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Sample records for ancestral pacific gondwana

  1. A tectonic reconstruction of accreted terranes along the paleo-Pacific margin of Gondwana

    Science.gov (United States)

    Bammel, Brandon

    The southern oceanic margin of Gondwana was nearly 40,000 km long or 24,854.8 miles. The southern margin was the result of the Terra Australis orogen. Spanning 18,000 km or 11,184.7 miles and is proposed as one of the largest and longest lived orogens in Earth history. The paleo-Pacific margin of Gondwana consisted of segments of the Australian-Antarctic craton, southern South America (modern Argentina and Chile), southern South Africa, Marie Byrdland, New Zealand and its adjacent continental shelf, the Ellsworth Mountains, and the Transantarctic Mountains. The process of terrane accretion has played a substantial part in the assembly of the continents as they look today. The paleo-Pacific margin of Gondwana was an active region of terrane accretion from the Neoproterozoic to the Late Mesozoic. This research study examines the accretion of terranes across the paleo-Pacific Gondwana margin to provide a comprehensive reconstruction. A paleogeographic basemap was created using PALEOMAP Project maps and the geology data was provided by the School of Geoscience from the University of Witwatersrand of South Africa. Location and data analyzed for terranes were collected building a PDF library of journal articles across numerous geological publications.

  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. 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

  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. 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

  6. Petrologic Aspects of Seamount and Guyot Volcanism on the Ancestral Mesozoic Pacific Plate: a Review

    Science.gov (United States)

    Natland, J. H.

    2007-12-01

    Hundreds of large seamounts and guyots are widely scattered almost in a "shotgun-blast" arrangement in an area about the size of the United States west of the Mississippi River on the Mesozoic Pacific plate between the Mariana Trench and the Gilbert Islands. Most of these formed between ~160-100 Ma while the Pacific plate was surrounded by spreading ridges and growing outward in all directions. There is little to no indication that the seamounts and guyots formed along linear seamount chains; existing radiometric-age data show no age progressions. The volcanoes appear to have formed in response to a uniform stress configuration across the plate, which was either not moving or moving very slowly at the time (1, 2), much like the modern Antarctic plate. When the growing plate started to encounter subduction systems in the western Pacific at ~90 Ma, consistent stress patterns began to develop, and the broad linear Gilbert and Line volcanic ridge systems began to form. Even then, however, considerable overlapping of volcanism occurred, and only the most general age progressions are evident in existing data. Petrologic data from samples obtained from dozens of volcanic summits by dredging and beneath several carbonate platforms by drilling reveal considerable diversity in development of differentiated alkalic magmatic lineages rooted in diverse parental basaltic rocks. These include transitional, alkalic and basanitic compositions, with differentiates of hawaiite, mugearite, trachyte and one phonolite. Many of the basaltic rocks are partly to significantly transformed by alteration under oxidative conditions (dredged rocks) and both oxidative and non-oxidative conditions (drilled rocks). This can make estimations of mantle geochemical provenance difficult. Nevertheless, the province has been linked by backtracking techniques to the modern SOPITA region of the South Pacific (3), and its rocks show enrichments in trace elements and isotopic characteristics similar to

  7. Mesozoic tectonics of the Otway Basin region: The legacy of Gondwana and the active Pacific margin: a review and ongoing research

    Energy Technology Data Exchange (ETDEWEB)

    Hill, K.A. [Monash Univ., Clayton, VIC (Australia). Department of Earth Sciences; Finlayson, D.M. [Australian Geological Survey Organisation, Canberra, ACT (Australia); Hill, K.C. [La Trobe Univ., Bundoora, VIC (Australia). School of Earth Sciences; Cooper, G.T. [Monash Univ., Clayton, VIC (Australia). Department of Earth Sciences

    1995-12-31

    Recent plate tectonic models for SE Australia and the formerly contiguous parts of Gondwana are reviewed in this paper in order to assess the Mesozoic evolution of the Otway Basin. Research around the Otway Basin is summarised to demonstrate how the application of new technology can address some of the outstanding questions regarding the Basin`s evolution on local to lithospheric scales. The geometry and geology of Australia`s southern margin are compared with Atlantic rift-drift margins to provide analogues for tectonics and hydrocarbon exploration in the Otway Basin. At least two stages of rifting were found to be evident in the Cretaceous and in the deep structure of the Otway basin. These are Early Cretaceous rifting which is manifested in numerous half-graben and accommodation zones, and Late Cretaceous rifting in the deep seismic data seaward of the Tartwaup, Timboon and Sorell fault zones. Major offsets of the spreading axis during break up, at the Tasman and Spencer Fracture Zones were probably controlled by the location of Paleozoic terrace boundaries. The Tasman Fracture System was reactivated during break-up, with considerable uplift and denudation of the Bass failed rift to the east, which controlled Otway Basin facies distribution. Paleozoic structures also had a significant effect in determining the half graben orientations within a general N-S extensional regime during early Cretaceous rifting. The late Cretaceous second stage of rifting, seaward of the Tartwaup, Timboon and Sorell fault zones, left stable failed rift margin to the north, but the attenuated lithosphere of the Otway-Sorell microplate to the south records repeated extension that led to continental separation and may be part of an Antarctic upper plate. 1 table. 16 figs., 4 photos., refs.

  8. STAGE MODEL FOR GONDWANA ASSEMBLY

    African Journals Online (AJOL)

    the Eastern Granulites, the Kitumbi rocks occur as small enclaves ... out of collision of India, Madagascar, parts of Easten Antarctica and the Kalahari craton (IMSLEK ... Hepworth (1972) describes other granulite occurrences in the western and central parts of ..... of Gondwana. In: A. Kroner (ed) Precambrian Plate Tectonics,.

  9. 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.

  10. 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.

  11. 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.

  12. From Rodinia to Gondwana : supercontinent evolution in the Transantarctic Mountains

    International Nuclear Information System (INIS)

    Goodge, J.W.

    2002-01-01

    The Transantarctic Mountains provide a cryptic but important record of Proterozoic and Early Paleozoic supercontinent history, including Rodinian assembly, Rodinian breakup, transition from a drifting to subducting margin, and active plate-margin activity during Gondwanan assembly. A linkage between Laurentia and East Antarctica as part of Neoproterozoic Rodinia is plausible, based on isotopic data from rare exposures of crystalline basement in the Transantarctic Mountains. However, testing of paleogeographic details is difficult because the crustal structure of the East Antarctic shield is poorly known along much of its perimeter and because we lack well-dated Proterozoic paleomagnetic poles. The timing of Rodinian breakup is poorly constrained globally, yet local mafic magmatism of 800-650 Ma age provides the best evidence in the Transantarctic Mountains for Late Neoproterozoic crustal extension and possible rifting. Still uncertain are the position of the rift margin, the geometry of rifting, the extent of crustal thinning, the extent of rift-margin sedimentation, the location of possible transform offset, and the influence of these structural patterns on later orogenesis. A transformation from drifting to active subducting mode is inferred for the Late Neoproterozoic, but the nature and specific timing of this event are unknown. The Vendian-Early Paleozoic Ross Orogen reflects convergent-margin activity associated temporally, if not causally, with the consolidation of Gondwana. Inception of a convergent Gondwana margin is signalled by the earliest Ross granitoids at c. 560 Ma and may be reflected in early structural inversion of craton-margin sedimentary succession. Protracted Ross tectonism between 560 and 480 Ma involved episodic deformation, calc-alkaline magmatism, and syn-orogenic deposition of arc-derived detritus in a sinistral-transpressive, continental-margin arc setting. Sedimentary provenance in siliciclastic rocks appears to have shifted by late

  13. 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.

  14. 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 ...

  15. 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.

  16. 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...

  17. 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 (...

  18. 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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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 Tasma...... 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...... 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. Trace element abundances in clinopyroxene are highly heterogeneous and vary from LREE-enriched, relatively flat and MORB...

  20. 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)

  1. 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.

  2. 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.

  3. Resolution effects in reconstructing ancestral genomes.

    Science.gov (United States)

    Zheng, Chunfang; Jeong, Yuji; Turcotte, Madisyn Gabrielle; Sankoff, David

    2018-05-09

    The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

  4. Re-evaluating Gondwana breakup: Magmatism, movement and microplates

    Science.gov (United States)

    Ferraccioli, F.; Jordan, T. A.

    2017-12-01

    Gondwana breakup is thought to have initiated in the Early- to Mid-Jurassic between South Africa and East Antarctica. The critical stages of continental extension and magmatism which preceded breakup remain controversial. It is agreed that extensive magmatism struck this region 180 Ma, and that significant extension occurred in the Weddell Sea Rift System (WSRS) and around the Falkland Plateau. However, the timing and volume of magmatism, extent and mechanism of continental extension, and the links with the wider plate circuit are poorly constrained. Jordan et al (Gondwana Research 2017) recently proposed a two-stage model for the formation of the WSRS: initial extension and movement of the Ellsworth Whitmore Mountains microplate along the margin of the East Antarctic continent on a sinistral strike slip fault zone, followed by transtensional extension closer to the continental margin. Here we identify some key questions raised by the two-stage model, and identify regions where these can be tested. Firstly, is the magmatism inferred to have facilitated extension in the WSRS directly linked to the onshore Dufek Intrusion? This question relates to both the uncertainty in the volume of magmatism and potentially the timing of extension, and requires improved resolution of aeromagnetic data in the eastern WSRS. Secondly, did extension in the WSRS terminate against a single strike slip fault zone or into a distributed fault system? By integrating new and existing aeromagnetic data along the margin of East Antarctica we evaluate the possibility of a distributed shear zone penetrating the East Antarctic continent, and identify critical remaining data gaps. Finally we question how extension within the WSRS could fit into the wider plate circuit. By integrating the two-stage model into Gplates reconstructions we identify regions of overlap and areas where tracers of past plate motion could be identified.

  5. Plate motions, Gondwana dinosaurs, Noah's arks, beached Viking funeral ships, ghost ships, and landspans.

    Science.gov (United States)

    Jacobs, Louis L; Strganac, Christopher; Scotese, Christopher

    2011-03-01

    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.

  6. 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.

  7. 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

  8. 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)

  9. ^<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.

  10. 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.

  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. Animal regeneration: ancestral character or evolutionary novelty?

    Science.gov (United States)

    Slack, Jonathan Mw

    2017-09-01

    An old question about regeneration is whether it is an ancestral character which is a general property of living matter, or whether it represents a set of specific adaptations to the different circumstances faced by different types of animal. In this review, some recent results on regeneration are assessed to see if they can throw any new light on this question. Evidence in favour of an ancestral character comes from the role of Wnt and bone morphogenetic protein signalling in controlling the pattern of whole-body regeneration in acoels, which are a basal group of bilaterian animals. On the other hand, there is some evidence for adaptive acquisition or maintenance of the regeneration of appendages based on the occurrence of severe non-lethal predation, the existence of some novel genes in regenerating organisms, and differences at the molecular level between apparently similar forms of regeneration. It is tentatively concluded that whole-body regeneration is an ancestral character although has been lost from most animal lineages. Appendage regeneration is more likely to represent a derived character resulting from many specific adaptations. © 2017 The Author.

  13. Gondwana Tales: an inquiry approach to plate tectonics

    Science.gov (United States)

    Domènech Casal, Jordi

    2014-05-01

    Plate tectonics and its effects on the constitution of seas and continents are key models in science education. Fossil evidences are usually taught in demostrative key when Wegener's discoverings about Pangea are introduced. In order to introduce inquiry-based science education (IBSE) approaches to this topic, we propose "Gondwana Tales", an activity where students are asked to use fossil data to reconstruct the geologic history of an imaginary planet. Grouped in independent teams, each team is furnished with stratigraphic columns from several sites containing faunistic successions of real organisms existing in the past in Earth. Students are told to reconstruct a model of the evolution of the continents, by making calculations of relative ages of the fossils, and relating each fossil to a geologic era. The different teams have incomplete and complementary information. After a first step where they have to propose a partial model based on incomplete data, each team receives a "visitor scientist" from another team, this implying an informal scientific communication event. This process is performed several times, engaging a discussion in each team and getting a final consensus model created by the whole class. Correct answer is not given to the students, even at the end of the activity, to keep the activity under the parameters of real scientific experience, where there is not a "correct answer" to compare. Instead of this, and following the IBSE standards, a reflection on the process is proposed to students. The lack of complete information and the need to collaborate are part of classroom dynamics focused to the understanding of the process of creation of the scientific knowledge. This activity is part of the C3 Project on Creation of Scientific Knowledge that is being applied in the school.

  14. Regional trend of coal metamorphism in the major Gondwana basins of India

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, A K; Alam, M M; Bunerjee, B

    1983-04-01

    The coal-bearing Gondwana sedimentaries are of great economic importance as they possess over 98% of coal resources of India. Within the Gondwana supergroup coal-bearing formations are confined in the Lower Gondwana sequence (Damuda group). The development of coal seams in the different basins were genetically related to the evolutionary pattern of each basin. The imprint of such diverse tectono-geomorphic conditions prevailing over the vast Peninsular Shield, and their regional impact in individual basins are well preserved in the different lithofacies of this thick-pile of sedimentary sequence. In fact constituting coal facies served as a sensitive recorder of the past episode enacted for long geological time span in each basin of the Gondwana grabens. In the present paper an attempt is made to incorporate the salient features of the operative processes in the major Gondwana basins with special reference to coal metamorphism. This has been done considering mass of analytical and sub-surface data available from the physico-chemical survey of coal seams of major coalfields, and extensive drilling operations carried out over the vast virgin tracts of important coalfields.

  15. 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.

  16. 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.

  17. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.

    Science.gov (United States)

    Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy

    2015-06-01

    Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist 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 which 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 relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. Copyright © 2015 by the Genetics Society of America.

  18. 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).

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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...

  7. 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.

  8. Ancestral Rocky Mountian Tectonics: A Sedimentary Record of Ancestral Front Range and Uncompahgre Exhumation

    Science.gov (United States)

    Smith, T. M.; Saylor, J. E.; Lapen, T. J.

    2015-12-01

    The Ancestral Rocky Mountains (ARM) encompass multiple crustal provinces with characteristic crystallization ages across the central and western US. Two driving mechanisms have been proposed to explain ARM deformation. (1) Ouachita-Marathon collision SE of the ARM uplifts has been linked to an E-to-W sequence of uplift and is consistent with proposed disruption of a larger Paradox-Central Colorado Trough Basin by exhumation of the Uncompahgre Uplift. Initial exhumation of the Amarillo-Wichita Uplift to the east would provide a unique ~530 Ma signal absent from source areas to the SW, and result in initial exhumation of the Ancestral Front Range. (2) Alternatively, deformation due to flat slab subduction along a hypothesized plate boundary to the SW suggests a SW-to-NE younging of exhumation. This hypothesis suggests a SW-derived Grenville signature, and would trigger uplift of the Uncompahgre first. We analyzed depositional environments, sediment dispersal patterns, and sediment and basement zircon U-Pb and (U-Th)/He ages in 3 locations in the Paradox Basin and Central Colorado Trough (CCT). The Paradox Basin exhibits an up-section transition in fluvial style that suggests a decrease in overbank stability and increased lateral migration. Similarly, the CCT records a long-term progradation of depositional environments from marginal marine to fluvial, indicating that sediment supply in both basins outpaced accommodation. Preliminary provenance results indicate little to no input from the Amarillo-Wichita uplift in either basin despite uniformly westward sediment dispersal systems in both basins. Results also show that the Uncompahgre Uplift was the source for sediment throughout Paradox Basin deposition. These observations are inconsistent with the predictions of scenario 1 above. Rather, they suggest either a synchronous response to tectonic stress across the ARM provinces or an SW-to-NE pattern of deformation.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

    Science.gov (United States)

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina

    2010-01-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle. PMID:21029545

  15. 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, ...

  16. 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.

  17. 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.

  18. 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

  19. Evidence of Middle Jurassic magmatism within the Seychelles microcontinent: Implications for the breakup of Gondwana

    Science.gov (United States)

    Shellnutt, J. G.; Lee, T.-Y.; Chiu, H.-Y.; Lee, Y.-H.; Wong, J.

    2015-12-01

    The breakup of East and West Gondwana occurred during the Jurassic, but the exact timing is uncertain due to the limited exposure of rocks suitable for radioisotopic dating. Trachytic rocks from Silhouette Island, Seychelles, yielded a range of zircon ages from Paleoproterozoic to Cenozoic. The 206Pb/238U age of the trachyte is 64.9 ± 1.6 Ma (Danian) but the majority of zircons yielded an age of 163.8 ± 1.8 Ma (Callovian) with a small subset yielding an age of 147.7 ± 4.5 Ma (Tithonian). The Hf isotopes of the Callovian (ɛHf(t) = +4.1 to +13.4) and Danian (ɛHf(t) = +1.9 to +7.1) zircons indicate that they were derived from moderately depleted mantle sources whereas the Tithonian zircons (ɛHf(t) = -7.0 to -7.3) were derived from an enriched source. The identification of middle Jurassic zircons indicates that rifting and magmatism were likely contemporaneous during the initial separation of East and West Gondwana.

  20. Episodic Jurassic to Lower Cretaceous intraplate compression in Central Patagonia during Gondwana breakup

    Science.gov (United States)

    Navarrete, César; Gianni, Guido; Echaurren, Andrés; Kingler, Federico Lince; Folguera, Andrés

    2016-12-01

    From Lower Jurassic to Lower Cretaceous, several intraplate compression events affected discrete sectors of Central Patagonia, under a general context of crustal extension associated with Gondwana breakup. This was demonstrated by means of 2D and 3D seismic and borehole data, which show partial inversion of Lower and Middle Jurassic extensional structures of the Chubut and Cañadón Asfalto basins, during the earliest stages of breakup. A comparison with surrounding areas in Patagonia, where similar Jurassic intraplate compression was described, allowed the discrimination of three discrete pulses of subtle compression (C1: ∼188-185 Ma; C2: ∼170-163; C3: ∼157-136? Ma). Interestingly, episodic intraplate compressional events are closely followed by high flux magmatic events linked to the westward expansion of the Karoo-Ferrar thermal anomaly, which impacted on the lithosphere of southwest Gondwana in Lower Jurassic. In addition, we determined the approximate direction of the main compressive strain (σ1) compatible with other Jurassic intraplate belts of South America. These observations led us to propose a linkage between a thermo mechanically weakened continental crust due to LIPs activity, changes in plate motions and ridge-push forces generated by the opening of the Weddell Sea, in order to explain intraplate shortening, interrupted while Karoo LIPs magmatic invigoration took place.

  1. 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.

  2. Nilonema gymnarchi Khalil, 1960 and N. senticosum (Baylis, 1922) (Nematoda: Dracunculoidea): Gondwana relicts?

    Science.gov (United States)

    Santos, Cláudia Portes; Gibson, David I

    2007-07-01

    Data-base searches of records of the helminth parasites of South American and African freshwater fishes revealed only two pairs of species from genera endemic to the two regions. One pair, species of the primitive amphilinid cestode genus Nesolecithus Dönges & Harder, 1966, has already been designated as likely Gondwana relicts. The second pair are the philometrid nematodes Nilonema gymnarchi Khalil, 1960 from Gymnarchus niloticus Cuvier (Gymnarchidae) in Africa and N. senticosum (Baylis, 1922) from the South American fish Arapaima gigas (Cuvier) (Arapaimidae). Both species are partly redescribed on the basis of light and scanning electron microscopical observations of the type-specimens, and their relationships are discussed. In view of the fact that both hosts are basal teleosts of the order Osteoglossiformes and they are the same two fish which harbour the amphilinid cestodes already indicated as Gondwana relics, the nematode pair is also deemed to be relictual. However, these species are suggested as being of limited potential value for calibrating a molecular clock.

  3. 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.

  4. Mississippian lamprophyre dikes in western Sierras Pampeanas, Argentina: Evidence of transtensional tectonics along the SW margin of Gondwana

    Science.gov (United States)

    Martina, Federico; Canelo, Horacio N.; Dávila, Federico M.; de Hollanda, María Helena M.; Teixeira, Wilson

    2018-04-01

    In the Famatina range, Sierras Pampeanas of Argentina (SW Gondwana), subvertical calc-alkaline lamprophyric dike swarms crop out through >300 km. The dikes cut Ordovician units with a prominent NW-SE trending and are covered by continental sedimentary successions of Pennsylvanian to Permian age. The dikes show a strong structural control associated with Riedel fault systems. Detailed field analysis suggested a ∼N-S opening direction oblique to the attitude of dike walls and a left-lateral transtensional tectonics during the emplacement. 40Ar/39Ar geochronology of a lamprophyric sample defined a crystallization age (plateau; whole rock) of 357.1 ± 7.1 Ma (MSWD = 2.3). Coetaneous ductile zones with dominant strike-slip motion, documented along western Argentina for >600 km, suggest a regional event in SW Gondwana during the Mississippian. We propose that this deformation was the result of the counterclockwise fast rotation of Gondwana between 365 and 345 Ma, when the Famatina range and western Argentina occupied a sub-polar position. A transform margin along SW Gondwana better explains our (and others) data rather than a subduction margin. This scenario is also consistent with the occurrence of A-type granites and normal-fault basins within the foreland as well as bimodal volcanics.

  5. Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

    Science.gov (United States)

    Holmes, Ian H

    2017-04-15

    Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  6. 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.

  7. 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.

  8. The ancestral selection graph under strong directional selection.

    Science.gov (United States)

    Pokalyuk, Cornelia; Pfaffelhuber, Peter

    2013-08-01

    The ancestral selection graph (ASG) was introduced by  Neuhauser and Krone (1997) in order to study populations of constant size which evolve under selection. Coalescence events, which occur at rate 1 for every pair of lines, lead to joint ancestry. In addition, splitting events in the ASG at rate α, the scaled selection coefficient, produce possible ancestors, such that the real ancestor depends on the ancestral alleles. Here, we use the ASG in the case without mutation in order to study fixation of a beneficial mutant. Using our main tool, a reversibility property of the ASG, we provide a new proof of the fact that a beneficial allele fixes roughly in time (2logα)/α if α is large. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. 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

  10. 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...

  11. 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...

  12. Infant and juvenile growth in ancestral Pueblo Indians.

    Science.gov (United States)

    Schillaci, Michael A; Nikitovic, Dejana; Akins, Nancy J; Tripp, Lianne; Palkovich, Ann M

    2011-06-01

    The present study examines patterns of infant and juvenile growth in a diachronic sample of ancestral Pueblo Indians (AD 1300-1680) from the American Southwest. An assessment of growth patterns is accompanied by an evaluation of pathological conditions often considered to be indicators of nutritional deficiencies and/or gastrointestinal infections. Growth patterns and the distribution of pathological conditions are interpreted relative to culturally relevant age categories defined by Puebloan rites of passage described in the ethnographic literature. A visual comparison of growth distance curves revealed that relative to a modern comparative group our sample of ancestral Pueblo infant and juveniles exhibited faltering growth beginning soon after birth to about 5 years of age. A comparison of curves describing growth relative to adult femoral length, however, indicated reduced growth occurring later, by around 2 years of age. Similar to previous studies, we observed a high proportion of nonsurvivors exhibiting porotic cranial lesions during the first 2 years of life. Contrary to expectations, infants and juveniles without evidence of porotic cranial lesions exhibited a higher degree of stunting. Our study is generally consistent with previous research reporting poor health and high mortality for ancestral Pueblo Indian infants and juveniles. Through use of a culturally relevant context defining childhood, we argue that the observed poor health and high mortality in our sample occur before the important transition from young to older child and the concomitant initial incorporation into tribal ritual organization. Copyright © 2011 Wiley-Liss, Inc.

  13. 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.

  14. 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.

  15. A stem acrodontan lizard in the Cretaceous of Brazil revises early lizard evolution in Gondwana.

    Science.gov (United States)

    Simões, Tiago R; Wilner, Everton; Caldwell, Michael W; Weinschütz, Luiz C; Kellner, Alexander W A

    2015-08-26

    Iguanians are one of the most diverse groups of extant lizards (>1,700 species) with acrodontan iguanians dominating in the Old World, and non-acrodontans in the New World. A new lizard species presented herein is the first acrodontan from South America, indicating acrodontans radiated throughout Gondwana much earlier than previously thought, and that some of the first South American lizards were more closely related to their counterparts in Africa and Asia than to the modern fauna of South America. This suggests both groups of iguanians achieved a worldwide distribution before the final breakup of Pangaea. At some point, non-acrodontans replaced acrodontans and became the only iguanians in the Americas, contrary to what happened on most of the Old World. This discovery also expands the diversity of Cretaceous lizards in South America, which with recent findings, suggests sphenodontians were not the dominant lepidosaurs in that continent as previously hypothesized.

  16. 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

  17. Record of Lower Gondwana megafloral assemblage from Lower Kamthi Formation of Ib River Coalfield, Orissa, India

    Energy Technology Data Exchange (ETDEWEB)

    Goswami, S. [Birbal Sahni Institute of Paleobotany, Lucknow (India)

    2006-03-15

    Recent investigations carried out in the Ib River Coalfield, Mahanadi Master Basin, Orissa, identified some fossiliferous beds in the Lower Gondwana deposits. Two exposures of the Lower Kamthi Formation yielded diverse and abundant plant remains, which include Neomariopteris, Vertebraria, and a scale leaf along with 14 Glossopteris species otherwise mapped as Barren Measures and Upper Kamthi formations. Glossopteris indica dominates the flora (22.78%) followed by G. communis (17.72%) and G. browniana (13.92%). Based on megafloral assemblages, different beds exposed at Gopalpur and Laxamanpur Pahar are assigned here to the Lower Kamthi Formation (Late Permian). The floristic composition suggests that a warm and humid climate prevailed during the Late Permian. The status of the Kamthi Formation in the Ib River Coalfield has been redefined in the present study.

  18. 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.

  19. Ancestral Variations in the Shape and Size of the Zygoma.

    Science.gov (United States)

    Oettlé, Anna C; Demeter, Fabrice P; L'abbé, Ericka N

    2017-01-01

    The variable development of the zygoma, dictating its shape and size variations among ancestral groups, has important clinical implications and valuable anthropological and evolutionary inferences. The purpose of the study was to review the literature regarding the variations in the zygoma with ancestry. Ancestral variation in the zygoma reflects genetic variations because of genetic drift as well as natural selection and epigenetic changes to adapt to diet and climate variations with possible intensification by isolation. Prominence of the zygoma, zygomaxillary tuberosity, and malar tubercle have been associated with Eastern Asian populations in whom these features intensified. Prominence of the zygoma is also associated with groups from Eastern Europe and the rest of Asia. Diffusion of these traits occurred across the Behring Sea to the Arctic areas and to North and South America. The greatest zygomatic projections are exhibited in Arctic groups as an adaptation to extreme cold conditions, while Native South American groups also present with other features of facial robusticity. Groups from Australia, Malaysia, and Oceania show prominence of the zygoma to a certain extent, possibly because of archaic occupations by undifferentiated Southeast Asian populations. More recent interactions with Chinese groups might explain the prominent cheekbones noted in certain South African groups. Many deductions regarding evolutionary processes and diversifications of early groups have been made. Cognisance of these ancestral variations also have implications for forensic anthropological assessments as well as plastic and reconstructive surgery. More studies are needed to improve accuracy of forensic anthropological identification techniques. Anat Rec, 300:196-208, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. 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.

  1. Reconstruction of ancestral RNA sequences under multiple structural constraints

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    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 .

  2. 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 .

  3. 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.

  4. Late Cambrian magmatic arc activity in peri-Gondwana: geochemical evidence from the Basal Allochthonous Units of NW Iberia

    Energy Technology Data Exchange (ETDEWEB)

    Andonaegui, P.; Abati, J.; Díez-Fernández, R.

    2017-07-01

    The North African section of the Gondwana margin was the site of voluminous, arc-related magmatism during the Late Neoproterozoic (Avalonian–Cadomian orogen). The lower (and older) metasedimentary sequence that constitutes the Basal Units of the Allochthonous Complexes of NW Iberia was deposited in that setting. In these units, sedimentation was followed by the intrusion of tonalites and granodiorites in the late Cambrian (ca. 493–489Ma). In the Late Paleozoic, the collision of Gondwana and Laurussia (Variscan orogeny) deformed and metamorphosed the whole ensemble. New whole rock geochemical analysis performed in seven samples of metatonalites and fourteen samples of metagranodiorites are characterized by: i) slight enrichment in incompatible elements (Rb, Ba, Th, U), ii) negative anomalies in Nb, Ta, P, and Ti, and iii) negative anomalies in Eu. These chemical features are in agreement with a subduction-related setting for the genesis of both types of magma, which is also supported by chemical discrimination using tectonic setting diagrams. Positive anomalies of Pb suggest a crustal component. The new geochemical data reveal that the convergent orogen that ruled the paleogeography of the Gondwana periphery during the Neoproterozoic (Cadomian orogen) remained active bey.

  5. 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.

  6. 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.

  7. 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

  8. Computational analysis and functional expression of ancestral copepod luciferase.

    Science.gov (United States)

    Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

    2013-10-10

    We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

  9. Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity

    Science.gov (United States)

    2013-01-01

    Background Ancestral environmental exposures to a variety of environmental factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The present work examined the potential transgenerational actions of the insecticide dichlorodiphenyltrichloroethane (DDT) on obesity and associated disease. Methods Outbred gestating female rats were transiently exposed to a vehicle control or DDT and the F1 generation offspring bred to generate the F2 generation and F2 generation bred to generate the F3 generation. The F1 and F3 generation control and DDT lineage rats were aged and various pathologies investigated. The F3 generation male sperm were collected to investigate methylation between the control and DDT lineage male sperm. Results The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats were not found to develop obesity. The F1 generation DDT lineage animals did develop kidney disease, prostate disease, ovary disease and tumor development as adults. Interestingly, the F3 generation (great grand-offspring) had over 50% of males and females develop obesity. Several transgenerational diseases previously shown to be associated with metabolic syndrome and obesity were observed in the testis, ovary and kidney. The transgenerational transmission of disease was through both female (egg) and male (sperm) germlines. F3 generation sperm epimutations, differential DNA methylation regions (DMR), induced by DDT were identified. A number of the genes associated with the DMR have previously been shown to be associated with obesity. Conclusions Observations indicate ancestral exposure to DDT can promote obesity and associated disease transgenerationally. The etiology of disease such as obesity may be in part due to environmentally induced epigenetic transgenerational inheritance. PMID:24228800

  10. Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

    Science.gov (United States)

    Legendre, Lucas J; Guénard, Guillaume; Botha-Brink, Jennifer; Cubo, Jorge

    2016-11-01

    Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Upper Carboniferous retroarc volcanism with submarine and subaerial facies at the western Gondwana margin of Argentina

    Science.gov (United States)

    Koukharsky, M.; Kleiman, L.; Etcheverría, M.; Quenardelle, S.; Bercowski, F.

    2009-04-01

    During Late Carboniferous times a continental magmatic arc developed at the western margin of Gondwana in South America, as several marine sedimentary basins were formed at the same time in the retroarc region. North of 33°S, at Cordón Agua del Jagüel, Precordillera of Mendoza, Argentina, a volcanic sequence crops out which was emplaced in a submarine environment with some subaerial exposures, and it is intercalated in marine sediments of Agua del Jagüel Formation, which fills of one of these retroarc basins. This paper presents, for the first time, a facies analyses together with geochemical and isotopic data of this volcanic suite, suggesting its deposition in an ensialic retroarc marine basin. The volcanic succession comprises debris flows with either sedimentary or volcanic fragments, base surge, resedimented massive and laminated dacitic-andesitic hyaloclastite, pillow lava, basic hyaloclastite and dacitic-andesitic lavas and hyaloclastite facies. Its composition is bimodal, either basaltic or dacitic-andesitic. The geochemistry data indicate a subalkaline, low K calk-alkaline and metaluminous affinity. The geochemistry of the basalts points to an origin of the magmas from a depleted mantle source with some crustal contamination. Conversely, the geochemistry of the dacites-andesites shows an important participation of both crustal components and subduction related fluids. A different magmatic source for the basalts than for the dacites-andesites is also supported by Sr and Nd isotopic initial ratios and Nd model ages. The characteristics of this magmatic suite suggest its emplacement in an extensional setting probably associated with the presence of a steepened subduction zone at this latitude during Upper Carboniferous times.

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

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    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.

  13. Electrical and gamma-ray logging in Gondwana and Tertiary coal fields of India

    International Nuclear Information System (INIS)

    Kayal, J.R.

    1979-01-01

    Electrical and gamma-ray logging have been very useful for identification and accurate determination of depth and thickness of coal seams in Gondwana and Tertiary coal fields of India. The characteristic resistance/resistivity peaks of coal seams in a particular area have been correlated, thus providing a picture of the subsurface structure. Physico-chemical properties of layers or sections of coal seams are responsive to electrical logs. Gamma-ray logs are found to be very useful for correlation and have sometimes been the only logs used in cased and dry boreholes for detection of coal seams. Under favourable conditions a single-point resistance log reveals a detailed picture of the formations and picks up thin coal seams as well as thin shale bands within the coal seam. But in some cases it fails to differentiate between coal and sandstone beds in spite of high contrast in true resistivities. Multi-electrode long-normal and lateral logs are found to be more useful in differentiating such formations because of higher penetration in this system. Long-normal and lateral curves can also be used to determine true resisvity of the formation. But long normal logs cannot pick up thin coal bands and/or thin shale partings within the coal seam because of the 'adjacent bed effect'. Gamma-ray logging can be done in both cased and uncased bore-holes or even in a dry borehole but its resolution for shaly coal or thin coal is not sufficient. Combined study has been found to yield the best results. (Auth.)

  14. 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.

  15. 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

  16. 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.

  17. Inference of Ancestral Recombination Graphs through Topological Data Analysis

    Science.gov (United States)

    Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

    2016-01-01

    The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

  18. Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

    Science.gov (United States)

    Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

    2017-03-01

    Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. 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.

  20. 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

  1. Escaping social-ecological traps through tribal stewardship on national forest lands in the Pacific Northwest, United States of America

    Science.gov (United States)

    Jonathan W. Long; Frank K. Lake

    2018-01-01

    Tribal communities in the Pacific Northwest of the United States of America (USA) have long-standing relationships to ancestral lands now managed by federal land management agencies. In recent decades, federal and state governments have increasingly recognized tribal rights to resources on public lands and to participate in their management. In support of a new...

  2. Ancestral gene reconstruction and synthesis of ancient rhodopsins in the laboratory.

    Science.gov (United States)

    Chang, Belinda S W

    2003-08-01

    Laboratory synthesis of ancestral proteins offers an intriguing opportunity to study the past directly. The development of Bayesian methods to infer ancestral sequences, combined with advances in models of molecular evolution, and synthetic gene technology make this an increasingly promising approach in evolutionary studies of molecular function. Visual pigments form the first step in the biochemical cascade of events in the retina in all animals known to possess visual capabilities. In vertebrates, the necessity of spanning a dynamic range of light intensities of many orders of magnitude has given rise to two different types of photoreceptors, rods specialized for dim-light conditions, and cones for daylight and color vision. These photoreceptors contain different types of visual pigment genes. Reviewed here are methods of inferring ancestral sequences, chemical synthesis of artificial ancestral genes in the laboratory, and applications to the evolution of vertebrate visual systems and the experimental recreation of an archosaur rod visual pigment. The ancestral archosaurs gave rise to several notable lineages of diapsid reptiles, including the birds and the dinosaurs, and would have existed over 200 MYA. What little is known of their physiology comes from fossil remains, and inference based on the biology of their living descendants. Despite its age, an ancestral archosaur pigment was successfully recreated in the lab, and showed interesting properties of its wavelength sensitivity that may have implications for the visual capabilities of the ancestral archosaurs in dim light.

  3. 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.

  4. 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.

  5. 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.

  6. The Microcephalin Ancestral Allele in a Neanderthal Individual

    Science.gov (United States)

    Lari, Martina; Rizzi, Ermanno; Milani, Lucio; Corti, Giorgio; Balsamo, Carlotta; Vai, Stefania; Catalano, Giulio; Pilli, Elena; Longo, Laura; Condemi, Silvana; Giunti, Paolo; Hänni, Catherine; De Bellis, Gianluca; Orlando, Ludovic; Barbujani, Guido; Caramelli, David

    2010-01-01

    Background The high frequency (around 0.70 worlwide) 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. PMID:20498832

  7. 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

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

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    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 assist with

  9. 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.

  10. 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.

  11. Tectonostratigraphic terranes of the frontier circum-Pacific region

    Energy Technology Data Exchange (ETDEWEB)

    Howell, D.G.; Jones, D.L.; Schermer, E.R.

    1983-03-01

    Many major exploration frontiers around the Pacific are in regions where complex geologic relations reflect plate-tectonic processes, crustal mobility, and accretion of exotic terranes. The destruction of the proto-Pacific ocean (Panthalassa) involved accretion of terranes to cratonal regions such as Gondwana and Laurasia. Terranes in southwestern New Zealand and eastern Antarctica were also probably accreted during the Paleozoic. The southern margin of Siberia, extending into China, underwent a protracted period of accretion from the late Precambrian through the early Mesozoic. Mid-Paleozoic accretion is reflected in the Innuitian foldbelt of the Arctic Ocean, the Black Clastic unit of the northern Rocky Mountains, and the Antler orogeny of the western US cordillera. The Mesozoic breakup of Pangaea and the acceleration of subduction aided in the rifting and dispersal of terranes from equatorial paleolatitudes. Fragments of these terranes now compose much of the continental margins of the Pacific basin, including New Zealand, Indochina, southern China, southeast Siberia, the North American cordillera, and South America. Some terranes are presently being further fragmented by post-accretionary dispersion processes such as strike-slip faulting in western North America and Japan. Although the character and distribution of terranes in the western US are fairly well documented, details are needed for other terranes around the Pacific basin. Interpretation of structure and stratigraphy at depth will be aided by more data on the timing of accretion and the nature of deformation associated with accretion and dispersion. Such data are needed for further define specific exploration targets in the circum-Pacific region.

  12. 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

  13. 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

  14. Provenance of Permian-Triassic Gondwana Sequence Units Accreted to the Banda Arc: Constraints from U/Pb and Hf Analysis of Zircons and Igneous Geochemistry

    Science.gov (United States)

    Flores, J. A.; Spencer, C. J.; Harris, R. A.; Hoiland, C.

    2011-12-01

    Analysis of zircons from Australian affinity Permo-Triassic units of the Timor region yield age distributions with large peaks at 230-400 Ma and 1750-1900 Ma (n=435). Similar zircon age peaks are also found in rocks from NE Australia and the eastern Cimmerian block. It is likely that these terranes, which are now widely separated, were once part of the northern edge of Gondwana near what is now the NW margin of Australia. The Cimmerian Block was removed from Gondwana during Early Permian rifting and initiation of the Neo-Tethys Ocean. Hf analysis of zircon from the Aileu Complex in Timor and Kisar shows bimodal (juvenial and evolved) magmatism in the Gondwana Sequence of NW Australia at ~300 Ma. The magmatic event produced basalt with rift valley and ocean floor geochemical affinities, and rhyolite. Similar rock types and isotopic signatures are also found in Permo-Triassic igneous units throughout the Cimmerian continental block. The part of the Cimmerian Block with zircon distributions most like the Gondwana Sequence of NW Australia is the terranes of northern Tibet and Malaysia. The large 1750-1900 Ma zircon peak is much more wide spread, and appears in terranes from Baoshan (SW China) to Borneo. The Permo-Triassic rocks of the Timor region fill syn-rift intracratonic basins that successfully rifted in the Jurassic to form the NW margin of Australia. This passive continental margin first entered the Sunda Trench in the Timor region at around 8 Ma causing the Permo-Triassic rocks to accrete to the edge of the Asian Plate and emerge as a series of mountainous islands in the young collision zone. Eventually, the Australian continental margin will collide with the southern edge of the Asian plate and these Gondwana terranes will rejoin. However, it may be difficult to reconstruct the various ventures of they made over the past 300 Ma.

  15. 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.

  16. The breakup of East Gondwana: Assimilating constraints from Cretaceous ocean basins around India into a best-fit tectonic model

    Science.gov (United States)

    Gibbons, Ana D.; Whittaker, Joanne M.; Müller, R. Dietmar

    2013-03-01

    models for the Cretaceous seafloor-spreading history of East Gondwana result in unlikely tectonic scenarios for at least one of the plate boundaries involved and/or violate particular constraints from at least one of the associated ocean basins. We link East Gondwana spreading corridors by integrating magnetic and gravity anomaly data from the Enderby Basin off East Antarctica within a regional plate kinematic framework to identify a conjugate series of east-west-trending magnetic anomalies, M4 to M0 ( 126.7-120.4 Ma). The mid-ocean ridge that separated Greater India from Australia-Antarctica propagated from north to south, starting at 136 Ma northwest of Australia, and reached the southern tip of India at 126 Ma. Seafloor spreading in the Enderby Basin was abandoned at 115 Ma, when a ridge jump transferred the Elan Bank and South Kerguelen Plateau to the Antarctic plate. Our revised plate kinematic model helps resolve the problem of successive two-way strike-slip motion between Madagascar and India seen in many previously published reconstructions and also suggests that seafloor spreading between them progressed from south to north from 94 to 84 Ma. This timing is essential for tectonic flow lines to match the curved fracture zones of the Wharton and Enderby basins, as Greater India gradually began to unzip from Madagascar from 100 Ma. In our model, the 85-East Ridge and Kerguelen Fracture Zone formed as conjugate flanks of a "leaky" transform fault following the 100 Ma spreading reorganization. Our model also identifies the Afanasy Nikitin Seamounts as products of the Conrad Rise hotspot.

  17. The Permo-Triassic uranium deposits of Southern Africa within the African-South American Gondwana framework

    International Nuclear Information System (INIS)

    Toens, P.D.; Le Roux, J.P.

    1981-01-01

    The discovery of uranium in the Permo-Triassic Gondwana in South America and Africa has served to highlight the intercontinental correlations. The purpose here is to examine the uranium deposits of Southern Africa in the light of the similarities that exist between the various Gondwana formations of the two continents. This hopefully will assist in gaining some understanding of the genesis of the uranium mineralization and the sedimentary environment in which such deposits are likely to occur. Between the Upper Carboniferous and the Jurassic a tectono-sedimentary terrain existed within Gondwanaland in which broadly similar conditions prevailed over large areas, thus producing numerous partly disconnected basins practically identical in character. The basal formations are composed of glacial tillite followed by a succession of sandstone and shale which attains a thickness of up to 12,000 m. Sedimentological studies confirm that major source areas composed largely of granitic and metamorphic rocks existed to the north and south of central South America and Southern Africa, as also in the divides between the basins. Uranium mineralization occurs sporadically throughout the succession and is usually restricted to palaeoriver channels containing carbon trash. There has been little subsequent enrichment and the Colorado model does not apply. With a few exceptions, the deposits tend to have a low overall uranium tenor and individual deposits are usually not very extensive in size. Collectively, however, they may eventually assume some importance. Uraniferous coals have been recorded from a number of localities and it is suggested that the significance of these deposits has as yet not been fully appreciated or investigated. (author)

  18. 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

  19. 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.

  20. Social capital and health: evidence that ancestral trust promotes health among children of immigrants.

    Science.gov (United States)

    Ljunge, Martin

    2014-12-01

    This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Environmental enrichment mitigates the impact of ancestral stress on motor skill and corticospinal tract plasticity.

    Science.gov (United States)

    McCreary, J Keiko; Erickson, Zachary T; Metz, Gerlinde A S

    2016-10-06

    An adverse fetal environment in utero has been associated with long-term alterations in brain structure and function, and a higher risk of neurological disorders in later life. A common consequence of early adverse experience is impaired motor system function. A causal relationship for stress-associated impairments and a suitable therapy, however, have not been determined yet. To investigate the impact of ancestral stress on corticospinal tract (CST) morphology and fine motor performance in rats, and to determine if adverse programming by ancestral stress can be mitigated by environmental enrichment therapy in rats. The study examined F3 offspring generated by three lineages; one with prenatal stress only in the F1 generation, one with compounding effects of multigenerational prenatal stress, and a non-stress control lineage. F3 offspring from each lineage were injected with biotinylated dextran amine (BDA) into the motor cortex for anterograde tracing of the CST. Examination of the CST revealed reduced axonal density in the ancestrally stressed lineages. These anatomical changes were associated with significant impairments in skilled walking, as indicated by reduced foot placement accuracy and disturbed inter-limb coordination. Therapeutic intervention by environmental enrichment reduced the neuromorphological consequences of ancestral stress and restored skilled walking ability. The data suggest a causal relationship between stress-induced abnormal CST function and loss of fine motor performance. Thus, ancestral stress may be a determinant of motor system development and motor skill. Environmental enrichment may represent an effective intervention for the adverse programming by ancestral stress and trauma. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Jing; Chen, Xi; Liu, Yanan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Xie, Qunhui [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Zhao, Bin, E-mail: binzhao@rcees.ac.cn [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Tang, Naijun, E-mail: tangnaijun@tijmu.edu.cn [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China)

    2015-12-01

    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.

  7. 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

  8. 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

  9. An ant genus-group (Prenolepis) illuminates the biogeography and drivers of insect diversification in the Indo-Pacific.

    Science.gov (United States)

    Matos-Maraví, Pável; Clouse, Ronald M; Sarnat, Eli M; Economo, Evan P; LaPolla, John S; Borovanska, Michaela; Rabeling, Christian; Czekanski-Moir, Jesse; Latumahina, Fransina; Wilson, Edward O; Janda, Milan

    2018-06-01

    The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini). We used a fossil-calibrated phylogeny to infer ancestral geographical ranges utilizing a biogeographic model that includes founder-event speciation. Ancestral state reconstructions of the ants' ecological preferences, and diversification rates were estimated for selected Indo-Pacific clades. Overall, we report that faunal interchange between Asia and Australia has occurred since at least 20-25 Ma, and early dispersal to the Fijian Basin happened during the early and mid-Miocene (ca. 10-20 Ma). Differences in diversification rates across Indo-Pacific clades may be related to ecological preference breadth, which in turn may have facilitated geographical range expansions. Ancient dispersal routes suggested by our results agree with the palaeogeography of the region. For this particular group of ants, the rapid orogenesis in New Guinea and possibly subsequent ecological shifts may have promoted their rapid diversification and widespread distribution across the Indo-Pacific. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. 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)

  11. 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.

  12. 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

  13. 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…

  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. The structured ancestral selection graph and the many-demes limit.

    Science.gov (United States)

    Slade, Paul F; Wakeley, John

    2005-02-01

    We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

  16. Indigenous ancestral sayings contribute to modern conservation partnerships: examples using Phormium tenax.

    Science.gov (United States)

    Wehi, Priscilla M

    2009-01-01

    Traditional ecological knowledge (TEK) is central to indigenous worldviews and practices and is one of the most important contributions that indigenous people can bring to conservation management partnerships. However, researchers and managers may have difficulty accessing such knowledge, particularly where knowledge transmission has been damaged. A new methodological approach analyzes ancestral sayings from Maori oral traditions for ecological information about Phormium tenax, a plant with high cultural value that is a dominant component in many threatened wetland systems, and frequently used in restoration plantings in New Zealand. Maori ancestral sayings record an association with nectar-feeding native parrots that has only rarely been reported, as well as indications of important environmental parameters (rainfall and drought) for this species. These sayings provide evidence of indigenous management that has not been reported from interviews with elders, including evidence of fire use to create Phormium cultivations. TEK in Maori ancestral sayings imply landscape-scale processes in comparison to intensive, small-scale management methods often reported in interviews. TEK in ancestral sayings can be used to generate new scientific hypotheses, negotiate collaborative pathways, and identify ecological management strategies that support biodiversity retention. TEK can inform restoration ecology, historical ecology, and conservation management of species and ecosystems, especially where data from pollen records and archaeological artifacts are incomplete.

  17. Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes.

    Science.gov (United States)

    Wu, Yonghua; Wang, Haifeng; Hadly, Elizabeth A

    2017-04-20

    Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

  18. Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.

    Science.gov (United States)

    Avdeyev, Pavel; Jiang, Shuai; Aganezov, Sergey; Hu, Fei; Alekseyev, Max A

    2016-03-01

    Since most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the "simplest" case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes. One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets. We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genome reconstruction tools.

  19. 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...

  20. Expression, purification and crystallization of the ancestral androgen receptor-DHT complex.

    Science.gov (United States)

    Colucci, Jennifer K; Ortlund, Eric A

    2013-09-01

    Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. 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...

  4. Ancestral diet leads to dynamic transgenerational plasticity for five generations in Drosophila melanogaster

    OpenAIRE

    Mikheyev, Alexander; Emborski, Carmen

    2018-01-01

    Ancestral exposures can influence phenotypic expression in subsequent generations, which influence diverse biological processes ranging from phenotypic plasticity to obesity. Currently, most transgenerational studies work under the assumption of transgenerational response stability and reproducibility through time and across exposure differences, relying on short-term (i.e. 2-3 generations) single-exposure experiments. Yet, little evidence exists in the literature to validate this assumption,...

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

    OpenAIRE

    Nadot S.; Sauquet H.; Damerval C.; Jabbour F.; Domenech B.

    2016-01-01

    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...

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

    Directory of Open Access Journals (Sweden)

    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. Sedimentology of Hirnantian glaciomarine deposits in the Balkan Terrane, western Bulgaria: Fixing a piece of the north peri-Gondwana jigsaw puzzle

    Science.gov (United States)

    Chatalov, Athanas

    2017-04-01

    Glaciomarine deposits of late Hirnantian age in the western part of the Palaeozoic Balkan Terrane have persistent thickness ( 7 m) and lateral uniformity in rock colour, bedding pattern, lithology, and sedimentary structures. Four lithofacies are distinguished from base to top: lonestone-bearing diamictites, interbedded structureless mudstones, crudely laminated diamictites, and finely laminated mudstones. The diamictites are clast-poor to clast-rich comprising muddy to sandy varieties. Their compositional maturity is evidenced by the very high amount of detrital quartz compared to the paucity of feldspar and unstable lithic grains. Other textural components include extraclasts derived from the local Ordovician basement, mudstone intraclasts, and sediment aggregates. Turbate structures, grain lineations, and soft sediment deformation of the matrix below larger grains are locally observed. Sedimentological analysis reveals that deposition occurred in an ice-intermediate to ice-distal, poorly agitated shelf environment by material supplied from meltwater buoyant plumes and rain-out from ice-rafted debris. Remobilization by mass-flow processes (cohesive debris flows and slumps) was an important mechanism particularly for the formation of massive diamictites. The glaciomarine deposits represent a typical deglaciation sequence reflecting retreat of the ice front (grounded or floating ice sheet), relative sea-level rise and gradually reduced sedimentation rate with increasing contribution from suspension fallout. This sequence was deposited on the non-glaciated shelf of the intracratonic North Gondwana platform along the southern margin of the Rheic Ocean. The Hirnantian strata of the Balkan Terrane can be correlated with similar glaciomarine deposits known from peri-Gondwana terranes elsewhere in Europe showing clear 'Armorican affinity'. Several lines of evidence suggest that the provenance of siliciclastic material was associated mainly with sedimentary recycling of

  8. 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.

  9. 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.

  10. 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)

  11. An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.

    Science.gov (United States)

    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 human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Gillette, Ross; Miller-Crews, Isaac; Skinner, Michael K; Crews, David

    2015-01-01

    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 (mPOA), lateral hypothalamus (LH), 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 mPOA. Epigenetic related genes were affected by stress in the ventromedial nucleus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the LH showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  14. 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.

  15. Pollination and reproduction of an invasive plant inside and outside its ancestral range

    Science.gov (United States)

    Petanidou, Theodora; Price, Mary V.; Bronstein, Judith L.; Kantsa, Aphrodite; Tscheulin, Thomas; Kariyat, Rupesh; Krigas, Nikos; Mescher, Mark C.; De Moraes, Consuelo M.; Waser, Nickolas M.

    2018-05-01

    Comparing traits of invasive species within and beyond their ancestral range may improve our understanding of processes that promote aggressive spread. Solanum elaeagnifolium (silverleaf nightshade) is a noxious weed in its ancestral range in North America and is invasive on other continents. We compared investment in flowers and ovules, pollination success, and fruit and seed set in populations from Arizona, USA ("AZ") and Greece ("GR"). In both countries, the populations we sampled varied in size and types of present-day disturbance. Stature of plants increased with population size in AZ samples whereas GR plants were uniformly tall. Taller plants produced more flowers, and GR plants produced more flowers for a given stature and allocated more ovules per flower. Similar functional groups of native bees pollinated in AZ and GR populations, but visits to flowers decreased with population size and we observed no visits in the largest GR populations. As a result, plants in large GR populations were pollen-limited, and estimates of fecundity were lower on average in GR populations despite the larger allocation to flowers and ovules. These differences between plants in our AZ and GR populations suggest promising directions for further study. It would be useful to sample S. elaeagnifolium in Mediterranean climates within the ancestral range (e.g., in California, USA), to study asexual spread via rhizomes, and to use common gardens and genetic studies to explore the basis of variation in allocation patterns and of relationships between visitation and fruit set.

  16. 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)

  17. 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....... The dominant motif is that of meters to tens of meters of exposure-capped cycles of carbonates, mixed carbonates, and siliciclastics and, in older stratigraphic levels, siliciclastics and gypsum. Halitegypsum-carbonate cycles developed in deeper, isolated basins. Individual cycles of carbonate and mixed...

  18. 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...

  19. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene.

    OpenAIRE

    Crawford, D H; Powell, L W; Leggett, B A; Francis, J S; Fletcher, L M; Webb, S I; Halliday, J W; Jazwinska, E C

    1995-01-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, ...

  20. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, D.H.G.; Powell, L.W.; Leggett, B.A. [Univ. of Queensland (Australia)] [and others

    1995-08-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, one copy, and no copies of the ancestral haplotype). We also examined iron indices in two groups of HC heterozygotes (those with the ancestral haplotype and those without) and in age-matched controls. These analyses indicate that (i) HC patients with two copies of the ancestral haplotype show significantly more severe expression of the disorder than those with one copy or those without, (ii) HC heterozygotes have partial clinical expression, which may be influenced by the presence of the ancestral haplotype in females but not in males, and (iii) the high population frequency of the HC gene may be the result of the selective advantage conferred by protecting heterozygotes against iron deficiency. 18 refs., 3 tabs.

  1. 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.

  2. Push from the Pacific

    Science.gov (United States)

    Jaccard, Samuel L.; Galbraith, Eric D.

    2018-05-01

    Enhanced upwelling and CO2 degassing from the subpolar North Pacific during a warm event 14,000 years ago may have helped keep atmospheric CO2 levels high enough to propel the Earth out of the last ice age.

  3. 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...

  4. 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

  5. Evolution of sexes from an ancestral mating-type specification pathway.

    Directory of Open Access Journals (Sweden)

    Sa Geng

    2014-07-01

    Full Text Available Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was

  6. What was the ancestral sex-determining mechanism in amniote vertebrates?

    Science.gov (United States)

    Johnson Pokorná, Martina; Kratochvíl, Lukáš

    2016-02-01

    Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic sex determination (GSD), sex is determined by a sex-specific genotype, i.e. by the combination of sex chromosomes at various stages of differentiation at conception. As well as influencing sex determination, sex-specific parts of genomes may, and often do, develop specific reproductive or ecological roles in their bearers. Accordingly, an individual with a mismatch between phenotypic (gonadal) and genotypic sex, for example an individual sex-reversed by environmental effects, should have a lower fitness due to the lack of specialized, sex-specific parts of their genome. In this case, evolutionary transitions from GSD to ESD should be less likely than transitions in the opposite direction. This prediction contrasts with the view that GSD was the ancestral sex-determining mechanism for amniote vertebrates. Ancestral GSD would require several transitions from GSD to ESD associated with an independent dedifferentiation of sex chromosomes, at least in the ancestors of crocodiles, turtles, and lepidosaurs (tuataras and squamate reptiles). In this review, we argue that the alternative theory postulating ESD as ancestral in amniotes is more parsimonious and is largely concordant with the theoretical expectations and current knowledge of the phylogenetic distribution and homology of sex-determining mechanisms. © 2014 Cambridge Philosophical Society.

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Pharo, Elizabeth A; De Leo, Alison A; Renfree, Marilyn B; Thomson, Peter C; Lefèvre, Christophe M; Nicholas, Kevin R

    2012-06-08

    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. 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. 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.

  10. 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.

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

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    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.

  12. The Fairway-Aotea Basin and the New Caledonia Trough, witnesses of the Pacific-Australian plate boundary evolution : from mid-Cretaceous cessation of subduction to Eocene subduction renewal

    Science.gov (United States)

    Collot, J.; Geli, L. B.; Lafoy, Y.; Sutherland, R.; Herzer, R. H.; Roest, W. R.

    2009-12-01

    The geodynamical history of the SW Pacific is controlled since the Mesozoic by the evolution of peri-Pacific subduction zones, in a trench retreat by slab roll-back process, which successively occurred along the Eastern Gondwana margin. In this context, most basins which formed after 45 Ma reached a stage of seafloor spreading, have recorded the inversions of the earth's magnetic field and present typical oceanic crust morphologies. By contrast, the New Caledonia and Fairway basins, which are narrower and present thick sedimentary covers have a less known and more controversial origin. Based on a regional geological synthesis and on interpretation of multichannel seismic reflection and refraction data, combined with drill hole data off New Zealand and a compilation of regional potential data, we distinguish 2 phases of the evolution of the Fairway-Aotea Basin (FAB) and the New Caledonia Trough (NCT), which reflect the evolution of the Gondwana-Pacific plate boundary: Phase 1: Mid Cretaceous formation of the FAB in a continental intra- or back- arc position of the Pacific-Gondwana subduction system. The formation of this shallow basin reflects the onset of continental breakup of the Eastern Gondwana margin during Cenomanian which was most probably caused by a dynamic change of the subduction zone through a « verticalization » of the slab. This event may be the result of the 99 Ma kinematic plate reorganization which probably led to subduction cessation along the Gondwana-Pacific plate boundary. A tectonic escape mechanism, in relation with the locking of the subduction zone by the Hikurangi Plateau, could also be responsible of the trench retreat leading to backarc extension. Phase 2: Regional Eocene-Oligocene uplift followed by rapid subsidence (3-4 km) of the system « Lord Howe Rise - FAB - Norfolk Ridge ». The structural style of this deformation leads us to suggest that detachment of the lower crust is the cause of subsidence. We therefore propose a model in

  13. 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

  14. 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

  15. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family.

    Science.gov (United States)

    Illa, Eudald; Sargent, Daniel J; Lopez Girona, Elena; Bushakra, Jill; Cestaro, Alessandro; Crowhurst, Ross; Pindo, Massimo; Cabrera, Antonio; van der Knaap, Esther; Iezzoni, Amy; Gardiner, Susan; Velasco, Riccardo; Arús, Pere; Chagné, David; Troggio, Michela

    2011-01-12

    Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  16. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

    Directory of Open Access Journals (Sweden)

    Velasco Riccardo

    2011-01-01

    Full Text Available Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  17. 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.

  18. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

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    Katherine Belov

    2006-03-01

    Full Text Available The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum sequence to construct the first map of a marsupial major histocompatibility complex (MHC. The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.

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

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    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.

  20. 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.

  1. Sexually dimorphic effects of ancestral exposure to vinclozolin on stress reactivity in rats.

    Science.gov (United States)

    Gillette, Ross; Miller-Crews, Isaac; Nilsson, Eric E; Skinner, Michael K; Gore, Andrea C; Crews, David

    2014-10-01

    How an individual responds to the environment depends upon both personal life history as well as inherited genetic and epigenetic factors from ancestors. Using a 2-hit, 3 generations apart model, we tested how F3 descendants of rats given in utero exposure to the environmental endocrine-disrupting chemical (EDC) vinclozolin reacted to stress during adolescence in their own lives, focusing on sexually dimorphic phenotypic outcomes. In adulthood, male and female F3 vinclozolin- or vehicle-lineage rats, stressed or nonstressed, were behaviorally characterized on a battery of tests and then euthanized. Serum was used for hormone assays, and brains were used for quantitative PCR and transcriptome analyses. Results showed that the effects of ancestral exposure to vinclozolin converged with stress experienced during adolescence in a sexually dimorphic manner. Debilitating effects were seen at all levels of the phenotype, including physiology, behavior, brain metabolism, gene expression, and genome-wide transcriptome modifications in specific brain nuclei. Additionally, females were significantly more vulnerable than males to transgenerational effects of vinclozolin on anxiety but not sociality tests. This fundamental transformation occurs in a manner not predicted by the ancestral exposure or the proximate effects of stress during adolescence, an interaction we refer to as synchronicity.

  2. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

    Science.gov (United States)

    Anselmetti, Yoann; Duchemin, Wandrille; Tannier, Eric; Chauve, Cedric; Bérard, Sèverine

    2018-05-09

    Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

  3. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    Science.gov (United States)

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  4. 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.

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

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    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

  6. The Gondwana Orogeny in northern North Patagonian Massif: Evidences from the Caita Có granite, La Seña and Pangaré mylonites, Argentina

    Directory of Open Access Journals (Sweden)

    Daniel A. Gregori

    2016-07-01

    Full Text Available Structural analyses in the northern part of the North Patagonia Massif, in the foliated Caita Có granite and in La Seña and Pangaré mylonites, indicate that the pluton was intruded as a sheet-like body into an opening pull-apart structure during the Gondwana Orogeny. Geochronological studies in the massif indicate a first, lower to middle Permian stage of regional deformation, related to movements during indentation tectonics, with emplacement of foliated granites in the western and central areas of the North Patagonian Massif. Between the upper Permian and lower Triassic, evidence indicates emplacement of undeformed granitic bodies in the central part of the North Patagonian Massif. A second pulse of deformation between the middle and upper Triassic is related to the emplacement of the Caita Có granite, the development of mylonitic belts, and the opening of the Los Menucos Basin. During this pulse of deformation, compression direction was from the eastern quadrant.

  7. 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.

  8. Modelos de cinemática de placas para Antártida durante la ruptura de Gondwana: una revisión

    OpenAIRE

    M.E. Ghidella; L.A. Lawver; S. Marenssi; L.M. Gahagan

    2007-01-01

    La historia de apertura del mar de Weddell y del Oc éano Atlántico Sur es crítica para comprender la ruptura de Gondwana y la evolución geológica de Antártida desde el Jurásico temprano. La dispersión de los fragmentos gondwánicos es importante para entender la circulación oceánica del pasado, descifrar la historia de las cuencas sedimentarias ubicadas al Este de la Península Antártica y establecer posibles rutas de dispersión de flora y fauna entre los continentes australes. Desafortunadamen...

  9. 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...

  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. 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

  12. 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.

  13. 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

  14. Petrological, geochemical, isotopic, and geochronological constraints for the Late Devonian-Early Carboniferous magmatism in SW Gondwana (27-32°LS): an example of geodynamic switching

    Science.gov (United States)

    Dahlquist, Juan A.; Alasino, Pablo H.; Basei, Miguel A. S.; Morales Cámera, Matías M.; Macchioli Grande, Marcos; da Costa Campos Neto, Mario

    2018-04-01

    We report a study integrating 13 new U-Pb LA-MC-ICP-MS zircon ages and Hf-isotope data from dated magmatic zircons together with complete petrological and whole-rock geochemistry data for the dated granitic rocks. Sample selection was strongly based on knowledge reported in previous investigations. Latest Devonian-Early Carboniferous granite samples were collected along a transect of 900 km, from the inner continental region (present-day Eastern Sierras Pampeanas) to the magmatic arc (now Western Sierras Pampeanas and Frontal Cordillera). Based on these data together with ca. 100 published whole-rock geochemical analyses we conclude that Late Devonian-Early Carboniferous magmatism at this latitude represents continuous activity (ranging from 322 to 379 Ma) on the pre-Andean margin of SW Gondwana, although important whole-rock and isotopic compositional variations occurred through time and space. Combined whole-rock chemistry and isotope data reveal that peraluminous A-type magmatism started in the intracontinental region during the Late Devonian, with subsequent development of synchronous Carboniferous peraluminous and metaluminous A-type magmatism in the retro-arc region and calc-alkaline magmatism in the western paleomargin. We envisage that magmatic evolution was mainly controlled by episodic fluctuations in the angle of subduction of the oceanic plate (between flat-slab and normal subduction), supporting a geodynamic switching model. Subduction fluctuations were relatively fast (ca. 7 Ma) during the Late Devonian and Early Carboniferous, and the complete magmatic switch-off and switch-on process lasted for 57 Ma. Hf T DM values of zircon (igneous and inherited) from some Carboniferous peraluminous A-type granites in the retro-arc suggest that Gondwana continental lithosphere formed during previous orogenies was partly the source of the Devonian-Carboniferous granitic magmas, thus precluding the generation of the parental magmas from exotic terranes.

  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....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

  16. 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...

  17. Researching Pacific island livelihoods:

    DEFF Research Database (Denmark)

    Egelund Christensen, Andreas; Mertz, Ole

    2010-01-01

    on contemporary theories of nissology and conceptual analytical frameworks for island research. Through a review of selected case-study-based island literature on changing livelihoods coming out of the South Pacific, we wish to illustrate and discuss advantages of finding common grounds for small island studies....... The focus is on two dimensions of island livelihood, migration and natural resource management, both of which are significant contributors in making island livelihoods and shaping Pacific seascapes. We argue that there is still a substantial lack of studies targeting small island dynamics that are empirical...

  18. 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,…

  19. Indo-Pacific echinoids in the tropical eastern Pacific

    Science.gov (United States)

    Lessios, H. A.; Kessing, B. D.; Wellington, G. M.; Graybeal, A.

    1996-06-01

    The existing literature reports that only one species of Indo-Pacific echinoid ( Echinometra oblonga), occurs in the eastern Pacific. In this study we confirm the presence of this species at Islas Revillagigedo and also report the presence of two species of Echinothrix (a genus hitherto unknown outside the Indo-Pacific) at Isla del Coco and at Clipperton Island. We also present evidence from isozymes and from mitochondrial DNA sequences indicating that at least one individual of Diadema at Clipperton may belong to a maternal lineage characteristic of the west Pacific species D. savignyi. These data are consistent with the hypothesis that the observed populations of Indo-Pacific echinoid species are recent arrivals to the eastern Pacific, as opposed to the view that they are relicts of Tethyan pan-tropical distributions. Echinothrix diadema, in particular, may have arrived at Isla del Coco during the 1982-1983 El Nifio. In addition to Indo-Pacific species, Clipperton, Isla del Coco and the Revillagigedos contain a complement of eastern Pacific echinoids. The echinoid faunas of these islands should, therefore, be regarded as mixtures of two biogeographic provinces. Though none of the Indo-Pacific species are known to have reached the coast of the American mainland, their presence at the offshore islands of the eastern Pacific suggests that, for some echinoids, the East Pacific Barrier is not as formidable an obstacle to migration as was previously thought.

  20. 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

  1. Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species.

    Science.gov (United States)

    Tewksbury, Joshua J; Manchego, Carlos; Haak, David C; Levey, Douglas J

    2006-03-01

    The biogeography of pungency in three species of wild chili in the chaco and surrounding highland habitats of southeastern Bolivia is described. We report that Capsicum chacoense, C. baccatum, and C. eximium are polymorphic for production of capsaicin and its analogs, such that completely pungent and completely nonpungent individuals co-occur in some populations. In C. chacoense, the density of plants and the proportion of pungent plants increased with elevation. Above 900 m, all individuals in all populations except two were pungent; nonpungent individuals in at least one of the two polymorphic populations were likely a result of spreading by humans. The occurrence of pungent and nonpungent individuals in three species of ancestral Capsicum and the geographic variation of pungency within species suggest that production of capsaicin and its analogs entails both costs and benefits, which shift from one locality to another. Determining the selection pressures behind such shifts is necessary to understand the evolution of pungency in chilies.

  2. Novel ancestral Dysferlin splicing mutation which migrated from the Iberian peninsula to South America.

    Science.gov (United States)

    Vernengo, Luis; Oliveira, Jorge; Krahn, Martin; Vieira, Emilia; Santos, Rosário; Carrasco, Luisa; Negrão, Luís; Panuncio, Ana; Leturcq, France; Labelle, Veronique; Bronze-da-Rocha, Elsa; Mesa, Rosario; Pizzarossa, Carlos; Lévy, Nicolas; Rodriguez, Maria-Mirta

    2011-05-01

    Primary dysferlinopathies are a group of recessive heterogeneous muscular dystrophies. The most common clinical presentations are Miyoshi myopathy and LGMD2B. Additional presentations range from isolated hyperCKemia to severe functional disability. Symptomatology begins in the posterior muscle compartment of the calf and its clinical course progresses slowly in Miyoshi myopathy whereas LGMD2B involves predominantly the proximal muscles of the lower limbs. The age of onset ranges from 13 to 60years in Caucasians. We present five patients that carry a novel mutation in the exon12/intron12 boundary: c.1180_1180+7delAGTGCGTG (r.1054_1284del). We provide evidence of a founder effect due to a common ancestral origin of this mutation, detected in heterozygosity in four patients and in homozygosity in one patient. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Loop Replacement Enhances the Ancestral Antibacterial Function of a Bifunctional Scorpion Toxin

    Directory of Open Access Journals (Sweden)

    Shangfei Zhang

    2018-06-01

    Full Text Available On the basis of the evolutionary relationship between scorpion toxins targeting K+ channels (KTxs and antibacterial defensins (Zhu S., Peigneur S., Gao B., Umetsu Y., Ohki S., Tytgat J. Experimental conversion of a defensin into a neurotoxin: Implications for origin of toxic function. Mol. Biol. Evol. 2014, 31, 546–559, we performed protein engineering experiments to modify a bifunctional KTx (i.e., weak inhibitory activities on both K+ channels and bacteria via substituting its carboxyl loop with the structurally equivalent loop of contemporary defensins. As expected, the engineered peptide (named MeuTXKα3-KFGGI remarkably improved the antibacterial activity, particularly on some Gram-positive bacteria, including several antibiotic-resistant opportunistic pathogens. Compared with the unmodified toxin, its antibacterial spectrum also enlarged. Our work provides a new method to enhance the antibacterial activity of bifunctional scorpion venom peptides, which might be useful in engineering other proteins with an ancestral activity.

  4. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

    Science.gov (United States)

    Bowles, Samuel

    2009-06-05

    Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

  5. 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

  6. 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.

  7. 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...

  8. 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.

  9. 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.

  10. 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

  11. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    Directory of Open Access Journals (Sweden)

    Paul H Williams

    Full Text Available Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC models and Poisson-tree-process (PTP models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and

  12. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    Science.gov (United States)

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

  13. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

    Science.gov (United States)

    Voss, Stephen R.; Kump, D. Kevin; Putta, Srikrishna; Pauly, Nathan; Reynolds, Anna; Henry, Rema J.; Basa, Saritha; Walker, John A.; Smith, Jeramiah J.

    2011-01-01

    Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12–17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution. PMID:21482624

  14. 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.

  15. Metamorphosis Is Ancestral for Crown Euarthropods, and Evolved in the Cambrian or Earlier.

    Science.gov (United States)

    Wolfe, Joanna M

    2017-09-01

    Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption. Based on a published morphological dataset encompassing 217 exceptionally preserved fossil and 96 extant taxa, fossils were directly incorporated into both the topology and age estimates, as in "tip dating" analyses. Using data from post-embryonic fossils representing 25 species throughout stem and crown arthropod lineages (as well as most of the 96 extant taxa), characters for metamorphosis were assigned based on inferred ecological changes in development (e.g., changes in habitat and adaptive landscape). Under all phylogenetic hypotheses, metamorphosis was supported as most likely ancestral to both ecdysozoans and euarthropods. Care must be taken to account for potential drastic post-embryonic morphological changes in evolutionary analyses. Many stem group euarthrpods may have had ecologically differentiated larval stages that did not preserve in the fossil record. Moreover, a complex life cycle and planktonic ecology may have evolved in the Ediacaran or earlier, and may have typified the pre-Cambrian explosion "wormworld" prior to the origin of crown group euarthropods. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  16. 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.

  17. 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

  18. 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...

  19. 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

    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...

  20. 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.

  1. 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....

  2. 187Re - 232Th - 238U nuclear geochronometry: constraining magmatism in East-Antarctica and the break-up of Gondwana

    Science.gov (United States)

    Roller, Goetz

    2017-04-01

    187Re - 232Th - 238U nuclear geochronometry is a new dating method for astronomy, earth and planetary sciences [1-4]. Nucleogeochronometric Rhenium-Osmium two-point-isochron (TPI) ages are calculated using a nuclear geochronometer as one data point in a two-point-isochron diagram [5-7]. The IVREA chronometer, for example, is one of five terrestrial nuclear geochronometers identified so far [8]. Here, it is used to constrain the magmatism of the Ferrar flood basalt province, which has been related to continental rifting and the break-up of Gondwana in the Jurassic.TPI ages for seven (basaltic) andesite whole rock samples from the Prince Albert Mountains (Victoria Land, Antarctica) are calculated. An isochron age of 172 ± 5 Ma (187Os/188Osi = 0.194 ± 0.023) has previously been published for these rocks [9]. Initial TPI 187Os/188Osi ratios show only minor scatter between 187Os/188Osi = 0.2149 ± 0.0064 and 187Os/188Osi = 0.22231 ± 0.00080, in agreement with the enigmatic, suprachondritic 187Os/188Osi = 0.194 ± 0.023 from the isochron [9]. TPI ages for the Mount Joyce samples range from 125.4 ± 9.9 Ma to 139 ± 17 Ma and thus constrain the youngest magmatic event(s) in the Transantarctic Mountains. For the Thumb Point basalt, a TPI age of 219 ± 81 Ma is calculated. Despite of its large uncertainty, the age itself is in agreement with the Triassic 224 Ma and 240 Ma events reported from North Patagonia [10]. The TPI age of 186.1 ± 8.1 Ma from the Ricker Hill basalt can be clearly distinguished from the Mount Murray TPI age of 158 ± 14 Ma, while at Brimstone Peak two TPI age groups of 155 ± 14 Ma and 175.3 ± 3.1 Ma are observed. From this it may be concluded that the seven TPI ages indicate episodic magmatic activity in East-Antarctica between 125 Ma and 219 Ma, leading to the break-up of Gondwana. This picture is consistent with the geochronology of the Antarctic Peninsula, Patagonia, the Karoo and the Ferrar mafic rocks [10]. Thus, besides constraining

  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. 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

  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

    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...

  7. The Pacific RANET Project

    Science.gov (United States)

    Postawko, S.; Ah Poe, A.; Morrissey, M.

    2004-12-01

    There are few places in the world more vulnerable to the effects of climate variability and change than the island nations of the tropical Pacific Ocean. The region also faces great challenges in communicating the issues related to climate to the general population. Lack of communications infrastructure, multiple languages, and knowledgeable personnel to deliver information, are all challenges for these countries. However, a recently developed international consortium is taking the first steps to addressing these challenges. The RANET (RAdio and interNET communications) project was originally developed for the countries of Africa, with initial funding from NOAA, to make weather, climate, and other environmental information more accessible to remote and resource-poor communities. The program is now expanding into Asia and the Pacific. RANET works to build telecommunication bridges between scientific-based products and remote communities that could benefit from such information.?The RANET project in the Pacific is a consortium of partners from the Pacific Island nations, the U.S., New Zealand, Australia, and others. Coordination of the project is loosely overseen by a Steering Committee, made up of representatives from the various interested partners. For regions where the appropriate technology exists (which includes the capital cities of nearly all of the island states of the Pacific), information is downloaded via a digital satellite receiver. This can then be broadcast within a country by many means, including Community FM Radio stations. The information distributed includes technical information needed by meteorological and related services to improve their own products and services, as well as a second level of information designed to serve communities, including weather forecasts, bulletins, warnings, etc. The primary challenge at this time is developing content that is both relevant and understandable to these remote communities. While some information will

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

    Directory of Open Access Journals (Sweden)

    Kyle S. McCommis

    2016-08-01

    Full Text Available Objective: Transport of pyruvate into the mitochondrial matrix by the Mitochondrial Pyruvate Carrier (MPC is an important and rate-limiting step in its metabolism. In pancreatic β-cells, mitochondrial pyruvate metabolism is thought to be important for glucose sensing and glucose-stimulated insulin secretion. Methods: To evaluate the role that the MPC plays in maintaining systemic glucose homeostasis, we used genetically-engineered Drosophila and mice with loss of MPC activity in insulin-producing cells. Results: In both species, MPC deficiency results in elevated blood sugar concentrations and glucose intolerance accompanied by impaired glucose-stimulated insulin secretion. In mouse islets, β-cell MPC-deficiency resulted in decreased respiration with glucose, ATP-sensitive potassium (KATP channel hyperactivity, and impaired insulin release. Moreover, treatment of pancreas-specific MPC knockout mice with glibenclamide, a sulfonylurea KATP channel inhibitor, improved defects in islet insulin secretion and abnormalities in glucose homeostasis in vivo. Finally, using a recently-developed biosensor for MPC activity, we show that the MPC is rapidly stimulated by glucose treatment in INS-1 insulinoma cells suggesting that glucose sensing is coupled to mitochondrial pyruvate carrier activity. 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. Keywords: Stimulus-coupled secretion, Insulin, β-Cell, Diabetes, Pyruvate, Mitochondria, Drosophila

  10. 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.

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. 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.

  14. Fixation Probability in a Two-Locus Model by the Ancestral Recombination–Selection Graph

    Science.gov (United States)

    Lessard, Sabin; Kermany, Amir R.

    2012-01-01

    We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill–Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller’s ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination. PMID:22095080

  15. 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.

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

    Science.gov (United States)

    Chen, Xiaorui; Hitchings, Matthew D.; Mendoza, José E.; Balanza, Virginia; Facey, Paul D.; Dyson, Paul J.; Bielza, Pablo; Del Sol, Ricardo

    2017-01-01

    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. PMID:29067021

  17. 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.

  18. 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.

  19. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.

    Science.gov (United States)

    Huang, Ruiqi; O'Donnell, Andrew J; Barboline, Jessica J; Barkman, Todd J

    2016-09-20

    Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

  20. Reinterpretation of Halokinetic Features in the Ancestral Rocky Mountains Paradox Salt Basin, Utah and Colorado

    Science.gov (United States)

    Thompson, J. A.; Giles, K. A.; Rowan, M. G.; Hearon, T. E., IV

    2016-12-01

    The Paradox Basin in southeastern Utah and southwestern Colorado is a foreland basin formed in response to flexural loading by the Pennsylvanian-aged Uncompaghre uplift during the Ancestral Rocky Mountain orogen. Thick sequences of evaporites (Paradox Formation) were deposited within the foreland basin, which interfinger with clastic sediments in the foredeep and carbonates around the basin margin. Differential loading of the Pennsylvanian-Jurassic sediments onto the evaporites drove synsedimentary halokinesis, creating a series of salt walls and adjacent minibasins within the larger foreland basin. The growing salt walls within the basin influenced patterns of sediment deposition from the Pennsylvanian through the Cretaceous. By integrating previously published mapping with recent field observations, mapping, and subsurface interpretations of well logs and 2D seismic lines, we present interpretations of the timing, geometry, and nature of halokinesis within the Paradox Basin, which record the complex salt tectonic history in the basin. Furthermore, we present recent work on the relationships between the local passive salt history and the formation of syndepositional counter-regional extensional fault systems within the foreland. These results will be integrated into a new regional salt-tectonic and stratigraphic framework of the Paradox Basin, and have broader implications for interpreting sedimentary records in other basins with a mobile substrate.

  1. 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

  2. Obesity and Native Hawaiians/Pacific Islanders

    Science.gov (United States)

    ... Population Profiles > Native Hawaiian/Other Pacific Islander > Obesity Obesity and Native Hawaiians/Pacific Islanders Native Hawaiians/Pacific ... youthonline . [Accessed 08/18/2017] HEALTH IMPACT OF OBESITY People who are overweight are more likely to ...

  3. The age of the Tunas formation in the Sauce Grande basin-Ventana foldbelt (Argentina): Implications for the Permian evolution of the southwestern margin of Gondwana

    Science.gov (United States)

    López-Gamundí, Oscar; Fildani, Andrea; Weislogel, Amy; Rossello, Eduardo

    2013-08-01

    New SHRIMP radiogenic isotope dating on zircons in tuffs (280.8 ± 1.9 Ma) confirms the Early Permian (Artinskian) age of the uppermost section of the Tunas Formation. Tuff-rich levels in the Tunas Formation are exposed in the Ventana foldbelt of central Argentina; they are part of a deltaic to fluvial section corresponding to the late overfilled stage of the Late Paleozoic Sauce Grande foreland basin. Recent SHRIMP dating of zircons from the basal Choiyoi volcanics exposed in western Argentina yielded an age of 281.4 ± 2.5 Ma (Rocha-Campos et al., 2011). The new data for the Tunas tuffs suggest that the volcanism present in the Sauce Grande basin can be considered as the distal equivalent of the earliest episodes of the Choiyoi volcanism of western Argentina. From the palaeoclimatic viewpoint the new Tunas SHRIMP age confirms that by early Artinskian glacial conditions ceased in the Sauce Grande basin and, probably, in adajacent basins in western Gondwana.

  4. Paleomagnetism of Jurassic and Cretaceous rocks in central Patagonia: a key to constrain the timing of rotations during the breakup of southwestern Gondwana?

    Science.gov (United States)

    Geuna, Silvana E.; Somoza, Rubén; Vizán, Haroldo; Figari, Eduardo G.; Rinaldi, Carlos A.

    2000-08-01

    A paleomagnetic study in Jurassic and Cretaceous rocks from the Cañadón Asfalto basin, central Patagonia, indicates the occurrence of about 25-30° clockwise rotation in Upper Jurassic-lowermost Cretaceous rocks, whereas the overlying mid-Cretaceous rocks do not show evidence of rotation. This constrains the tectonic rotation to be related to a major regional unconformity in Patagonia, which in turn seems to be close in time with the early opening of the South Atlantic Ocean. The sense and probably the timing of this rotation are similar to those of other paleomagnetically detected rotations in different areas of southwestern Gondwana, suggesting a possible relationship between these and major tectonic processes related with fragmentation of the supercontinent. On the other hand, the mid-Cretaceous rocks in the region yield a paleopole located at Lat. 87° South, Long. 159° East, A95=3.8°. This pole position is consistent with coeval high-quality paleopoles of other plates when transferred to South American coordinates, implying it is an accurate determination of the Aptian (circa 116 Ma) geomagnetic field in South America.

  5. 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.

  6. Pteridophytes from Lower Gondwana formations of the Ib River Coalfield, Orissa and their diversity and distribution in the Permian of India

    Energy Technology Data Exchange (ETDEWEB)

    Goswami, S.; Singh, K.J.; Chandra, S. [Fakir Mohan University, Balasore (India). PG Dept. of Environmental Science

    2006-12-15

    Recent extensive investigations carried out in the Ib River Coalfield, Mahanadi Master Basin, Orissa, identified numerous fossiliferous beds in the lower Gondwana deposits. Six exposures of the Barakar and lower Kamthi formations yielded diverse and abundant plant remains. The flora includes twenty-three genera representing nine groups viz., Lycopodiales, Equisetales, Sphenophyllales, Filicales, Cordaitales, Coniferales, Ginkgoales, Cycadales and Glossopteridales. Systematic descriptions of the pteridophyte taxa namely Cyclodendron (Lycopodiales), Schizoneura, Raniganjia, Bengalia, equisetaceous stems (Equisetales), Trizygia, Benlightfootia (Sphenophyllales), Neomariopteris, and Dichotomopteris (Filicales) are presented in this paper. Pteridophytic leaves comprising nine taxa viz., Cyclodendron leslii, Schizoneura gondwanensis, Raniganjia bengalensis, Bengalia raniganjensis, Trizygia speciosa, Benlightfootia indica, Neomariopteris hughesii, N. talchirensis, and Dichotomopteris sp. together with equisetaceous stems constitute about 7.88% (72 specimens) of the total plant assemblage collected from this coalfield. Among the pteridophytes, equisetaceous stems are most abundant (40.3%; 29 specimens) followed by Schizoneura gondwanensis (20.8%, 15 specimens) and Trizygia speciosa (13.9%, 10 specimens). A summary of the known diversity of pteridophytes in the Indian Permian as a whole is provided.

  7. A-type granitoid in Hasansalaran complex, northwestern Iran: Evidence for extensional tectonic regime in northern Gondwana in the Late Paleozoic

    Science.gov (United States)

    Azizi, Hossein; Kazemi, Tahmineh; Asahara, Yoshihiro

    2017-07-01

    The Hasansalaran plutonic complex is one of the main intrusive bodies with a wide range of granite, monzonite, diorite and syenite that crop out in northwest Iran. This body includes Paleozoic granitoids that are surrounded and cut by Cretaceous granitoids. Zircon U-Pb age dating shows that the crystallization of this body occurred at 360 Ma ago in the Early Carboniferous. Whole rock compositions of the investigated intrusive body, show high contents of Ga (11.1-76.3 ppm), Zr (73.5-1280 ppm), Zn (43.7-358 ppm), Y(17.9-177 ppm), enrichment of rare earth elements (REEs) together with high Ga/Al ratios and a strong Eu negative anomaly, fairly consistent with typical A-type signature. The low εNd(t = 360 Ma) value (model for evolution of northwest Iran in the Late Paleozoic. Based on our model, the upwelling of a mantle plume, probably due to the proto-Tethys oceanic rollback activity beneath northern Gondwana, had a crucial role in the uplifting of the continental crust and resulted in the crystallization of A-type granitoids with some gabbroic rocks in northwest Iran.

  8. 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.

  9. Power in the pacific

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    Highlights of the fourth Pacific Basin Nuclear Conference are presented, with the emphasis on opportunities for Canadian nuclear exports to the region. Japan and Korea are pressing ahead with nuclear generating programs to reduce their dependence on imported oil. Korea aims to increase the Korean content of its nuclear industry, and to participate in international ventures. China plans several nuclear power stations. In Canada and the U.S.A., no recent domestic orders have been received. Mexico is financially constrained to delay its nuclear program for about ten years. Indonesia is starting with a research reactor

  10. Arbutus menziesii Pursh. Pacific madrone

    Science.gov (United States)

    Philip M. McDonald

    1990-01-01

    Pacific madrone (Arbutus menziesii) is one of the most widely distributed tree species native to the Pacific coast. Named for its discoverer, Archibald Menzies, a 19th century Scottish physician and naturalist, the species is called arbutus in Canada, and madrone, madroña, or madroño in the United States. The latter name is...

  11. 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.

  12. 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

  13. 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.

  14. Effects of ancestral populations on entrepreneurial founding and failure: private liquor stores in Alberta, 1994--2003

    OpenAIRE

    Glen Dowell; Robert J. David

    2011-01-01

    Until 1993, all liquor stores in the Canadian province of Alberta were government owned and run. In the fall of 1993, the provincial government exited liquor retailing, all government stores were shut down, and entrepreneurs were allowed to open private liquor stores. In this article, we take advantage of this abrupt regulatory change in the Alberta liquor-retailing industry to address two related issues that have received little empirical attention. First, we investigate how an ancestral pop...

  15. Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade.

    Science.gov (United States)

    Jackson, Hazel; Strubbe, Diederik; Tollington, Simon; Prys-Jones, Robert; Matthysen, Erik; Groombridge, Jim J

    2015-08-01

    Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is paramount for elucidating mechanisms underlying biological invasions. Among birds, the ring-necked parakeet (Psittacula krameri) is one of the most successful invasive species, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring-necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Successful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences. © 2015 John Wiley & Sons Ltd.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. COMPONENTES NUTRICIONALES Y ANTIOXIDANTES DE DOS ESPECIES DE GUAJE (Leucaena spp.: UN RECURSO ANCESTRAL SUBUTILIZADO

    Directory of Open Access Journals (Sweden)

    Nallely Román-Cortés

    2014-01-01

    Full Text Available El guaje ( Leucaena spp. es una planta de vaina y semillas comestibles, un recurso ancestral subutilizado por los pueblos mesoamericanos. El valor nutricional y nutracéutico del guaje se desconoce pese a su consumo vigente en las poblaciones rurales. El objetivo de este trabajo fue evaluar el contenido de minerales, compo - nentes nutricionales y antioxidantes para contribuir a la revalorización alimentaria del guaje rojo ( L. esculenta Benth. y verde ( L. leucocephala Lam.. Los contenidos de antocianinas, flavonoides, fenoles totales, taninos y actividad antioxidante se cuantificaron, así como la composición proximal y mineral. Las semillas de guaje rojo superaron a las de guaje verde en los contenidos de N, Mg, Mn, P y Zn; en contraste, las semillas de guaje verde presentaron niveles mayores de Na y de Fe. El contenido de fibra cruda fue 10.55 y 10.07 % en guaje rojo y verde, respectivamente, mientras que el de proteína fue 33.12 % en guaje rojo y 31.7 % en el verde. El alto contenido de compuestos fenólicos fue mayor en las semillas frescas de guaje rojo (1,088.70 mg equivalentes de ácido gálico [EAG]·100 g -1 p. f. que en las verdes (969.09 mg EAG·100 g -1 p. f., pero las últimas presen - taron mayor cantidad de taninos. La elevada actividad secuestradora de radicales libres (97.22 a 98.11 % obtenida por el método ABTS ( á cido 2,2’-azino-bis(3-etilben-zotiazolin-6-sulfónico, puede estar asociada al contenido de compuestos fenólicos. En conclusión, las semillas de guaje podrían considerarse un alimento funcional, principalmente las de guaje rojo debido a su calidad nutricional y mayor actividad antioxidante.

  3. 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

  4. Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate?

    Science.gov (United States)

    Holland, L. Z.; Holland, N. D.

    2001-01-01

    Recent studies of protochordates (ascidian tunicates and amphioxus) have given insights into possible ancestors of 2 of the characteristic features of the vertebrate head: neural crest and placodes. The neural crest probably evolved from cells on either side of the neural plate-epidermis boundary in a protochordate ancestral to the vertebrates. In amphioxus, homologues of several vertebrate neural crest marker genes (BMP2/4, Pax3/7, Msx, Dll and Snail) are expressed at the edges of the neural plate and/or adjacent nonneural ectoderm. Some of these markers are also similarly expressed in tunicates. In protochordates, however, these cells, unlike vertebrate neural crest, neither migrate as individuals through embryonic tissues nor differentiate into a wide spectrum of cell types. Therefore, while the protochordate ancestor of the vertebrates probably had the beginnings of a genetic programme for neural crest formation, this programme was augmented in the earliest vertebrates to attain definitive neural crest. Clear homologues of vertebrate placodes are lacking in protochordates. However, both amphioxus and tunicates have ectodermal sensory cells. In tunicates these are all primary neurons, sending axons to the central nervous system, while in amphioxus, the ectodermal sensory cells include both primary neurons and secondary neurons lacking axons. Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons. Similarly, biochemical, morphological and gene expression data suggest that amphioxus and tunicates also have homologues of the adenohypophysis, one of the few vertebrate structures derived from nonneurogenic placodes. In contrast, the origin of the other vertebrate placodes is very uncertain.

  5. Functions of two distinct prolactin-releasing peptides evolved from a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Tetsuya eTachibana

    2014-11-01

    Full Text Available Prolactin-releasing peptide (PrRP is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius RFa (C-RFa, which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.

  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. 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.

  8. 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.

  9. 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...

  10. Origin of pegmatites and fluids at Ponta Negra (RJ, Brazil) during late- to post-collisional stages of the Gondwana Assembly

    Science.gov (United States)

    Bongiolo, Everton Marques; Renac, Christophe; Piza, Patricia d'Almeida de Toledo; Schmitt, Renata da Silva; Mexias, André Sampaio

    2016-01-01

    the pegmatites. A linear trend of decreasing CO2 content and δ13CCO2 is consistent with mixtures between (i) carbon derived from organic matter or volatilization of skarns and (ii) inorganic carbon (carbonate). Based on the data obtained, we propose that the pegmatites of Ponta Negra are close to an LCT-type geochemical signature (highly peraluminous magmas with normative corundum), and originated by partial melting of the metasedimentary Palmital succession at depth, during the waning stages of the Búzios Orogeny. The primary melts of the PNP cross-cut both the Neoproterozoic supracrustals and the Paleoproterozoic orthogneissic basement during its ascent and emplacement at higher crustal levels. Variable melt sources explain the slight differences in geochemical compositions among the studied rocks within the metasedimentary succession, which probably include Mn-bearing exhalites, as well as differentiation processes. The 454 ± 5 Ma U-Pb (zircon) age of the Cajú syenogranite overlaps previous geochronological data of 440 ± 11 Ma obtained on a pegmatite dyke at Ponta Negra, bracketing and extending the time interval for the Gondwana assembly collapse magmatism in the region. The heat that triggered this magmatic event could still be a consequence of the collisional orogeny, increasing contents of heat-producing elements, or, a large intraplate extension that followed the Gondwana amalgamation and initiated the formation of Paleozoic basins.

  11. Geology and metallogeny of the Ar Rayn terrane, eastern Arabian shield: Evolution of a Neoproterozoic continental-margin arc during assembly of Gondwana within the East African orogen

    Science.gov (United States)

    Doebrich, J.L.; Al-Jehani, A. M.; Siddiqui, A.A.; Hayes, T.S.; Wooden, J.L.; Johnson, P.R.

    2007-01-01

    characteristics of the Ar Rayn terrane are analogous to the Andean continental margin of Chile, with opposite subduction polarity. The Ar Rayn terrane represents a continental margin arc that lay above a west-dipping subduction zone along a continental block represented by the Afif composite terrane. The concentration of epithermal, porphyry Cu and IOCG mineral systems, of central arc affiliation, along the AAF suggests that the AAF is not an ophiolitic suture zone, but originated as a major intra-arc fault that localized magmatism and mineralization. West-directed oblique subduction and ultimate collision with a land mass from the east (East Gondwana?) resulted in major transcurrent displacement along the AAF, bringing the eastern part of the arc terrane to its present exposed position, juxtaposed across the AAF against a back-arc basin assemblage represented by the Abt schist of the Ad Dawadimi terrane. Our findings indicate that arc formation and accretionary processes in the Arabian shield were still ongoing into the latest Neoproterozoic (Ediacaran), to about 620-600 Ma, and lead us to conclude that evolution of the Ar Rayn terrane (arc formation, accretion, syn- to postorogenic plutonism) defines a final stage of assembly of the Gondwana supercontinent along the northeastern margin of the East African orogen. ?? 2007 Elsevier B.V. All rights reserved.

  12. 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)

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

    International Nuclear Information System (INIS)

    Ortiz, Agustin; Hauser, Natalia

    2015-01-01

    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)

  14. Australian provenance for Upper Permian to Cretaceous rocks forming accretionary complexes on the New Zealand sector of the Gondwana land margin

    International Nuclear Information System (INIS)

    Pickard, A.L.; Barley, M.E.

    2000-01-01

    U-Pb (SHRIMP) detrital zircon age patterns are reported for 12 samples of Permian to Cretaceous turbiditic quartzo-feldspathic sandstone from the Torlesse and Waipapa suspect terranes of New Zealand. Their major Permian to Triassic, and minor Early Palaeozoic and Mesoproterozoic, age components indicate that most sediment was probably derived from the Carboniferous to Triassic New England Orogen in northeastern Australia. Rapid deposition of voluminous Torlesse/Waipapa turbidite fans during the Late Permian to Late Triassic appears to have been directly linked to uplift and exhumation of the magmatically active orogen during the 265-230 Ma Hunter-Bowen event. This period of cordilleran-type orogeny allowed transport of large volumes of quartzo-feldspathic sediment across the convergent Gondwana land margin. Post-Triassic depocentres also received (recycled?) sediment from the relict orogen as well as from Jurassic and Cretaceous volcanic provinces now offshore from southern Queensland and northern New South Wales. The detailed provenance-age fingerprints provided by the detrital zircon data are also consistent with progressive southward derivation of sediment: from northeastern Queensland during the Permian, southeastern Queensland during the Triassic, and northeastern New South Wales - Lord Howe Rise - Norfolk Ridge during the Jurassic to Cretaceous. Although the dextral sense of displacement is consistent with the tectonic regime during this period, detailed characterisation of source terranes at this scale is hindered by the scarcity of published zircon age data for igneous and sedimentary rocks in Queensland and northern New South Wales. Mesoproterozoic and Neoproterozoic age components cannot be adequately matched with likely source terranes in the Australian-Antarctic Precambrian craton, and it is possible they originated in the Proterozoic cores of the Cathaysia and Yangtze Blocks of southeast China. Copyright (1999) Geological Society of Australia

  15. 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.

  16. 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.

  17. 76 FR 33641 - Safety Zone; The Pacific Grove Feast of Lanterns, Fireworks Display, Pacific Grove, CA

    Science.gov (United States)

    2011-06-09

    ...-AA00 Safety Zone; The Pacific Grove Feast of Lanterns, Fireworks Display, Pacific Grove, CA AGENCY... support of the Pacific Grove Feast of Lanterns Fireworks Display. This safety zone is established to... Purpose Pacific Grove Feast of Lanterns will sponsor the Pacific Grove Feast of Lanterns Fireworks Display...

  18. Pacific Northwest regional AGU meeting

    Science.gov (United States)

    Hyndman, Roy

    The 27th Annual Pacific Northwest Regional American Geophysical Union Meeting, held September 25 and 26, 1980, was hosted by the Pacific Geoscience Centre at the Institute of Ocean Sciences, near Victoria, British Columbia. A total of 79 papers was presented to the 150 registrants in six general sessions: seismology; electromagnetic induction; general geophysics; volcanology; hydrology; and oceanography, and in three special symposia: ‘The Queen Charlotte-Fairweather fault system and other active faults of the Pacific Northwest’ ‘Coastal circulation in the northeast Pacific’ and ‘Studies of the eruption of Mount St. Helens.’

  19. 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.

  20. 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.

  1. A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts.

    Directory of Open Access Journals (Sweden)

    Xiaodong Jiao

    report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin.

  2. 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...

  3. A Cambrian mixed carbonate-siliciclastic platform in SW Gondwana: evidence from the Western Sierras Pampeanas (Argentina) and implications for the early Paleozoic paleogeography of the proto-Andean margin

    Science.gov (United States)

    Ramacciotti, Carlos D.; Casquet, César; Baldo, Edgardo G.; Galindo, Carmen; Pankhurst, Robert J.; Verdecchia, Sebastián O.; Rapela, Carlos W.; Fanning, Mark

    2018-05-01

    The Western Sierras Pampeanas (WSP) of Argentina record a protracted geological history from the Mesoproterozoic assembly of the Rodinia supercontinent to the early Paleozoic tectonic evolution of SW Gondwana. Two well-known orogenies took place at the proto-Andean margin of Gondwana in the Cambrian and the Ordovician, i.e., the Pampean (545-520 Ma) and Famatinian (490-440 Ma) orogenies, respectively. Between them, an extensive continental platform was developed, where mixed carbonate-siliciclastic sedimentation occurred. This platform was later involved in the Famatinian orogeny when it underwent penetrative deformation and metamorphism. The platform apparently extended from Patagonia to northwestern Argentina and the Eastern Sierras Pampeanas, and has probable equivalents in SW Africa, Peru, and Bolivia. The WSP record the outer (deepest) part of the platform, where carbonates were deposited in addition to siliciclastic sediments. Detrital zircon U-Pb SHRIMP ages from clastic metasedimentary successions and Sr-isotope compositions of marbles from the WSP suggest depositional ages between ca. 525 and 490 Ma. The detrital zircon age patterns further suggest that clastic sedimentation took place in two stages. The first was sourced mainly from re-working of the underlying Neoproterozoic metasedimentary rocks and the uplifted core of the early Cambrian Pampean orogen, without input from the Paleoproterozoic Río de la Plata craton. Sediments of the second stage resulted from the erosion of the still emerged Pampean belt and the Neoproterozoic Brasiliano orogen in the NE with some contribution from the Río de la Plata craton. An important conclusion is that the WSP basement was already part of SW Gondwana in the early Cambrian, and not part of the exotic Precordillera/Cuyania terrane, as was previously thought.

  4. 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.

  5. Wave energy: a Pacific perspective.

    Science.gov (United States)

    Paasch, Robert; Ruehl, Kelley; Hovland, Justin; Meicke, Stephen

    2012-01-28

    This paper illustrates the status of wave energy development in Pacific rim countries by characterizing the available resource and introducing the region's current and potential future leaders in wave energy converter development. It also describes the existing licensing and permitting process as well as potential environmental concerns. Capabilities of Pacific Ocean testing facilities are described in addition to the region's vision of the future of wave energy.

  6. Reducing Maori and Pacific Inequalities

    OpenAIRE

    The Treasury

    2001-01-01

    Over the last fifty years the Maori and non-Maori populations have slowly and unevenly become more similar on a range of key demographic, social and economic outcomes. This has principally been driven by increased geographic and social proximity between the two groups. There is evidence that similar processes may be operating for migrant peoples from the Pacific. Many Maori and Pacific people do better than the population median. Conversely, on most outcomes, a much greater number of people o...

  7. Reestablishment of the Ancestral Cascades Arc in Western Nevada and Eastern California by Rollback of the Shallow Farallon Slab

    Science.gov (United States)

    Henry, C. D.; Cousens, B.; John, D. A.; Colgan, J. P.

    2009-12-01

    The character and even existence of an ancestral Tertiary Cascades arc in western Nevada and eastern California south of the modern arc are controversial. Based on extensive published and new data on the regional distribution, timing, style, and composition of magmatism, we conclude that an ancestral arc was established by WSW migration of magmatism into western NV and the northeastern Sierra Nevada in the Oligocene and Miocene as a result of progressive rollback of the shallow subducted slab. Magma migration started with the well-known southward sweep through NE NV and NW UT between ~46 and 36 Ma. By ~30 Ma, migration of the leading edge and central belt of activity was much more WSW, especially after removing younger ~E-W extension. Locally sourced, initially dispersed and small volume, intermediate to mafic lavas erupted in western NV and northeastern CA by ~30 Ma and the eastern Sierra Nevada by ~28 Ma, contemporaneous with the much more voluminous ignimbrite flare-up in central NV. As migration continued, the ignimbrite flare-up tapered off. A voluminous, NNW-trending, dominantly effusive volcanic belt developed by ~22-18 Ma in western NV and was continuous from the Bodie Hills (CA/NV) to the Warner Range (northeast CA) by ~16-15 Ma. The volcanic belt was dominated by intermediate to mafic magmas compositionally similar to those of the modern south Cascades arc but reflecting melting of an old, subduction-modified lithosphere (Cousens et al. 2008; Geosphere). Extensive middle Miocene bimodal rocks related to the Yellowstone hotspot cover these rocks in NW NV, NE CA, and SE OR, but 30-23 Ma, intermediate to mafic and lesser silicic rocks are voluminous wherever older rocks are exposed below the middle Miocene rocks. Between ~25 Ma and the present, magmatism migrated WSW at an average rate of ~8 km/Ma but was at least partly stepwise, as exemplified by an ~50 km westward step at 2 Ma in the Lassen area (Guffanti et al. 1990, JGR). The magmatic belt was as much

  8. Founder haplotype analysis of Fanconi anemia in the Korean population finds common ancestral haplotypes for a FANCG variant.

    Science.gov (United States)

    Park, Joonhong; Kim, Myungshin; Jang, Woori; Chae, Hyojin; Kim, Yonggoo; Chung, Nack-Gyun; Lee, Jae-Wook; Cho, Bin; Jeong, Dae-Chul; Park, In Yang; Park, Mi Sun

    2015-05-01

    A common ancestral haplotype is strongly suggested in the Korean and Japanese patients with Fanconi anemia (FA), because common mutations have been frequently found: c.2546delC and c.3720_3724delAAACA of FANCA; c.307+1G>C, c.1066C>T, and c.1589_1591delATA of FANCG. Our aim in this study was to investigate the origin of these common mutations of FANCA and FANCG. We genotyped 13 FA patients consisting of five FA-A patients and eight FA-G patients from the Korean FA population. Microsatellite markers used for haplotype analysis included four CA repeat markers which are closely linked with FANCA and eight CA repeat markers which are contiguous with FANCG. As a result, Korean FA-A patients carrying c.2546delC or c.3720_3724delAAACA did not share the same haplotypes. However, three unique haplotypes carrying c.307+1G>C, c.1066C > T, or c.1589_1591delATA, that consisted of eight polymorphic loci covering a flanking region were strongly associated with Korean FA-G, consistent with founder haplotypes reported previously in the Japanese FA-G population. Our finding confirmed the common ancestral haplotypes on the origins of the East Asian FA-G patients, which will improve our understanding of the molecular population genetics of FA-G. To the best of our knowledge, this is the first report on the association between disease-linked mutations and common ancestral haplotypes in the Korean FA population. © 2015 John Wiley & Sons Ltd/University College London.

  9. 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.

  10. 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

  11. 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

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

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E; Bedoya, Gabriel

    2015-01-01

    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.

  13. Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases.

    Science.gov (United States)

    Castro-Fernandez, Víctor; Herrera-Morande, Alejandra; Zamora, Ricardo; Merino, Felipe; Gonzalez-Ordenes, Felipe; Padilla-Salinas, Felipe; Pereira, Humberto M; Brandão-Neto, Jose; Garratt, Richard C; Guixe, Victoria

    2017-09-22

    One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales , Methanosarcinales , and Methanococcales , as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Estimation of the net acid load of the diet of ancestral preagricultural Homo sapiens and their hominid ancestors.

    Science.gov (United States)

    Sebastian, Anthony; Frassetto, Lynda A; Sellmeyer, Deborah E; Merriam, Renée L; Morris, R Curtis

    2002-12-01

    Natural selection has had diet resulting from the inventions of agriculture and animal husbandry. The objective was to estimate the net systemic load of acid (net endogenous acid production; NEAP) from retrojected ancestral preagricultural diets and to compare it with that of contemporary diets, which are characterized by an imbalance of nutrient precursors of hydrogen and bicarbonate ions that induces a lifelong, low-grade, pathogenically significant systemic metabolic acidosis. Using established computational methods, we computed NEAP for a large number of retrojected ancestral preagricultural diets and compared them with computed and measured values for typical American diets. The mean (+/- SD) NEAP for 159 retrojected preagricultural diets was -88 +/- 82 mEq/d; 87% were net base-producing. The computational model predicted NEAP for the average American diet (as recorded in the third National Health and Nutrition Examination Survey) as 48 mEq/d, within a few percentage points of published measured values for free-living Americans; the model, therefore, was not biased toward generating negative NEAP values. The historical shift from negative to positive NEAP was accounted for by the displacement of high-bicarbonate-yielding plant foods in the ancestral diet by cereal grains and energy-dense, nutrient-poor foods in the contemporary diet-neither of which are net base-producing. The findings suggest that diet-induced metabolic acidosis and its sequelae in humans eating contemporary diets reflect a mismatch between the nutrient composition of the diet and genetically determined nutritional requirements for optimal systemic acid-base status.

  15. 76 FR 6402 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-02-04

    ... Pacific Fishery Management Council's (Pacific Council) Groundfish Essential Fish Habitat Review Committee... review of Essential Fish Habitat (EFH) descriptions for Pacific Coast groundfish species. Major topics of...

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

    Science.gov (United States)

    Caspeta, Luis; Nielsen, Jens

    2015-07-21

    A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using 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. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number 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. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes. Yeast thermotolerance can significantly reduce the production costs of biomass

  17. 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

    to the other PV proteins. The PV sequences were fused to a T cell adjuvant, the murine invariant chain and encoded in a recombinant adenoviral vector which was administered to naïve outbred mice. By measuring T cell responses induced by these different vaccines and towards peptide pools representing 3...... 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...

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

    2018-06-01

    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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  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. Asthma and Native Hawaiians/Pacific Islanders

    Science.gov (United States)

    ... Population Profiles > Native Hawaiian/Other Pacific Islander > Asthma Asthma and Native Hawaiians/Pacific Islanders National data for ... very limited. While all of the causes of asthma remain unclear, children exposed to secondhand tobacco smoke ...

  10. Immunizations and Asians and Pacific Islanders

    Science.gov (United States)

    ... and Data > Minority Population Profiles > Asian American > Immunizations Immunizations and Asians and Pacific Islanders Asian/Pacific Islander ... 35 months reached the Healthy People goal for immunizations for hepatitis B, MMR (measles-mumps-rubella), polio ...

  11. 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...

  12. 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

  13. 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

  14. 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

  15. 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

  16. Pacific Rim log trade: determinants and trends.

    Science.gov (United States)

    Donald F. Flora; Andrea L. Anderson; Wendy J. McGinnls

    1991-01-01

    Pacific Rim trade in softwood logs amounts to about $3 billion annually, of which the U.S. share is about $2 billion. Log exporting is a significant part of the forest economy in the Pacific Northwest. The 10 major Pacific Rim log-trading client and competitor countries differ widely in their roles in trade and in their policies affecting the industry.

  17. 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.

  18. 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.

  19. 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).

  20. Triassic arc-derived detritus in the Triassic Karakaya accretionary complex was not derived from either the S Eurasian margin (Istanbul terrane) or the N Gondwana margin (Taurides)

    Science.gov (United States)

    Ustaömer, Timur; Ayda Ustaömer, Petek; Robertson, Alastair H. F.; Gerdes, Axel; Zulauf, Gernold

    2014-05-01

    We present new U-Pb zircon source age data for Upper Triassic sandstones of the Istanbul Terrane (S Eurasian margin) and also for Triassic sandstones of the Taurides (N Gondwana margin). The main aim is to detect and quantify the contribution of Triassic magmatism as detritus to either of these crustal blocks. This follows the recent discovery of a Triassic magmatic arc source for the Triassic sandstones of the Palaeotethyan Karakaya subduction-accretion complex (Ustaömer et al. 2013; this meeting). Carboniferous (Variscan) zircon grains also form a significant detrital population, plus several more minor populations. Six sandstone samples were studied, two from the İstanbul Terrane (Bakırlıkıran Formation of the Kocaeli Triassic Basin) and four from the Tauride Autochthon (latest Triassic Üzümdere Formation and Mid-Triassic Kasımlar Formations; Beyşehir region). Detrital zircon grains were dated by the laser ablation-inductively coupled plasma-mass spectrometer (LA-ICP-MS) U-Pb method at Goethe University, Frankfurt. Our results do not reveal Triassic detritus in the Üzümdere Formation. The U-Pb age of the analysed zircon grains ranges from 267 Ma to 3.2 Ga. A small fraction of Palaeozoic zircons are Permian (267 to 296 Ma), whereas the remainder are Early Palaeozoic. Ordovician grains (4%) form two age clusters, one at ca. 450 Ma and the other at ca. 474 Ma. Cambrian-aged grains dominate the zircon population, while the second largest population is Ediacaran (576 to 642 Ma). Smaller populations occur at 909-997 Ma, 827-839 Ma, 1.8-2.0 Ga and 2.4-2.6 Ga. The sandstones of the Kasımlar Formation have similar zircon age cluster to those of the somewhat younger Üzümdere Formation, ranging from 239 Ma to 2.9 Ga. A few grains gave Anisian ages. Cambrian zircon grains are less pronounced than in the Kasımlar Formation compared to the Üzümdere Formation. The detrital zircon record of Tauride sandstones, therefore, not indicates significant contribution

  1. 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…

  2. 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

  3. 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.

  4. 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.

  5. ¿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.

  6. Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates.

    Science.gov (United States)

    Melin, Amanda D; Matsushita, Yuka; Moritz, Gillian L; Dominy, Nathaniel J; Kawamura, Shoji

    2013-05-22

    Tarsiers are small nocturnal primates with a long history of fuelling debate on the origin and evolution of anthropoid primates. Recently, the discovery of M and L opsin genes in two sister species, Tarsius bancanus (Bornean tarsier) and Tarsius syrichta (Philippine tarsier), respectively, was interpreted as evidence of an ancestral long-to-middle (L/M) opsin polymorphism, which, in turn, suggested a diurnal or cathemeral (arrhythmic) activity pattern. This view is compatible with the hypothesis that stem tarsiers were diurnal; however, a reversion to nocturnality during the Middle Eocene, as evidenced by hyper-enlarged orbits, predates the divergence of T. bancanus and T. syrichta in the Late Miocene. Taken together, these findings suggest that some nocturnal tarsiers possessed high-acuity trichromatic vision, a concept that challenges prevailing views on the adaptive origins of the anthropoid visual system. It is, therefore, important to explore the plausibility and antiquity of trichromatic vision in the genus Tarsius. Here, we show that Sulawesi tarsiers (Tarsius tarsier), a phylogenetic out-group of Philippine and Bornean tarsiers, have an L opsin gene that is more similar to the L opsin gene of T. syrichta than to the M opsin gene of T. bancanus in non-synonymous nucleotide sequence. This result suggests that an L/M opsin polymorphism is the ancestral character state of crown tarsiers and raises the possibility that many hallmarks of the anthropoid visual system evolved under dim (mesopic) light conditions. This interpretation challenges the persistent nocturnal-diurnal dichotomy that has long informed debate on the origin of anthropoid primates.

  7. 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.

  8. 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.

  9. Major zircon megacryst suites of the Indo-Pacific lithospheric margin (ZIP) and their petrogenetic and regional implications

    Science.gov (United States)

    Sutherland, Lin; Graham, Ian; Yaxley, Gregory; Armstrong, Richard; Giuliani, Gaston; Hoskin, Paul; Nechaev, Victor; Woodhead, Jon

    2016-04-01

    Zircon megacrysts (± gem corundum) appear in basalt fields of Indo-Pacific origin over a 12,000 km zone (ZIP) along West Pacific continental margins. Age-dating, trace element, oxygen and hafnium isotope studies on representative zircons (East Australia-Asia) indicate diverse magmatic sources. The U-Pb (249 to 1 Ma) and zircon fission track (ZFT) ages (65 to 1 Ma) suggest thermal annealing during later basalt transport, with < 1 to 203 Ma gaps between the U-Pb and ZFT ages. Magmatic growth zonation and Zr/Hf ratios (0.01-0.02) suggest alkaline magmatic sources, while Ti—in—zircon thermometry suggests that most zircons crystallized within ranges between 550 and 830 °C. Chondrite-normalised multi-element plots show variable enrichment patterns, mostly without marked Eu depletion, indicating little plagioclase fractionation in source melts. Key elements and ratios matched against zircons from magmatic rocks suggest a range of ultramafic to felsic source melts. Zircon O-isotope ratios (δ18O in the range 4 to 11‰) and initial Hf isotope ratios (ɛHf in the range +2 to +14) encompass ranges for both mantle and crustal melts. Calculated Depleted Mantle (TDM 0.03-0.56 Ga) and Crustal Residence (0.20-1.02 Ga) model ages suggest several mantle events, continental break-ups (Rodinia and Gondwana) and convergent margin collisions left imprints in the zircon source melts. East Australian ZIP sites reflect prolonged intraplate magmatism (~85 Ma), often during times of fast-migrating lithosphere. In contrast, East Asian-Russian ZIP sites reflect later basaltic magmatism (<40 Ma), often linked to episodes of back-arc rifting and spreading, slow-migrating lithosphere and slab subduction.

  10. 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...

  11. 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.

  12. United States Pacific Command, Asia-Pacific Economic Update.

    Science.gov (United States)

    1998-04-01

    export process more efficient and effective by reducing export barriers and expanding markets abroad. The strategy coordinates the U.S. Government’s...investment from Western companies, such as Boeing and Mercedes - Benz , since China opened to the outside world the late 1970s.12 North Korea’s arms... markets for American trade and investment. Expanding wealth and opportunity in many Asia-Pacific countries have facilitated a transition to greater

  13. 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

    Science.gov (United States)

    Soejono, Igor; Janoušek, Vojtěch; Žáčková, Eliška; Sláma, Jiří; Konopásek, Jiří; Machek, Matěj; Hanžl, Pavel

    2017-09-01

    Cadomian magmatic complexes of the Brunovistulian Domain crop out at the eastern termination of the Bohemian Massif. However, the age, nature and geotectonic affinity of some of pre-Variscan (meta-)igneous rock complexes from this domain are still unknown. Geochronological and geochemical study of the granitic rocks across the Brunovistulian Domain reveals new information about the timing and nature of this magmatic activity originally situated along the northern margin of Gondwana. Zircon U-Pb data (601 ± 3 Ma, Brno Massif; 634 ± 6 Ma, paraautochtonous core of the Svratka Dome; 568 ± 3 Ma, Bíteš orthogneiss) from the allochtonous Moravicum indicate the prolonged magmatic activity within the Brunovistulian Domain during the Ediacaran. The major- and trace-element and Sr-Nd isotopic signatures show heterogeneous geochemical characteristics of the granitic rocks and suggest a magmatic-arc geotectonic setting. The two-stage Depleted Mantle Nd model ages ( c. 1.3-2.0 Ga) indicate derivation of the granitic rocks from a relatively primitive crustal source, as well as from an ancient and evolved continental crust of the Brunovistulian Domain. These results constrain the magmatic-arc activity to c. 635-570 Ma and provide a further evidence for a long-lived (at least c. 65 Myr) and likely episodic subduction-related magmatism at the northern margin of Gondwana. The presence of granitic intrusions derived from variously mature crustal sources at different times suggests heterogeneous crustal segments to having been involved in the magmatic-arc system during its multistage evolution.

  14. Sources of basalt suites in the Campos and Pelotas basins (South-Southeast of Brazil) and geo dynamic breakup models for Western Gondwana; Tipos de fontes associadas as suites basalticas de Campos e de Pelotas (Sul-Sudeste) e modelos geodinamicos de ruptura do Gondwana ocidental

    Energy Technology Data Exchange (ETDEWEB)

    Lobo, Janaina Teixeira; Valente, Sergio de Castro; Szatmari, Peter; Duarte, Beatriz Paschoal [Universidade Estadual do Rio de Janeiro, RJ (Brazil). Faculdade de Geologia. Pos-graduacao]. E-mail: janaina_lobo@hotmail.com

    2006-05-15

    Based essentially on geochemical data, this work aims at defining constrain to the petrogenesis of the Eocretacious basalts from the Campos and Pelotas marginal rift basins (South-Southeast Brazil). Geochemical modeling, including quantification of mantle sources and binary mixing methods, were performed in order to contribute to the elaboration of geo dynamic models related to the initial stages of Gondwana breakup. Basalts from Campos and Pelotas basins comprise two transitional series with tholeiitic affinities. All basalts from the Campos Basin can be assigned to a low-TiO2 suite (TiO2 1.20 +- 0.12 wt %; Ti/Y = 272); whereas basalts from the Pelotas Basin comprise a low-(TiO2 = 1.19 +- 0.02 wt %; Ti/Y = 288) and a high-TiO2 suites (TiO2 = 2.10 +- 0.19 wt %; Ti/Y = 387). Non-modal batch partial melting modeling showed that the La/YbN = 5.78 generation ratio of the Campos Basin suite was obtained from 21% of partial melting of lherzolite garnet. The same model required a source with smaller amounts of garnet (melted at 28%) to generate the La/YbN generation ratio of the low-TiO2 suite of the Pelotas Basin. Larger amounts of grenade and less partial melting (22%) were necessary to generate the La/YbN ratio of the high-TiO2 suite of the Pelotas Basin. The simple binary model shows that parent compositions of Campos and Pelotas cannot result from the mixture of T C (Tristao da Cunha) and SCLM (Sub continental Lithospheric Mantle). The best results obtained suggest the participation of component N-Morb in the generation of basalt suites of the Campos and Pelotas basins (respectively 61% and 93% of partial melting). Tristao da Cunha seems to have been an important component to the generation of the basalt suite of the Campos Basin (at 39% of partial melting). In Pelotas, the model indicates restricted contribution of SCLM reservoirs. (author)

  15. 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.

  16. 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

  17. 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

  18. Gridded multibeam bathymetry of Baker 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 Baker Island, within the Pacific Remote Island Areas - Central Pacific Ocean. Bottom coverage was achieved in depths...

  19. 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...

  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. 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...

  2. 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...

  3. 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...

  4. 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

  5. Sediment Evaluation Framework for the Pacific Northwest

    Science.gov (United States)

    The Sediment Evaluation Framework provides a regional framework for assessment, characterization and management of sediments in the Pacific Northwest to determine suitability for unconfined in-water disposal.

  6. Pacific oyster culture in British Columbia

    National Research Council Canada - National Science Library

    Quayle, D. B; Quayle, Daniel Branch

    1988-01-01

    .... Harvesting, processing, and storage methods are described. The problems of Pacific oyster culture include industrial and sewage pollution, paralytic shellfish poisoning along with predators and disease...

  7. 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.

  8. 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.

  9. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

    Science.gov (United States)

    Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

    2016-07-01

    This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

  10. 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.

  11. Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia.

    Science.gov (United States)

    Rodriguez, Libia M; Giraldo, Mabel C; Velasquez, Laura I; Alvarez, Cristiam M; Garcia, Luis F; Jimenez-Del-Rio, Marlene; Velez-Pardo, Carlos

    2015-03-01

    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. 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.

  13. Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation.

    Science.gov (United States)

    Bampi, Giovana B; Bisso-Machado, Rafael; Hünemeier, Tábita; Gheno, Tailise C; Furtado, Gabriel V; Veliz-Otani, Diego; Cornejo-Olivas, Mario; Mazzeti, Pillar; Bortolini, Maria Cátira; Jardim, Laura B; Saraiva-Pereira, Maria Luiza

    2017-12-01

    Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder characterized by progressive cerebellar ataxia and epilepsy. The disease is caused by a pentanucleotide ATTCT expansion in intron 9 of the ATXN10 gene on chromosome 22q13.3. SCA10 has shown a geographical distribution throughout America with a likely degree of Amerindian ancestry from different countries so far. Currently available data suggest that SCA10 mutation might have spread out early during the peopling of the Americas. However, the ancestral origin of SCA10 mutation remains under speculation. Samples of SCA10 patients from two Latin American countries were analysed, being 16 families from Brazil (29 patients) and 21 families from Peru (27 patients) as well as 49 healthy individuals from Indigenous Quechua population and 51 healthy Brazilian individuals. Four polymorphic markers spanning a region of 5.2 cM harbouring the ATTCT expansion were used to define the haplotypes, which were genotyped by different approaches. Our data have shown that 19-CGGC-14 shared haplotype was found in 47% of Brazilian and in 63% of Peruvian families. Frequencies from both groups are not statistically different from Quechua controls (57%), but they are statistically different from Brazilian controls (12%) (p Quechuas, 19-15-CGGC-14-10, is found in 50% of Brazilian and in 65% of Peruvian patients with SCA10. These findings bring valuable evidence that ATTCT expansion may have arisen in a Native American chromosome.

  14. RESEARCH ON NON-DESTRUCTIVE TESTING TECHNOLOGY IN CONSERVATION REPAIR PROJECT OF ANCESTRAL TEMPLE IN MUKDEN PALACE

    Directory of Open Access Journals (Sweden)

    J. Yang

    2017-08-01

    Full Text Available 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.

  15. 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.

  16. 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.

  17. On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu.

    Science.gov (United States)

    Vielberg, Marie-Theres; Bauer, Verena C; Groll, Michael

    2018-03-02

    The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral β-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallized Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases. In contrast to their typical architecture, the Anbu protomer is a tightly interacting dimer that can assemble into a helical superstructure. Although Anbu features a catalytic triad of Thr1O γ , Asp17O δ1 and Lys32N ε , it is unable to hydrolyze standard protease substrates. The lack of activity might be caused by the incapacity of Thr1NH 2 to function as a Brønsted acid during substrate cleavage due to its missing activation via hydrogen bonding. Altogether, we demonstrate that the topology of the proteasomal fold is conserved in Anbu, but whether it acts as a protease still needs to be clarified. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. 76 FR 55363 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-09-07

    ... Pacific Fishery Management Council's (Pacific Council) Groundfish Management Team (GMT) [[Page 55364... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National...; telephone: (206) 526-6150. Council address: Pacific Fishery Management Council, 7700 NE Ambassador Place...

  19. 78 FR 25955 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-05-03

    ... Pacific Fishery Management Council's (Pacific Council) Highly Migratory Species Management Team (HMSMT... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... be implemented pursuant to the precautionary management framework for North Pacific albacore...

  20. 77 FR 75614 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-12-21

    ... Pacific Fishery Management Council's (Pacific Council) Highly Migratory Species Management Team (HMSMT... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National.... Council address: Pacific Fishery Management Council, 7700 NE. Ambassador Place, Suite 101, Portland, OR...

  1. 78 FR 27367 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-05-10

    ... Pacific Fishery Management Council's (Pacific Council) Highly Migratory Species Management Team (HMSMT... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... be implemented pursuant to the precautionary management framework for North Pacific albacore...

  2. 75 FR 49890 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-08-16

    ... Pacific Fishery Management Council's (Pacific Council) Coastal Pelagic Species Management Team (CPSMT) and... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... will be available at the following location: Pacific Fishery Management Council, Small Conference Room...

  3. 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.

  4. The pig story (tiboi sakkoko Storytelling of kinship, memories of the past, and rights to plots of ancestral land in Mentawai

    Directory of Open Access Journals (Sweden)

    Juniator Tulius

    2016-07-01

    Full Text Available This paper examines some significant elements of the pig story (tiboi sakkoko. This tale contains crucial information about the collective identity, ancestors and historical events affecting particular Mentawai kin-groups. As families do not preserve their culture and traditions in written form, storytellers of kin-groups have narrated the pig story from generation to generation so as to preserve it carefully. In the course of time, storytellers establish particular ways of telling their stories so as to remember the content and plot of the stories easily. Through the pig story, members of kin groups also recollect their ancestral place of origin and plots of ancestral lands. The role of human memory is indispensable to recalling all these important elements. Therefore, this paper analyses memories of the past of different family generations. To achieve its aims, this paper also evaluates the roles of family stories in the culture and traditions of Mentawai society.

  5. Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles.

    Science.gov (United States)

    Griffith, Oliver W; Blackburn, Daniel G; Brandley, Matthew C; Van Dyke, James U; Whittington, Camilla M; Thompson, Michael B

    2015-09-01

    To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses. © 2015 Wiley Periodicals, Inc.

  6. Archaeology of the Afro-Ecuadorians in La Concepción, Ancestral Territory of the Chota-Mira Valley (Carchi-Ecuador)

    OpenAIRE

    Balanzategui , Daniela Catalina

    2017-01-01

    Historical Archaeology of the African Diaspora in the Americas urges for interdisciplinary, collaborative, and intercultural approaches to shed light on how the material culture reflects conditions of enslavement and racialization, but also process of resistance and historical reparation. This investigation is organized in five articles connected around the topic of the cultural construction of the African Diaspora identities in the Afro-Ecuadorian Ancestral Territory of the Chota-Mira Valley...

  7. 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.

  8. The South Pacific Forestry Development Programme

    Science.gov (United States)

    Tang Hon Tat

    1992-01-01

    Only a few countries in the South Pacific are large enough for industrial forestry to be a key component of the national economy, but forests provide benefits to many people. The United Nations FA0 South Pacific Forestry Development Programme was established in April 1988, at Port Vila, Vanuatu, with a $385,000 budget, and 14 nations participating. The Programme's...

  9. Forestry research in Asia and Pacific

    Science.gov (United States)

    Jim Chamberlain; Erin Moore

    1992-01-01

    Much research has been done in Asia and the Pacific that might help Pacific Island countries produce more biomass and better manage their natural resources. National forestry research institutes throughout the region have examined many important aspects of forestry. Not all research findings are directly transferable between countries, but research methods and results...

  10. South Pacific Nuclear Free Zone Treaty

    International Nuclear Information System (INIS)

    1987-03-01

    The document contains the 3 Protocols to the South Pacific Nuclear Free Zone Treaty (INFCIRC-331) adopted by the South Pacific Forum at its 17th session in Suva on 8 August 1986. The treaty entered into force on 11 December 1986

  11. 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

  12. 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...

  13. Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus.

    Science.gov (United States)

    Kawasaki, Junna; Kawamura, Maki; Ohsato, Yoshiharu; Ito, Jumpei; Nishigaki, Kazuo

    2017-10-15

    Recombination events induce significant genetic changes, and this process can result in virus genetic diversity or in the generation of novel pathogenicity. We discovered a new recombinant feline leukemia virus (FeLV) gag gene harboring an unrelated insertion, termed the X region, which was derived from Felis catus endogenous gammaretrovirus 4 (FcERV-gamma4). The identified FcERV-gamma4 proviruses have lost their coding capabilities, but some can express their viral RNA in feline tissues. Although the X-region-carrying recombinant FeLVs appeared to be replication-defective viruses, they were detected in 6.4% of tested FeLV-infected cats. All isolated recombinant FeLV clones commonly incorporated a middle part of the FcERV-gamma4 5'-leader region as an X region. Surprisingly, a sequence corresponding to the portion contained in all X regions is also present in at least 13 endogenous retroviruses (ERVs) observed in the cat, human, primate, and pig genomes. We termed this shared genetic feature the commonly shared (CS) sequence. Despite our phylogenetic analysis indicating that all CS-sequence-carrying ERVs are classified as gammaretroviruses, no obvious closeness was revealed among these ERVs. However, the Shannon entropy in the CS sequence was lower than that in other parts of the provirus genome. Notably, the CS sequence of human endogenous retrovirus T had 73.8% similarity with that of FcERV-gamma4, and specific signals were detected in the human genome by Southern blot analysis using a probe for the FcERV-gamma4 CS sequence. Our results provide an interesting evolutionary history for CS-sequence circulation among several distinct ancestral viruses and a novel recombined virus over a prolonged period. IMPORTANCE Recombination among ERVs or modern viral genomes causes a rapid evolution of retroviruses, and this phenomenon can result in the serious situation of viral disease reemergence. We identified a novel recombinant FeLV gag gene that contains an unrelated

  14. Manganese in the North Pacific

    International Nuclear Information System (INIS)

    Bruland, K.W.; Landing, W.M.

    1980-01-01

    A quantitative and precise method for determination of dissolved M (nmol)/kg level in seawater has been developed and used to study the distribution of Mn in the northeast Pacific. Mn concentrations in the surface mixed layer decrease from 1.0 to 0.6 nmol/kg between the central gyre and the western boundary of the California Current, then increase to values from 2 to 6 nmol/kg near the coastal boundary (in contrast to the distribution of 210 Pb). Particulate Mn in the surface waters accounts for only about 1% of the total. Vertical distributions of Mn are characterized by surface maxima, minima near 300 m, maxima at mid-depth coinciding with the oxygen minimum and the labile nutrient maxima, and concentrations in Pacific bottom waters of approximately 0.2 nmol/kg. The oceanic distribution of Mn appears to be dominated by external inputs superimposed upon ovberall scavenging which can lead to Mn maxima in (1) the surface waters due to riverine and atmospheric sources; (2) the deep ocean as a result of hydrothermal injection and/or sediment resuspension; and (3) the oxygen minimum region resulting from in-situ breakdown of organic matter, in-situ MnO 2 reduction, and/or advective-diffusive transport of dissolved Mn from anoxic slope sediments. (orig.)

  15. 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.

  16. Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders.

    Science.gov (United States)

    Pineda, Sandy S; Sollod, Brianna L; Wilson, David; Darling, Aaron; Sunagar, Kartik; Undheim, Eivind A B; Kely, Laurence; Antunes, Agostinho; Fry, Bryan G; King, Glenn F

    2014-03-05

    Spiders have evolved pharmacologically complex venoms that serve to rapidly subdue prey and deter predators. The major toxic factors in most spider venoms are small, disulfide-rich peptides. While there is abundant evidence that snake venoms evolved by recruitment of genes encoding normal body proteins followed by extensive gene duplication accompanied by explosive structural and functional diversification, the evolutionary trajectory of spider-venom peptides is less clear. Here we present evidence of a spider-toxin superfamily encoding a high degree of sequence and functional diversity that has evolved via accelerated duplication and diversification of a single ancestral gene. The peptides within this toxin superfamily are translated as prepropeptides that are posttranslationally processed to yield the mature toxin. The N-terminal signal sequence, as well as the protease recognition site at the junction of the propeptide and mature toxin are conserved, whereas the remainder of the propeptide and mature toxin sequences are variable. All toxin transcripts within this superfamily exhibit a striking cysteine codon bias. We show that different pharmacological classes of toxins within this peptide superfamily evolved under different evolutionary selection pressures. Overall, this study reinforces the hypothesis that spiders use a combinatorial peptide library strategy to evolve a complex cocktail of peptide toxins that target neuronal receptors and ion channels in prey and predators. We show that the ω-hexatoxins that target insect voltage-gated calcium channels evolved under the influence of positive Darwinian selection in an episodic fashion, whereas the κ-hexatoxins that target insect calcium-activated potassium channels appear to be under negative selection. A majority of the diversifying sites in the ω-hexatoxins are concentrated on the molecular surface of the toxins, thereby facilitating neofunctionalisation leading to new toxin pharmacology.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Evolution and functional insights of different ancestral orthologous clades of chitin synthase genes in the fungal tree of life

    Directory of Open Access Journals (Sweden)

    Mu eLi

    2016-02-01

    Full Text Available Chitin synthases (CHSs are key enzymes in the biosynthesis of chitin, an important structural component of fungal cell walls that can trigger innate immune responses in host plants and animals. Members of CHS gene family perform various functions in fungal cellular processes. Previous studies focused primarily on classifying diverse CHSs into different classes, regardless of their functional diversification, or on characterizing their functions in individual fungal species. A complete and systematic comparative analysis of CHS genes based on their orthologous relationships will be valuable for elucidating the evolution and functions of different CHS genes in fungi. Here, we identified and compared members of the CHS gene family across the fungal tree of life, including 18 divergent fungal lineages. Phylogenetic analysis revealed that the fungal CHS gene family is comprised of at least 10 ancestral orthologous clades, which have undergone multiple independent duplications and losses in different fungal lineages during evolution. Interestingly, one of these CHS clades (class III was expanded in plant or animal pathogenic fungi belonging to different fungal lineages. Two clades (classes VIb and VIc identified for the first time in this study occurred mainly in plant pathogenic fungi from Sordariomycetes and Dothideomycetes. Moreover, members of classes III and VIb were specifically up-regulated during plant infection, suggesting important roles in pathogenesis. In addition, CHS-associated networks conserved among plant pathogenic fungi are involved in various biological processes, including sexual reproduction and plant infection. We also identified specificity-determining sites, many of which are located at or adjacent to important structural and functional sites that are potentially responsible for functional divergence of different CHS classes. Overall, our results provide new insights into the evolution and function of members of CHS gene

  2. Ancestral Relationships Using Metafounders

    DEFF Research Database (Denmark)

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

    2015-01-01

    Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist...

  3. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

    KAUST Repository

    DiBattista, Joseph; Whitney, Jonathan; Craig, Matthew T.; Hobbs, Jean-Paul A.; Rocha, Luiz A.; Feldheim, Kevin A.; Berumen, Michael L.; Bowen, Brian W.

    2016-01-01

    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 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Chronic Liver Disease and Asian Americans/Pacific Islanders

    Science.gov (United States)

    ... Cancer Asian/Pacific Islander Women Non-Hispanic White Women Asian/Pacific Islander/ Non-Hispanic White Ratio All Sites ... Cancer Asian/Pacific Islander Women Non-Hispanic White Women Asian/Pacific Islander/ Non-Hispanic White Ratio Liver & IBD* ...

  11. 77 FR 45591 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-08-01

    ... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... Pacific Fishery Management Council's (Pacific Council) Ad Hoc South of Humbug Pacific Halibut Workgroup..., monitoring, and allocation history of Pacific halibut in the area south of Humbug Mt. DATES: The conference...

  12. 76 FR 20959 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-04-14

    ... Pacific Fishery Management Council (Pacific Council) will convene a Pacific mackerel Stock Assessment... of the meeting is to review the Pacific mackerel stock assessment for 2011, in order to inform... action under Section 305(c) of the Magnuson-Stevens Fishery Conservation and Management Act, provided the...

  13. 21 CFR 161.170 - Canned Pacific salmon.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Canned Pacific salmon. 161.170 Section 161.170... § 161.170 Canned Pacific salmon. (a) Identity. (1) Canned Pacific salmon is the food prepared from one... forms of canned Pacific salmon are processed from fish prepared by removing the head, gills, and tail...

  14. 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.

  15. The IAEA '97 Pacific Ocean expedition

    International Nuclear Information System (INIS)

    Povinec, P.P.; Huynh-Ngoc, L.; Liong Wee Kwong, L.

    1999-01-01

    The International Atomic Energy Agency's Marine Environment Laboratory (IAEA-MEL) started in 1995 a five-year project 'Research on World-wide Marine Radioactivity', generously supported by the Government of Japan. In the framework of the project, IAEA-MEL conducted the 'IAEA '97 Pacific Ocean Expedition' to the NW Pacific Ocean from 21 October to 20 November, 1997. The objectives of the expedition were to provide new data on the current marine radioactivity in order to compare them with data sets obtained during national and international surveys at sites used for radioactive waste dumping or nuclear bomb testing in the NW Pacific Ocean and its marginal seas

  16. 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.

  17. 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

  18. ¿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.

  19. 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

  20. 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

  1. Australia's role in Pacific energy trade

    International Nuclear Information System (INIS)

    McColl, G.

    1989-01-01

    This paper discusses Australia's resources and the expansion of its steaming coal exports. The author reviews Australia's development of its natural gas resources and future prospects for exporting to the Pacific region

  2. 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

  3. U.S. Pacific Command > Leadership

    Science.gov (United States)

    USPACOM U.S. Pacific Command Search USPACOM: Search Search Search USPACOM: Search Home Leadership Directory Media Inquiries Home : Leadership Admiral Harry B. Harris, Jr., U.S. Navy Read the full biography

  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. 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...

  6. Out of the Pacific and back again

    DEFF Research Database (Denmark)

    Foote, Andrew David; Morin, Phillip A.; Durban, John W.

    2011-01-01

    or have been consolidated upon secondary contact due to resource competition. The estimated timing of bidirectional migration between the North Pacific and North Atlantic coincided with the previous inter-glacial when the leakage of fauna from the Indo-Pacific into the Atlantic via the Agulhas current......Killer whales (Orcinus orca) are the most widely distributed marine mammals and have radiated to occupy a range of ecological niches. Disparate sympatric types are found in the North Atlantic, Antarctic and North Pacific oceans, however, little is known about the underlying mechanisms driving...... 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...

  7. 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,...

  8. 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)

  9. 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- ...

  10. Heart Disease and Asians and Pacific Islanders

    Science.gov (United States)

    ... Data > Minority Population Profiles > Asian American > Heart Disease Heart Disease and Asians and Pacific Islanders Overall, Asian American ... are less likely than white adults to have heart disease and they are less likely to die from ...

  11. 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.

  12. The US Pivot Towards Asia-Pacific

    DEFF Research Database (Denmark)

    Ulrich, Philip Christian

    An analysis of the US new Asia-Pacific strategy. The brief seeks to set the new strategy in the context of American foreign policy since the end of the Cold War.......An analysis of the US new Asia-Pacific strategy. The brief seeks to set the new strategy in the context of American foreign policy since the end of the Cold War....

  13. Pacific salmonines in the Great Lakes Basin

    Science.gov (United States)

    Claramunt, Randall M.; Madenjian, Charles P.; Clapp, David; Taylor, William W.; Lynch, Abigail J.; Léonard, Nancy J.

    2012-01-01

    Pacific salmon (genus Oncorhynchus) are a valuable resource, both within their native range in the North Pacific rim and in the Great Lakes basin. Understanding their value from a biological and economic perspective in the Great Lakes, however, requires an understanding of changes in the ecosystem and of management actions that have been taken to promote system stability, integrity, and sustainable fisheries. Pacific salmonine introductions to the Great Lakes are comprised mainly of Chinook salmon, coho salmon, and steelhead and have accounted for 421, 177, and 247 million fish, respectively, stocked during 1966-2007. Stocking of Pacific salmonines has been effective in substantially reducing exotic prey fish abundances in several of the Great Lakes (e.g., lakes Michigan, Huron, and Ontario). The goal of our evaluation was to highlight differences in management strategies and perspectives across the basin, and to evaluate policies for Pacific salmonine management in the Great Lakes. Currently, a potential conflict exists between Pacific salmonine management and native fish rehabilitation goals because of the desire to sustain recreational fisheries and to develop self-sustaining populations of stocked Pacific salmonines in the Great Lakes. We provide evidence that suggests Pacific salmonines have not only become naturalized to the food webs of the Great Lakes, but that their populations (specifically Chinook salmon) may be fluctuating in concert with specific prey (i.e., alewives) whose populations are changing relative to environmental conditions and ecosystem disturbances. Remaining questions, however, are whether or not “natural” fluctuations in predator and prey provide enough “stability” in the Great Lakes food webs, and even more importantly, would a choice by managers to attempt to reduce the severity of predator-prey oscillations be antagonistic to native fish restoration efforts. We argue that, on each of the Great Lakes, managers are pursuing

  14. Asia-Pacific: A Selected Bibliography

    Science.gov (United States)

    2013-01-01

    Institute of Southeast Asian Studies, 2011. 540pp. (DS35.2 .M65 2011) Myers, Stephen C. Military Cooperation Frameworks: Effective Models to Address... Undesirable Multilateral Security Order?" Pacific Review 24, no. 2 (May 2011): 137-158. Taylor & Francis "The Quality of Democracy in Asia Pacific...2009): 205-219. Sage Turner, Mark, Sonam Chuki, and Jit Tshering. "Democratization by Decree: The Case of Bhutan." Democratization 18, no. 1 (February

  15. 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 ...

  16. 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.)

  17. Molecular phylogenetic reconstruction and localization of the (TTAGGn telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863 suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera

    Directory of Open Access Journals (Sweden)

    Tássia Tatiane Pontes Pereira

    2018-01-01

    Full Text Available Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known. The main exception is Acromyrmex striatus (Roger, 1863, which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH with telomeric probes with (TTAGG6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus. Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.

  18. 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.

  19. 76 FR 32929 - Western Pacific Pelagic Fisheries; American Samoa Longline Gear Modifications To Reduce Turtle...

    Science.gov (United States)

    2011-06-07

    ... are revised from ``Indo-Pacific blue marlin, Makaira mazara'' to ``Pacific blue marlin, Makaira... Istiompax indica striped marlin Kajikia audax * * * * * Pacific blue marlin Makaira nigricans [[Page 32932...

  20. Latest Miocene-earliest Pliocene evolution of the ancestral Rio Grande at the Española-San Luis Basin boundary, northern New Mexico

    Science.gov (United States)

    Daniel J. Koning,; Aby, Scott B.; Grauch, V. J.; Matthew J. Zimmerer,

    2016-01-01

    We use stratigraphic relations, paleoflow data, and 40Ar/39Ar dating to interpret net aggradation, punctuated by at least two minor incisional events, along part of the upper ancestral Rio Grande fluvial system between 5.5 and 4.5 Ma (in northern New Mexico). The studied fluvial deposits, which we informally call the Sandlin unit of the Santa Fe Group, overlie a structural high between the San Luis and Española Basins. The Sandlin unit was deposited by two merging, west- to southwest-flowing, ancestral Rio Grande tributaries respectively sourced in the central Taos Mountains and southern Taos Mountains-northeastern Picuris Mountains. The river confluence progressively shifted southwestward (downstream) with time, and the integrated river (ancestral Rio Grande) flowed southwards into the Española Basin to merge with the ancestral Rio Chama. Just prior to the end of the Miocene, this fluvial system was incised in the southern part of the study area (resulting in an approximately 4–7 km wide paleovalley), and had sufficient competency to transport cobbles and boulders. Sometime between emplacement of two basalt flows dated at 5.54± 0.38 Ma and 4.82±0.20 Ma (groundmass 40Ar/39Ar ages), this fluvial system deposited 10–12 m of sandier sediment (lower Sandlin subunit) preserved in the northern part of this paleovalley. The fluvial system widened between 4.82±0.20 and 4.50±0.07 Ma, depositing coarse sand and fine gravel up to 14 km north of the present-day Rio Grande. This 10–25 m-thick sediment package (upper Sandlin unit) buried earlier south- to southeast-trending paleovalleys (500–800 m wide) inferred from aeromagnetic data. Two brief incisional events are recognized. The first was caused by the 4.82±0.20 Ma basalt flow impounding south-flowing paleodrainages, and the second occurred shortly after emplacement of a 4.69±0.09 Ma basalt flow in the northern study area. Drivers responsible for Sandlin unit aggradation may include climate

  1. 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.

  2. 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.

  3. 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.

  4. The Pacific sea surface temperature

    Energy Technology Data Exchange (ETDEWEB)

    Douglass, David H., E-mail: douglass@pas.rochester.edu [Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627-0171 (United States)

    2011-12-05

    The Pacific sea surface temperature data contains two components: N{sub L}, a signal that exhibits the familiar El Niño/La Niña phenomenon and N{sub H}, a signal of one-year period. Analysis reveals: (1) The existence of an annual solar forcing F{sub S}; (2) N{sub H} is phase locked directly to F{sub S} while N{sub L} is frequently phase locked to the 2nd or 3rd subharmonic of F{sub S}. At least ten distinct subharmonic time segments of N{sub 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{sub L} is the familiar El Niño/La Niña effect. ► The second N{sub H} component has a period of 1 cycle/year. ► N{sub 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.

  5. Exploring the 'cultural' in cultural competencies in Pacific mental health.

    Science.gov (United States)

    Samu, Kathleen Seataoai; Suaalii-Sauni, Tamasailau

    2009-02-01

    Cultural competency is about the ability of individuals and systems to respond respectfully and effectively to the cultural needs of peoples of all cultures. Its general attributes include knowledge, attitudes, skills and professional judgment. In Pacific mental health, 'the cultural' is generally understood to be ethnic culture. Accordingly, Pacific cultural competencies assume ethnic specific markers. In mental health Pacific cultural competencies has seen a blending of cultural and clinical beliefs and practices. This paper provides an overview of five key theme areas arising from Auckland-based ethnic-specific Pacific workshop data: language, family, tapu relationships, skills and organisation policy. Workshop participants comprised of Pacific mental health providers, Pacific consumers, family members of Pacific consumers and members of the Pacific community members. This paper purports that identifying the perceptions of different Pacific groups on ethnic-specific elements of cultural competencies are necessary to build and strengthen the capacity and capability of mental health services to provide culturally relevant services.

  6. 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.

  7. PRÁCTICAS SOSTENIBLES BASADAS EN EL CONOCIMIENTO ANCESTRAL Y LA TECNOLOGÍA. APLICACIÓN EN EL CULTIVO DE MAÍZ

    Directory of Open Access Journals (Sweden)

    Tony JinsopYangüés Pappa

    2012-11-01

    Full Text Available Este trabajo fue desarrollado en la microcuenca Membrillo del cantón Bolívar, provincia de Manabí, su objetivo fue incrementar la productividad del cultivo de maíz aplicando prácticas sostenibles basadas en el conocimiento ancestral y la tecnología. Para lograr el objetivo propuesto se realizó un Diagnóstico Rural Participativo (DRP y se aplicaron las Metodologías de Escuelas de Aprendizaje (ERAs. Entre los principales resultados obtenidos se destacan el incremento de la productividad promedio del cultivo del maíz a 120 qq/ha con prácticas alternativas sostenibles basadas en el conocimiento ancestral y la tecnología en las comunidades donde se aplicaron las experiencias, alcanzando estas mayores ingresos que satisfacen las necesidades de los productores y consecuentemente se logró reducir la presión hacia los bosques por la producción intensiva alcanzada. Se capacitaron a los agricultores involucrados en técnicas de elaboración de bioinsumos que se utilizaron para la producción de maíz, alternativas para el manejo técnico sostenible y amigable con el ambiente en este cultivo. También se demostró que las prácticas implementadas en el desarrollo de este trabajo contribuyen al desarrollo sostenible de la Microcuenca Membrillo.

  8. [High frequency of ancestral allele of the TJP1 polymorphism rs2291166 in Mexican population, conformational effect and applications in surgery and medicine].

    Science.gov (United States)

    Ramirez-Garcia, Sergio Alberto; Flores-Alvarado, Luis Javier; Topete-González, Luz Rosalba; Charles-Niño, Claudia; Mazariegos-Rubi, Manuel; Dávalos-Rodríguez, Nory Omayra

    2016-01-01

    TJP1 gene encodes a ZO-1 protein that is required for the recruitment of occludins and claudins in tight junction, and is involved in cell polarisation. It has different variations, the frequency of which has been studied in different populations. In Mexico there are no studies of this gene. These are required because their polymorphisms can be used in studies associated with medicine and surgery. Therefore, the aim of this study was to estimate the frequency of alleles and genotypes of rs2291166 gene polymorphism TJP1 in Mexico Mestizos population, and to estimate the conformational effect of an amino acid change. A total of 473 individuals were included. The rs2291166 polymorphism was identified PASA PCR-7% PAGE, and stained with silver nitrate. The conformational effect of amino acid change was performed in silico, and was carried out with servers ProtPraram Tool and Search Database with Fasta. The most frequent allele in the two populations is the ancestral allele (T). A genotype distribution similar to other populations was found. The polymorphism is in Hardy-Weinberg, p>0.05. Changing aspartate to alanine produced a conformational change. The study reveals a high frequency of the ancestral allele at rs2291166 polymorphism in the Mexican population. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

  9. Miocene magmatism in the Bodie Hills volcanic field, California and Nevada: A long-lived eruptive center in the southern segment of the ancestral Cascades arc

    Science.gov (United States)

    John, David A.; du Bray, Edward A.; Blakely, Richard J.; Fleck, Robert J.; Vikre, Peter; Box, Stephen E.; Moring, Barry C.

    2012-01-01

    The Middle to Late Miocene Bodie Hills volcanic field is a >700 km2, long-lived (∼9 Ma) but episodic eruptive center in the southern segment of the ancestral Cascades arc north of Mono Lake (California, U.S.). It consists of ∼20 major eruptive units, including 4 trachyandesite stratovolcanoes emplaced along the margins of the field, and numerous, more centrally located silicic trachyandesite to rhyolite flow dome complexes. Bodie Hills volcanism was episodic with two peak periods of eruptive activity: an early period ca. 14.7–12.9 Ma that mostly formed trachyandesite stratovolcanoes and a later period between ca. 9.2 and 8.0 Ma dominated by large trachyandesite-dacite dome fields. A final period of small silicic dome emplacement occurred ca. 6 Ma. Aeromagnetic and gravity data suggest that many of the Miocene volcanoes have shallow plutonic roots that extend to depths ≥1–2 km below the surface, and much of the Bodie Hills may be underlain by low-density plutons presumably related to Miocene volcanism.Compositions of Bodie Hills volcanic rocks vary from ∼50 to 78 wt% SiO2, although rocks with Bodie Hills rocks are porphyritic, commonly containing 15–35 vol% phenocrysts of plagioclase, pyroxene, and hornblende ± biotite. The oldest eruptive units have the most mafic compositions, but volcanic rocks oscillated between mafic and intermediate to felsic compositions through time. Following a 2 Ma hiatus in volcanism, postsubduction rocks of the ca. 3.6–0.1 Ma, bimodal, high-K Aurora volcanic field erupted unconformably onto rocks of the Miocene Bodie Hills volcanic field.At the latitude of the Bodie Hills, subduction of the Farallon plate is inferred to have ended ca. 10 Ma, evolving to a transform plate margin. However, volcanism in the region continued until 8 Ma without an apparent change in rock composition or style of eruption. Equidimensional, polygenetic volcanoes and the absence of dike swarms suggest a low differential horizontal stress regime

  10. The pacific island health care project.

    Science.gov (United States)

    Person, Donald Ames

    2014-01-01

    US Associated/Affiliated Pacific Islands (USAPI) include three freely associated states: Marshall Islands, Federated States of Micronesia, Palau, and three Territories: American Samoa, Guam, and Commonwealth of the Northern Mariana Islands. The Pacific Island Health Care Project (PIHCP) provides humanitarian medical referral/consultation/care to >500,000 indigenous people of these remote islands. In the mid-1990s, we developed a simple store-and-forward program to link the USAPI with Tripler Army Medical Center. This application allowed image attachment to email consultations. More than 8000 Pacific Islanders have benefited from the program. Three thousand 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. 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.).

  11. 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

  12. 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.

  13. 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.

  14. The parasite Ichthyophonus sp. in Pacific herring from the coastal NE Pacific.

    Science.gov (United States)

    Hershberger, P K; Gregg, J L; Hart, L M; Moffitt, S; Brenner, R; Stick, K; Coonradt, E; Otis, E O; Vollenweider, J J; Garver, K A; Lovy, J; Meyers, T R

    2016-04-01

    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. © 2015 John Wiley & Sons Ltd.

  15. 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.

  16. 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

  17. 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.

  18. Asia Pacific Mangrove Information Network (APMIN): A conceptual model

    Digital Repository Service at National Institute of Oceanography (India)

    Chavan, V.S.; Jagtap, T.G.; Untawale, A.G.

    Asia Pacific Mangrove Information Network (APMIN), its structure and scope, is discussed in this paper. Establishment of National Mangrove Information Centers (NMIC) in 20 Asia-Pacific countries, would contribute towards development of databases...

  19. 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 ...

  20. 75 FR 55745 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-09-14

    ... Pacific Fishery Management Council's (Pacific Council) Coastal Pelagic Species Management Team (CPSMT) and... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... sardine stock assessment for 2010. Other issues relevant to Coastal Pelagic Species fisheries management...

  1. 75 FR 33245 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-06-11

    ... Pacific Fishery Management Council's (Council) Groundfish Management Team (GMT) will hold a working... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... be held at the Pacific Fishery Management Council office, Large Conference Room, 7700 NE Ambassador...

  2. 78 FR 77658 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-12-24

    ... Pacific Fishery Management Council's (Pacific Council) Highly Migratory Species Management Team (HMSMT... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National.... Potential changes to management measures for the west coast drift gillnet fishery. 2. Developments to...

  3. 78 FR 56659 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-09-13

    ... Pacific Fishery Management Council's (Pacific Council) Groundfish Management Team (GMT) will hold a... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National...-16 groundfish harvest specifications and management measures, long-term impact analysis, and...

  4. 75 FR 80470 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-12-22

    ... Pacific Fishery Management Council's (Council) Groundfish Management Team (GMT) will hold a working... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National.... Council address: Pacific Fishery Management Council, 7700 NE. Ambassador Place, Suite 101, Portland, OR...

  5. 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...

  6. 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...

  7. 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.

  8. 76 FR 80890 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-12-27

    ... Airport Hotel, 7900 NE 82nd Avenue, Portland, OR 97220. Council address: Pacific Fishery Management.... Kerry Griffin, Staff Officer, Pacific Council; (503) 820-2280. SUPPLEMENTARY INFORMATION: The purpose of...

  9. 76 FR 43987 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-07-22

    ... Pacific Fishery Management Council's (Pacific Council) ad hoc groundfish Essential Fish Habitat Review... of groundfish Essential Fish Habitat (EFH). DATES: The work session will be held Thursday, October 6...

  10. 78 FR 49477 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-08-14

    ... Pacific Fishery Management Council (Pacific Council) will convene a meeting of its Groundfish Essential Fish Habitat Review Committee (EFHRC). DATES: The meeting will be held Wednesday September 4 through...

  11. 75 FR 17901 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-04-08

    ... June 2010 meeting of the Pacific Council. The CPSMT will also discuss the pending Essential Fish Habitat five-year review; the 2010 Stock Assessment and Fishery Evaluation document; Pacific mackerel...

  12. Tropical Pacific Observing for the Next Decade

    Science.gov (United States)

    Legler, David M.; Hill, Katherine

    2014-06-01

    More than 60 scientists and program officials from 13 countries met at the Scripps Institution of Oceanography for the Tropical Pacific Observing System (TPOS) 2020 Workshop. The workshop, although motivated in part by the dramatic decline of NOAA's Tropical Atmosphere Ocean (TAO) buoy reporting from mid-2012 to early 2014 (see http://www.bloomberg.com/news/2014-03-07/aging-el-nino-buoys-getting-fixed-as-weather-forecasts-at-risk.html), evaluated the needs for tropical Pacific observing and initiated efforts to develop a more resilient and integrative observing system for the future.

  13. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  14. 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...

  15. CRED 5 m Gridded bathymetry of Jarvis 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 Jarvis Island, 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 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...

  18. THE FUTURE OF PACIFIC NORTHWEST SALMON: ANATOMY OF A CRISIS

    Science.gov (United States)

    Salmon are categorized biologically into two groups: Pacific salmon or Atlantic salmon. All seven species of Pacific salmon on both sides of the North Pacific Ocean have declined substantially from historic levels, but large runs still occur in northern British Columbia, Yukon,...

  19. 76 FR 58472 - North Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-09-21

    ... North Pacific Fishery Management Council's (Council) Pacific Northwest Crab Industry Advisory Committee. SUMMARY: The Pacific Northwest Crab Industry Advisory Committee will meet October 13, 2011 at the Leif...: (907) 271-2809. SUPPLEMENTARY INFORMATION: Agenda--Alaska Department of Fish & Game/ NMFS scientists...

  20. 77 FR 53179 - North Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-08-31

    .... SUMMARY: The North Pacific Fishery Management Council's (NPFMC) Crab Plan Team (CPT) will meet in Seattle... Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS..., WA. Council address: North Pacific Fishery Management Council, 605 W. 4th Avenue, Suite 306...

  1. 75 FR 20985 - North Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2010-04-22

    .... SUMMARY: The North Pacific Fishery Management Council's Crab Plan Team (CPT) will meet in Alaska on May 10... Pacific Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS... Room - May 14. Council address: North Pacific Fishery Management Council, 605 W. 4th Avenue, Suite 306...

  2. 78 FR 26616 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2013-05-07

    ... Pacific Fishery Management Council's (Pacific Council) Groundfish Management Team (GMT) will hold a... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National... number) and use the access code 802-457-985 when prompted. Council address: Pacific Fishery Management...

  3. 77 FR 74469 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2012-12-14

    ... Pacific Fishery Management Council's (Pacific Council) Groundfish Management Team (GMT) will hold a week... Fishery Management Council; Public Meeting AGENCY: National Marine Fisheries Service (NMFS), National...) 634-2000. Council address: Pacific Fishery Management Council, 7700 NE Ambassador Place, Suite 101...

  4. 76 FR 54217 - Pacific Fishery Management Council; Public Meeting

    Science.gov (United States)

    2011-08-31

    ... Pacific Fishery Management Council (Pacific Council) will convene a meeting of the Stock Assessment Review... 2011 stock assessment for Pacific sardine, which will be used to develop management measures for the... 305(c) of the Magnuson-Stevens Fishery Conservation and Management Act, provided the public has been...

  5. Patterns of change in climate and Pacific salmon production

    Science.gov (United States)

    Nathan J. Mantua

    2009-01-01

    For much of the 20th century a clear north-south inverse production pattern for Pacific salmon had a time dynamic that closely followed that of the Pacific Decadal Oscillation (PDO), which is the dominant pattern of North Pacific sea surface temperature variability. Total Alaska salmon production was high during warm regimes of the PDO, and total Alaska salmon...

  6. 78 FR 33240 - International Fisheries; Pacific Tuna Fisheries; Fishing Restrictions in the Eastern Pacific Ocean

    Science.gov (United States)

    2013-06-04

    ... States, Vanuatu, and Venezuela. Bolivia and the Cook Islands are cooperating non-members. International... Pacific bluefin mortality. In addition, the Department of the Interior, Office of Environmental Policy and...

  7. Alcances translocales de cultos ancestrales: El caso de las danzas rituales aztecas (Translocales reaches of ancestral cults: The case of the Aztec ritual dances

    Directory of Open Access Journals (Sweden)

    Renée de la Torre

    2007-03-01

    Full Text Available Este trabajo trata sobre las transformaciones de identidad que se gestan en los grupos de danza conocidos como aztecas o concheros en su intercambio cultural y encuentro con redes espirituales alternativas o conocidas como movimientos de espiritualidad Nueva Era (o New Age. El objetivo de este trabajo es dar cuenta de los procesos a partir de los cuales la tradición dancística conchera o azteca está siendo trasformada por las dinámicas de la globalización cultural, haciendo de esta tradición mexicana y ancestral, un eslabón de una amplia red New Age de alcances planetarios.

  8. A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia.

    Science.gov (United States)

    Ogedengbe, Mosun E; Qvarnstrom, Yvonne; da Silva, Alexandre J; Arrowood, Michael J; Barta, John R

    2015-05-01

    The near complete mitochondrial genome for Cyclospora cayetanensis is 6184 bp in length with three protein-coding genes (Cox1, Cox3, CytB) and numerous lsrDNA and ssrDNA fragments. Gene arrangements were conserved with other coccidia in the Eimeriidae, but the C. cayetanensis mitochondrial genome is not circular-mapping. Terminal transferase tailing and nested PCR completed the 5'-terminus of the genome starting with a 21 bp A/T-only region that forms a potential stem-loop. Regions homologous to the C. cayetanensis mitochondrial genome 5'-terminus are found in all eimeriid mitochondrial genomes available and suggest this may be the ancestral start of eimeriid mitochondrial genomes. Copyright © 2015 Australian Society for Parasitology Inc. All rights reserved.

  9. Field-trip guide to subaqueous volcaniclastic facies in the Ancestral Cascades arc in southern Washington State—The Ohanapecosh Formation and Wildcat Creek beds

    Science.gov (United States)

    Jutzeler, Martin; McPhie, Jocelyn

    2017-06-27

    Partly situated in the idyllic Mount Rainier National Park, this field trip visits exceptional examples of Oligocene subaqueous volcaniclastic successions in continental basins adjacent to the Ancestral Cascades arc. The >800-m-thick Ohanapecosh Formation (32–26 Ma) and the >300-m-thick Wildcat Creek (27 Ma) beds record similar sedimentation processes from various volcanic sources. Both show evidence of below-wave-base deposition, and voluminous accumulation of volcaniclastic facies from subaqueous density currents and suspension settling. Eruption-fed facies include deposits from pyroclastic flows that crossed the shoreline, from tephra fallout over water, and from probable Surtseyan eruptions, whereas re-sedimented facies comprise subaqueous density currents and debris flow deposits.

  10. 78 FR 7385 - Western Pacific Fisheries; Fishing in the Marianas Trench, Pacific Remote Islands, and Rose Atoll...

    Science.gov (United States)

    2013-02-01

    ...-BA98 Western Pacific Fisheries; Fishing in the Marianas Trench, Pacific Remote Islands, and Rose Atoll... Presidential proclamations that created the Marianas Trench, Pacific Remote Islands, and Rose Atoll Marine..., 2009). Proclamation 8337 of January 6, 2009, ``Establishment of the Rose Atoll Marine National Monument...

  11. Geological and Geophysical Integration Regarding a Structural Evolution Modelling of a Suture Zone Controlled by a Cratonic Buttress - The Case of Dom Feliciano Orogenic Belt, SSE Brazil, Implications for Western Gondwana Assembly

    Science.gov (United States)

    Bruno, H.; Almeida, J.; Heilbron, M. C. P. L.; Salomão, M.

    2017-12-01

    The matters surrounding the amalgamation of tectonic blocks during the Brasiliano / Pan-African orogeny have been the main subject of study of several works in recent years. The main objective of this work is the hierarchy and discrimination of the boundaries between the known tectonic blocks, integrating geological and geophysical data. The geology of the study area is dominated by Precambrian terranes; Luís Alves Terrane, the vulcanosedimentary sequences of the Itajaí and Campo Alegre Basins, the metasedimentary sequences of the Brusque and Paranaguá Terranes and their granitic suites besides the granitoids of the Florianópolis Terrane. The shear zones and faults that separate these crustal blocks were developed during the Brasiliano / Pan-African orogenic cycle that led to the formation of the supercontinent Gondwana. These tectonic boundaries generally separate blocks of different rheology and crustal thickness. The integration of geological and geophysical data allowed the identification of important structural lineaments and crustal boundaries. The presented geodynamic model suggests that the suture between the block composed of the Brusque, Paranaguá and Florianópolis Terranes and the block composed by the Luís Alves Terrane is the Itajaí Perimbó Shear Zone, and not the Major Gercino Shear Zone as previously suggested. Considering the Itajaí Perimbó Shear Zone as the suture zone, the metassediments of the Brusque Terrane were deposited on the basement of the Florianópolis Terrane, hereby declared as part of the Angola Craton, and are correlated to the metassediments of the Paranaguá Terrane as a passive margin that in approximately ca. 650 My became active margin, functioning as a forearc basin. The oblique collision between the blocks would have occurred with the development of a dextral transpression in the Itajaí Perimbó Shear Zone, separating the Luís Alves Terrane from the Brusque Terrane, a sinistral transcurrence represented by the

  12. Environmental control on concretion-forming processes: Examples from Paleozoic terrigenous sediments of the North Gondwana margin, Armorican Massif (Middle Ordovician and Middle Devonian) and SW Sardinia (Late Ordovician)

    Science.gov (United States)

    Dabard, Marie-Pierre; Loi, Alfredo

    2012-08-01

    Concretions of various compositions are common in the Paleozoic terrigenous successions of the north Gondwana margin. This study focuses on phosphatic (P) and siliceous (Si) concretions present in some successions of the Armorican Massif (NW France) and SW Sardinia (W Italy). It shows that they consist of mudstones, fine- to very fine-grained sandstones or shellbeds with a more or less abundant P-cement and form a continuum between a phosphatic end-member and a siliceous biogenic end-member. The P2O5 contents are ranging from 0.26% to 21.5% and are related to apatite. The SiO2 contents vary from 25% to 82% and are linked both to a terrigenous phase and to a biogenic silica phase. Concretions showing the lower P-contents (P2O5 5). Comparison with the surrounding sediments shows that all the concretions are enriched in chlorite and in Middle Rare Earth Elements (Las/Gds: 0.12-0.72) and some of them in Y (up to 974 ppm), Rare Earth Elements (more than 300 ppm) and Sr (260-880 ppm). The concretions with highest biogenic silica concentrations are contained in the outer shelf sediments whereas the other concretions are present from the proximal part of the inner shelf to the outer shelf. A genetic model in two stages is proposed. During early diagenesis, the dissolution of shells and degradation of organic matter progressively enrich the pore water in dissolved Si, Ca and P. When the suboxic zone is reached, P-precipitation begins, leading to the formation of protoconcretions. In shallow environments, the relative permeability of sediments and the winnowing or reworking of the upper few centimetres by bottom currents allow for suboxic conditions to be maintained, leading to P-rich concretion formation. In deeper environments, the anoxic zone is reached more rapidly, thereby preventing extensive phosphogenesis. Nevertheless in the protoconcretions the early P-cement preserves pore spaces from compaction. In the presence of biogenic siliceous particles, the fluids are

  13. Migration for Environmentally Displaced Pacific Peoples: Legal Options in the Pacific Rim

    OpenAIRE

    Tabucanon, Gil Marvel

    2012-01-01

    This paper explores the complex relationship between the environment and migration, namely the various protection options available for environmentally-displaced Pacific peoples under the laws of the United States, Canada, Australia, and New Zealand. It seeks to ascertain whether flexibility exists in these countries' domestic laws for environmental migrants from neighboring Pacific countries. It asks if humanitarian and ministerial discretion admissions and preferential admission schemes suf...

  14. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  15. Processed foods available in the Pacific Islands

    Science.gov (United States)

    2013-01-01

    Background There is an increasing reliance on processed foods globally, yet food composition tables include minimal information on their nutrient content. The Pacific Islands share common trade links and are heavily reliant on imported foods. The objective was to develop a dataset for the Pacific Islands on nutrient composition of processed foods sold and their sources. Methods Information on the food labels, including country of origin, nutrient content and promotional claims were recorded into a standardised dataset. Data were cleaned, converted to per 100 g data as needed and then checked for anomalies and recording errors. Setting: Five representative countries were selected for data collection, based on their trading patterns: Fiji, Guam, Nauru, New Caledonia, and Samoa. Data were collected in the capitals, in larger stores which import their own foods. Subjects: Processed foods in stores. Results The data from 6041 foods and drinks were recorded. Fifty four countries of origin were identified, with the main provider of food for each Pacific Island country being that with which it was most strongly linked politically. Nutrient data were not provided for 6% of the foods, imported from various countries. Inaccurate labels were found on 132 products. Over one-quarter of the foods included some nutrient or health-related claims. Conclusions The globalisation of the food supply is having considerable impacts on diets in the Pacific Islands. While nutrient labels can be informative for consumers looking for healthier options, difficulties still exist with poor labelling and interpretation can be challenging. PMID:24160249

  16. The Asian-Pacific world in transition

    International Nuclear Information System (INIS)

    McLean, D.

    1990-01-01

    Analyzing the modern situation in the Asian-Pacific Region, with account for strategic concerns on the part of China, Japan, USSR and USA the author considers prospects for meaningful disarmament or arms-control (including nuclear weapons) negotiations in the region

  17. Delimiting communities in the Pacific Northwest.

    Science.gov (United States)

    Ellen M. Donoghue

    2003-01-01

    The paper presents an approach for delimiting communities in the Northwest Forest Plan (NWFP) region of the Pacific Northwest that responds to the need to assess impacts and issues associated with broad-scale ecosystem management. Census block groups are aggregated to provide an alternative to more commonly used geographic delimitations of communities, specifically...

  18. SCIENCE, POLITICS, AND PACIFIC NORTHWEST SALMON RECOVERY

    Science.gov (United States)

    Throughout the Pacific Northwest, since 1850, all wild salmon runs have declined and some have disappeared. Billions of dollars have been spent in a so-far failed attempt to reverse the long-term decline. Each year, hundreds of millions of dollars continue to be spent in variou...

  19. Pacific Island rugby: Histories, mobilities, comparisons

    NARCIS (Netherlands)

    Besnier, N.

    2014-01-01

    The migration of rugby players from Fiji and neighbouring Pacific Island nations poses fundamental questions about the way in which sport is embedded in historical, political, social and global dynamics, all of which give specific meanings to sports and those who play it. An approach that bestows a

  20. Modeling the population dynamics of Pacific yew.

    Science.gov (United States)

    Richard T. Busing; Thomas A. Spies

    1995-01-01

    A study of Pacific yew (Taxus brevifolia Nutt.) population dynamics in the mountains of western Oregon and Washington was based on a combination of long-term population data and computer modeling. Rates of growth and mortality were low in mature and old-growth forest stands. Diameter growth at breast height ranged from 0 to 3 centimeters per decade...

  1. Biogeographic congruence in the south Pacific

    DEFF Research Database (Denmark)

    Seberg, Ole

    1991-01-01

    Ever since J. D. Hooker's famous 'Introductory Essay' to Flora NOVE-Zelandise, a classical problem in biogeography has been to give a casual explanation of southern hemisphere distribution patterns. An attempt is made to see whether the cladograms for the circum-Pacific areas (South America, New ...

  2. The Third Pacific Basin Biofuels Workshop: Proceedings

    Science.gov (United States)

    Among the many compelling reasons for the development of biofuels on remote Pacific islands, several of the most important include: (1) a lack of indigenous fossil fuels necessitates their import at great economic loss to local island economics, (2) ideal conditions for plant growth exist on many Pacific islands to produce yields of biomass feedstocks, (3) gaseous and liquid fuels such as methane, methanol and ethanol manufactured locally from biomass feedstocks are the most viable alternatives to gasoline and diesel fuels for transportation, and (4) the combustion of biofuels is cleaner than burning petroleum products and contributes no net atmospheric CO2 to aggravate the greenhouse effect and the subsequent threat of sea level rise to low islands. Dr. Vic Phillips, HNEI Program Manager of the Hawaii Integrated Biofuels Research Program welcomed 60 participants to the Third Pacific Basin Biofuels Workshop at the Sheraton Makaha Hotel, Waianae, Oahu, on March 27 and 28, 1989. The objectives of the workshop were to update progress since the Second Pacific Basin Biofuels Workshop in April 1987 and to develop a plan for action for biofuels R and D, technology transfer, and commercialization now (immediate attention), in the near-term (less than two years), in the mid-term (three to five years), and in the long-term (more than six years). An emerging theme of the workshop was how the production, conversion, and utilization of biofuels can help increase environmental and economic security locally and globally. Individual papers are processed separately for the data base.

  3. Solar Energy for Pacific Northwest Buildings.

    Science.gov (United States)

    Reynolds, John S.

    Data presented in this report indicate that solar space and water heating are possible in the Pacific Northwest. The first section of the report contains solar records from several stations in the region illustrating space heating needs that could be met, on an average daily basis, by solar energy. The data are summarized, and some preliminary…

  4. Asian & Pacific Islander American Health Forum

    Science.gov (United States)

    ... Report.pdf [1.2MB] Obesity and Overweight Among Asian American Children and Adolescents 2016.04.28-OBESITY AND ... Month Stay Connected! Receive the latest APIAHF updates Asian & Pacific Islander American Health Forum. All rights reserved. One Kaiser Plaza, ...

  5. SeaWiFS: North Pacific Storm

    Science.gov (United States)

    2002-01-01

    An extratropical storm can be seen swirling over the North Pacific just south of Alaska. This SeaWiFS image was collected yesterday at 23:20 GMT. Credit: Provided by the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE

  6. Albert Einstein the roads to pacifism

    CERN Document Server

    Anta, Claudio Giulio

    2017-01-01

    Albert Einstein (1879-1955) is universally known as the father of the theory of relativity; however, he was also one of the most eminent pacifists of the first half of the twentieth century. Through his active, pragmatic and nuanced breed of pacifism, he sought to confront the dilemmas and problems of his time.

  7. INTELSAT et al. in the South Pacific.

    Science.gov (United States)

    Pelton, Joseph N.

    1985-01-01

    Discusses services provided to the island countries of the South Pacific Basin by the International Telecommunications Satellite Organization (INTELSAT), a 110 member-country cooperative that operates a global satellite system. The services include provision of basic satellite communications facilities, technical assistance and training, and free…

  8. Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

    Science.gov (United States)

    Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

    2009-10-01

    We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa.

  9. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.

    Directory of Open Access Journals (Sweden)

    Daniel Magee

    2017-02-01

    Full Text Available Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods. In this paper, we compare these two methods, while also using a primitive method without BSSVS, and highlight the differences in phylogenies created by each. We test six coalescent priors and six random sequence samples of H3N2 influenza during the 2014-15 flu season in the U.S. We show that the GLMs yield significantly greater root state posterior probabilities than the two alternative methods under five of the six priors, and significantly greater Kullback-Leibler divergence values than the two alternative methods under all priors. Furthermore, the GLMs strongly implicate temperature and precipitation as driving forces of this flu season and nearly unanimously identified a single root state, which exhibits the most tropical climate during a typical flu season in the U.S. The GLM, however, appears to be highly susceptible to sampling bias compared with the other methods, which casts doubt on whether its reconstructions should be favored over those created by alternate methods. We report that a BSSVS approach with a Poisson prior demonstrates less bias toward sample size under certain conditions than the GLMs or primitive models, and believe that the connection between reconstruction method and sampling bias warrants further investigation.

  10. The impact of ancestral heath management on soils and landscapes. A reconstruction based on paleoecological analyses of soil records in the middle and southeast Netherlands.

    Science.gov (United States)

    van Mourik, Jan; Doorenbosch, Marieke

    2016-04-01

    The evolution of heath lands during the Holocene has been registered in various soil records . Paleoecological analyses of these records enable to reconstruct the changing economic and cultural management of heaths and the consequences for landscape and soils. Heaths are characteristic components of cultural landscape mosaics on sandy soils in the Netherlands. The natural habitat of heather species was moorland. At first, natural events like forest fires and storms caused small-scale forest degradation, in addition on the forest degradation accelerated due to cultural activities like forest grazing, wood cutting and shifting cultivation. Heather plants invaded on degraded forest soils and heaths developed. People learned to use the heaths for economic and cultural purposes. The impact of the heath management on landscape and soils was registered in soil records of barrows, drift sand sequences and plaggic Anthrosols. Based on pollen diagrams of such records we could reconstruct that heaths were developed and used for cattle grazing before the Bronze Age. During the Late Neolithic, the Bronze Age and Iron Age, people created the barrow landscape on the ancestral heaths. After the Iron Age people probably continued with cattle grazing on the heaths and plaggic agriculture until the Early Middle Ages. After 1000 AD two events affected the heaths. At first deforestation for the sale of wood resulted in the first regional extension of sand drifting and heath degradation. After that the introduction of the deep stable economy and heath sods digging resulted in acceleration of the rise of plaggic horizons, severe heath degradation and the second extension of sand drifting. At the end of the 19th century the heath lost its economic value due to the introduction of chemical fertilizers. The heaths were transformed into 'new' arable fields and forests and due to deep ploughing most soil archives were destroyed. Since 1980 AD, the remaining relicts of the ancestral heaths are

  11. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

    Directory of Open Access Journals (Sweden)

    Michael B Walker

    Full Text Available Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

  12. Pacific Basin Heavy Oil Refining Capacity

    Directory of Open Access Journals (Sweden)

    David Hackett

    2013-02-01

    Full Text Available The United States today is Canada’s largest customer for oil and refined oil products. However, this relationship may be strained due to physical, economic and political influences. Pipeline capacity is approaching its limits; Canadian oil is selling at substantive discounts to world market prices; and U.S. demand for crude oil and finished products (such as gasoline, has begun to flatten significantly relative to historical rates. Lower demand, combined with increased shale oil production, means U.S. demand for Canadian oil is expected to continue to decline. Under these circumstances, gaining access to new markets such as those in the Asia-Pacific region is becoming more and more important for the Canadian economy. However, expanding pipeline capacity to the Pacific via the proposed Northern Gateway pipeline and the planned Trans Mountain pipeline expansion is only feasible when there is sufficient demand and processing capacity to support Canadian crude blends. Canadian heavy oil requires more refining and produces less valuable end products than other lighter and sweeter blends. Canadian producers must compete with lighter, sweeter oils from the Middle East, and elsewhere, for a place in the Pacific Basin refineries built to handle heavy crude blends. Canadian oil sands producers are currently expanding production capacity. Once complete, the Northern Gateway pipeline and the Trans Mountain expansion are expected to deliver an additional 500,000 to 1.1 million barrels a day to tankers on the Pacific coast. Through this survey of the capacity of Pacific Basin refineries, including existing and proposed facilities, we have concluded that there is sufficient technical capacity in the Pacific Basin to refine the additional Canadian volume; however, there may be some modifications required to certain refineries to allow them to process Western Canadian crude. Any additional capacity for Canadian oil would require refinery modifications or

  13. A decadal tropical Pacific condition unfavorable to central Pacific El Niño

    Science.gov (United States)

    Zhong, Wenxiu; Zheng, Xiao-Tong; Cai, Wenju

    2017-08-01

    The frequency of central Pacific (CP) El Niño events displays strong decadal variability but the associated dynamics are unclear. The Interdecadal Pacific Oscillation (IPO) and the tropical Pacific decadal variability (TPDV) are two dominant modes of tropical Pacific decadal variability that can interact with high-frequency activities. Using a 500 year control integration from the Geophysical Fluid Dynamics Laboratory Earth System Model, we find that the difference in mean state between the low-frequency and high-frequency CP El Niño periods is similar to the decadal background condition concurrently contributed by a negative IPO and a positive TPDV. This decadal state features strengthened trade winds west of the International Date Line and anomalous cool sea surface temperatures across the central tropical Pacific. As such, positive zonal advection feedback is difficult to be generated over the central to western tropical Pacific during the CP El Niño developing season, resulting in the low CP El Niño frequency.

  14. Pacific ethnic groups and frequent hospital presentation: A fair target?

    Science.gov (United States)

    Irvine, Zoe

    2016-06-01

    In New Zealand, Pacific health figures are traditionally presented for all Pacific ethnic groups combined. Use of EDs and urgent care clinics is high compared with Maori and non-Maori, non-Pacific (nMnP) use. By controlling for proximity to the hospital and socioeconomic status, we demonstrate greater variation between Pacific ethnic groups than between Pacific and nMnP, or between Maori and nMnP groups. We discuss the significance of subpopulation variation in use of urgent care services. © 2016 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

  15. Pacific Lamprey Research and Restoration : Annual Report 1997.

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Aaron D.; Hatch, Douglas R.; Close, David A.

    1998-08-05

    The once abundant stocks of Pacific lamprey (Lampetra tridentata) above Bonneville Dam are currently depressed (Close et al. 1995). It is likely that many of the same factors that led to the decline of wild stocks of Columbia River Pacific salmon and steelhead have impacted Pacific lamprey populations as well. The Pacific Lamprey Research and Restoration Project, funded by Bonneville Power Administration, is a cooperative effort between the Confederated Tribes of the Umatilla Indian Reservation, the Columbia River Inter-Tribal Fish Commission, and Oregon State University with the goal to increase Pacific lamprey stocks above Bonneville Dam.

  16. The History of the Pacific Superplume

    Science.gov (United States)

    Suzuki, N.; Utsunomiya, A.; Maruyama, S.

    2001-12-01

    To understand the birth place and episodic activity of the Pacific superplume, we reconstructed the paleogeograhy of continents and oceanic plates from 1.0 Ga supercontinent Rodinia until now by adopting the most confident available data set to determine paleopositions of oceanic plateaus, seamounts, and oceanic arc, in addition to major continents, by using plate trajectory for the last 150Ma and for the farther back to 1.0Ga, by the paleomagnetic constraints tied with geologic connections. Our main focus is the frequency change of ancient activity of plume rocks that are now preserved in the accretionary complex around the circum-Pacific orogenic belts. Several conclusions are led through our reconstruction. (1) Cretaceous oceanic plateaus which present widespread in western Pacific (e.g., Manihiki Plateau, Shatsky Rise, Hess Rise, Mid-Pacific Mountain, Nauru Basin) are traced back and concentrated to the present active region of the Pacific superplume. This suggests that those were once formed a huge composite volcanoes as large as 4000 km x 2400 km across during the Cretaceous by superplume activity. These are equivalent to Australia or Tharsis bulge volcanic complex on Mars. The estimated thickness of oceanic crust ca. 30-40 km suggests that major parts may have been above sea-level during the Cretaceous time. The Cretaceous global warming may be related to this hyper-active superplume event which have carried mantle CO2 to the surface of 3.2 x 1021 g, assuming 0.3 wt% x 350 million km3 (magma volume) x 3.07 g/cm3 during 150-75 Ma. This CO2 output amount occupies as much as 37 wt% among the total output from mantle estimated by using erupted basaltic volume estimated by Larson (1991, Geology, 549-550) and present output rate of CO2. The similar episodic activity of Pacific superplume seems to have occurred at 750-700 Ma, 550-500Ma, 300-250Ma by considering the frequency of occurrences of greenstones in the accretionary complexes of the world. (2) Rodinia

  17. Lithofacies Correlation in Early Permian Fluvial Gondwana ...

    Indian Academy of Sciences (India)

    64

    Stratigraphy of South-eastern India using Cross Association. Statistics. Zahid A. Khan1 ... It has been successfully applied to correlate vertical succession of ..... and Associate Editor of the Journal of Earth System Science for critical assessment.

  18. Derived (mutated)-types of TRPV6 channels elicit greater Ca²+ influx into the cells than ancestral-types of TRPV6: evidence from Xenopus oocytes and mammalian cell expression system.

    Science.gov (United States)

    Sudo, Yuka; Matsuo, Kiyotaka; Tetsuo, Tomoyuki; Tsutsumi, Satoshi; Ohkura, Masamichi; Nakai, Junichi; Uezono, Yasuhito

    2010-01-01

    The frequency of the allele containing three derived nonsynonymous SNPs (157C, 378M, 681M) of the gene encoding calcium permeable TRPV6 channels expressed in the intestine has been increased by positive selection in non-African populations. To understand the nature of these SNPs, we compared the properties of Ca²+ influx of ancestral (in African populations) and derived-TRPV6 (in non-African populations) channels with electrophysiological, Ca²+-imaging, and morphological methods using both the Xenopus oocyte and mammalian cell expression systems. Functional electrophysiological and Ca²+-imaging analyses indicated that the derived-TRPV6 elicited more Ca²+ influx than the ancestral one in TRPV6-expressing cells where both channels were equally expressed in the cells. Ca²+-inactivation properties in the ancestral- and derived-TRPV6 were almost the same. Furthermore, fluorescence resonance energy transfer (FRET) analysis showed that both channels have similar multimeric formation properties, suggesting that derived-TRPV6 itself could cause higher Ca²+ influx. These findings suggest that populations having derived-TRPV6 in non-African areas may absorb higher Ca²+ from the intestine than ancestral-TRPV6 in the African area.

  19. Neodymium isotopic variations in Northwest Pacific waters

    Science.gov (United States)

    Amakawa, Hiroshi; Nozaki, Yoshiyuki; Alibo, Dia Sotto; Zhang, Jing; Fukugawa, Kiyotaka; Nagai, Hisao

    2004-02-01

    Four vertical profiles of the concentration and isotopic composition of Nd in seawater were obtained in the western North Pacific. Two profiles from the Kuroshio Current regime showed congruently that although the Nd concentration increases gradually with depth, its isotopic composition varies significantly with depth depending upon the water mass occupying the water column. The high-salinity Kuroshio waters originating from the North Pacific Tropical Water (NPTW) carry the least radiogenic Nd (ɛ Nd = -7.4 to -8.7) to this region at ˜250 m from the western margin continental shelves, most likely from the East China Sea. The Nd isotopic compositions in the North Pacific Intermediate Water (NPIW) that occurs at 600 to 1000 m in the subtropical region are fairly uniform at ɛ Nd = -3.7. The profile data from the ˜38° to 40°N Kuroshio/Oyashio mixed water region off Sanriku of Honshu, Japan, also suggest that the newest NPIW with ɛ Nd = -3.2 is formed there by the mixing of various source waters, and the radiogenic component of Nd is derived mainly from the Oyashio waters. In the Pacific Deep Water (PDW) below ˜1000 m, the Nd isotopic composition is neither vertically nor horizontally homogeneous, suggesting that it serves as a useful tracer for sluggish deep water circulation as well. Two profiles from the Izu-Ogasawara Trench showed a minimum ɛ Nd value at ˜2000 m, suggesting that there exists a horizontal advective flow in the vicinity of Honshu, Japan. There is some evidence from other chemical properties to support this observation. The waters below 4000 m including those within the trench in the subtropical region have ɛ Nd values of around -5, suggesting that the deep waters are fed from the south along the western boundary, ultimately from the Antarctic Bottom Water (AABW) in the South Pacific. This extends up to ˜40°N along the Japanese Islands. In the subarctic region (>˜42°N), the waters have more radiogenic Nd with ɛ Nd > -4.0 throughout the

  20. A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry

    Science.gov (United States)

    Chang, Chi-Shan; Liu, Hsiao-Lei; Moncada, Ximena; Seelenfreund, Andrea; Seelenfreund, Daniela; Chung, Kuo-Fang

    2015-01-01

    The peopling of Remote Oceanic islands by Austronesian speakers is a fascinating and yet contentious part of human prehistory. Linguistic, archaeological, and genetic studies have shown the complex nature of the process in which different components that helped to shape Lapita culture in Near Oceania each have their own unique history. Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China, whereas alternative models favor South China to North Vietnam or a Southeast Asian origin. We test these propositions by studying phylogeography of paper mulberry, a common East Asian tree species introduced and clonally propagated since prehistoric times across the Pacific for making barkcloth, a practical and symbolic component of Austronesian cultures. Using the hypervariable chloroplast ndhF-rpl32 sequences of 604 samples collected from East Asia, Southeast Asia, and Oceanic islands (including 19 historical herbarium specimens from Near and Remote Oceania), 48 haplotypes are detected and haplotype cp-17 is predominant in both Near and Remote Oceania. Because cp-17 has an unambiguous Taiwanese origin and cp-17–carrying Oceanic paper mulberries are clonally propagated, our data concur with expectations of Taiwan as the Austronesian homeland, providing circumstantial support for the “out of Taiwan” hypothesis. Our data also provide insights into the dispersal of paper mulberry from South China “into North Taiwan,” the “out of South China–Indochina” expansion to New Guinea, and the geographic origins of post-European introductions of paper mulberry into Oceania. PMID:26438853