormous potential for growth. How fuel demand and quality is related to engine type is discussed. The three basic grades of baseoils are described, and the Asia-Pacific lube demand and the Asia-Pacific lube oil supply are discussed. There are 15 diagrams giving data on: (i) finished lubes in world markets as a percentage of total; (ii) how lube demand follows GDP per capita in Asia; (iii) AP baseoil capacity relationships; (iv) AP baseoil disposition by end use; (v) AP changing shares of baseoil demand; (vi) AP finished lube demand by subregion; (vii) AP finished lube demand growth, indexed; (viii) AP baseoil capacity by region; Singapore baseoil vs. Dubai crude prices, 1992-99; (ix) Singapore baseoil vs. crude prices, 1992-99; (x) AP baseoil deficit moved to surplus; (xi) AP baseoil production; (xii) East Asia net percentage change in lube sales, 1997-1999. (xiii) Southeast Asia net percentage change in lube sales, 1997-1999; (xiv) South East Asia and Australia net percentage change in lube sales, 1997-1999 and (xv) Asia-Pacific major lube marketers

  5. Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope.

    Science.gov (United States)

    Doria-Rose, N A; Learn, G H; Rodrigo, A G; Nickle, D C; Li, F; Mahalanabis, M; Hensel, M T; McLaughlin, S; Edmonson, P F; Montefiori, D; Barnett, S W; Haigwood, N L; Mullins, J I

    2005-09-01

    Human immunodeficiency virus type 1 (HIV-1) is a difficult target for vaccine development, in part because of its ever-expanding genetic diversity and attendant capacity to escape immunologic recognition. Vaccine efficacy might be improved by maximizing immunogen antigenic similarity to viruses likely to be encountered by vaccinees. To this end, we designed a prototype HIV-1 envelope vaccine using a deduced ancestral state for the env gene. The ancestral state reconstruction method was shown to be >95% accurate by computer simulation and 99.8% accurate when estimating the known inoculum used in an experimental infection study in rhesus macaques. Furthermore, the deduced ancestor gene differed from the set of sequences used to derive the ancestor by an average of 12.3%, while these latter sequences were an average of 17.3% different from each other. A full-length ancestral subtype B HIV-1 env gene was constructed and shown to produce a glycoprotein of 160 kDa that bound and fused with cells expressing the HIV-1 coreceptor CCR5. This Env was also functional in a virus pseudotype assay. When either gp160- or gp140-expressing plasmids and recombinant gp120 were used to immunize rabbits in a DNA prime-protein boost regimen, the artificial gene induced immunoglobulin G antibodies capable of weakly neutralizing heterologous primary HIV-1 strains. The results were similar for rabbits immunized in parallel with a natural isolate, HIV-1 SF162. Further design efforts to better present conserved neutralization determinants are warranted.

  6. Mapuche Ancestral Recovery of Land. The Lof Inkaial WalMapu Meu case of study (Nahuel Huapí National Park, Río Negro, Argentina

    Directory of Open Access Journals (Sweden)

    Guido Galafassi

    2012-07-01

    Full Text Available The aim of this paper is to present and analyze the case of a recent social mobilization which involved a Mapuche community in the southern region of Argentina, known as Patagonia. An “ancestral recovery of land” was claimed to be the objective of the action. Several conflicts emerged due to the fact that the land in conflict is part of the Nahuel Huapi National Park, which implied a straightforward questioning of the National State rights over territory. Apart from that, the recovery process was strongly rejected by local residents. This brought about a new conflict that required the local government's mediation.

  7. Personal and Social Transformation in the Health Area through Education: A Brief Journey from the Ancestral Indigenous Wisdom to the Modern Tyranny of Healthiness

    Directory of Open Access Journals (Sweden)

    Andrés de Muller

    2015-09-01

    Full Text Available This paper aims at claiming the ancestral wisdom of indigenous people in the health area. It analyzes how health has been commodified in the interest of large companies (particularly those related to the pharmaceutical industry to the detriment of a holistic definition of wellness through education. Furthermore, the concept of health as a right disagrees with such commodification or sale to the highest bidder, which prompts dehumanization of health services and public misinformation. The abundance of self-proclaimed gurus or healers who appeal to autosuggestion contributes both to confusion and to an unhealthy cult of healthiness.

  8. Proto-Jabutí: a first attempt to reconstruct the ancestral language of the Arikapú and the Djeoromitxí

    Directory of Open Access Journals (Sweden)

    Hein van der Voort

    2007-08-01

    Full Text Available The Arikapú and Djeoromitxí languages form a small linguistic family in southern Rondônia, known as Jabutí. The languages are highly endangered and high quality data have become available only recently. This article is intended to create a basis of evidence for Curt Nimuendajú’s hypothesis that the Jabutí language family belongs to the Macro-Jê linguistic stock. After short descriptive sketches of both Jabutí languages and the historical and sociocultural background, the article focusses on the reconstruction of the ancestral language, Proto-Jabutí, following the principles of the historical-comparative method.

  9. The parasite Ichthyophonus sp. in Pacific herring from the coastal NE Pacific

    Science.gov (United States)

    Hershberger, Paul K.; Gregg, Jacob L.; Hart, Lucas M.; Moffitt, Steve; Brenner, Richard L.; Stick, K.; Coonradt, Eric; Otis, E. O.; Vollenweider, Johanna J.; Garver, Kyle A.; Lovy, Jan; Meyers, T.R.

    2016-01-01

    The protistan parasite Ichthyophonus occurred in populations of Pacific herring Clupea pallasii Valenciennes throughout coastal areas of the NE Pacific, ranging from Puget Sound, WA north to the Gulf of Alaska, AK. Infection prevalence in local Pacific herring stocks varied seasonally and annually, and a general pattern of increasing prevalence with host size and/or age persisted throughout the NE Pacific. An exception to this zoographic pattern occurred among a group of juvenile, age 1+ year Pacific herring from Cordova Harbor, AK in June 2010, which demonstrated an unusually high infection prevalence of 35%. Reasons for this anomaly were hypothesized to involve anthropogenic influences that resulted in locally elevated infection pressures. Interannual declines in infection prevalence from some populations (e.g. Lower Cook Inlet, AK; from 20–32% in 2007 to 0–3% during 2009–13) or from the largest size cohorts of other populations (e.g. Sitka Sound, AK; from 62.5% in 2007 to 19.6% in 2013) were likely a reflection of selective mortality among the infected cohorts. All available information for Ichthyophonus in the NE Pacific, including broad geographic range, low host specificity and presence in archived Pacific herring tissue samples dating to the 1980s, indicate a long-standing host–pathogen relationship.

  10. The Rise and Decline of Japanese Pacifism

    Directory of Open Access Journals (Sweden)

    Yuan Cai

    2008-12-01

    Full Text Available The Japanese pacifist constitution has been a symbol of Japan’s commitment to peace and more importantly its renunciation of wartime militarism. There has been strong support for its continuing existence amongst the Japanese populace despite persistent attempts by the Japanese government to amend it. However, the prevalent pacifist sentiment is showing signs of fading vitality in recent times. This article purports to examine the underlying forces that contributed to the development and the decline of Japanese pacifism. A host of domestic and international factors were responsible for the growth of pacifism and its subsequent decline, but only three important domestic factors will be examined in detail: the concept of victimhood in the development of pacifism and its implication for its continuing strength, the importance of peace education and the role played by the influential Japan’s Teachers’ Union on the formation of pacifist conscience and finally, the influence of leftist organisations on the organised peace movement.

  11. The Pacific northwest stream quality assessment

    Science.gov (United States)

    Van Metre, Peter C.; Morace, Jennifer L.; Sheibley, Rich W.

    2015-01-01

    In 2015, the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) program is assessing stream quality in the Pacific Northwest. The goals of the Pacific Northwest Stream Quality Assessment (Pacific Northwest study) are to assess the quality of streams in the region by characterizing multiple water-quality factors that are stressors to aquatic life and to evaluate the relation between these stressors and biological communities. The effects of urbanization and agriculture on stream quality for the Puget Lowlands and Willamette Valley are the focus of this regional study. Findings will provide the public and policymakers with information regarding which human and environmental factors are the most critical in affecting stream quality and, thus, provide insights about possible approaches to protect or improve the health of streams in the region.

  12. Regional climate change for the Pacific Northwest

    International Nuclear Information System (INIS)

    McBean, G.A.; Thomas, G.

    1991-01-01

    The Pacific Northwest climate is dominated by topography and the Pacific Ocean; the forests have become adapted to the present climate. Within short distances there are large changes in precipitation and temperature, with resultant changes in ecosystems. As the atmospheric concentrations of greenhouse gases increase, global climate is expected to warm and precipitation to increase. Global climate model simulations show enhanced warming at high northern latitudes. For the Pacific Northwest, models show 2-6 degree C warming and increased precipitation in the winter for doubled atmospheric CO 2 concentration. However, the regional details of these models are presently not very reliable. The results and limitations of present global climate models are reviewed. The roles of the oceans, clouds, and other feedback mechanisms are described along with some of the possible impacts of climate change on forest resources. 24 refs., 2 figs., 1 tab

  13. Asia-Pacific Economic Cooperation (APEC) - Center for Global Health

    Science.gov (United States)

    As the leading economic forum in the Asia-Pacific region, APEC facilitates economic growth and prosperity in the Asia-Pacific region through trade and investment liberalization, business facilitation, and economic and technical cooperation.

  14. 78 FR 27365 - North Pacific Fishery Management Council; Public Meetings

    Science.gov (United States)

    2013-05-10

    ... items include: Receive the report on the 2013 performance evaluation; review the electronic monitoring... Pacific Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS.... SUMMARY: The North Pacific Fishery Management Council's (Council) Observer Advisory Committee (OAC) will...

  15. 78 FR 47675 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-08-06

    ... Pacific Fishery Management Council's (Pacific Council) Ad Hoc Groundfish Electronic Monitoring Committee and Ad Hoc Trawl Groundfish Electronic Monitoring Technical Advisory Committee (GEM Committees) will... meeting is to discuss and develop potential alternatives for electronic monitoring (EM) for vessels...

  16. 78 FR 77659 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-12-24

    ... Pacific Fishery Management Council's (Pacific Council) Ad Hoc Trawl Groundfish Electronic Monitoring... further analysis a range of alternatives for electronic monitoring (EM) of the West Coast groundfish trawl... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National...

  17. 78 FR 69649 - North Pacific Fishery Management Council; Public Meetings

    Science.gov (United States)

    2013-11-20

    ... Permit (EFP) for electronic Monitoring (T); Individual Fishing Quota (IFQ) Implementation Committee... Pacific Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS.... SUMMARY: The North Pacific Fishery Management Council (Council) and its advisory committees will hold...

  18. Pacific Albacore Troll and Pole-and-line Fisheries

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The North Pacific and South Pacific Albacore Troll and Pole-and-line Fisheries project contains landings, logbooks, and size composition data from U.S.A. troll and...

  19. 78 FR 70283 - Pacific Fishery Management Council; Online Webinar

    Science.gov (United States)

    2013-11-25

    ... Fishery Management Council; Online Webinar AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of online webinar. SUMMARY: The Pacific Fishery Management Council's (Pacific Council's) Scientific and Statistical Committee (SSC...

  20. 78 FR 25956 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-05-03

    ... National Oceanic and Atmospheric Administration RIN 0648-XC652 Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ] ACTION: Notice, public meeting. SUMMARY: The Pacific Fishery Management Council...

  1. 78 FR 54239 - North Pacific Fishery Management Council; Public Meetings

    Science.gov (United States)

    2013-09-03

    ... National Oceanic and Atmospheric Administration RIN 0648-XC845 North Pacific Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of public meetings. SUMMARY: The North Pacific Fishery Management...

  2. 78 FR 25955 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-05-03

    ... National Oceanic and Atmospheric Administration RIN 0648-XC657 Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice; public meeting. SUMMARY: The Pacific Fishery Management Council's...

  3. 77 FR 58527 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-09-21

    ... National Oceanic and Atmospheric Administration RIN 0648-XC248 Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of a public meeting. SUMMARY: The Pacific Fishery Management Council...

  4. 78 FR 54240 - North Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-09-03

    ... National Oceanic and Atmospheric Administration RIN 0648-XC844 North Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of a public meeting. SUMMARY: The North Pacific Fishery...

  5. 78 FR 2371 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-01-11

    ... National Oceanic and Atmospheric Administration RIN 0648-XC436 Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice, public meeting. SUMMARY: The Pacific Fishery Management Council...

  6. 77 FR 31327 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-05-25

    ... National Oceanic and Atmospheric Administration RIN 0648-XC039 Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of public meetings. SUMMARY: The Pacific Fishery Management Council's...

  7. 77 FR 67633 - North Pacific Fishery Management Council; Public Meetings

    Science.gov (United States)

    2012-11-13

    ... National Oceanic and Atmospheric Administration RIN 0648-XC349 North Pacific Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of public meetings. SUMMARY: The North Pacific Fishery Management...

  8. 77 FR 65535 - North Pacific Fishery Management Council; Public Meetings

    Science.gov (United States)

    2012-10-29

    ... National Oceanic and Atmospheric Administration RIN 0648-XC314 North Pacific Fishery Management Council; Public Meetings AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice of public meetings. SUMMARY: The North Pacific Fishery Management...

  9. AFSC/REFM: Pacific cod Localized Depletion Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data from Localized Depletion study for Pacific cod 2001-2005. Study was conducted using cod pot gear to measure localized abundance of Pacific cod inside and...

  10. Infant Mortality and Native Hawaiians/Pacific Islanders

    Science.gov (United States)

    ... Hawaiian/Other Pacific Islander > Infant Health & Mortality Infant Mortality and Native Hawaiians/Pacific Islanders While the overall ... data for this ethnic group is limited. Infant Mortality Rate Infant mortality rate per 1,000 live ...

  11. CRED Reson 8101 multibeam backscatter data of Baker Island, Pacific Remote Island Areas, Central Pacific in netCDF format

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Multibeam backscatter imagery extracted from gridded bathymetry of the shelf and slope environments of Baker Island, Pacific Island Areas, Central Pacific. These...

  12. CRED Reson 8101 multibeam backscatter data of Howland Island, Pacific Remote Island Areas, Central Pacific in netCDF format

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Multibeam backscatter imagery extracted from gridded bathymetry of the shelf and slope environments of Howland Island, Pacific Island Areas, Central Pacific. These...

  13. CRED 40 m Gridded bathymetry of Howland Island, Pacific Remote Island Areas, Central Pacific (Arc ASCII Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (40 m cell size) bathymetry of the shelf and slope environments of Howland Island, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...

  14. CRED 5 m Gridded bathymetry of Palmyra Atoll, Pacific Remote Island Areas, Central Pacific (Arc ASCII Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (5 m cell size) bathymetry of the lagoon, shelf and slope environments of Palmyra Atoll, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...

  15. CRED 5 m Gridded bathymetry of Johnston Atoll, Pacific Remote Island Areas, Central Pacific (Arc ASCII Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded bathymetry (5 m cell size) of the shelf and slope environments of Johnston Atoll, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...

  16. CRED 5 m Gridded bathymetry of Baker Island, Pacific Remote Island Areas, Central Pacific (Arc ASCII Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (5 m cell size) bathymetry of the shelf and slope environments of Baker Island, Pacific Remote Isand Areas, Central Pacific. Almost complete bottom coverage...

  17. CRED 5 m Gridded bathymetry of Palmyra Atoll, Pacific Remote Island Areas, Central Pacific (NetCDF Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (5 m cell size) bathymetry of the lagoon, shelf and slope environments of Palmyra Atoll, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...

  18. CRED 40 m Gridded bathymetry of Baker Island, Pacific Remote Island Areas, Central Pacific (Arc ASCII Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (40 m cell size) bathymetry of the shelf and slope environments of Baker Island, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...

  19. CRED 5 m Gridded bathymetry of Baker Island, Pacific Remote Island Areas, Central Pacific (NetCDF Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (5 m cell size) bathymetry of the shelf and slope environments of Baker Island, Pacific Remote Island Areas, Central Pacific. Almost complete bottom coverage...

  20. CRED 40 m Gridded bathymetry of Baker Island, Pacific Remote Island Areas, Central Pacific (NetCDF Format)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded (40 m cell size) bathymetry of the shelf and slope environments of Baker Island, Pacific Remote Island Areas, Central Pacific. Almost complete bottom...