Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.

Science.gov (United States)

Kropáčková, Lucie; Těšický, Martin; Albrecht, Tomáš; Kubovčiak, Jan; Čížková, Dagmar; Tomášek, Oldřich; Martin, Jean-François; Bobek, Lukáš; Králová, Tereza; Procházka, Petr; Kreisinger, Jakub

2017-10-01

Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM. © 2017 John Wiley & Sons Ltd.

Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

Science.gov (United States)

Vélez-Zuazo, Ximena; Agnarsson, Ingi

2011-02-01

Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

Molecular phylogeny of Neotropical monogeneans (Platyhelminthes: Monogenea) from catfishes (Siluriformes)

Czech Academy of Sciences Publication Activity Database

Mendoza-Palmero, Carlos Alonso; Blasco-Costa, I.; Scholz, Tomáš

2015-01-01

Roč. 8, MAR 18 2015 (2015), s. 164 ISSN 1756-3305 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Phylogeny * Monogenea * Dactylogyridae * Neotropical region * Diversity * Siluriformes * 28S rRNA Subject RIV: EG - Zoology Impact factor: 3.234, year: 2015

Molecular phylogeny and morphological change in the Psittacula parakeets.

Science.gov (United States)

Groombridge, Jim J; Jones, Carl G; Nichols, Richard A; Carlton, Mark; Bruford, Michael W

2004-04-01

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.

Phylogeny and subgeneric taxonomy of Aspergillus

DEFF Research Database (Denmark)

Peterson, S.W.; Varga, Janos; Frisvad, Jens Christian

2008-01-01

The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence...

Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera

Czech Academy of Sciences Publication Activity Database

Han, M.L.; Chen, Y.-Y.; Shen, L.-L.; Song, J.; Vlasák, Josef; Dai, Y.-C.; Cui, B.-K.

2016-01-01

Roč. 80, č. 1 (2016), s. 343-373 ISSN 1560-2745 Institutional support: RVO:60077344 Keywords : Fomitopsidaceae * Multi-marker analysis * Phylogeny Subject RIV: EF - Botanics Impact factor: 13.465, year: 2016

Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

Science.gov (United States)

D. Jean Lodge; Mahajabeen Padamsee; P. Brandon Matheny; M. Catherine Aime; Sharon A. Cantrell; David Boertmann; Alexander Kovalenko; Alfredo Vizzini; Bryn T.M. Dentinger; Paul M. Kirk; A. Martin Ainsworth; Jean-Marc Moncalvo; Rytas Vilgalys; Ellen Larsson; Robert Lucking; Gareth W. Griffith; Matthew E. Smith; Lorilei L. Norvell; Dennis E. Desjardin; Scott A. Redhead; Clark L. Ovrebo; Edgar B. Lickey; Enrico Ercole; Karen W. Hughes; Regis Courtecuisse; Anthony Young; Manfred Binder; Andrew M. Minnis; Daniel L. Lindner; Beatriz Ortiz-Santana; John Haight; Thomas Laessoe; Timothy J. Baroni; Jozsef Geml; Tsutomu Hattori

2013-01-01

Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe,...

Using genomic data to unravel the root of the placental mammal phylogeny.

Science.gov (United States)

Murphy, William J; Pringle, Thomas H; Crider, Tess A; Springer, Mark S; Miller, Webb

2007-04-01

The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-01-01

Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-02-01

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

Resolution of ray-finned fish phylogeny and timing of diversification.

Science.gov (United States)

Near, Thomas J; Eytan, Ron I; Dornburg, Alex; Kuhn, Kristen L; Moore, Jon A; Davis, Matthew P; Wainwright, Peter C; Friedman, Matt; Smith, W Leo

2012-08-21

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

Circular revisit orbits design for responsive mission over a single target

Science.gov (United States)

Li, Taibo; Xiang, Junhua; Wang, Zhaokui; Zhang, Yulin

2016-10-01

The responsive orbits play a key role in addressing the mission of Operationally Responsive Space (ORS) because of their capabilities. These capabilities are usually focused on supporting specific targets as opposed to providing global coverage. One subtype of responsive orbits is repeat coverage orbit which is nearly circular in most remote sensing applications. This paper deals with a special kind of repeating ground track orbit, referred to as circular revisit orbit. Different from traditional repeat coverage orbits, a satellite on circular revisit orbit can visit a target site at both the ascending and descending stages in one revisit cycle. This typology of trajectory allows a halving of the traditional revisit time and does a favor to get useful information for responsive applications. However the previous reported numerical methods in some references often cost lots of computation or fail to obtain such orbits. To overcome this difficulty, an analytical method to determine the existence conditions of the solutions to revisit orbits is presented in this paper. To this end, the mathematical model of circular revisit orbit is established under the central gravity model and the J2 perturbation. A constraint function of the circular revisit orbit is introduced, and the monotonicity of that function has been studied. The existent conditions and the number of such orbits are naturally worked out. Taking the launch cost into consideration, optimal design model of circular revisit orbit is established to achieve a best orbit which visits a target twice a day in the morning and in the afternoon respectively for several days. The result shows that it is effective to apply circular revisit orbits in responsive application such as reconnoiter of natural disaster.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Directory of Open Access Journals (Sweden)

David Lee Erickson

2014-11-01

Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

Directory of Open Access Journals (Sweden)

Strassmann Joan E

2004-03-01

Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

Directory of Open Access Journals (Sweden)

Stajich Jason E

2006-11-01

Full Text Available Abstract Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available. Results A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD, and their close

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Science.gov (United States)

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

Archaebacterial phylogeny: perspectives on the urkingdoms

Science.gov (United States)

Woese, C. R.; Olsen, G. J.

1986-01-01

Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

Science.gov (United States)

Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea)

Czech Academy of Sciences Publication Activity Database

Tkach, V.V.; Kudlai, Olena; Kostadinova, Aneta

2016-01-01

Roč. 46, č. 3 (2016), s. 171-185 ISSN 0020-7519 R&D Projects: GA ČR(CZ) GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Echinostomatoidea * Molecular phylogeny * Systematics * Echinostomatidae (sensu stricto) * Caballerotrematidae n. fam. * Himasthlidae * Echinochasmidae * Host associations Subject RIV: EG - Zoology Impact factor: 3.730, year: 2016

Phylogeny of Selaginellaceae: There is value in morphology after all!

Science.gov (United States)

Weststrand, Stina; Korall, Petra

2016-12-01

The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian-Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

Science.gov (United States)

Singh, Reema; Schilde, Christina; Schaap, Pauline

2016-11-17

Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

Science.gov (United States)

Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

2012-01-01

Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

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Nan Song

Full Text Available Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha,Cicadomorpha,Heteroptera, and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

High-Performance Phylogeny Reconstruction

Energy Technology Data Exchange (ETDEWEB)

Tiffani L. Williams

2004-11-10

Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

Phylogeny mandalas for illustrating the Tree of Life.

Science.gov (United States)

Hasegawa, Masami

2017-12-01

A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogenetic analysis of pelecaniformes (aves based on osteological data: implications for waterbird phylogeny and fossil calibration studies.

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Nathan D Smith

2010-10-01

Full Text Available Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group's fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving and temporal diversification (e.g., the origins of modern families. Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification.Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae, Prophaethon and Lithoptila (successive sister taxa to Phaethontidae, and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae. These relationships are invariant when 'backbone' constraints based on recent avian phylogenies are imposed.Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though

Direct maximum parsimony phylogeny reconstruction from genotype data.

Science.gov (United States)

Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

2007-12-05

Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

Direct maximum parsimony phylogeny reconstruction from genotype data

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Ravi R

2007-12-01

Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria

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Laura J. May-Collado

2015-02-01

Full Text Available Marsupials or metatherians are a group of mammals that are distinct in giving birth to young at early stages of development and in having a prolonged investment in lactation. The group consists of nearly 350 extant species, including kangaroos, koala, possums, and their relatives. Marsupials are an old lineage thought to have diverged from early therian mammals some 160 million years ago in the Jurassic, and have a remarkable evolutionary and biogeographical history, with extant species restricted to the Americas, mostly South America, and to Australasia. Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. Here we present the first Methaterian species-level phylogeny to include 80% of the extant marsupial species and five nuclear and five mitochondrial markers obtained from Genbank and a recently published retroposon matrix. Our primary goal is to provide a summary phylogeny that will serve as a tool for comparative research. We evaluate the extent to which the phylogeny recovers current phylogenetic knowledge based on the recovery of “benchmark clades” from prior studies—unambiguously supported key clades and undisputed traditional taxonomic groups. The Bayesian phylogenetic analyses recovered nearly all benchmark clades but failed to find support for the suborder Phalagiformes. The most significant difference with previous published topologies is the support for Australidelphia as a group containing Microbiotheriidae, nested within American marsupials. However, a likelihood ratio test shows that alternative topologies with monophyletic Australidelphia and Ameridelphia are not significantly different than the preferred tree. Although further data are needed to solidify understanding of Methateria phylogeny, the new phylogenetic hypothesis provided here offers a well

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae

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Kingston Sarah E

2009-10-01

Full Text Available Abstract Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae

Czech Academy of Sciences Publication Activity Database

Dogga, S.K.; Bartošová-Sojková, Pavla; Lukeš, Julius; Soldati-Favre, D.

2015-01-01

Roč. 166, č. 6 (2015), s. 659-676 ISSN 1434-4610 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Apicomplexa * Coccidia * Goussia janae * phylogeny * ultrastructure * invasion * central carbon metabolism. Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed

Czech Academy of Sciences Publication Activity Database

Maslov, D. A.; Votýpka, Jan; Yurchenko, V.; Lukeš, Julius

2013-01-01

Roč. 29, č. 1 (2013), s. 43-52 ISSN 1471-4922 R&D Projects: GA ČR GA204/09/1667 Institutional support: RVO:60077344 Keywords : biodiversity * Kinetoplastea * insect trypanosomatids * monoxenous parasites * phylogeny * taxonomy * Trypanosomatidae Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.217, year: 2013

Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

Czech Academy of Sciences Publication Activity Database

Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

2017-01-01

Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).

Science.gov (United States)

Schmidt, Ray C; Bart, Henry L; Nyingi, Wanja Dorothy

2017-06-01

The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa. Copyright © 2017 Elsevier Inc. All rights reserved.

Higher-level molecular phylogeny of the water mites (Acariformes: Prostigmata: Parasitengonina: Hydrachnidiae).

Science.gov (United States)

Dabert, Miroslawa; Proctor, Heather; Dabert, Jacek

2016-08-01

With nearly 6000 named species, water mites (Hydrachnidiae) represent the largest group of arachnids to have invaded and extensively diversified in freshwater habitats. Water mites together with three other lineages (the terrestrial Erythraiae and Trombidiae, and aquatic Stygothrombiae), make up the hyporder Parasitengonina, which is characterized by having parasitic larvae and predatory nymphs and adults. Relationships between the Hydrachnidiae and other members of the Parasitengonina are unclear, as are relationships among the major lineages of water mites. Monophyly of water mites has been asserted, with the possible exception of the morphologically distinctive Hydrovolzioidea. Here we infer the phylogeny of water mites using multiple molecular markers and including representatives of all superfamilies of Hydrachnidiae and of almost all other Parasitengonina. Our results support a monophyletic Parasitengonina including Trombidiae, Stygothrombiae, and Hydrachnidiae. A monophyletic Hydrachnidiae, including Hydrovolzioidea, is strongly supported. Terrestrial Parasitengonina do not form a monophyletic sister group to water mites. Stygothrombiae is close to water mites but is not nested within this clade. Water mites appear to be derived from ancestors close to Stygothrombiae or the erythraoid group Calyptostomatoidea; however, this relationship is not clear because of extremely short branches in this part of the parasitengonine tree. We recovered with strong support all commonly accepted water mite superfamilies except for Hydryphantoidea, which is clearly paraphyletic. Our data support the previously proposed clades Protohydrachnidia (Hydrovolzioidea and Eylaoidea), Euhydrachnidia (all remaining superfamilies), and the euhydrachnid subclade Neohydrachnidia (Lebertioidea, Hydrachnoidea, Hygrobatoidea, and Arrenuroidea). We found that larval leg structure and locomotory behavior are strongly congruent with the molecular phylogeny. Other morphological and behavioral

Molecular phylogeny of Systellognatha (Plecoptera: Arctoperlaria) inferred from mitochondrial genome sequences.

Science.gov (United States)

Chen, Zhi-Teng; Zhao, Meng-Yuan; Xu, Cheng; Du, Yu-Zhou

2018-05-01

The infraorder Systellognatha is the most species-rich clade in the insect order Plecoptera and includes six families in two superfamilies: Pteronarcyoidea (Pteronarcyidae, Peltoperlidae, and Styloperlidae) and Perloidea (Perlidae, Perlodidae, and Chloroperlidae). To resolve the debatable phylogeny of Systellognatha, we carried out the first mitochondrial phylogenetic analysis covering all the six families, including three newly sequenced mitogenomes from two families (Perlodidae and Peltoperlidae) and 15 published mitogenomes. The three newly reported mitogenomes share conserved mitogenomic features with other sequenced stoneflies. For phylogenetic analyses, we assembled five datasets with two inference methods to assess their influence on topology and nodal support within Systellognatha. The results indicated that inclusion of the third codon positions of PCGs, exclusion of rRNA genes, the use of nucleotide datasets and Bayesian inference could improve the phylogenetic reconstruction of Systellognatha. The monophyly of Perloidea was supported in the mitochondrial phylogeny, but Pteronarcyoidea was recovered as paraphyletic and remained controversial. In this mitochondrial phylogenetic study, the relationships within Systellognatha were recovered as (((Perlidae + (Perlodidae + Chloroperlidae)) + (Pteronarcyidae + Styloperlidae)) + Peltoperlidae). Copyright © 2018 Elsevier B.V. All rights reserved.

Juvenile morphology in baleen whale phylogeny.

Science.gov (United States)

Tsai, Cheng-Hsiu; Fordyce, R Ewan

2014-09-01

Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

On simulated annealing phase transitions in phylogeny reconstruction.

Science.gov (United States)

Strobl, Maximilian A R; Barker, Daniel

2016-08-01

Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Studies in Phylogeny. I. On the relation of Taxonomy, Phylogeny and Biogeography

NARCIS (Netherlands)

Lam, H.J.

1938-01-01

Taxonomy is static, its symbols are therefore two-dimensional, representing 1. differences or resemblances and 2. diversity (eventually are also area). Phylogeny is dynamic and its symbols are three-dimensional, representing 1. Time, 2. differences or resemblances and 3. diversity (eventually also

Ribosomal RNA: a key to phylogeny

Science.gov (United States)

Olsen, G. J.; Woese, C. R.

1993-01-01

As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.

Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

Czech Academy of Sciences Publication Activity Database

Doležalová, J.; Vallo, Peter; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, M.; Lukeš, J.; Scholz, T.; Modrý, D.

2015-01-01

Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA ČR GA524/06/0264; GA ČR GA206/09/0927 Institutional support: RVO:68081766 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

New insights in Russula subsect. Rubrinae: phylogeny and the quest for synapomorphic characters

Czech Academy of Sciences Publication Activity Database

Caboň, M.; Eberhardt, U.; Looney, B.; Hampe, F.; Kolařík, Miroslav; Jančovičová, S.; Verbeken, A.; Adamčík, S.

2017-01-01

Roč. 16, č. 9 (2017), s. 877-892 ISSN 1617-416X Grant - others:AV ČR(CZ) SAV-16-06 Program:Bilaterální spolupráce Institutional support: RVO:61388971 Keywords : Sulphovanillin * Incrustations * Multi-locus phylogeny Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.616, year: 2016

Algorithms For Phylogeny Reconstruction In a New Mathematical Model

NARCIS (Netherlands)

Lenzini, Gabriele; Marianelli, Silvia

1997-01-01

The evolutionary history of a set of species is represented by a tree called phylogenetic tree or phylogeny. Its structure depends on precise biological assumptions about the evolution of species. Problems related to phylogeny reconstruction (i.e., finding a tree representation of information

Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism

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Ron S. Ronimus

2003-01-01

Full Text Available Enzymes of the gluconeogenic/glycolytic pathway (the Embden-Meyerhof-Parnas (EMP pathway, the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle and the Entner-Doudoroff pathway are widely distributed and are often considered to be central to the origins of metabolism. In particular, several enzymes of the lower portion of the EMP pathway (the so-called trunk pathway, including triosephosphate isomerase (TPI; EC 5.3.1.1, glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12/13, phosphoglycerate kinase (PGK; EC 2.7.2.3 and enolase (EC 4.2.1.11, are extremely well conserved and universally distributed among the three domains of life. In this paper, the distribution of enzymes of gluconeogenesis/glycolysis in hyperthermophiles—microorganisms that many believe represent the least evolved organisms on the planet—is reviewed. In addition, the phylogenies of the trunk pathway enzymes (TPIs, GAPDHs, PGKs and enolases are examined. The enzymes catalyzing each of the six-carbon transformations in the upper portion of the EMP pathway, with the possible exception of aldolase, are all derived from multiple gene sequence families. In contrast, single sequence families can account for the archaeal and hyperthermophilic bacterial enzyme activities of the lower portion of the EMP pathway. The universal distribution of the trunk pathway enzymes, in combination with their phylogenies, supports the notion that the EMP pathway evolved in the direction of gluconeogenesis, i.e., from the bottom up.

An alu-based phylogeny of lemurs (infraorder: Lemuriformes.

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Adam T McLain

Full Text Available LEMURS (INFRAORDER: Lemuriformes are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55-60 million years ago (mya. Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs, to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the

Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae).

Science.gov (United States)

Martin, Gavin J; Branham, Marc A; Whiting, Michael F; Bybee, Seth M

2017-02-01

Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis. Copyright © 2016 Elsevier Inc. All rights reserved.

Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Czech Academy of Sciences Publication Activity Database

Haddad, S.; Shin, S.; Lemmon, A. R.; Lemmon, E. M.; Švácha, Petr; Farrell, B.; Ślipiński, A.; Windsor, D.; McKenna, D. D.

2018-01-01

Roč. 43, č. 1 (2018), s. 68-89 ISSN 0307-6970 Institutional support: RVO:60077344 Keywords : Chrysomeloidea * Cerambycidae * molecular phylogeny Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 4.474, year: 2016 http://onlinelibrary.wiley.com/doi/10.1111/syen.12257/abstract

The phylogeny of Arthrotardigrada

DEFF Research Database (Denmark)

Hansen, Jesper Guldberg

2011-01-01

The order Arthrotardigrada, or water bears, constitutes a small group of 160 species of marine, microscopical invertebrates, within the phylum Tardigrada. Although the position of tardigrades in the Animal Kingdom has received much attention focusing on the metazoan phylogeny, the phylogenetic...

Phylogeny and morphological variability of trypanosomes from African pelomedusid turtles with redescription of Trypanosoma mocambicum Pienaar, 1962

Czech Academy of Sciences Publication Activity Database

Dvořáková, N.; Čepička, I.; Qablan, M. A.; Gibson, W.; Blažek, Radim; Široký, P.

2015-01-01

Roč. 166, č. 6 (2015), s. 599-608 ISSN 1434-4610 Institutional support: RVO:68081766 Keywords : Trypanosoma * turtle * Pelusios * polymorphism * phylogeny * SSU rRNA gene Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

The evolution of the mitochondrial genetic code in arthropods revisited.

Science.gov (United States)

Abascal, Federico; Posada, David; Zardoya, Rafael

2012-04-01

A variant of the invertebrate mitochondrial genetic code was previously identified in arthropods (Abascal et al. 2006a, PLoS Biol 4:e127) in which, instead of translating the AGG codon as serine, as in other invertebrates, some arthropods translate AGG as lysine. Here, we revisit the evolution of the genetic code in arthropods taking into account that (1) the number of arthropod mitochondrial genomes sequenced has triplicated since the original findings were published; (2) the phylogeny of arthropods has been recently resolved with confidence for many groups; and (3) sophisticated probabilistic methods can be applied to analyze the evolution of the genetic code in arthropod mitochondria. According to our analyses, evolutionary shifts in the genetic code have been more common than previously inferred, with many taxonomic groups displaying two alternative codes. Ancestral character-state reconstruction using probabilistic methods confirmed that the arthropod ancestor most likely translated AGG as lysine. Point mutations at tRNA-Lys and tRNA-Ser correlated with the meaning of the AGG codon. In addition, we identified three variables (GC content, number of AGG codons, and taxonomic information) that best explain the use of each of the two alternative genetic codes.

Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

Czech Academy of Sciences Publication Activity Database

Doležalová, J.; Vallo, P.; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, Milan; Lukeš, Julius; Scholz, Tomáš; Modrý, David

2015-01-01

Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR GA206/09/0927 Institutional support: RVO:60077344 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches.

Science.gov (United States)

Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

2009-02-11

Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations

Inference of Large Phylogenies Using Neighbour-Joining

DEFF Research Database (Denmark)

Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm

2011-01-01

The neighbour-joining method is a widely used method for phylogenetic reconstruction which scales to thousands of taxa. However, advances in sequencing technology have made data sets with more than 10,000 related taxa widely available. Inference of such large phylogenies takes hours or days using...... the Neighbour-Joining method on a normal desktop computer because of the O(n^3) running time. RapidNJ is a search heuristic which reduce the running time of the Neighbour-Joining method significantly but at the cost of an increased memory consumption making inference of large phylogenies infeasible. We present...... two extensions for RapidNJ which reduce the memory requirements and \\makebox{allows} phylogenies with more than 50,000 taxa to be inferred efficiently on a desktop computer. Furthermore, an improved version of the search heuristic is presented which reduces the running time of RapidNJ on many data...

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus.

Science.gov (United States)

Figueroa, Alex; McKelvy, Alexander D; Grismer, L Lee; Bell, Charles D; Lailvaux, Simon P

2016-01-01

With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Science.gov (United States)

McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P.

2016-01-01

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes. PMID:27603205

The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

Directory of Open Access Journals (Sweden)

Ó'Fágáin Ciarán

2008-03-01

Full Text Available Abstract Background The mammalian heme peroxidases (MHPs are a medically important group of enzymes. Included in this group are myeloperoxidase, eosinophil peroxidase, lactoperoxidase, and thyroid peroxidase. These enzymes are associated with such diverse diseases as asthma, Alzheimer's disease and inflammatory vascular disease. Despite much effort to elucidate a clearer understanding of the function of the 4 major groups of this multigene family, we still do not have a clear understanding of their relationships to each other. Results Sufficient signal exists for the resolution of the evolutionary relationships of this family of enzymes. We demonstrate, using a root mean squared deviation statistic, how the removal of the fastest evolving sites aids in the minimisation of the effect of long branch attraction and the generation of a highly supported phylogeny. Based on this phylogeny we have pinpointed the amino acid positions that have most likely contributed to the diverse functions of these enzymes. Many of these residues are in close proximity to sites implicated in protein misfolding, loss of function or disease. Conclusion Our analysis of all available genomic sequence data for the MHPs from all available completed mammalian genomes, involved sophisticated methods of phylogeny reconstruction and data treatment. Our study has (i fully resolved the phylogeny of the MHPs and the subsequent pattern of gene duplication, and (ii, we have detected amino acids under positive selection that have most likely contributed to the observed functional shifts in each type of MHP.

Fossils and decapod phylogeny

NARCIS (Netherlands)

Schram, Frederick R.; Dixon, Christopher

2003-01-01

An expanded series of morphological characters developed for a cladistic analysis of extant decapods has yielded a new hypothesis for the phylogeny of the group. Application of this database to selected fossil genera produces some interesting results and demonstrates the feasibility of treating

Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola

Czech Academy of Sciences Publication Activity Database

Nováková, Eva; Hypša, Václav; Klein, J.; Foottit, R. G.; von Dohlen, C.D.; Moran, N. A.

2013-01-01

Roč. 68, č. 1 (2013), s. 42-54 ISSN 1055-7903 R&D Projects: GA ČR GD206/09/H026 Institutional support: RVO:60077344 Keywords : Aphid * Evolution * Buchnera * Phylogeny * Informative markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.018, year: 2013

Molecular Phylogeny of the Bamboo Sharks (Chiloscyllium spp.

Directory of Open Access Journals (Sweden)

Noor Haslina Masstor

2014-01-01

Full Text Available Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences’ lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate that can clearly be used to differentiate each species.

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.

Science.gov (United States)

Zeng, Liping; Zhang, Ning; Zhang, Qiang; Endress, Peter K; Huang, Jie; Ma, Hong

2017-05-01

Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Phylogeny of species and cytotypes of mole rats (Spalacidae) in Turkey inferred from mitochondrial cytochrome b gene sequencees

Czech Academy of Sciences Publication Activity Database

Kandemir, I.; Sozen, M.; Matur, F.; Kankilic, T.; Martínková, Natália; Colak, F.; Ozkurt, S. O.; Colak, E.

2012-01-01

Roč. 61, č. 1 (2012), s. 25-33 ISSN 0139-7893 Institutional support: RVO:68081766 Keywords : Nannospalax * molecular phylogeny * chromosomal form * Anatolia * Thrace Subject RIV: EG - Zoology Impact factor: 0.494, year: 2012

A molecular phylogeny of the Cephinae (Hymenoptera, Cephidae based on mtDNA COI gene: a test of traditional classification

Directory of Open Access Journals (Sweden)

Mahir Budak

2011-09-01

Full Text Available Cephinae is traditionally divided into three tribes and about 24 genera based on morphology and host utilization. There has been no study testing the monophyly of taxa under a strict phylogenetic criterion. A molecular phylogeny of Cephinae based on a total of 68 sequences of mtDNA COI gene, representing seven genera of Cephinae, is reconstructed to test the traditional limits and relationships of taxa. Monophyly of the traditional tribes is not supported. Monophyly of the genera are largely supported except for Pachycephus. A few host shift events are suggested based on phylogenetic relationships among taxa. These results indicate that a more robust phylogeny is required for a more plausible conclusion. We also report two species of Cephus for the first time from Turkey.

Archigregarines of the English Channel revisited: New molecular data on Selenidium species including early described and new species and the uncertainties of phylogenetic relationships.

Directory of Open Access Journals (Sweden)

Sonja Rueckert

Full Text Available Gregarines represent an important transition step from free-living predatory (colpodellids s.l. and/or photosynthetic (Chromera and Vitrella apicomplexan lineages to the most important pathogens, obligate intracellular parasites of humans and domestic animals such as coccidians and haemosporidians (Plasmodium, Toxoplasma, Eimeria, Babesia, etc.. While dozens of genomes of other apicomplexan groups are available, gregarines are barely entering the molecular age. Among the gregarines, archigregarines possess a unique mixture of ancestral (myzocytosis and derived (lack of apicoplast, presence of subpellicular microtubules features.In this study we revisited five of the early-described species of the genus Selenidium including the type species Selenidium pendula, with special focus on surface ultrastructure and molecular data. We were also able to describe three new species within this genus. All species were characterized at morphological (light and scanning electron microscopy data and molecular (SSU rDNA sequence data levels. Gregarine specimens were isolated from polychaete hosts collected from the English Channel near the Station Biologique de Roscoff, France: Selenidium pendula from Scolelepis squamata, S. hollandei and S. sabellariae from Sabellaria alveolata, S. sabellae from Sabella pavonina, Selenidium fallax from Cirriformia tentaculata, S. spiralis sp. n. and S. antevariabilis sp. n. from Amphitritides gracilis, and S. opheliae sp. n. from Ophelia roscoffensis. Molecular phylogenetic analyses of these data showed archigregarines clustering into five separate clades and support previous doubts about their monophyly.Our phylogenies using the extended gregarine sampling show that the archigregarines are indeed not monophyletic with one strongly supported clade of Selenidium sequences around the type species S. pendula. We suggest the revision of the whole archigregarine taxonomy with only the species within this clade remaining in the genus

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa

Czech Academy of Sciences Publication Activity Database

Bryja, J.; Mikula, Ondřej; Šumbera, R.; Meheretu, Y.; Aghová, T.; Lavrenchenko, L. A.; Mazoch, V.; Oguge, N.; Mbau, J. S.; Welegerima, K.; Amundala, N.; Colyn, M.; Leirs, H.; Verheyen, E.

2014-01-01

Roč. 14, č. 256 (2014) ISSN 1471-2148 R&D Projects: GA ČR GAP506/10/0983 Institutional support: RVO:67985904 Keywords : biogeography * tropical Africa * molecular phylogeny Subject RIV: EG - Zoology Impact factor: 3.368, year: 2014

A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats

KAUST Repository

Hundt, Peter J.

2014-01-01

The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100. bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies. © 2013 Elsevier Inc.

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

Directory of Open Access Journals (Sweden)

Beaulieu Jeremy M

2009-02-01

Full Text Available Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae with 13,533 species and 1,401 sites. Conclusion By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously

A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China.

Directory of Open Access Journals (Sweden)

Xin Zhao

Full Text Available The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens. Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.

Molecular data and phylogeny of family

International Nuclear Information System (INIS)

Shinwari, Z.K.; Shinwari, S.

2010-01-01

Family Smilacaceae's higher order taxonomy remained disputed for many years. It was treated as an order 'Smilacales' and was also placed under Liliales by several taxonomists. Even some considered as part of family Liliacaeae. In present paper, we investigated the family's higher order phylogeny and also compared its rbcL gene sequence data with related taxa to elucidate its phylogeny. The data suggests that its family stature is beyond dispute because of its advanced karyotype, woody climbing habit and DNA sequence data. The data suggest that Smilacaceae may be a sister group of order Liliales and it forms a clear clade with the order. (author)

Molecular phylogeny of Acerentomidae (Protura), with description of Acerentuloides bernardi sp. nov. from North America

Czech Academy of Sciences Publication Activity Database

Shrubovych, J.; Starý, Josef; D'Haese, C.A.

2017-01-01

Roč. 100, č. 2 (2017), s. 433-443 ISSN 0015-4040 R&D Projects: GA MŠk ME08019 Institutional support: RVO:60077344 Keywords : Acerentulus * DNA barcoding * Indiana * phylogeny * Podolinella * USA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 0.964, year: 2016

Building a Twig Phylogeny

Science.gov (United States)

Flinn, Kathryn M.

2015-01-01

In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a…

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

Science.gov (United States)

Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies.

Science.gov (United States)

Min, Xiaoping; Zhang, Mouzhao; Yuan, Sisi; Ge, Shengxiang; Liu, Xiangrong; Zeng, Xiangxiang; Xia, Ningshao

2017-12-26

In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.

Directory of Open Access Journals (Sweden)

Emmanuelle Lerat

2003-10-01

Full Text Available The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205 of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.

Bayesian phylogeny analysis via stochastic approximation Monte Carlo

KAUST Repository

Cheon, Sooyoung

2009-11-01

Monte Carlo methods have received much attention in the recent literature of phylogeny analysis. However, the conventional Markov chain Monte Carlo algorithms, such as the Metropolis-Hastings algorithm, tend to get trapped in a local mode in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method is compared with two popular Bayesian phylogeny software, BAMBE and MrBayes, on simulated and real datasets. The numerical results indicate that our method outperforms BAMBE and MrBayes. Among the three methods, SAMC produces the consensus trees which have the highest similarity to the true trees, and the model parameter estimates which have the smallest mean square errors, but costs the least CPU time. © 2009 Elsevier Inc. All rights reserved.

eWOM, Revisit Intention, Destination Trust and Gender

OpenAIRE

Abubakar, Abubakar Mohammed; Ilkan, Mustafa; Al-Tal, Raad Meshall; Eluwole, Kayode

2017-01-01

This article investigates the impact of eWOM on intention to revisit and destination trust, and the moderating role of gender in medical tourism industry. Result from structural equation modeling (n=240) suggests the following: (1) that eWOM influences intention to revisit and destination trust; (2) that destination trust influences intention to revisit; (3) that the impact of eWOM on intention to revisit is about 1.3 times higher in men; (4) that the impact of eWOM on destination trust is ab...

PHY∙FI: fast and easy online creation and manipulation of phylogeny color figures

DEFF Research Database (Denmark)

Fredslund, Jakob

2006-01-01

the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create...... types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing...... a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus...

Phylogeny and adaptation shape the teeth of insular mice.

Science.gov (United States)

Ledevin, Ronan; Chevret, Pascale; Ganem, Guila; Britton-Davidian, Janice; Hardouin, Emilie A; Chapuis, Jean-Louis; Pisanu, Benoit; da Luz Mathias, Maria; Schlager, Stefan; Auffray, Jean-Christophe; Renaud, Sabrina

2016-02-10

By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. © 2016 The Author(s).

A transcriptome approach to ecdysozoan phylogeny.

Science.gov (United States)

Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

2014-11-01

The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Complex phylogenetic placement of ilex species (aquifoliaceae): a case study of molecular phylogeny

International Nuclear Information System (INIS)

Yi, F.; Sun, L.; Xiao, P.G.; Hao, D.C.

2017-01-01

To investigate the phylogenetic relationships among Ilex species distributed in China, we analyzed two alignments including 4,698 characters corresponding to six plastid sequences (matK, rbcL, atpB-rbcL, trnL-F, psbA-trnH, and rpl32-trnL) and 1,748 characters corresponding to two nuclear sequences (ITS and nepGS). Using different partitioning strategies and approaches (i.e., Bayesian inference, maximum likelihood, and maximum parsimony) for phylogeny reconstruction, different topologies and clade supports were determined. A total of 18 Ilex species was divided into two major groups (group I and II) in both plastid and nuclear phylogenies with some incongruences. Potential hybridization events may account, in part, for those phylogenetic uncertainties. The analyses, together with previously identified sequences, indicated that all 18 species were recovered within Eurasia or Asia/North America groups based on plastid data. Meanwhile, the species in group II in the nuclear phylogeny were placed in the Aquifolium clade, as inferred from traditional classification, whereas the species in group I belonged to several other clades. The divergence time of most of the 18 Ilex species was estimated to be not more than 10 million years ago. Based on the results of this study, we concluded that paleogeographical events and past climate changes during the same period might have played important roles in these diversifications. (author)

Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization

Directory of Open Access Journals (Sweden)

Blanc Michel

2007-01-01

Full Text Available Abstract Background The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and breed in empty gastropod shells is probably the most peculiar. Although shell-breeding arose several times in the evolutionary history of the lamprologines, all obligatory and most facultative shell-breeders belong to the so called "ossified group", a monophyletic lineage within the lamprologine cichlids. Since their distinctive life style enables these species to live and breed in closest vicinity, we hypothesized that these cichlids might be particularly prone to accidental hybridization, and that introgression might have affected the evolutionary history of this cichlid lineage. Results Our analyses revealed discrepancies between phylogenetic hypotheses based on mitochondrial and nuclear (AFLP data. While the nuclear phylogeny was congruent with morphological, behavioral and ecological characteristics, several species – usually highly specialized shell-breeders – were placed at contradicting positions in the mitochondrial phylogeny. The discordant phylogenies strongly suggest repeated incidents of introgressive hybridization between several distantly related shell-breeding species, which reticulated the phylogeny of this group of cichlids. Long interior branches and high bootstrap support for many interior nodes in the mitochondrial phylogeny argue against a major effect of ancient incomplete lineage sorting on the phylogenetic reconstruction. Moreover, we provide morphological and genetic (mtDNA and microsatellites evidence for ongoing hybridization among distantly related shell-breeders. In these cases, the territorial males of the inferred paternal species are too large to enter the shells of their mate, such that they have to release their sperm over the entrance of the shell to fertilize the eggs. With sperm

Phylogeny of the Acanthocephala based on morphological characters.

Science.gov (United States)

Monks, S

2001-02-01

Only four previous studies of relationships among acanthocephalans have included cladistic analyses, and knowledge of the phylogeny of the group has not kept pace with that of other taxa. The purpose of this study is to provide a more comprehensive analysis of the phylogenetic relationships among members of the phylum Acanthocephala using morphological characters. The most appropriate outgroups are those that share a common early cell-cleavage pattern (polar placement of centrioles), such as the Rotifera, rather than the Priapulida (meridional placement of centrioles) to provide character polarity based on common ancestry rather than a general similarity likely due to convergence of body shapes. The phylogeny of 22 species of the Acanthocephala was evaluated based on 138 binary and multistate characters derived from comparative morphological and ontogenetic studies. Three assumptions of cement gland structure were tested: (i) the plesiomorphic type of cement glands in the Rotifera, as the sister group, is undetermined; (ii) non-syncytial cement glands are plesiomorphic; and (iii) syncytial cement glands are plesiomorphic. The results were used to test an early move of Tegorhynchus pectinarius to Koronacantha and to evaluate the relationship between Tegorhynchus and Illiosentis. Analysis of the data-set for each of these assumptions of cement gland structure produced the same single most parsimonious tree topology. Using Assumptions i and ii for the cement glands, the trees were the same length (length = 404 steps, CI = 0.545, CIX = 0.517, HI = 0.455, HIX = 0.483, RI = 0.670, RC = 0.365). Using Assumption iii, the tree was three steps longer (length = 408 steps, CI = 0.539, CIX = 0.512, HI = 0.461, HIX = 0.488, RI = 0.665, RC = 0.359). The tree indicates that the Palaeacanthocephala and Eoacanthocephala both are monophyletic and are sister taxa. The members of the Archiacanthocephala are basal to the other two clades, but do not themselves form a clade. The results

PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

Directory of Open Access Journals (Sweden)

Fredslund Jakob

2006-06-01

Full Text Available Abstract Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates". The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go

Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

Directory of Open Access Journals (Sweden)

Ferla Matteo P

2009-01-01

Full Text Available Abstract Background The phylogeny of Eumalacostraca (Crustacea remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders has either combined evidence from multiple loci, or combined molecular and morphological evidence. Results We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades. Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed

Molecular phylogeny and morphological change in the Psittacula parakeets

OpenAIRE

Groombridge, Jim J.; Jones, Carl G.; Nichols, Richard A.; Carlton, Mark; Bruford, Michael W.

2004-01-01

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800 bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that ext...

The shape of mammalian phylogeny

DEFF Research Database (Denmark)

Purvis, Andy; Fritz, Susanne A; Rodríguez, Jesús

2011-01-01

an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions...

Phylogeny of the 'orchid-like' bladderworts (gen. Utricularia sect. Orchidioides and Iperua: Lentibulariaceae) with remarks on the stolon-tuber system

Czech Academy of Sciences Publication Activity Database

Rodrigues, F. G.; Marulanda, N. F.; Silva, S. R.; Płachno, B.J.; Adamec, Lubomír; Miranda, V.F.O.

2017-01-01

Roč. 120, č. 5 (2017), s. 709-723 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : molecular phylogeny * anatomy * tubers Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides).

Science.gov (United States)

Jønsson, Knud Andreas; Fabre, Pierre-Henri; Kennedy, Jonathan D; Holt, Ben G; Borregaard, Michael K; Rahbek, Carsten; Fjeldså, Jon

2016-01-01

The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not. Copyright © 2015 Elsevier Inc. All rights reserved.

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).

Science.gov (United States)

Goodheart, Jessica A; Bazinet, Adam L; Valdés, Ángel; Collins, Allen G; Cummings, Michael P

2017-10-26

The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of marine specialized consumers for which reliable phylogenies exist hampers attempts to test the role of trophic specialization in evolution. In this study, RNA-Seq data is used to produce a phylogeny of Cladobranchia, a group of marine invertebrates that feed on a diverse array of prey taxa but mostly specialize on cnidarians. The broad range of prey type preferences allegedly present in two major groups within Cladobranchia suggest that prey type shifts are relatively common over evolutionary timescales. In the present study, we generated a well-supported phylogeny of the major lineages within Cladobranchia using RNA-Seq data, and used ancestral state reconstruction analyses to better understand the evolution of prey preference. These analyses answered several fundamental questions regarding the evolutionary relationships within Cladobranchia, including support for a clade of species from Arminidae as sister to Tritoniidae (which both preferentially prey on Octocorallia). Ancestral state reconstruction analyses supported a cladobranchian ancestor with a preference for Hydrozoa and show that the few transitions identified only occur from lineages that prey on Hydrozoa to those that feed on other types of prey. There is strong phylogenetic correlation with prey preference within Cladobranchia, suggesting that prey type specialization within this group has inertia. Shifts between different types of prey have occurred rarely throughout the evolution of

A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity.

Science.gov (United States)

Milla, Liz; van Nieukerken, Erik J; Vijverberg, Ruben; Doorenweerd, Camiel; Wilcox, Stephen A; Halsey, Mike; Young, David A; Jones, Therésa M; Kallies, Axel; Hilton, Douglas J

2018-03-01

Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Identifying the Basal Angiosperm Node in Chloroplast GenomePhylogenies: Sampling One's Way Out of the Felsenstein Zone

Energy Technology Data Exchange (ETDEWEB)

Leebens-Mack, Jim; Raubeson, Linda A.; Cui, Liying; Kuehl,Jennifer V.; Fourcade, Matthew H.; Chumley, Timothy W.; Boore, JeffreyL.; Jansen, Robert K.; dePamphilis, Claude W.

2005-05-27

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca and Typha), a water lily (Nuphar), a ranunculid(Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein datasets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiospermphylogeny. However, their relative positions proved to be dependent on method of analysis, with parsimony favoring Amborella as sister to all other angiosperms, and maximum likelihood and neighbor-joining methods favoring an Amborella + Nympheales clade as sister. The maximum likelihood phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single gene phylogenies, estimated divergence dates and conflicting in del characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiospermphylogeny. Molecular dating analyses provided median age estimates of 161 mya for the most recent common ancestor of all extant angiosperms and 145 mya for the most recent common ancestor of monocots, magnoliids andeudicots. Whereas long sequences reduce variance in

Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny.

Science.gov (United States)

Dumack, Kenneth; Mylnikov, Alexander P; Bonkowski, Michael

2017-07-01

The genus Kraken represents a distinct lineage of filose amoebae within the Cercozoa. Currently a single species, Kraken carinae, has been described. SSU rDNA phylogeny showed an affiliation to the Cercomonadida, branching with weak support at its base, close to Paracercomonas, Metabolomonas, and Brevimastigomonas. Light microscopical analyses showed several unique features of the genus Kraken, but ultrastructure data were lacking. In this study, K. carinae has been studied by electron microscopy, these data conjoined with a two-gene phylogeny were used to give more insight into the evolutionary relationship of the genus Kraken within Cercozoa. The data confirmed the absence of flagella, but also showed novel characteristics, such as the presence of extrusomes, osmiophilic bodies, and mitochondria with flat cristae. Surprising was the presence of single-tier scales which are carried by cell outgrowths, much of what is expected of the last common ancestor of the class Imbricatea. The phylogenetic analyses however confirmed previous results, indicating Kraken as a sister group to Paracercomonas in Sarcomonadea with an increased but still low support of 0.98 PP/63 BP. Based on the unique features of Kraken we establish the Krakenidae fam. nov. that we, due to contradictory results in morphology and phylogeny, assign incertae sedis, Monadofilosa. Copyright © 2017 Elsevier GmbH. All rights reserved.

A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment

Directory of Open Access Journals (Sweden)

Lindgren Annie R

2012-07-01

Full Text Available Abstract Background The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology. Results Our study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively. Discussion Our study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that

Bootstrapping phylogenies inferred from rearrangement data

Directory of Open Access Journals (Sweden)

Lin Yu

2012-08-01

Full Text Available Abstract Background Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. Results We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Conclusions Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its

Bootstrapping phylogenies inferred from rearrangement data.

Science.gov (United States)

Lin, Yu; Rajan, Vaibhav; Moret, Bernard Me

2012-08-29

Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver

A dated phylogeny complements macroecological analysis to explain the diversity patterns in Geonoma (Arecaceae)

DEFF Research Database (Denmark)

Roncal, Julissa; Overgaard, Anne Blach; Borchsenius, Finn

2011-01-01

pattern. To test for a time-for-diversification effect, we correlated four different species richness measures with the diversification time of the earliest large lineage that is characteristic of each cluster. In support of this hypothesis, we found that geographic areas with higher richness contained...... coherent floristic clusters. We then evaluated the extent to which the spatial variation in species composition reflects present-day environmental variation vs. nonenvironmental spatial effects, as expected if the pattern reflects historical biogeography. We also examined the degree of geographic structure...... in the Geonoma phylogeny. Finally, we used a dated phylogeny to assess whether species richness within the floristic clusters was constrained by a specific historical biogeographic driver, namely time-for-diversification. A cluster analysis identified six spatially coherent floristic clusters, four of which were...

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences.

Science.gov (United States)

Lyra, Goia de M; Costa, Emmanuelle da S; de Jesus, Priscila B; de Matos, João Carlos G; Caires, Taiara A; Oliveira, Mariana C; Oliveira, Eurico C; Xi, Zhenxiang; Nunes, José Marcos de C; Davis, Charles C

2015-04-01

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well-supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae. © 2015 Phycological Society of America.

Molecular phylogeny of extant Holothuroidea (Echinodermata).

Science.gov (United States)

Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

2017-06-01

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown

A six-gene phylogeny provides new insights into choanoflagellate evolution.

Science.gov (United States)

Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

2017-02-01

Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Book review: Insect morphology and phylogeny

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Susanne Randolf

2014-05-01

Full Text Available Beutel RG, Friedrich F, Ge S-Q, Yang X-K (2014 Insect Morphology and Phylogeny: A textbook for students of entomology. De Gruyter, Berlin/Boston, 516 pp., softcover. ISBN 978-3-11-026263-6.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

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Sun, Zhonglou; Pan, Tao; Hu, Chaochao; Sun, Lu; Ding, Hengwu; Wang, Hui; Zhang, Chenling; Jin, Hong; Chang, Qing; Kan, Xianzhao; Zhang, Baowei

2017-01-01

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

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Zhonglou Sun

Full Text Available The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes. Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma. Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma. Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

Molecular phylogeny of Subtribe Artemisiinae (Asteraceae), including Artemisia and its allied and segregate genera

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Watson, Linda E; Bates, Paul L; Evans, Timothy M; Unwin, Matthew M; Estes, James R

2002-01-01

Background Subtribe Artemisiinae of Tribe Anthemideae (Asteraceae) is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemisia, as well as several smaller genera and Seriphidium, that altogether comprise the Artemisia-group. Circumscription and taxonomic boundaries of Artemisia and the placements of these small segregate genera is currently unresolved. Results We constructed a molecular phylogeny for the subtribe using the internal transcribed spacers (ITS) of nuclear ribosomal DNA analyzed with parsimony, likelihood, and Bayesian criteria. The resulting tree is comprised of three major clades that correspond to the radiate genera (e.g., Arctanthemum and Dendranthema), and two clades of Artemisia species. All three clades have allied and segregate genera embedded within each. Conclusions The data support a broad concept of Artemisia s.l. that includes Neopallasia, Crossostephium, Filifolium, Seriphidium, and Sphaeromeria. However, the phylogeny excludes Elachanthemum, Kaschgaria, and Stilnolepis from the Artemisia-group. Additionally, the monophyly of the four subgenera of Artemisia is also not supported, with the exception of subg. Dracunculus. Homogamous, discoid capitula appear to have arisen in parallel four to seven times, with the loss of ray florets. Thus capitular morphology is not a reliable taxonomic character, which traditionally has been one of the defining characters. PMID:12350234

Bayesian inference of the metazoan phylogeny

DEFF Research Database (Denmark)

Glenner, Henrik; Hansen, Anders J; Sørensen, Martin V

2004-01-01

Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has...

Molecular characterization and phylogeny of four new species of the genus trichonympha (Parabasalia, trichonymphea) from lower termite hindguts

Czech Academy of Sciences Publication Activity Database

Boscaro, V.; James, E. R.; Fiorito, R.; Hehenberger, E.; Karnkowska, A.; del Campo, J.; Kolísko, Martin; Irwin, N. A.T.; Mathur, V.; Scheffrahn, R. H.; Keeling, P. J.

2017-01-01

Roč. 67, č. 9 (2017), s. 3570-3575, č. článku 002169. ISSN 1466-5026 Institutional support: RVO:60077344 Keywords : parabasalids * SSU rRNA phylogeny * termite symbionts * trichonympha Subject RIV: EB - Gene tics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.134, year: 2016

The Effects of Korean Medical Service Quality and Satisfaction on Revisit Intention of the United Arab Emirates Government Sponsored Patients.

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Lee, Seoyoung; Kim, Eun-Kyung

2017-06-01

The purpose of this study was to investigate medical service quality, satisfaction and to examine factors influencing hospital revisit intention of the United Arab Emirates government sponsored patients in Korea. A total of 152 UAE government sponsored patients who visited Korean hospitals participated in the questionnaire survey from August to November 2016. Stepwise multiple regression was used to identify the factors that affected the revisit intention of the participants. The mean scores of medical service quality, satisfaction, and revisit intention were 5.72 out of 7, 88.88 out of 100, 4.59 out of 5, respectively. Medical service quality and satisfaction, Medical service quality and revisit intention, satisfaction and revisit intention were positively correlated. Medical service of physician, visiting routes and responsiveness of medical service quality explained about 23.8% of revisit intention. There are needs for physicians to communicate with patients while ensuring sufficient consultation time based on excellent medical skills and nurses to respond immediately for the patients' needs through an empathic encounter in order to improve medical service quality and patient satisfaction so that to increase the revisit intention of the United Arab Emirates government sponsored patients. Further, it is necessary for the hospitals to have support plans for providing country specialized services in consideration of the UAE culture to ensure that physicians' and nurses' competencies are not undervalued by non-medical service elements such as interpreters and meals. Copyright © 2017. Published by Elsevier B.V.

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa

Czech Academy of Sciences Publication Activity Database

Bryja, Josef; Mikula, Ondřej; Šumbera, R.; Meheretu, Y.; Aghová, Tatiana; Lavrenchenko, L. A.; Mazoch, Vladimír; Oguge, N.; Mbau, J. S.; Welegerima, K.; Amundala, N.; Colyn, M.; Leirs, H.; Verheyen, E.

2014-01-01

Roč. 14, č. 256 (2014), s. 256 ISSN 1471-2148 R&D Projects: GA ČR GAP506/10/0983 Institutional support: RVO:68081766 Keywords : Biogeography * Tropical Africa * Molecular phylogeny * Pygmy mice * Plio-Pleistocene climatic fluctuations * Divergence timing * Muridae (Murinae) * Mus minutoides * Phylogeography * DNA barcoding Subject RIV: EG - Zoology Impact factor: 3.368, year: 2014

A web-database of mammalian morphology and a reanalysis of placental phylogeny

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Asher Robert J

2007-07-01

Full Text Available Abstract Background Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny. Results The results reinforce the growing consensus regarding the extant placental mammal clades of Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria. Bayesian analyses of morphology, indels, and DNA support both a basal position for Afrotheria and the position of Cretaceous eutherians outside of crown Placentalia. Depending on treatment of third codon positions, the affinity of several fossils (Leptictis,Paleoparadoxia, Plesiorycteropus and Zalambdalestes vary, highlighting the potential effect of sequence data on fossils for which such data are missing. Conclusion The combined dataset supports the location of the placental mammal root at Afrotheria or Xenarthra, not at Erinaceus or rodents. Even a small morphological dataset can have a marked influence on the location of the root in a combined-data analysis. Additional morphological data are desirable to better reconstruct the position of several fossil taxa; and the graphic-rich, web-based morphology data matrix presented here will make it easier to incorporate more taxa into a larger data matrix.

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

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Giribet, Gonzalo; Edgecombe, Gregory D.; Wheeler, Ward C.; Babbitt, Courtney

2002-01-01

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. c2002 The Willi Hennig Society.

Phylogeny of economically important insect pests that infesting several crops species in Malaysia

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Ghazali, Siti Zafirah; Zain, Badrul Munir Md.; Yaakop, Salmah

2014-09-01

This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the fern's pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabola's order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences.

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Kochzius, Marc; Söller, Rainer; Khalaf, Maroof A; Blohm, Dietmar

2003-09-01

This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) "Pterois" clade (Pterois miles and Pterois volitans), and (2) "Pteropterus-Dendrochirus" clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the "Pteropterus-Dendrochirus" clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.

Lakatos Revisited.

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Court, Deborah

1999-01-01

Revisits and reviews Imre Lakatos' ideas on "Falsification and the Methodology of Scientific Research Programmes." Suggests that Lakatos' framework offers an insightful way of looking at the relationship between theory and research that is relevant not only for evaluating research programs in theoretical physics, but in the social…

Phylogeny of Cirsium spp. in North America: Host Specificity Does Not Follow Phylogeny

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Tracey A. Bodo Slotta

2012-10-01

Full Text Available Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native Great Plains Cirsium spp. and other thistles to determine if host specificity follows phylogeny. The monophyly of Cirsium spp. and Carduus within the tribe Cardinae was confirmed with native North American and European lineages of the Cirsium spp. examined. We did not detect interspecific hybridization between the introduced invasive and the native North American Cirsium spp. Selected host-biological control agent interactions were mapped onto the phylogenic tree derived by maximum likelihood analysis to examine the co-occurrence of known hosts with biological control agents. Within Cirsium-Cardueae, the insect biological control agents do not associate with host phylogenetic lines. Thus, more comprehensive testing of species in host-specificity trials, rather than relying on a single representative of a given clade may be necessary; because the assumption that host-specificity follows phylogeny does not necessarily hold. Since the assumption does not always hold, it will also be important to evaluate ecological factors to provide better cues for host specificity.

Explaining evolution via constrained persistent perfect phylogeny

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2014-01-01

Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

Science.gov (United States)

Graham Reynolds, R; Niemiller, Matthew L; Revell, Liam J

2014-02-01

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers

A Bayesian approach to the evolution of metabolic networks on a phylogeny.

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Aziz Mithani

2010-08-01

Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

Microsporidian genus Berwaldia (Opisthosporidia, Microsporidia), infecting daphnids (Crustacea, Branchiopoda): Biology, structure, molecular phylogeny and description of two new species

Czech Academy of Sciences Publication Activity Database

Vávra, Jiří; Hyliš, M.; Fiala, Ivan; Sacherová, V.; Vossbrinck, C. R.

2017-01-01

Roč. 61, October (2017), s. 1-12 ISSN 0932-4739 R&D Projects: GA ČR(CZ) GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Daphnia * fungi * Microsporidia * parasite * SSU rDNA phylogeny * transmission Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.581, year: 2016

Oxidative phosphorylation revisited

DEFF Research Database (Denmark)

Nath, Sunil; Villadsen, John

2015-01-01

The fundamentals of oxidative phosphorylation and photophosphorylation are revisited. New experimental data on the involvement of succinate and malate anions respectively in oxidative phosphorylation and photophosphorylation are presented. These new data offer a novel molecular mechanistic...

Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata: phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

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Jang Kuem

2009-04-01

Full Text Available Abstract Background The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny. Results The complete mitochondrial genome (15,433 bp of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata, one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of F. hispida (Bryozoa, Gymnolaemata, Ctenostomata, which has only 36 components with loss of tRNAser(ucn genes. The B. neritina mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida and a chiton Katharina tunicate than to that of F. hispida. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (B. neritina and F. hispida was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta. Conclusion This study presents the complete mitochondrial genome of a

A molecular phylogeny of living primates.

Science.gov (United States)

Perelman, Polina; Johnson, Warren E; Roos, Christian; Seuánez, Hector N; Horvath, Julie E; Moreira, Miguel A M; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C; Silva, Artur; O'Brien, Stephen J; Pecon-Slattery, Jill

2011-03-01

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

A Molecular Phylogeny of Living Primates

Science.gov (United States)

Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

2011-01-01

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

A molecular phylogeny of living primates.

Directory of Open Access Journals (Sweden)

Polina Perelman

2011-03-01

Full Text Available Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb from 186 primates representing 61 (~90% of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

Evolution of electric communication signals in the South American ghost knifefishes (Gymnotiformes: Apteronotidae): A phylogenetic comparative study using a sequence-based phylogeny.

Science.gov (United States)

Smith, Adam R; Proffitt, Melissa R; Ho, Winnie W; Mullaney, Claire B; Maldonado-Ocampo, Javier A; Lovejoy, Nathan R; Alves-Gomes, José A; Smith, G Troy

2016-10-01

The electric communication signals of weakly electric ghost knifefishes (Gymnotiformes: Apteronotidae) provide a valuable model system for understanding the evolution and physiology of behavior. Apteronotids produce continuous wave-type electric organ discharges (EODs) that are used for electrolocation and communication. The frequency and waveform of EODs, as well as the structure of transient EOD modulations (chirps), vary substantially across species. Understanding how these signals have evolved, however, has been hampered by the lack of a well-supported phylogeny for this family. We constructed a molecular phylogeny for the Apteronotidae by using sequence data from three genes (cytochrome c oxidase subunit 1, recombination activating gene 2, and cytochrome oxidase B) in 32 species representing 13 apteronotid genera. This phylogeny and an extensive database of apteronotid signals allowed us to examine signal evolution by using ancestral state reconstruction (ASR) and phylogenetic generalized least squares (PGLS) models. Our molecular phylogeny largely agrees with another recent sequence-based phylogeny and identified five robust apteronotid clades: (i) Sternarchorhamphus+Orthosternarchus, (ii) Adontosternarchus, (iii) Apteronotus+Parapteronotus, (iv) Sternarchorhynchus, and (v) a large clade including Porotergus, 'Apteronotus', Compsaraia, Sternarchogiton, Sternarchella, and Magosternarchus. We analyzed novel chirp recordings from two apteronotid species (Orthosternarchus tamandua and Sternarchorhynchus mormyrus), and combined data from these species with that from previously recorded species in our phylogenetic analyses. Some signal parameters in O. tamandua were plesiomorphic (e.g., low frequency EODs and chirps with little frequency modulation that nevertheless interrupt the EOD), suggesting that ultra-high frequency EODs and "big" chirps evolved after apteronotids diverged from other gymnotiforms. In contrast to previous studies, our PGLS analyses using the

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

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Suchard Marc A

2007-03-01

Full Text Available Abstract Background Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments. Results We introduce a novel Markov chain transition kernel that improves computational efficiency by proposing non-local topology rearrangements and by block sampling alignment and topology parameters. In addition, we extend our previous indel model to increase biological realism by placing indels preferentially on longer branches. We demonstrate the ability of indel information to increase phylogenetic resolution in examples drawn from within-host viral sequence samples. We also demonstrate the importance of taking alignment uncertainty into account when using such information. Finally, we show that codon-based substitution models can significantly affect alignment quality and phylogenetic inference by unrealistically forcing indels to begin and end between codons. Conclusion These results indicate that indel information can improve phylogenetic resolution of recently diverged pathogens and that alignment uncertainty should be considered in such analyses.

The higher phylogeny of Leptophlebiidae (Insecta: Ephemeroptera), with description of a new species of Calliarcys Eaton, 1881

Czech Academy of Sciences Publication Activity Database

Godunko, Roman J.; Sroka, Pavel; Soldán, Tomáš; Bojková, J.

2015-01-01

Roč. 73, č. 2 (2015), s. 259-280 ISSN 1863-7221 R&D Projects: GA ČR GA206/08/1389 Institutional support: RVO:60077344 Keywords : Calliarcyinae * systematics * phylogeny Subject RIV: EG - Zoology Impact factor: 1.655, year: 2015 http://www.senckenberg.de/files/content/forschung/publikationen/arthropodsystematics/asp_73_2/03_asp_73_2_godunko_259-279.pdf

Molecular phylogeny of Ranunculaceae based on internal ...

African Journals Online (AJOL)

STORAGESEVER

2009-10-19

Oct 19, 2009 ... evidence regarding the systematic classification of Ranunculaceae plants, we used molecular ... Ranunculaceae is a family of flowering plants known as ... and in the analysis of the evolutionary rate for lower level phylogeny ...

A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

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Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

2014-01-01

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean

Phylogeny mandalas of birds using the lithographs of John Gould's folio bird books.

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Hasegawa, Masami; Kuroda, Sayako

2017-12-01

The phylogeny mandala, which is a circular phylogeny with photos or drawings of species, is a suitable way to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. In this article, in order to demonstrate the recent progress of avian molecular phylogenetics, six phylogeny mandalas of various taxonomic groups of birds are presented with the lithographs of John Gould's folio bird books; i.e., (1) whole Aves, (2) Passeriformes, (3) Paradisaeidae in Corvoidea (Passeriformes), (4) Meliphagoidea (Passeriformes), (5) Trochili in Apodiformes, and (6) Galliformes. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogeny, diet, and cranial integration in australodelphian marsupials.

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Anjali Goswami

2007-10-01

Full Text Available Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials.

Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

Science.gov (United States)

Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

2004-06-01

A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host.

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Gilbert, Maarten J; Duim, Birgitta; Timmerman, Arjen J; Zomer, Aldert L; Wagenaar, Jaap A

2017-08-21

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.

Phylogeny and biogeography of hawkmoths (Lepidoptera: Sphingidae: evidence from five nuclear genes.

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Akito Y Kawahara

2009-05-01

Full Text Available The 1400 species of hawkmoths (Lepidoptera: Sphingidae comprise one of most conspicuous and well-studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes.The data set consisted of 131 sphingid species and 6793 bp of sequence from five protein-coding nuclear genes. Maximum likelihood and parsimony analyses provided strong support for more than two-thirds of all nodes, including strong signal for or against nearly all of the fifteen current subfamily, tribal and sub-tribal groupings. Monophyly was strongly supported for some of these, including Macroglossinae, Sphinginae, Acherontiini, Ambulycini, Philampelini, Choerocampina, and Hemarina. Other groupings proved para- or polyphyletic, and will need significant redefinition; these include Smerinthinae, Smerinthini, Sphingini, Sphingulini, Dilophonotini, Dilophonotina, Macroglossini, and Macroglossina. The basal divergence, strongly supported, is between Macroglossinae and Smerinthinae+Sphinginae. All genes contribute significantly to the signal from the combined data set, and there is little conflict between genes. Ancestral state reconstruction reveals multiple separate origins of New World and Old World radiations.Our study provides the first comprehensive phylogeny of one of the most conspicuous and well-studied insects. The molecular phylogeny challenges current concepts of Sphingidae based on morphology, and provides a foundation for a new classification. While there are multiple independent origins of New World and Old World radiations, we conclude that broad-scale geographic distribution in hawkmoths

Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.

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Chen, Meng-Yun; Liang, Dan; Zhang, Peng

2017-08-01

The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae

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Chen Ling-Yun

2012-03-01

Full Text Available Abstract Background Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters. Results Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite and divergence time estimates (BEAST resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma. Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states. Conclusions

Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae.

Science.gov (United States)

Chen, Ling-Yun; Chen, Jin-Ming; Gituru, Robert Wahiti; Wang, Qing-Feng

2012-03-10

Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters. Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite) and divergence time estimates (BEAST) resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma). Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges) probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states. Our study has shed light on the previously controversial

Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

Science.gov (United States)

Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

2012-11-01

The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. Copyright © 2012 Elsevier Inc. All rights reserved.

Rooting phylogenies using gene duplications: an empirical example from the bees (Apoidea).

Science.gov (United States)

Brady, Seán G; Litman, Jessica R; Danforth, Bryan N

2011-09-01

The placement of the root node in a phylogeny is fundamental to characterizing evolutionary relationships. The root node of bee phylogeny remains unclear despite considerable previous attention. In order to test alternative hypotheses for the location of the root node in bees, we used the F1 and F2 paralogs of elongation factor 1-alpha (EF-1α) to compare the tree topologies that result when using outgroup versus paralogous rooting. Fifty-two taxa representing each of the seven bee families were sequenced for both copies of EF-1α. Two datasets were analyzed. In the first (the "concatenated" dataset), the F1 and F2 copies for each species were concatenated and the tree was rooted using appropriate outgroups (sphecid and crabronid wasps). In the second dataset (the "duplicated" dataset), the F1 and F2 copies were aligned to each another and each copy for all taxa were treated as separate terminals. In this dataset, the root was placed between the F1 and F2 copies (e.g., paralog rooting). Bayesian analyses demonstrate that the outgroup rooting approach outperforms paralog rooting, recovering deeper clades and showing stronger support for groups well established by both morphological and other molecular data. Sequence characteristics of the two copies were compared at the amino acid level, but little evidence was found to suggest that one copy is more functionally conserved. Although neither approach yields an unambiguous root to the tree, both approaches strongly indicate that the root of bee phylogeny does not fall near Colletidae, as has been previously proposed. We discuss paralog rooting as a general strategy and why this approach performs relatively poorly with our particular dataset. Copyright © 2011 Elsevier Inc. All rights reserved.

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

Science.gov (United States)

Panero, Jose L; Freire, Susana E; Ariza Espinar, Luis; Crozier, Bonnie S; Barboza, Gloria E; Cantero, Juan J

2014-11-01

A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae. Copyright © 2014 Elsevier Inc. All rights reserved.

Evidence for a Higher Number of Species of Odontotermes (Isoptera) than Currently Known from Peninsular Malaysia from Mitochondrial DNA Phylogenies

Science.gov (United States)

Cheng, Shawn; Kirton, Laurence G.; Panandam, Jothi M.; Siraj, Siti S.; Ng, Kevin Kit-Siong; Tan, Soon-Guan

2011-01-01

Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O. malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa. PMID:21687629

Phylogeny of Bembidion and related ground beetles (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidiina).

Science.gov (United States)

Maddison, David R

2012-06-01

The phylogeny of the large genus Bembidion and related genera is inferred from four nuclear protein-coding genes (CAD, wingless, arginine kinase, and topoisomerase I), ribosomal DNA (28S and 18S), and the mitochondrial gene cytochrome oxidase I (COI). 230 of the more than 1200 species of Bembidion are sampled, as well as 26 species of five related genera, and 14 outgroups. Nuclear copies (numts) of COI were found sparsely scattered through sampled species. The resulting phylogeny, based upon individual gene analyses and combined analyses using maximum likelihood and parsimony, is very well supported at most nodes. Additional analyses explored the evidence, and corroborate the phylogeny. Seven analyses, each with one of the seven genes removed from the combined matrix, were also conducted, and yielded maximum likelihood bootstrap trees sharing over 92% of their nodes with the original, well-resolved bootstrap trees based on the complete set of seven genes. All key nodes were present in all seven analyses missing a single gene, indicating that support for these nodes comes from at least two genes. In addition, the inferred maximum likelihood tree based on the combined matrix is well-behaved and self-predicting, in that simulated evolution of sequences on the inferred tree under the inferred model of evolution yields a matrix from which all but one of the model tree's clades are recovered with bootstrap value >50, suggesting that internal branches in the tree may be of a length to yield sequences sufficient to allow their inference. All likelihood analyses were conducted under both a proportion-invariable plus gamma site-to-site rate variation model, as well as a simpler gamma model. The choice of model did not have a major effect on inferred phylogenies or their bootstrap values. The inferred phylogeny shows that Bembidarenas is not closely related to Bembidiina, and Phrypeus is likely distant as well; the remaining genera of Bembidiina form a monophyletic group

Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family.

Science.gov (United States)

Germot, A; Philippe, H

1999-01-01

Trichomonads, together with diplomonads and microsporidia, emerge at the base of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny. However, phylogenies based on protein sequences such as tubulin are markedly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could be a reliable phylogenetic marker. In eukaryotes, HSP70s are found in cytosol, endoplasmic reticulum, and organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly complete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitochondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters considered. Almost all the undoubtedly monophyletic groups, defined by ultrastructural characters, were recovered. However, due to the long branch attraction phenomenon, the evolutionary rates were the main factor determining the position of species, even with the use of a close outgroup, which is an important advantage of HSP70 with respect to many other markers. Numerous variable sites are peculiar to Trichomonas and probably generated the artefactual placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of species; and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.

Klein's double discontinuity revisited

DEFF Research Database (Denmark)

Winsløw, Carl; Grønbæk, Niels

2014-01-01

Much effort and research has been invested into understanding and bridging the ‘gaps’ which many students experience in terms of contents and expectations as they begin university studies with a heavy component of mathematics, typically in the form of calculus courses. We have several studies...... of bridging measures, success rates and many other aspects of these “entrance transition” problems. In this paper, we consider the inverse transition, experienced by university students as they revisit core parts of high school mathematics (in particular, calculus) after completing the undergraduate...... mathematics courses which are mandatory to become a high school teacher of mathematics. To what extent does the “advanced” experience enable them to approach the high school calculus in a deeper and more autonomous way ? To what extent can “capstone” courses support such an approach ? How could it be hindered...

A human genome-wide library of local phylogeny predictions for whole-genome inference problems

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Schwartz Russell

2008-08-01

Full Text Available Abstract Background Many common inference problems in computational genetics depend on inferring aspects of the evolutionary history of a data set given a set of observed modern sequences. Detailed predictions of the full phylogenies are therefore of value in improving our ability to make further inferences about population history and sources of genetic variation. Making phylogenetic predictions on the scale needed for whole-genome analysis is, however, extremely computationally demanding. Results In order to facilitate phylogeny-based predictions on a genomic scale, we develop a library of maximum parsimony phylogenies within local regions spanning all autosomal human chromosomes based on Haplotype Map variation data. We demonstrate the utility of this library for population genetic inferences by examining a tree statistic we call 'imperfection,' which measures the reuse of variant sites within a phylogeny. This statistic is significantly predictive of recombination rate, shows additional regional and population-specific conservation, and allows us to identify outlier genes likely to have experienced unusual amounts of variation in recent human history. Conclusion Recent theoretical advances in algorithms for phylogenetic tree reconstruction have made it possible to perform large-scale inferences of local maximum parsimony phylogenies from single nucleotide polymorphism (SNP data. As results from the imperfection statistic demonstrate, phylogeny predictions encode substantial information useful for detecting genomic features and population history. This data set should serve as a platform for many kinds of inferences one may wish to make about human population history and genetic variation.

Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs.

Science.gov (United States)

Ha, Young-Ho; Kim, Changkyun; Choi, Kyung; Kim, Joo-Hwan

2018-01-01

Tribe Forsythieae (Oleaceae), containing two genera ( Abeliophyllum and Forsythia ) and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 ( cyc2 ) DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe. The chloroplast genomes of the 11 Forsythieae species are highly conserved, except for a deletion of about 400 bp in the accD - psaI region detected only in Abeliophyllum . Within Forsythieae species, analysis of repetitive sequences revealed a total of 51 repeats comprising 26 forward repeats, 22 palindromic repeats, and 3 reverse repeats. Of those, 19 repeats were common and 32 were unique to one or more Forsythieae species. Our phylogenetic analyses supported the monophyly of Forsythia and its sister group is Abeliophyllum using the concatenated dataset of 78 chloroplast genes. Within Forsythia , Forsythia likiangensis and F. giraldiana were basal lineages followed by F. europaea ; the three species are characterized by minutely serrate or entire leaf margins. The remaining species, which are distributed in East Asia, formed two major clades. One clade included F. ovata , F. velutina , and F. japonica ; they are morphologically supported by broadly ovate leaves. Another clade of F. suspensa , F. saxatilis , F. viridissima , and F. koreana characterized by lanceolate leaves (except F. suspensa which have broad ovate leaves). Although cyc2 phylogeny is largely congruent to chloroplast genome phylogeny, we find the discordance between two phylogenies in the position of F. ovata suggesting that introgression of the chloroplast genome from one species into the nuclear background of another by interspecific hybridization in East Asian

Molecular Phylogeny and Dating of Forsythieae (Oleaceae Provide Insight into the Miocene History of Eurasian Temperate Shrubs

Directory of Open Access Journals (Sweden)

Young-Ho Ha

2018-02-01

Full Text Available Tribe Forsythieae (Oleaceae, containing two genera (Abeliophyllum and Forsythia and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 (cyc2 DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe. The chloroplast genomes of the 11 Forsythieae species are highly conserved, except for a deletion of about 400 bp in the accD–psaI region detected only in Abeliophyllum. Within Forsythieae species, analysis of repetitive sequences revealed a total of 51 repeats comprising 26 forward repeats, 22 palindromic repeats, and 3 reverse repeats. Of those, 19 repeats were common and 32 were unique to one or more Forsythieae species. Our phylogenetic analyses supported the monophyly of Forsythia and its sister group is Abeliophyllum using the concatenated dataset of 78 chloroplast genes. Within Forsythia, Forsythia likiangensis and F. giraldiana were basal lineages followed by F. europaea; the three species are characterized by minutely serrate or entire leaf margins. The remaining species, which are distributed in East Asia, formed two major clades. One clade included F. ovata, F. velutina, and F. japonica; they are morphologically supported by broadly ovate leaves. Another clade of F. suspensa, F. saxatilis, F. viridissima, and F. koreana characterized by lanceolate leaves (except F. suspensa which have broad ovate leaves. Although cyc2 phylogeny is largely congruent to chloroplast genome phylogeny, we find the discordance between two phylogenies in the position of F. ovata suggesting that introgression of the chloroplast genome from one species into the nuclear background of another by interspecific hybridization in East Asian

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

Science.gov (United States)

Reck-Kortmann, Maikel; Silva-Arias, Gustavo Adolfo; Segatto, Ana Lúcia Anversa; Mäder, Geraldo; Bonatto, Sandro Luis; de Freitas, Loreta Brandão

2014-12-01

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

Further studies on Boreonectes Angus, 2010, with a molecular phylogeny of the Palaearctic species of the genus.

Science.gov (United States)

Angus, Robert B; Ribera, Ignacio; Jia, Fenglong

2017-01-01

Karyotypes are given for Boreonectes emmerichi (Falkenström, 1936) from its type locality at Kangding, China, and for B. alpestris (Dutton & Angus, 2007) from the St Gotthard and San Bernardino passes in the Swiss Alps. A phylogeny based on sequence data from a combination of mitochondrial and nuclear genes recovered western Palaearctic species of Boreonectes as monophyletic with strong support. Boreonectes emmerichi was placed as sister to the north American forms of B. griseostriatus (De Geer, 1774), although with low support. The diversity of Palaearctic species of the B. griseostriatus species group is discussed.

Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina

Czech Academy of Sciences Publication Activity Database

Yurchenko, V.; Votýpka, Jan; Tesařová, Martina; Klepetková, H.; Kraeva, N.; Jirků, Milan; Lukeš, Julius

2014-01-01

Roč. 61, č. 2 (2014), s. 97-112 ISSN 0015-5683 R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Kinetoplastida * Trypanosomatidae * monoxenous kientoplastids * Leishmaniinae * molecular taxonomy * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.147, year: 2014

Molecular phylogeny of Ranunculaceae based on internal ...

African Journals Online (AJOL)

The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic analysis of 92 ...

Phylogeny and biogeography of Maclura (Moraceae) and the origin of an anachronistic fruit.

Science.gov (United States)

Gardner, Elliot M; Sarraf, Paya; Williams, Evelyn W; Zerega, Nyree J C

2017-12-01

Maclura (ca. 12spp., Moraceae) is a widespread genus of trees and woody climbers found on five continents. Maclura pomifera, the Osage orange, is considered a classic example of an anachronistic fruit. Native to the central USA, the grapefruit-sized Osage oranges are unpalatable and have no known extant native dispersers, leading to speculation that the fruits were adapted to extinct megafauna. Our aim was to reconstruct the phylogeny, estimate divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group. Employing Bayesian and maximum-likelihood methods, we reconstructed the Maclura phylogeny using two nuclear and five chloroplast loci from all Maclura species and outgroups representing all Moraceae tribes. We reconstructed ancestral ranges and syncarp sizes using a family level dated tree, and used Ornstein-Uhlenbeck models to test for significant changes in syncarp size in the Osage orange lineage. Our analyses support a monophyletic Maclura with a Paleocene crown. Subgeneric sections were monophyletic except for the geographically-disjunct Cardiogyne. There was strong support for current species delineations except in the widespread M. cochinchinensis. South America was reconstructed as the ancestral range for Maclura with subsequent colonization of Africa and the northern hemisphere. The clade containing M. pomifera likely diverged in the Oligocene, closely coinciding with crown divergence dates of the mammoth/mastodon and sloth clades that contain possible extinct dispersers. The best fitting model for syncarp size evolution indicated an increase in both syncarp size and the rate of syncarp size evolution in the Osage orange lineage. We conclude that our findings are consistent with the hypothesis that M. pomifera was adapted to dispersal by extinct megafauna. In addition, we consider dispersal rather than vicariance to

Bayesian phylogeny analysis via stochastic approximation Monte Carlo

KAUST Repository

Cheon, Sooyoung; Liang, Faming

2009-01-01

in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method

Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

Science.gov (United States)

Herrera, James P; Dávalos, Liliana M

2016-09-01

Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. © 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.

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae).

Science.gov (United States)

Vuataz, Laurent; Rutschmann, Sereina; Monaghan, Michael T; Sartori, Michel

2016-09-21

Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups

Revisiting Okun's Relationship

NARCIS (Netherlands)

Dixon, R.; Lim, G.C.; van Ours, Jan

2016-01-01

Our paper revisits Okun's relationship between observed unemployment rates and output gaps. We include in the relationship the effect of labour market institutions as well as age and gender effects. Our empirical analysis is based on 20 OECD countries over the period 1985-2013. We find that the

Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence.

Science.gov (United States)

Zhang, Liang; Zhang, Li-Bing

2018-01-01

The brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major clades identified earlier are recovered here and we further identified a new major clade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

DISTRIBUTION, MORPHOLOGY, AND PHYLOGENY OF KLEBSORMIDIUM (KLEBSORMIDIALES, CHAROPHYCEAE) IN URBAN ENVIRONMENTS IN EUROPE(1).

Science.gov (United States)

Rindi, Fabio; Guiry, Michael D; López-Bautista, Juan M

2008-12-01

Klebsormidium is a cosmopolitan genus of green algae, widespread in terrestrial and freshwater habitats. The classification of Klebsormidium is entirely based on morphological characters, and very little is understood about its phylogeny at the species level. We investigated the diversity and phylogenetic relationships of Klebsormidium in urban habitats in Europe by a combination of approaches including examination of field-collected material, culture experiments conducted in many different combinations of factors, and phylogenetic analyses of the rbcL gene. Klebsormidium in European cities mainly occurs at the base of old walls, where it may produce green belts up to several meters in extent. Specimens from different cities showed a great morphological uniformity, consisting of long filaments 6-9 μm in width, with thin-walled cylindrical cells and smooth wall, devoid of false branches, H-shaped pieces, and biseriate parts. Conversely, the rbcL phylogeny showed a higher genetic diversity than expected from morphology. The strains were separated in four different clades supported by high bootstrap values and posterior probabilities. In culture, these clades differed in several characters, such as production of a superficial hydro-repellent layer, tendency to break into short fragments, and inducibility of zoosporulation. On the basis of the taxonomic information available in the literature, most strains could not be identified unambiguously at the species level. The rbcL phylogeny showed no correspondence with classification based on morphology and suggested that the identity of many species, in particular the type species K. flaccidum (kütz.) P.C. Silva, Mattox et W. H. Blackw., needs critical reassessment. © 2008 Phycological Society of America.

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda)

Czech Academy of Sciences Publication Activity Database

de Chambrier, A.; Waeschenbach, A.; Fisseha, M.; Scholz, Tomáš; Mariaux, J.

2015-01-01

Roč. 500, 27 Apr 2015 (2015), s. 25-59 ISSN 1313-2989 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Eucestoda * Proteocephalidae * systematics * molecular phylogeny * host-parasite associations * Spasskyellina Subject RIV: EG - Zoology Impact factor: 0.938, year: 2015

Comprehensive molecular sampling yields a robust phylogeny for geometrid moths (Lepidoptera: Geometridae.

Directory of Open Access Journals (Sweden)

Pasi Sihvonen

Full Text Available BACKGROUND: The moth family Geometridae (inchworms or loopers, with approximately 23,000 described species, is the second most diverse family of the Lepidoptera. Apart from a few recent attempts based on morphology and molecular studies, the phylogeny of these moths has remained largely uninvestigated. METHODOLOGY/PRINCIPAL FINDINGS: We performed a rigorous and extensive molecular analysis of eight genes to examine the geometrid affinities in a global context, including a search for its potential sister-taxa. Our maximum likelihood analyses included 164 taxa distributed worldwide, of which 150 belong to the Geometridae. The selected taxa represent all previously recognized subfamilies and nearly 90% of recognized tribes, and originate from all over world. We found the Geometridae to be monophyletic with the Sematuridae+Epicopeiidae clade potentially being its sister-taxon. We found all previously recognized subfamilies to be monophyletic, with a few taxa misplaced, except the Oenochrominae+Desmobathrinae complex that is a polyphyletic assemblage of taxa and the Orthostixinae, which was positioned within the Ennominae. The Sterrhinae and Larentiinae were found to be sister to the remaining taxa, followed by Archiearinae, the polyphyletic assemblage of Oenochrominae+Desmobathrinae moths, Geometrinae and Ennominae. CONCLUSIONS/SIGNIFICANCE: Our study provides the first comprehensive phylogeny of the Geometridae in a global context. Our results generally agree with the other, more restricted studies, suggesting that the general phylogenetic patterns of the Geometridae are now well-established. Generally the subfamilies, many tribes, and assemblages of tribes were well supported but their interrelationships were often weakly supported by our data. The Eumeleini were particularly difficult to place in the current system, and several tribes were found to be para- or polyphyletic.

Detection, phylogeny and population dynamics of syntrophic propionate - oxidizing bacteria in anaerobic granular sludge

NARCIS (Netherlands)

Harmsen, H.J.M.

1996-01-01

The research described this thesis concerns the diversity and phylogeny of syntrophic propionate-oxidizing bacteria and their ecology in granular sludge, from which they were obtained. 16S rRNA was used as a molecular marker to study both the phylogeny and the ecology of these bacteria.

Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae).

Science.gov (United States)

Williams, Evelyn W; Gardner, Elliot M; Harris, Robert; Chaveerach, Arunrat; Pereira, Joan T; Zerega, Nyree J C

2017-03-01

The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region. To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred. Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed. Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric

Tourists' perceptions and intention to revisit Norway

OpenAIRE

Lazar, Ana Florina; Komolikova-Blindheim, Galyna

2016-01-01

Purpose - The overall purpose of this study is to explore tourists' perceptions and their intention to revisit Norway. The aim is to find out what are the factors that drive the overall satisfaction, the willingness to recommend and the revisit intention of international tourists that spend their holiday in Norway. Design-Method-Approach - the Theory of Planned Behavior (Ajzen 1991), is used as a framework to investigate tourists' intention and behavior towards Norway as destination. The o...

Asian horses deepen the MSY phylogeny.

Science.gov (United States)

Felkel, S; Vogl, C; Rigler, D; Jagannathan, V; Leeb, T; Fries, R; Neuditschko, M; Rieder, S; Velie, B; Lindgren, G; Rubin, C-J; Schlötterer, C; Rattei, T; Brem, G; Wallner, B

2018-02-01

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages. © 2018 Stichting International Foundation for Animal Genetics.

Predictors and Outcomes of Revisits in Older Adults Discharged from the Emergency Department.

Science.gov (United States)

de Gelder, Jelle; Lucke, Jacinta A; de Groot, Bas; Fogteloo, Anne J; Anten, Sander; Heringhaus, Christian; Dekkers, Olaf M; Blauw, Gerard J; Mooijaart, Simon P

2018-04-01

To study predictors of emergency department (ED) revisits and the association between ED revisits and 90-day functional decline or mortality. Multicenter cohort study. One academic and two regional Dutch hospitals. Older adults discharged from the ED (N=1,093). At baseline, data on demographic characteristics, illness severity, and geriatric parameters (cognition, functional capacity) were collected. All participants were prospectively followed for an unplanned revisit within 30 days and for functional decline and mortality 90 days after the initial visit. The median age was 79 (interquartile range 74-84), and 114 participants (10.4%) had an ED revisit within 30 days of discharge. Age (hazard ratio (HR)=0.96, 95% confidence interval (CI)=0.92-0.99), male sex (HR=1.61, 95% CI=1.05-2.45), polypharmacy (HR=2.06, 95% CI=1.34-3.16), and cognitive impairment (HR=1.71, 95% CI=1.02-2.88) were independent predictors of a 30-day ED revisit. The area under the receiver operating characteristic curve to predict an ED revisit was 0.65 (95% CI=0.60-0.70). In a propensity score-matched analysis, individuals with an ED revisit were at higher risk (odds ratio=1.99 95% CI=1.06-3.71) of functional decline or mortality. Age, male sex, polypharmacy, and cognitive impairment were independent predictors of a 30-day ED revisit, but no useful clinical prediction model could be developed. However, an early ED revisit is a strong new predictor of adverse outcomes in older adults. © 2018 The Authors. The Journal of the American Geriatrics Society published by Wiley Periodicals, Inc. on behalf of The American Geriatrics Society.

Sensemaking Revisited

DEFF Research Database (Denmark)

Holt, Robin; Cornelissen, Joep

2014-01-01

We critique and extend theory on organizational sensemaking around three themes. First, we investigate sense arising non-productively and so beyond any instrumental relationship with things; second, we consider how sense is experienced through mood as well as our cognitive skills of manipulation ...... research by revisiting Weick’s seminal reading of Norman Maclean’s book surrounding the tragic events of a 1949 forest fire at Mann Gulch, USA....

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

OpenAIRE

Marx, Felix G.; Fordyce, R. Ewan

2015-01-01

A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36?30?Ma), a shift towards bulk filter-feeding (30?23?Ma) and a climate-driven diversity loss around 3?Ma. Evolutionary rates and...

Nuclear and original DNA application in Oryza taxonomy and phylogeny

International Nuclear Information System (INIS)

Romero, Gabriel O.

1998-01-01

Conventional taxonomy and phylogeny of germplasm are based on the tedious characterization of morphological variation. The ability to assay DNA variation that underlies morphological variation offers great promise as a convenient alternative for the genetic characterization of germplasm. Restriction fragment length polymorphism (RFLP) was used to survey DNA variation in 22 species of the genus Oryza. At the ribosomal DNA (rDNA) multigene family, 15 rDNA spacer length (sl) variants were identified using restriction enzyme Sst1 and wheatrDNA unit as probe. Particular sl variants predominated in certain isozyme groups of O. sativa, indicating a potential of sl ploymorphism in varietal classification. The distribution of sl variants supports the origin of O. sativa and O. nivara from O. rufipogon, and that O. spontanea arose from introgressions among O. sativa, O. nivara, and O. rufipogon. The distribution also suggests that the CCgenome, of all the genomes in the Officinalis complex, may be closest to the Sativa complex genomes, and it affirms the genetic position of the Officinalis complex intermediate between the Sativa and Ridleyi complexes. Variation at the Oryza organelle genomes was probed with a maize mitochondrial gene, atpA, a wheat chloroplast inverted repeat segment, p6. Results indicated that the complexes can be differentiated by their mitochondrial genome, but not their chloroplast genome when digested by Sst1 or BamH1. Therefore, the natural DNA variation in the nuclear and mitochondrial genomes has demonstrated great potential in complementing the conventional basis of taxa classification and phylogeny in the genus Oryza. (Author)

Molecular phylogeny of Indo-Pacific carpenter ants (Hymenoptera: Formicidae, Camponotus) reveals waves of dispersal and colonization from diverse source areas

Czech Academy of Sciences Publication Activity Database

Clouse, R. M.; Janda, Milan; Blanchard, B.; Sharma, P.; Hoffmann, B. D.; Andersen, A. N.; Czekanski-Moir, J. E.; Krushelnycky, P.; Rabeling, C.; Wilson, E. O.; Economo, E. P.; Sarnat, E. M.; General, D. M.; Alpert, G. D.; Wheeler, W. C.

2015-01-01

Roč. 31, č. 4 (2015), s. 424-437 ISSN 0748-3007 R&D Projects: GA ČR GAP505/12/2467 Grant - others:Marie Curie Felloswhip(CZ) PIOFGA2009-25448 Institutional support: RVO:60077344 Keywords : Hymenoptera * Camponotus * molecular phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.952, year: 2015 http://onlinelibrary.wiley.com/doi/10.1111/cla.12099/epdf

Shortest triplet clustering: reconstructing large phylogenies using representative sets

Directory of Open Access Journals (Sweden)

Sy Vinh Le

2005-04-01

Full Text Available Abstract Background Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. Results We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC, to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2 time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at http://www.bi.uni-duesseldorf.de/software/stc/. Conclusion The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy.

Revisiting the electrochemical oxidation of ammonia on carbon-supported metal nanoparticle catalysts

International Nuclear Information System (INIS)

Li, Zhe-Fei; Wang, Yuxuan; Botte, Gerardine G.

2017-01-01

Highlights: • A procedure to pretreat electrocatalysts to study the ammonia oxidation is provided. • N ads and O/OH ads were identified as the major deactivation species that prevent ammonia oxidatoin. • The electrocatalytic activity, thermodynamics, and possible deactivation mechanisms for ammonia oxidation were elucidated. • The onset potential for ammonia oxidation is related to the hydrogen binding energy of the catalyst. • Ammonia electro-oxidation involves a complex decoupled electron and proton transfer process. - Abstract: The ammonia electro-oxidation reaction (AOR) has been studied due to its promising applications in ammonia electrolysis, wastewater remediation, direct ammonia fuel cells, and sensors. However, it is difficult to compare and analyze the reported electrocatalytic activity of AOR reliably, likely due to the variation in catalyst synthesis, electrode composition, electrode morphology, and testing protocol. In this paper, the electro-oxidation of ammonia on different carbon-supported precious metal nanoparticle catalysts was revisited. The effect of experimental conditions, electrochemical test parameters, electrocatalytic activity, thermodynamics, and possible deactivation mechanism of the catalysts were investigated. Pt/C catalyst possesses the highest electrocatalytic activity, while Ir/C and Rh/C show lower overpotential. The onset potential of the AOR is related to the hydrogen binding energy of the catalyst. N ads is one major cause of deactivation accompanied with the formation of surface O/OH ads at high potentials. The coulombic efficiency of N ads formation on Pt is about 1% initially and gradually decreases with reaction time. Increase in ammonia concentration leads to increase in current density, while increase in hydroxyl ions concentration can enhance the current density and reduce the overpotential simultaneously. The slopes of AOR onset potential and hydrogen adsorption/desorption potential of Pt/C as a function of p

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

OpenAIRE

Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

2009-01-01

Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylog...

Rural-Nonrural Disparities in Postsecondary Educational Attainment Revisited

Science.gov (United States)

Byun, Soo-yong; Meece, Judith L.; Irvin, Matthew J.

2013-01-01

Using data from the National Educational Longitudinal Study, this study revisited rural-nonrural disparities in educational attainment by considering a comprehensive set of factors that constrain and support youth's college enrollment and degree completion. Results showed that rural students were more advantaged in community social resources compared to nonrural students, and these resources were associated with a significant increase in the likelihood of bachelor's degree attainment. Yet results confirmed that rural students lagged behind nonrural students in attaining a bachelor's degree largely due to their lower socioeconomic background. The findings present a more comprehensive picture of the complexity of geographic residence in shaping college enrollment and degree attainment. PMID:24285873

Molecular phylogeny of Eriocaulon (Eriocaulaceae)

DEFF Research Database (Denmark)

Ito, Yu; Tanaka, Norio; Barfod, Anders

Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an Africa...... the genus. In this talk, we provide preliminary results of our molecular phylogenetic analysis of the genus aiming to i) assess the biogeographic origin, ii) explore phylogenetic origins of submerged species, and iii) address the evolutionary role of polyploids.......Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an African...... origin for Eriocaulon as a sister relationship between the genus and an African endemic one was recovered. The species of Eriocaulon primarily grow in wetlands while some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. Polyploidy is known from...

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada, Tardigrada)

DEFF Research Database (Denmark)

Fujimoto, Shinta; Jørgensen, Aslak; Hansen, Jesper Guldberg

2017-01-01

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phy...... of the inferred phylogeny....

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

Science.gov (United States)

Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

2016-01-01

Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

Arthropod phylogeny based on eight molecular loci and morphology

Science.gov (United States)

Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

2001-01-01

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters

Science.gov (United States)

Tarasov, Sergei; Génier, François

2015-01-01

Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a

A Structural Equation Model of Risk Perception of Rockfall for Revisit Intention

OpenAIRE

Ya-Fen Lee; Yun-Yao Chi

2014-01-01

The study aims to explore the relationship between risk perception of rockfall and revisit intention using a Structural Equation Modeling (SEM) analysis. A total of 573 valid questionnaires are collected from travelers to Taroko National Park, Taiwan. The findings show the majority of travelers have the medium perception of rockfall risk, and are willing to revisit the Taroko National Park. The revisit intention to Taroko National Park is influenced by hazardous preferences, willingness-to-pa...

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades.

Science.gov (United States)

Arnold, E N

1990-05-22

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown

Phylogeny and Species Diversity of Gulf of California Oysters

Data.gov (United States)

U.S. Environmental Protection Agency — Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North...

The Faraday effect revisited

DEFF Research Database (Denmark)

Cornean, Horia; Nenciu, Gheorghe

2009-01-01

This paper is the second in a series revisiting the (effect of) Faraday rotation. We formulate and prove the thermodynamic limit for the transverse electric conductivity of Bloch electrons, as well as for the Verdet constant. The main mathematical tool is a regularized magnetic and geometric...

Remembered Experiences and Revisit Intentions

DEFF Research Database (Denmark)

Barnes, Stuart; Mattsson, Jan; Sørensen, Flemming

2016-01-01

Tourism is an experience-intensive sector in which customers seek and pay for experiences above everything else. Remembering past tourism experiences is also crucial for an understanding of the present, including the predicted behaviours of visitors to tourist destinations. We adopt a longitudinal...... approach to memory data collection from psychological science, which has the potential to contribute to our understanding of tourist behaviour. In this study, we examine the impact of remembered tourist experiences in a safari park. In particular, using matched survey data collected longitudinally and PLS...... path modelling, we examine the impact of positive affect tourist experiences on the development of revisit intentions. We find that longer-term remembered experiences have the strongest impact on revisit intentions, more so than predicted or immediate memory after an event. We also find that remembered...

Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

Science.gov (United States)

Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

2011-10-01

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of

Gene structure, phylogeny and expression profile of the sucrose ...

Indian Academy of Sciences (India)

Gene structure, phylogeny and expression profile of the sucrose synthase gene family in .... 24, 701–713. Bate N. and Twell D. 1998 Functional architecture of a late pollen .... Manzara T. and Gruissem W. 1988 Organization and expression.

The genus Gloriosa (Colchicaceae) : ethnobotany, phylogeny and taxonomy

NARCIS (Netherlands)

Maroyi, A.

2012-01-01

This thesis focuses on the ethnobotany, phylogeny and taxonomy of the genus Gloriosa L. over its distributional range. Some Gloriosa species are known to have economic and commercial value, but the genus is also well known for its complex alpha taxonomy. An appropriate taxonomy for this group is of

A reassessment of the phylogeny and circumscription of Zaluzianskya (Scrophulariaceae).

Science.gov (United States)

Archibald, Jenny K; Cook, Jacqueline; Anderson, Bruce; Johnson, Steven D; Mort, Mark E

2017-07-01

The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of floral and ecological traits. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. We present molecular data suggesting that this genus requires expansion via incorporation of species from other genera and recognition of unnamed cryptic species. This study advances prior molecular phylogenies of the southern African genus through the addition of DNA regions and 51 populations that had not previously been sampled in a published phylogeny. A total of 82 species of Zaluzianskya and related genera are included, adding 48 to those previously sampled. Results are presented from analyses of five DNA regions, including nuclear ITS and four rapidly evolving chloroplast regions (trnL-trnF, rpl16, rps16, and trnS-trnfM). Our primary finding is that the genus Phyllopodium is polyphyletic as currently circumscribed, with some species placed within Zaluzianskya and others grouping with Polycarena, indicating the need for further phylogenetic work on these genera. Preliminary support for the incorporation of Reyemia into Zaluzianskya is reinforced here by the first molecular analysis to include both species of Reyemia and a strong sampling of species across Zaluzianskya and major clades of tribe Limoselleae. The two disjunct, tropical African species of Zaluzianskya are also confirmed as members of this genus. Finally, a broad sampling of 21 populations of Z. microsiphon establishes their phylogenetic division into two to five separate lineages. Hybridization, coevolution, and cryptic speciation may each play a role in the evolution of Z. microsiphon. Further resolution within a clade comprising sections Nycterinia and Macrocalyx is needed to better understand their relationships. Copyright © 2017 Elsevier Inc. All rights reserved.

Revisiting the Okun relationship

NARCIS (Netherlands)

Dixon, R. (Robert); Lim, G.C.; J.C. van Ours (Jan)

2017-01-01

textabstractOur article revisits the Okun relationship between observed unemployment rates and output gaps. We include in the relationship the effect of labour market institutions as well as age and gender effects. Our empirical analysis is based on 20 OECD countries over the period 1985–2013. We

Bounded Intention Planning Revisited

OpenAIRE

Sievers Silvan; Wehrle Martin; Helmert Malte

2014-01-01

Bounded intention planning provides a pruning technique for optimal planning that has been proposed several years ago. In addition partial order reduction techniques based on stubborn sets have recently been investigated for this purpose. In this paper we revisit bounded intention planning in the view of stubborn sets.

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

International Nuclear Information System (INIS)

Medina, Monica; Collins, Allen G.; Silberman, Jeffrey; Sogin, Mitchell L.

2001-01-01

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of amonophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny

Molecular phylogeny of Anopheles hyrcanus group (Diptera: Culicidae) based on mtDNA COI.

Science.gov (United States)

Fang, Yuan; Shi, Wen-Qi; Zhang, Yi

2017-05-08

The Anopheles hyrcanus group, which includes at least 25 species, is widely distributed in the Oriental and Palearctic regions. Some group members have been incriminated as vectors of malaria and other mosquito-borne diseases. It is difficult to identify Hyrcanus Group members by morphological features. Thus, molecular phylogeny has been proposed as an important complementary method to traditional morphological taxonomy. Based on the GenBank database and our original study data, we used 466 mitochondrial DNA COI sequences belonging to 18 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its worldwide geographic range. The results are as follows. 1) The average conspecific K2P divergence was 0.008 (range 0.002-0.017), whereas sequence divergence between congroup species averaged 0.064 (range 0.026-0.108). 2) The topology of COI tree of the Hyrcanus Group was generally consistent with classical morphological taxonomy in terms of species classification, but disagreed in subgroup division. In the COI tree, the group was divided into at least three main clusters. The first cluster contained An. nimpe; the second was composed of the Nigerrimus Subgroup and An. argyropus; and the third cluster was comprised of the Lesteri Subgroup and other unassociated species. 3) Phylogenetic analysis of COI indicated that ancient hybridizations probably occurred among the three closely related species, An. sinensis, An. belenrae, and An. kleini. 4) The results supported An. paraliae as a probable synonym of An. lesteri, and it was possible that An. pseudopictus and An. hyrcanus were the same species, as evident from their extremely low interspecific genetic divergence (0.020 and 0.007, respectively) and their phylogenetic positions. In summary, we reconstructed the molecular phylogeny and analysed genetic divergence of the Hyrcanus Group using mitochondrial COI sequences. Our results suggest that in the future of malaria surveillance, we should not only pay

Revisiting Nursing Research in Nigeria

African Journals Online (AJOL)

2016-08-18

Aug 18, 2016 ... health care research, it is therefore pertinent to revisit the state of nursing research in the country. .... platforms, updated libraries with electronic resource ... benchmarks for developing countries of 26%, [17] the amount is still ...

Time functions revisited

Science.gov (United States)

Fathi, Albert

2015-07-01

In this paper we revisit our joint work with Antonio Siconolfi on time functions. We will give a brief introduction to the subject. We will then show how to construct a Lipschitz time function in a simplified setting. We will end with a new result showing that the Aubry set is not an artifact of our proof of existence of time functions for stably causal manifolds.

Pan-genome and phylogeny of Bacillus cereus sensu lato.

Science.gov (United States)

Bazinet, Adam L

2017-08-02

produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

Science.gov (United States)

Zhang, Yan-Cong; Lin, Kui

2015-01-01

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles.

Science.gov (United States)

Pereira, Anieli G; Sterli, Juliana; Moreira, Filipe R R; Schrago, Carlos G

2017-08-01

Despite their complex evolutionary history and the rich fossil record, the higher level phylogeny and historical biogeography of living turtles have not been investigated in a comprehensive and statistical framework. To tackle these issues, we assembled a large molecular dataset, maximizing both taxonomic and gene sampling. As different models provide alternative biogeographical scenarios, we have explicitly tested such hypotheses in order to reconstruct a robust biogeographical history of Testudines. We scanned publicly available databases for nucleotide sequences and composed a dataset comprising 13 loci for 294 living species of Testudines, which accounts for all living genera and 85% of their extant species diversity. Phylogenetic relationships and species divergence times were estimated using a thorough evaluation of fossil information as calibration priors. We then carried out the analysis of historical biogeography of Testudines in a fully statistical framework. Our study recovered the first large-scale phylogeny of turtles with well-supported relationships following the topology proposed by phylogenomic works. Our dating result consistently indicated that the origin of the main clades, Pleurodira and Cryptodira, occurred in the early Jurassic. The phylogenetic and historical biogeographical inferences permitted us to clarify how geological events affected the evolutionary dynamics of crown turtles. For instance, our analyses support the hypothesis that the breakup of Pangaea would have driven the divergence between the cryptodiran and pleurodiran lineages. The reticulated pattern in the ancestral distribution of the cryptodiran lineage suggests a complex biogeographic history for the clade, which was supposedly related to the complex paleogeographic history of Laurasia. On the other hand, the biogeographical history of Pleurodira indicated a tight correlation with the paleogeography of the Gondwanan landmasses. Copyright © 2017 Elsevier Inc. All rights

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

Science.gov (United States)

Longdon, Ben; Hadfield, Jarrod D.; Webster, Claire L.

2011-01-01

Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts. PMID:21966271

The current status of the New World monkey phylogeny

Directory of Open Access Journals (Sweden)

SCHNEIDER HORACIO

2000-01-01

Full Text Available Four DNA datasets were combined in tandem (6700 bp and Maximum parsimony and Neighbor-Joining analyses were performed. The results suggest three groups emerging almost at the same time: Atelidae, Pitheciidae and Cebidae. The total analysis strongly supports the monophyly of the Cebidae family, grouping Aotus, Cebus and Saimiri with the small callitrichines. In the callitrichines, the data link Cebuela to Callithrix, place Callimico as a sister group of Callithrix/Cebuella, and show Saguinus to be the earliest offshoot of the callitrichines. In the family Pithecidae, Callicebus is the basal genus. Finally, combined molecular data showed congruent branching in the atelid clade, setting up Alouatta as the basal lineage and Brachyteles-Lagothrix as a sister group and the most derived branch. Two major points remain to be clarified in the platyrrhine phylogeny: (i what is the exact branching pattern of Aotus, Cebus, Saimiri and the small callitrichines, and (ii, which two of these three lineages, pitheciines, atelines or cebids, are more closely related?

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

Directory of Open Access Journals (Sweden)

Rønsted Nina

2012-09-01

Full Text Available Abstract Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE and binding to the serotonin reuptake transporter (SERT are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.

The phylogeny of amphibian metamorphosis.

Science.gov (United States)

Reiss, John O

2002-01-01

Frogs have one of the most extreme metamorphoses among vertebrates. How did this metamorphosis evolve? By combining the methods previously proposed by Mabee and Humphries (1993) and Velhagen (1997), I develop a phylogenetic method suited for rigorous analysis of this question. In a preliminary analysis using 12 transformation sequence characters and 36 associated event sequence characters, all drawn from the osteology of the skull, the evolution of metamorphosis is traced on an assumed phylogeny. This phylogeny has lissamphibians (frogs, salamanders, and caecilians) monophyletic, with frogs the sister group of salamanders. Successive outgroups used are temnospondyls and discosauriscids, both of which are fossil groups for which ontogenetic data are available. In the reconstruction of character evolution, an unambiguous change (synapomorphy) along the branch leading to lissamphibians is a delay in the lengthening of the maxilla until metamorphosis, in accordance with my previous suggestion (Reiss, 1996). However, widening of the interpterygoid vacuity does not appear as a synapomophy of lissamphibians, due to variation in the character states in the outgroups. From a more theoretical perspective, the reconstructed evolution of amphibian metamorphosis involves examples of heterochrony, through the shift of ancestral premetamorphic events to the metamorphic period, caenogenesis, through the origin of new larval features, and terminal addition, through the origin of new adult features. Other changes don't readily fit these categories. This preliminary study provides evidence that metamorphic changes in frogs arose as further modifications of changes unique to lissamphibians, as well as a new method by which such questions can be examined.

A supertree approach to shorebird phylogeny

Directory of Open Access Journals (Sweden)

Thomas Gavin H

2004-08-01

Full Text Available Abstract Background Order Charadriiformes (shorebirds is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree. Results Three main lineages are revealed: i the plovers and allies; ii the gulls and allies; and iii the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny. Conclusion The supertree hypothesis presented herein is (to our knowledge the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion, we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.

Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies.

Science.gov (United States)

Hagen, Oskar; Andermann, Tobias; Quental, Tiago B; Antonelli, Alexandre; Silvestro, Daniele

2018-05-01

The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more

Revisiting climate change adaptation through proactive policy designing and institutional mechanism

Directory of Open Access Journals (Sweden)

Ashish K. Chaturvedi

2018-04-01

Full Text Available Climate change is a foremost challenge for agricultural productivity. The vulnerability is predominantly located in tropical regions with marginal farmers of developing countries. Enhancement of the adaptive capacity to climate change could be possible through revisiting the policy options with institutional reforms for adapting to the climate risks and sustaining the resilience in India. Innovative win-win approaches with key policy framework include innovative institutions, technologies, management systems and necessary financing mechanisms. Areas for utmost importance comprise agricultural research, irrigation, information technologies, market support, rural roads and extension services. Support from stakeholders to ensure effective adaptation/ mitigation strategy implementation and to provide financial support for addressing climate change issue is very essential. Along with these principles, a strong public-private partnership with successful institutional mechanisms may lead to the formulation of climate change adaptation strategies.

Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.

Science.gov (United States)

Spooner, David M; Ruess, Holly; Iorizzo, Massimo; Senalik, Douglas; Simon, Philipp

2017-02-01

We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid ( Dc MP). Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus . Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named Dc MP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus , (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid. © 2017 Spooner et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons public domain license (CC0 1.0).

Revisiting tourist behavior via destination brand worldness

Directory of Open Access Journals (Sweden)

Murat Kayak

2016-11-01

Full Text Available Taking tourists’ perspective rather than destination offerings as its core concept, this study introduces “perceived destination brand worldness” as a variable. Perceived destination brand worldness is defined as the positive perception that a tourist has of a country that is visited by tourists from all over the world. Then, the relationship between perceived destination brand worldness and intention to revisit is analyzed using partial least squares regression. This empirical study selects Taiwanese tourists as its sample, and the results show that perceived destination brand worldness is a direct predictor of intention to revisit. In light of these empirical findings and observations, practical and theoretical implications are discussed.

Revisitation: a trans phenomenology of the media image

Directory of Open Access Journals (Sweden)

Cael M Keegan

2016-12-01

Full Text Available How might certain moving images move us into transgender becoming? The recent proliferation of transgender images in the media of the Global North has been widely regarded as supporting transgender political and social equality. But do these images do justice to the complexity of transgender lives? Who are images of transgender identity made for, and whose interests do they serve? Instead of discussing media that produce a transgender object for public consumption, this essay’s author is interested in theorizing a trans point of media reception for the popular image. This essay illustrates how transgender subjects might fashion their own archives of becoming through encounters with media that unintentionally support transgender embodiment as a possibility in the world. Revisiting his phenomenological encounters with the film Under the Skin and the “Milk: It Does a Body Good” ad campaign, the author analyzes how certain media objects have the unexpected power to “move” the transgender subject into becoming.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Science.gov (United States)

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes).

Science.gov (United States)

Marki, Petter Z; Jønsson, Knud A; Irestedt, Martin; Nguyen, Jacqueline M T; Rahbek, Carsten; Fjeldså, Jon

2017-02-01

With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3Mya, 95% HPD 25.2-38.2Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change. Copyright © 2016 Elsevier Inc. All rights reserved.

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.

Science.gov (United States)

Shepherd, Lara D; Holland, Barbara R; Perrie, Leon R

2008-07-01

A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Science.gov (United States)

Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

2010-05-01

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

A plastid phylogeny and character evolution of the Old World fern genus Pyrrosia (Polypodiaceae) with the description of a new genus: Hovenkampia (Polypodiaceae).

Science.gov (United States)

Zhou, Xin-Mao; Zhang, Liang; Chen, Cheng-Wei; Li, Chun-Xiang; Huang, Yao-Moan; Chen, De-Kui; Lu, Ngan Thi; Cicuzza, Daniele; Knapp, Ralf; Luong, Thien Tam; Nitta, Joel H; Gao, Xin-Fen; Zhang, Li-Bing

2017-09-01

The Old World fern genus Pyrrosia (Polypodiaceae) offers a rare system in ferns to study morphological evolution because almost all species of this genus are well studied for their morphology, anatomy, and spore features, and various hypotheses have been proposed in terms of the phylogeny and evolution in this genus. However, the molecular phylogeny of the genus lags behind. The monophyly of the genus has been uncertain and a modern phylogenetic study of the genus based on molecular data has been lacking. In the present study, DNA sequences of five plastid markers of 220 accessions of Polypodiaceae representing two species of Drymoglossum, 14 species of Platycerium, 50 species of Pyrrosia, and the only species of Saxiglossum (subfamily Platycerioideae), and 12 species of other Polypodiaceae representing the remaining four subfamilies are used to infer a phylogeny of the genus. Major results and conclusions of this study include: (1) Pyrrosia as currently circumscribed is paraphyletic in relation to Platycerium and can be divided into two genera: Pyrrosia s.s. and Hovenkampia (gen. nov.), with Hovenkampia and Platycerium forming a strongly supported clade sister to Pyrrosia s.s.; (2) Subfamily Platycerioideae should contain three genera only, Hovenkampia, Platycerium, and Pyrrosia s.s.; (3) Based on the molecular phylogeny, macromorphology, anatomical features, and spore morphology, four major clades in the genus are identified and three of the four are further resolved into four, four, and six subclades, respectively; (4) Three species, P. angustissima, P. foveolata, and P. mannii, not assigned to any groups by Hovenkamp (1986) because of their unusual morphology, each form monospecific clades; (5) Drymoglossum is not monophyletic and those species previously assigned to this genus are resolved in two different subclades; (6) Saxiglossum is resolved as the first lineage in the Niphopsis clade; and (7) The evolution of ten major morphological characters in the

Revisiting Inter-Genre Similarity

DEFF Research Database (Denmark)

Sturm, Bob L.; Gouyon, Fabien

2013-01-01

We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...... not perform well, even for data that satisfies all its assumptions....

A Hydrostatic Paradox Revisited

Science.gov (United States)

Ganci, Salvatore

2012-01-01

This paper revisits a well-known hydrostatic paradox, observed when turning upside down a glass partially filled with water and covered with a sheet of light material. The phenomenon is studied in its most general form by including the mass of the cover. A historical survey of this experiment shows that a common misunderstanding of the phenomenon…

Molecular Phylogeny of the Small Ermine Moth Genus Yponomeuta (Lepidoptera, Yponomeutidae) in the Palaearctic

Science.gov (United States)

Turner, Hubert; Lieshout, Niek; Van Ginkel, Wil E.; Menken, Steph B. J.

2010-01-01

Background The small ermine moth genus Yponomeuta (Lepidoptera, Yponomeutidae) contains 76 species that are specialist feeders on hosts from Celastraceae, Rosaceae, Salicaceae, and several other plant families. The genus is a model for studies in the evolution of phytophagous insects and their host-plant associations. Here, we reconstruct the phylogeny to provide a solid framework for these studies, and to obtain insight into the history of host-plant use and the biogeography of the genus. Methodology/Principal Findings DNA sequences from an internal transcribed spacer region (ITS-1) and from the 16S rDNA (16S) and cytochrome oxidase (COII) mitochondrial genes were collected from 20–23 (depending on gene) species and two outgroup taxa to reconstruct the phylogeny of the Palaearctic members of this genus. Sequences were analysed using three different phylogenetic methods (parsimony, likelihood, and Bayesian inference). Conclusions/Significance Roughly the same patterns are retrieved irrespective of the method used, and they are similar among the three genes. Monophyly is well supported for a clade consisting of the Japanese (but not the Dutch) population of Yponomeuta sedellus and Y. yanagawanus, a Y. kanaiellus–polystictus clade, and a Rosaceae-feeding, western Palaearctic clade (Y. cagnagellus–irrorellus clade). Within these clades, relationships are less well supported, and the patterns between the different gene trees are not so similar. The position of the remaining taxa is also variable among the gene trees and rather weakly supported. The phylogenetic information was used to elucidate patterns of biogeography and resource use. In the Palaearctic, the genus most likely originated in the Far East, feeding on Celastraceae, dispersing to the West concomitant with a shift to Rosaceae and further to Salicaceae. The association of Y. cagnagellus with Euonymus europaeus (Celastraceae), however, is a reversal. The only oligophagous species, Y. padellus, belongs

THE INFLUENCE OF DESTINATION IMAGE AND TOURIST SATISFACTION TOWARD REVISIT INTENTION OF SETU BABAKAN BETAWI CULTURAL VILLAGE

OpenAIRE

Wibowo, Setyo Ferry; Sazali, Adnan; Kresnamurti R. P., Agung

2016-01-01

The purpose of this research are: 1) To find out the description of destination image, tourist satisfaction, and revisit intention of Betawi cultural village Setu Babakan, 2) test empirically the influence of destination image toward revisit intention of Betawi cultural village Setu Babakan, 3) test empirically the influence of tourist satisfaction toward revisit intention of Betawi cultural village Setu Babakan, 4) test empirically the influence of destination image toward revisit intention ...

Molecular phylogeny and evolution of mosquito parasitic Microsporidia (Microsporidia: Amblyosporidae)

Czech Academy of Sciences Publication Activity Database

Vossbrinck, C. R.; Andreadis, T.; Vávra, Jiří; Becnel, J. J.

2004-01-01

Roč. 51, č. 1 (2004), s. 88-95 ISSN 1066-5234 Institutional research plan: CEZ:AV0Z6022909 Keywords : Microsporidia * molecular phylogeny * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.403, year: 2004

Seven Issues, Revisited

OpenAIRE

Whitehead, Jim; De Bra, Paul; Grønbæk, Kaj; Larsen, Deena; Legget, John; schraefel, monica m.c.

2002-01-01

It has been 15 years since the original presentation by Frank Halasz at Hypertext'87 on seven issues for the next generation of hypertext systems. These issues are: Search and Query Composites Virtual Structures Computation in/over hypertext network Versioning Collaborative Work Extensibility and Tailorability Since that time, these issues have formed the nucleus of multiple research agendas within the Hypertext community. Befitting this direction-setting role, the issues have been revisited ...

'Felson Signs' revisited

International Nuclear Information System (INIS)

George, Phiji P.; Irodi, Aparna; Keshava, Shyamkumar N.; Lamont, Anthony C.

2014-01-01

In this article we revisit, with the help of images, those classic signs in chest radiography described by Dr Benjamin Felson himself, or other illustrious radiologists of his time, cited and discussed in 'Chest Roentgenology'. We briefly describe the causes of the signs, their utility and the differential diagnosis to be considered when each sign is seen. Wherever possible, we use CT images to illustrate the basis of some of these classic radiographic signs.

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora.

Science.gov (United States)

Calvente, Alice; Zappi, Daniela C; Forest, Félix; Lohmann, Lúcia G

2011-03-01

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55; 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided. Copyright © 2011 Elsevier Inc. All rights reserved.

THE INFLUENCE OF DESTINATION IMAGE AND TOURIST SATISFACTION TOWARD REVISIT INTENTION OF SETU BABAKAN BETAWI CULTURAL VILLAGE

Directory of Open Access Journals (Sweden)

Setyo Ferry Wibowo

2016-04-01

Full Text Available The purpose of this research are: 1 To find out the description of destination image, tourist satisfaction, and revisit intention of Betawi cultural village Setu Babakan, 2 test empirically the influence of destination image toward revisit intention of Betawi cultural village Setu Babakan, 3 test empirically the influence of tourist satisfaction toward revisit intention of Betawi cultural village Setu Babakan, 4 test empirically the influence of destination image toward revisit intention of Betawi cultural village Setu Babakan. The object of this research was 200 respondents who have ever visit to Betawi cultural village Setu Babakan at one time. The results of descriptive test explained that the destination image provided is good according to the tourist, so that the tourist is satisfied and want to revisit intention of Betawi cultural village Setu Babakan. The hypothesis test shows: 1 the influence of destination image toward revisit intention by -30%, 2 the influence of tourist satisfaction toward revisit intention by 118%, 3 the influence of destination image toward tourist satisfaction by 92%.

Host phylogeny determines viral persistence and replication in novel hosts.

Directory of Open Access Journals (Sweden)

Ben Longdon

2011-09-01

Full Text Available Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

Mitogenomic perspectives on the origin and phylogeny of living amphibians.

Science.gov (United States)

Zhang, Peng; Zhou, Hui; Chen, Yue-Qin; Liu, Yi-Fei; Qu, Liang-Hu

2005-06-01

Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for "missing" fossils, and can benefit comparative studies of amphibian evolution.

Re-visiting the electrophysiology of language.

Science.gov (United States)

Obleser, Jonas

2015-09-01

This editorial accompanies a special issue of Brain and Language re-visiting old themes and new leads in the electrophysiology of language. The event-related potential (ERP) as a series of characteristic deflections ("components") over time and their distribution on the scalp has been exploited by speech and language researchers over decades to find support for diverse psycholinguistic models. Fortunately, methodological and statistical advances have allowed human neuroscience to move beyond some of the limitations imposed when looking at the ERP only. Most importantly, we currently witness a refined and refreshed look at "event-related" (in the literal sense) brain activity that relates itself more closely to the actual neurobiology of speech and language processes. It is this imminent change in handling and interpreting electrophysiological data of speech and language experiments that this special issue intends to capture. Copyright © 2015 Elsevier Inc. All rights reserved.

The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes).

Science.gov (United States)

Amaral, Cesar R L; Pereira, Filipe; Silva, Dayse A; Amorim, António; de Carvalho, Elizeu F

2017-09-20

Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all over the world's seas, including some of the ocean's largest fishes. The group dates back about 400 million years near the Devonian-Silurian boundary, being nowadays represented by several derivative lineages, mainly related to Mesozoic forms. Although considered of ecological, commercial and conservation importance, the phylogeny of this old group is poorly studied and still under debate. Here we apply a molecular systematic approach on 82 complete mitochondrial genomes to investigate the phylogeny of the Elasmobranchii. By using maximum likelihood (ML) and Bayesian analyses, we found a clear separation within the shark clade between the Galeomorphii and the Squalomorphii, as well as sister taxa relationships between the Carcharhiniformes and the Lamniformes. Moreover, we found that Pristoidei clusters within the Rhinobatoidei, having been recovered as the sister taxon of the Rhinobatos genus in a clade which also includes the basal Zapteryx. Our results also reject the Hypnosqualea hypothesis, which proposes that the Batoidea should be placed within the Selachii.

Phylogeny and species traits predict bird detectability

Science.gov (United States)

Solymos, Peter; Matsuoka, Steven M.; Stralberg, Diana; Barker, Nicole K. S.; Bayne, Erin M.

2018-01-01

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.

Whole genome association mapping by incompatibilities and local perfect phylogenies

DEFF Research Database (Denmark)

Mailund, Thomas; Besenbacher, Søren; Schierup, Mikkel Heide

2006-01-01

around each marker that is compatible with a single phylogenetic tree. This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree. The rationale for this is that the perfect phylogeny near a disease affecting mutation should...... a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls. The method searches for significant clustering of case chromosomes in the "perfect" phylogenetic tree defined by the largest region...... provide more information about the affected/unaffected classification than random trees. If regions of compatibility contain few markers, due to e.g. large marker spacing, the algorithm can allow the inclusion of incompatibility markers in order to enlarge the regions prior to estimating their phylogeny...

A large phylogeny of turtles (Testudines) using molecular data

NARCIS (Netherlands)

Guillon, J.-M.; Guéry, L.; Hulin, V.; Girondot, M.

2012-01-01

Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA

Phylogeny of not-yet-cultured spirochetes from termite guts

DEFF Research Database (Denmark)

Paster, B.J.; Dewhirst, F.E.; Cooke, S.M.

1996-01-01

Comparisons of 16S rDNA sequences were used to determine the phylogeny of not-yet-cultured spirochetes from hindguts of the African higher termite, Nasutitermes lujae (Wasmann). The 16S rRNA genes were amplified directly from spirochete-rich hindguts by using universal primers, and the amplified...

Leadership and Management Theories Revisited

DEFF Research Database (Denmark)

Madsen, Mona Toft

2001-01-01

The goal of the paper is to revisit and analyze key contributions to the understanding of leadership and management. As a part of the discussion a role perspective that allows for additional and/or integrated leader dimensions, including a change-centered, will be outlined. Seemingly, a major...

Phylogenies of symbiotic genes of Bradyrhizobium symbionts of legumes of economic and environmental importance in Brazil support the definition of the new symbiovars pachyrhizi and sojae.

Science.gov (United States)

Delamuta, Jakeline Renata Marçon; Menna, Pâmela; Ribeiro, Renan Augusto; Hungria, Mariangela

2017-07-01

Bradyrhizobium comprises most tropical symbiotic nitrogen-fixing strains, but the correlation between symbiotic and core genes with host specificity is still unclear. In this study, the phylogenies of the nodY/K and nifH genes of 45 Bradyrhizobium strains isolated from legumes of economic and environmental importance in Brazil (Arachis hypogaea, Acacia auriculiformis, Glycine max, Lespedeza striata, Lupinus albus, Stylosanthes sp. and Vigna unguiculata) were compared to 16S rRNA gene phylogeny and genetic diversity by rep-PCR. In the 16S rRNA tree, strains were distributed into two superclades-B. japonicum and B. elkanii-with several strains being very similar within each clade. The rep-PCR analysis also revealed high intra-species diversity. Clustering of strains in the nodY/K and nifH trees was identical: 39 strains isolated from soybean grouped with Bradyrhizobium type species symbionts of soybean, whereas five others occupied isolated positions. Only one strain isolated from Stylosanthes sp. showed similar nodY/K and nifH sequences to soybean strains, and it also nodulated soybean. Twenty-one representative strains of the 16S rRNA phylogram were selected and taxonomically classified using a concatenated glnII-recA phylogeny; nodC sequences were also compared and revealed the same clusters as observed in the nodY/K and nifH phylograms. The analyses of symbiotic genes indicated that a large group of strains from the B. elkanii superclade comprised the novel symbiovar sojae, whereas for another group, including B. pachyrhizi, the symbiovar pachyrhizi could be proposed. Other potential new symbiovars were also detected. The co-evolution hypotheses is discussed and it is suggested that nodY/K analysis would be useful for investigating the symbiotic diversity of the genus Bradyrhizobium. Copyright © 2017 Elsevier GmbH. All rights reserved.

Schroedinger's variational method of quantization revisited

International Nuclear Information System (INIS)

Yasue, K.

1980-01-01

Schroedinger's original quantization procedure is revisited in the light of Nelson's stochastic framework of quantum mechanics. It is clarified why Schroedinger's proposal of a variational problem led us to a true description of quantum mechanics. (orig.)

Relationships of Reproductive Traits with the Phylogeny of the African Noctuid Stem Borers

Directory of Open Access Journals (Sweden)

Paul-André Calatayud

2016-01-01

Full Text Available The display of the reproductive behavior in most noctuid Lepidoptera follows a diel periodicity and is limited to a precise period of either the day or the night. These behavioral traits and the sex pheromone chemistry can be species specific and thus might be linked to the phylogeny. The objective of this study was to test the relationship of these reproductive traits with phylogeny. The study was undertaken using eight closely related species of noctuid stem borers, which are easy to rear under artificial conditions, namely, Busseola fusca, B. nairobica, B . sp. nr. segeta, Manga melanodonta, M . sp. nr. nubifera, Pirateolea piscator, Sesamia calamistis , and S. nonagrioides . For each species, the adult emergence period, the mating time, and the oviposition period were estimated, referred as biological traits. The components of the sex pheromones emitted by the females of each species were also analyzed by gas chromatography–mass spectrometry. Among the biological traits measured, only those linked to the oviposition pattern (timing and egg loads per night were significantly correlated with the phylogeny of these species. For the sex pheromone components, among the 13 components identified in all species, only four, namely, Z9-tetradecenyl acetate (Z9-TDA, Z11-TDA, E11-TDA, and Z11-hexadecenyl acetate (Z11-HDA, showed the highest significant correlations with the phylogeny. These results suggest that among the different reproductive traits evaluated, only few are phylogenetically constrained. Their involvement in the reinforcement of ecological speciation in noctuid stem borers is discussed.

Ontogeny and Phylogeny from an Epigenetic Point of View.

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Lovtrup, Soren

1984-01-01

The correlation between ontogeny and phylogeny is analyzed through the discussion of four theories on the reality, history, epigenetic, and ecological aspects of the mechanism of evolution. Also discussed are historical and creative aspects of evolution and three epigenetic mechanisms instantiated in the case of the amphibian embryo. (Author/RH)

Host and parasite morphology influence congruence between host and parasite phylogenies.

Science.gov (United States)

Sweet, Andrew D; Bush, Sarah E; Gustafsson, Daniel R; Allen, Julie M; DiBlasi, Emily; Skeen, Heather R; Weckstein, Jason D; Johnson, Kevin P

2018-03-23

Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution. Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

A practical method of predicting client revisit intention in a hospital setting.

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Lee, Kyun Jick

2005-01-01

Data mining (DM) models are an alternative to traditional statistical methods for examining whether higher customer satisfaction leads to higher revisit intention. This study used a total of 906 outpatients' satisfaction data collected from a nationwide survey interviews conducted by professional interviewers on a face-to-face basis in South Korea, 1998. Analyses showed that the relationship between overall satisfaction with hospital services and outpatients' revisit intention, along with word-of-mouth recommendation as intermediate variables, developed into a nonlinear relationship. The five strongest predictors of revisit intention were overall satisfaction, intention to recommend to others, awareness of hospital promotion, satisfaction with physician's kindness, and satisfaction with treatment level.

Live phylogeny with polytomies: Finding the most compact parsimonious trees.

Science.gov (United States)

Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

2017-08-01

Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phylogenomic analysis of kinetoplastids supports that trypanosomatids arose from within bodonids

DEFF Research Database (Denmark)

Deschamps, Philippe; Lara, Enrique; Marande, William

2011-01-01

Kinetoplastids are a large group of free-living and parasitic eukaryotic flagellates, including the medically important trypanosomatids (e.g., Trypanosoma and Leishmania) and the widespread free-living and parasitic bodonids. Small subunit rRNA- and conserved protein-based phylogenies support...

Mitochondrial phylogeny and biogeographic history of the Greek endemic land-snail genus Codringtonia Kobelt 1898 (Gastropoda, Pulmonata, Helicidae).

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Kotsakiozi, Panayiota; Parmakelis, Aristeidis; Giokas, Sinos; Papanikolaou, Irene; Valakos, Efstratios D

2012-02-01

The aim of this work was to infer the phylogeny of the Greek endemic land-snail genus Codringtonia Kobelt 1898, estimate the time frame of the radiation of the genus, and propose a biogeographic scenario that could explain the contemporary distribution of Codringtonia lineages. The study took place in the districts of Peloponnese, Central Greece and Epirus of mainland Greece. Sequence data originating from three mtDNA genes (COI, COII, and 16S rDNA) were used to infer the phylogeny of the eight nominal Codringtonia species. Furthermore, the radiation time-frame of extant Codringtonia species was estimated using a relaxed molecular clock analysis and mtDNA substitution rates of land snails. The phylogenetic analysis supported the existence of six Codringtonia lineages in Greece and indicated that one nominal species (Codringtonia neocrassa) might belong to a separate genus distantly related to Codringtonia. The time frame of differentiation of Codringtonia species was placed in the Late Miocene-Pleistocene epoch. The dispersal-vicariance analysis performed indicated that most probably Codringtonia exhibited a north-to-south spread with the ancestral area being that of central Greek mainland, accompanied with duplication (speciation) and vicariance events. Copyright © 2011 Elsevier Inc. All rights reserved.

Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

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Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

2014-08-04

Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

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Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K

2012-09-01

The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates. Published by Elsevier Inc.

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae.

Science.gov (United States)

Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin; Blattner, Frank R

2017-06-16

Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Science.gov (United States)

Chesser, R. Terry; Yeung, Carol K.L.; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien

2010-01-01

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

Environmental niche models for riverine desert fishes and their similarity according to phylogeny and functionality

Science.gov (United States)

Whitney, James E.; Whittier, Joanna B.; Paukert, Craig P.

2017-01-01

Environmental filtering and competitive exclusion are hypotheses frequently invoked in explaining species' environmental niches (i.e., geographic distributions). A key assumption in both hypotheses is that the functional niche (i.e., species traits) governs the environmental niche, but few studies have rigorously evaluated this assumption. Furthermore, phylogeny could be associated with these hypotheses if it is predictive of functional niche similarity via phylogenetic signal or convergent evolution, or of environmental niche similarity through phylogenetic attraction or repulsion. The objectives of this study were to investigate relationships between environmental niches, functional niches, and phylogenies of fishes of the Upper (UCRB) and Lower (LCRB) Colorado River Basins of southwestern North America. We predicted that functionally similar species would have similar environmental niches (i.e., environmental filtering) and that closely related species would be functionally similar (i.e., phylogenetic signal) and possess similar environmental niches (i.e., phylogenetic attraction). Environmental niches were quantified using environmental niche modeling, and functional similarity was determined using functional trait data. Nonnatives in the UCRB provided the only support for environmental filtering, which resulted from several warmwater nonnatives having dam number as a common predictor of their distributions, whereas several cool- and coldwater nonnatives shared mean annual air temperature as an important distributional predictor. Phylogenetic signal was supported for both natives and nonnatives in both basins. Lastly, phylogenetic attraction was only supported for native fishes in the LCRB and for nonnative fishes in the UCRB. Our results indicated that functional similarity was heavily influenced by evolutionary history, but that phylogenetic relationships and functional traits may not always predict the environmental distribution of species. However, the

Revisiting the Decision of Death in Hurst v. Florida.

Science.gov (United States)

Cooke, Brian K; Ginory, Almari; Zedalis, Jennifer

2016-12-01

The United States Supreme Court has considered the question of whether a judge or a jury must make the findings necessary to support imposition of the death penalty in several notable cases, including Spaziano v. Florida (1984), Hildwin v. Florida (1989), and Ring v. Arizona (2002). In 2016, the U.S. Supreme Court revisited the subject in Hurst v. Florida Florida Statute § 921.141 allows the judge, after weighing aggravating and mitigating circumstances, to enter a sentence of life imprisonment or death. Before Hurst, Florida's bifurcated sentencing proceedings included an advisory sentence from jurors and a separate judicial hearing without juror involvement. In Hurst, the Court revisited the question of whether Florida's capital sentencing scheme violates the Sixth Amendment, which requires a jury, not a judge, to find each fact necessary to impose a sentence of death in light of Ring In an eight-to-one decision, the Court reversed the judgment of the Florida Supreme Court, holding that the Sixth Amendment requires a jury to find the aggravating factors necessary for imposing the death penalty. The role of Florida juries in capital sentencing proceedings was thereby elevated from advisory to determinative. We examine the Court's decision and offer commentary regarding this shift from judge to jury in the final imposition of the death penalty and the overall effect of this landmark case. © 2016 American Academy of Psychiatry and the Law.

Genome rearrangements and phylogeny reconstruction in Yersinia pestis.

Science.gov (United States)

Bochkareva, Olga O; Dranenko, Natalia O; Ocheredko, Elena S; Kanevsky, German M; Lozinsky, Yaroslav N; Khalaycheva, Vera A; Artamonova, Irena I; Gelfand, Mikhail S

2018-01-01

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis . Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.

Phylogeny of the gymnosperm genus Cycas L. (Cycadaceae) as inferred from plastid and nuclear loci based on a large-scale sampling: Evolutionary relationships and taxonomical implications.

Science.gov (United States)

Liu, Jian; Zhang, Shouzhou; Nagalingum, Nathalie S; Chiang, Yu-Chung; Lindstrom, Anders J; Gong, Xun

2018-05-18

The gymnosperm genus Cycas is the sole member of Cycadaceae, and is the largest genus of extant cycads. There are about 115 accepted Cycas species mainly distributed in the paleotropics. Based on morphology, the genus has been divided into six sections and eight subsections, but this taxonomy has not yet been tested in a molecular phylogenetic framework. Although the monophyly of Cycas is broadly accepted, the intrageneric relationships inferred from previous molecular phylogenetic analyses are unclear due to insufficient sampling or uninformative DNA sequence data. In this study, we reconstructed a phylogeny of Cycas using four chloroplast intergenic spacers and seven low-copy nuclear genes and sampling 90% of extant Cycas species. The maximum likelihood and Bayesian inference phylogenies suggest: (1) matrices of either concatenated cpDNA markers or of concatenated nDNA lack sufficient informative sites to resolve the phylogeny alone, however, the phylogeny from the combined cpDNA-nDNA dataset suggests the genus can be roughly divided into 13 clades and six sections that are in agreement with the current classification of the genus; (2) although with partial support, a clade combining sections Panzhihuaenses + Asiorientales is resolved as the earliest diverging branch; (3) section Stangerioides is not monophyletic because the species resolve as a grade; (4) section Indosinenses is not monophyletic as it includes Cycas macrocarpa and C. pranburiensis from section Cycas; (5) section Cycas is the most derived group and its subgroups correspond with geography. Copyright © 2018 Elsevier Inc. All rights reserved.

Recapitulating phylogenies using k-mers: from trees to networks.

Science.gov (United States)

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Mitochondrial DNA phylogeny of camel spiders (Arachnida: Solifugae) from Iran.

Science.gov (United States)

Maddahi, Hassan; Khazanehdari, Mahsa; Aliabadian, Mansour; Kami, Haji Gholi; Mirshamsi, Amin; Mirshamsi, Omid

2017-11-01

In the present study, the mitochondrial DNA phylogeny of five solifuge families of Iran is presented using phylogenetic analysis of mitochondrial cytochrome c oxidase, subunit 1 (COI) sequence data. Moreover, we included available representatives from seven families from GenBank to examine the genetic distance between Old and New World taxa and test the phylogenetic relationships among more solifuge families. Phylogenetic relationships were reconstructed based on the two most probabilistic methods, Maximum Likelihood (ML) and Bayesian inference (BI) approaches. Resulting topologies demonstrated the monophyly of the families Daesiidae, Eremobatidae, Galeodidae, Karschiidae and Rhagodidae, whereas the monophyly of the families Ammotrechidae and Gylippidae was not supported. Also, within the family Eremobatidae, the subfamilies Eremobatinae and Therobatinae and the genus Hemerotrecha were paraphyletic or polyphyletic. According to the resulted topologies, the taxonomic placements of Trichotoma michaelseni (Gylippidae) and Nothopuga sp. 1 (Ammotrechidae) are still remain under question and their revision might be appropriate. According to the results of this study, within the family Galeodidae, the validity of the genus Galeodopsis is supported, while the validity of the genus Paragaleodes still remains uncertain. Moreover, our results revealed that the species Galeodes bacillatus, and Rhagodes melanochaetus are junior synonyms of G. caspius, and R. eylandti, respectively.

Antifungal susceptibility and phylogeny of opportunistic members of the order mucorales.

NARCIS (Netherlands)

Vitale, R.G.; Hoog, G.S. de; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; Sande, W.W. van de; Dolatabadi, S.; Meis, J.F.G.M.; Walther, G.

2012-01-01

The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales

NARCIS (Netherlands)

R.G. Vitale (Roxana); G.S. de Hoog; P. Schwarz (Peter); E. Dannaoui (Eric); S. Deng (Shuwen); M. Machouart (Marie); K. Voigt (Kerstin); W.W.J. van de Sande (Wendy); S. Dolatabadi (Somayeh); J.F. Meis; G. Walther

2012-01-01

textabstractThe in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the

Antifungal Susceptibility and Phylogeny of Opportunistic Members of the Order Mucorales

NARCIS (Netherlands)

Vitale, R.G.; de Hoog, G.S.; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; de Sande, W.W.J.v.; Dolatabadi, S.; Meis, J.F.; Walther, G.

2012-01-01

The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

Science.gov (United States)

Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

2017-04-01

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. Copyright © 2016 Elsevier GmbH. All rights reserved.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Directory of Open Access Journals (Sweden)

Xing-Xing Shen

2016-12-01

Full Text Available Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence and two data matrices (amino acids or the first two codon positions yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Science.gov (United States)

Shen, Xing-Xing; Zhou, Xiaofan; Kominek, Jacek; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis

2016-01-01

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast. PMID:27672114

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

Directory of Open Access Journals (Sweden)

W John Kress

2010-11-01

Full Text Available Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Phylogeny-guided (meta)genome mining approach for the targeted discovery of new microbial natural products.

Science.gov (United States)

Kang, Hahk-Soo

2017-02-01

Genomics-based methods are now commonplace in natural products research. A phylogeny-guided mining approach provides a means to quickly screen a large number of microbial genomes or metagenomes in search of new biosynthetic gene clusters of interest. In this approach, biosynthetic genes serve as molecular markers, and phylogenetic trees built with known and unknown marker gene sequences are used to quickly prioritize biosynthetic gene clusters for their metabolites characterization. An increase in the use of this approach has been observed for the last couple of years along with the emergence of low cost sequencing technologies. The aim of this review is to discuss the basic concept of a phylogeny-guided mining approach, and also to provide examples in which this approach was successfully applied to discover new natural products from microbial genomes and metagenomes. I believe that the phylogeny-guided mining approach will continue to play an important role in genomics-based natural products research.

Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

Science.gov (United States)

Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

2014-04-01

Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

Science.gov (United States)

2013-01-01

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

The Faraday effect revisited: General theory

DEFF Research Database (Denmark)

Cornean, Horia Decebal; Nenciu, Gheorghe; Pedersen, Thomas Garm

This paper is the first in a series revisiting the Faraday effect, or more generally, the theory of electronic quantum transport/optical response in bulk media in the presence of a constant magnetic field. The independent electron approximation is assumed. For free electrons, the transverse...

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada, Heterotardigrada)

DEFF Research Database (Denmark)

Guil, Noemi; Jørgensen, Aslak; Giribet, Gonzalo

2013-01-01

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ...

Revisited

DEFF Research Database (Denmark)

Tegtmeier, Silke; Meyer, Verena; Pakura, Stefanie

2017-01-01

were captured when they described entrepreneurs. Therefore, this paper aims to revisit gender role stereotypes among young adults. Design/methodology/approach: To measure stereotyping, participants were asked to describe entrepreneurs in general and either women or men in general. The Schein......Purpose: Entrepreneurship is shaped by a male norm, which has been widely demonstrated in qualitative studies. The authors strive to complement these methods by a quantitative approach. First, gender role stereotypes were measured in entrepreneurship. Second, the explicit notions of participants......: The images of men and entrepreneurs show a high and significant congruence (r = 0.803), mostly in those adjectives that are untypical for men and entrepreneurs. The congruence of women and entrepreneurs was low (r = 0.152) and insignificant. Contrary to the participants’ beliefs, their explicit notions did...

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

Science.gov (United States)

Ahrenfeldt, Johanne; Skaarup, Carina; Hasman, Henrik; Pedersen, Anders Gorm; Aarestrup, Frank Møller; Lund, Ole

2017-01-05

Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods. Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator strain grow in the lab for 8 consecutive days, each day splitting the culture in two while also collecting samples for sequencing. The result is a data set consisting of 101 whole genome sequences with known phylogenetic relationship. Among the sequenced samples 51 correspond to internal nodes in the phylogeny because they are ancestral, while the remaining 50 correspond to leaves. We also used the newly created data set to compare three different online available methods that infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and REALPHY. One complication when comparing the output of these methods with the known phylogeny is that phylogenetic methods typically build trees where all observed sequences are placed as leafs, even though some of them are in fact ancestral. We therefore devised a method for post processing the inferred trees by collapsing short branches (thus relocating some leafs to internal nodes), and also present two new measures of tree similarity that takes into account the identity of both internal and leaf nodes. Based on this analysis we find that, among the investigated methods, CSI Phylogeny had the best performance, correctly identifying 73% of all branches in the

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae, a mammalian family that experienced rapid speciation

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Ryder Oliver A

2007-10-01

Full Text Available Abstract Background Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family represents a typical example of rapid evolutionary radiation. Previous analyses with a single mitochondrial (mt gene or a small number of mt genes either provide weak support or a large unresolved polytomy for ursids. We revisit the contentious relationships within Ursidae by analyzing complete mt genome sequences and evaluating the performance of both entire mt genomes and constituent mtDNA genes in recovering a phylogeny of extremely recent speciation events. Results This mitochondrial genome-based phylogeny provides strong evidence that the spectacled bear diverged first, while within the genus Ursus, the sloth bear is the sister taxon of all the other five ursines. The latter group is divided into the brown bear/polar bear and the two black bears/sun bear assemblages. These findings resolve the previous conflicts between trees using partial mt genes. The ability of different categories of mt protein coding genes to recover the correct phylogeny is concordant with previous analyses for taxa with deep divergence times. This study provides a robust Ursidae phylogenetic framework for future validation by additional independent evidence, and also has significant implications for assisting in the resolution of other similarly difficult phylogenetic investigations. Conclusion Identification of base composition bias and utilization of the combined data of whole mitochondrial genome sequences has allowed recovery of a strongly supported phylogeny that is upheld when using multiple alternative outgroups for the Ursidae, a mammalian family that underwent a rapid radiation since the mid- to late Pliocene. It remains to be seen if the reliability of mt genome analysis will hold up in studies of other

Who should do the dishes now? Revisiting gender and housework in contemporary urban South Wales

OpenAIRE

Mannay, Dawn

2016-01-01

This chapter revisits Jane Pilcher’s (1994) seminal work ‘Who should do the dishes? Three generations of Welsh women talking about men and housework’, which was originally published in Our Sister’s Land: the changing identities of women in Wales. As discussed in the introductory chapter, I began revisiting classic Welsh studies as part of my doctoral study Mothers and daughters on the margins: gender, generation and education (Mannay, 2012); this lead to the later publication of a revisiting ...

The Faraday effect revisited: General theory

DEFF Research Database (Denmark)

Cornean, Horia Decebal; Nenciu, Gheorghe; Pedersen, Thomas Garm

2006-01-01

This paper is the first in a series revisiting the Faraday effect, or more generally, the theory of electronic quantum transport/optical response in bulk media in the presence of a constant magnetic field. The independent electron approximation is assumed. At zero temperature and zero frequency...

A molecular phylogeny of selected species of genus Prunus L ...

African Journals Online (AJOL)

(Syn. Prunus amygdalus) and Prunus cornuta (Wall. ex. Royle) Steudel. These are indigenous to Pakistan. In the ITS strict consensus results for example, the clade consisting of Laurocerasus, Padus and Cerasus subgenera are sister to the rest of the clades in the phylogenetic tree. Key words: Phylogeny, Prunus, Pakistan, ...

Pulling the sting out of nettle systematics - A comprehensive phylogeny of the genus Urtica L. (Urticaceae).

Science.gov (United States)

Grosse-Veldmann, Bernadette; Nürk, Nicolai M; Smissen, Rob; Breitwieser, Ilse; Quandt, Dietmar; Weigend, Maximilian

2016-09-01

The genus Urtica L. is subcosmopolitan, found on all continents (except Antarctica) and most extratropical islands and ranges from Alaska to Patagonia, Spitzbergen to the Cape and Camtschatka to the subantarctic islands. However, throughout its geographical range morphologically nearly indistinguishable species are found alongside morphologically quite disparate species, with the overall diversity of morphological characters extremely limited. The systematics of Urtica have puzzled scientists for the past 200years and no single comprehensive attempt at understanding infrageneric relationships has been published in the past, nor are species delimitations unequivocally established. We here provide the first comprehensive phylogeny of the genus including 61 of the 63 species recognized, represented by 144 ingroup accessions and 14 outgroup taxa. The markers ITS1-5.8S-ITS2, psbA-trnH intergenic spacer, trnL-trnF and trnS-trnG are used. The phylogeny is well resolved. The eastern Asian Zhengyia shennongensis T. Deng, D.G. Zhang & H. Sun is retrieved as sister to Urtica. Within Urtica, a clade comprising the western Eurasian species U. pilulifera L. and U. neubaueri Chrtek is sister to all other species of the genus. The phylogenetic analyses retrieve numerous well-supported clades, suggesting previously unsuspected relationships and implying that classically used taxonomic characters such as leaf morphology and growth habit are highly homoplasious. Species delimitation is problematical, and several accessions assigned to Urtica dioica L. (as subspecies) are retrieved in widely different places in the phylogeny. The genus seems to have undergone numerous dispersal-establishment events both between continents and onto different islands. Three recent species radiations are inferred, one in America centered in the Andes, one in New Zealand, and one in northern Eurasia which includes Urtica dioica s.str. sensu Henning et al. (2014). The present study provides the basis of a

The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes.

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Janssen, Toon; Vizoso, Dita B; Schulte, Gregor; Littlewood, D Timothy J; Waeschenbach, Andrea; Schärer, Lukas

2015-11-01

The Macrostomorpha-an early branching and species-rich clade of free-living flatworms-is attracting interest because it contains Macrostomum lignano, a versatile model organism increasingly used in evolutionary, developmental, and molecular biology. We elucidate the macrostomorphan molecular phylogeny inferred from both nuclear (18S and 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40 representatives. Although our phylogeny does not recover the Macrostomorpha as a statistically supported monophyletic grouping, it (i) confirms many taxa previously proposed based on morphological evidence, (ii) permits the first placement of many families and genera, and (iii) reveals a number of unexpected placements. Specifically, Myozona and Bradynectes are outside the three classic families (Macrostomidae, Microstomidae and Dolichomacrostomidae) and the asexually fissioning Myomacrostomum belongs to a new subfamily, the Myozonariinae nov. subfam. (Dolichomacrostomidae), rather than diverging early. While this represents the first evidence for asexuality among the Dolichomacrostomidae, we show that fissioning also occurs in another Myozonariinae, Myozonaria fissipara nov. sp. Together with the placement of the (also fissioning) Microstomidae, namely as the sister taxon of Dolichomacrostomidae, this suggests that fissioning is not basal within the Macrostomorpha, but rather restricted to the new taxon Dolichomicrostomida (Dolichomacrostomidae+Microstomidae). Furthermore, our phylogeny allows new insights into the evolution of the reproductive system, as ancestral state reconstructions reveal convergent evolution of gonads, and male and female genitalia. Finally, the convergent evolution of sperm storage organs in the female genitalia appears to be linked to the widespread occurrence of hypodermic insemination among the Macrostomorpha. Copyright © 2015 Elsevier Inc. All rights reserved.

A new molecular phylogeny of the Laurencia complex (Rhodophyta, Rhodomelaceae) and a review of key morphological characters result in a new genus, Coronaphycus, and a description of C. novus.

Science.gov (United States)

Metti, Yola; Millar, Alan J K; Steinberg, Peter

2015-10-01

Within the Laurencia complex (Rhodophyta, Rhodomelaceae), six genera have been recognized based on both molecular analyses and morphology: Laurencia, Osmundea, Chondrophycus, Palisada, Yuzurua, and Laurenciella. Recently, new material from Australia has been collected and included in the current molecular phylogeny, resulting in a new clade. This study examined the generic delineations using a combination of morphological comparisons and phylogenetic analysis of chloroplast (rbcL) nucleotide sequence. The molecular phylogeny recovered eight (rather than six) clades; Yuzurua, Laurenciella, Palisada, and Chondrophycus showed as monophyletic clades each with strong support. However, the genera Osmundea and Laurencia were polyphyletic. Consequently, the new genus Coronaphycus is proposed, resulting in the new combination Coronaphycus elatus and a description of the new species C. novus. © 2015 Phycological Society of America.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

KAUST Repository

Dí az-Arce, Natalia; Arrizabalaga, Haritz; Murua, Hilario; Irigoien, Xabier; Rodrí guez-Ezpeleta, Naiara

2016-01-01

conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough

Phantoms of Gondwana?-phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

DEFF Research Database (Denmark)

Frick, Holger; Scharff, Nikolaj

2014-01-01

This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiin...

Multi-gene analysis provides a well-supported phylogeny of Rosales.

Science.gov (United States)

Zhang, Shu-dong; Soltis, Douglas E; Yang, Yang; Li, De-zhu; Yi, Ting-shuang

2011-07-01

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae. Copyright © 2011 Elsevier Inc. All rights reserved.

When naked became armored: an eight-gene phylogeny reveals monophyletic origin of theca in dinoflagellates.

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Russell J S Orr

Full Text Available The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium.

When Naked Became Armored: An Eight-Gene Phylogeny Reveals Monophyletic Origin of Theca in Dinoflagellates

Science.gov (United States)

Orr, Russell J. S.; Murray, Shauna A.; Stüken, Anke; Rhodes, Lesley; Jakobsen, Kjetill S.

2012-01-01

The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium. PMID:23185516

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

Science.gov (United States)

Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

2015-10-01

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

Directory of Open Access Journals (Sweden)

Holland Barbara R

2006-07-01

Full Text Available Abstract Background Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. Results Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. Conclusion Using the most treelike distance matrices, as

Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction

Czech Academy of Sciences Publication Activity Database

Pečnerová, P.; Martínková, Natália

2012-01-01

Roč. 41, č. 3 (2012), s. 211-219 ISSN 0300-3256 Institutional research plan: CEZ:AV0Z60930519 Keywords : phylogeny * Sciurus * biogeography * colonisation Subject RIV: EG - Zoology Impact factor: 2.793, year: 2012

Examining Relationships of Destination Image, Service Quality, e-WOM, and Revisit Intention to Sabang Island, Indonesia

Directory of Open Access Journals (Sweden)

Rangga Restu Prayogo

2016-12-01

Full Text Available The purpose of this research is to study the relationship among destination image, service quality, e-WOM, and revisit intentions in the tourism industry. A questionnaire given to tourists who visit one of the farrest island in western part of Indonesia, Sabang Island and using sampling through the convenience sampling. A structural equation model (SEM test with WarpPLS 3.0 was used to test the relationship between research variables. This research gathered from 150 respondents. The empirical results from PLS-SEM showed that; the destination image positive affect e-WOM and revisit intention; service quality affect e-WOM and revisit intention; e-WOM positive affect to revisit intention tourists. The implications and future research issues were discussed.

Chromosomal phylogeny of Lagothrix, Brachyteles, and Cacajao.

Science.gov (United States)

Viegas Péquignot, E; Koiffmann, C P; Dutrillaux, B

1985-01-01

Based on a comparison of the karyotypes of two Plathyrrhini species, Cacajao melanocephalus (Pitheciinae) and Brachyteles arachnoides (Atelinae), with those of two previously studied species, Lagothrix lagothrica (Atelinae) and C calvus rubicundus (Pitheciinae), it appears that the two Cacajao species have undergone the same number of chromosome rearrangements since they diverged from their common ancestor and that the karyotype of Brachyteles is ancestral to that of Lagothrix. The chromosomal phylogeny of these four species is proposed. A Y-autosome translocation is present in the karyotypes of the two Cacajao species.

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae).

Science.gov (United States)

Musilová, Zuzana; Rícan, Oldrich; Janko, Karel; Novák, Jindrich

2008-02-01

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.

Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny

Science.gov (United States)

Marr, Henry S.; Tarigo, Jaime L.; Cohn, Leah A.; Bird, David M.; Scholl, Elizabeth H.; Levy, Michael G.; Wiegmann, Brian M.; Birkenheuer, Adam J.

2016-01-01

The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon) are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi) with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis) and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae) while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward understanding the

Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny.

Directory of Open Access Journals (Sweden)

Megan E Schreeg

Full Text Available The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward

Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.

Science.gov (United States)

Kreipe, Victoria; Corral-Hernández, Elena; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

2015-06-01

Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

Deterministic Graphical Games Revisited

DEFF Research Database (Denmark)

Andersson, Daniel; Hansen, Kristoffer Arnsfelt; Miltersen, Peter Bro

2008-01-01

We revisit the deterministic graphical games of Washburn. A deterministic graphical game can be described as a simple stochastic game (a notion due to Anne Condon), except that we allow arbitrary real payoffs but disallow moves of chance. We study the complexity of solving deterministic graphical...... games and obtain an almost-linear time comparison-based algorithm for computing an equilibrium of such a game. The existence of a linear time comparison-based algorithm remains an open problem....

Molecular phylogeny of Neotropical bioluminescent beetles (Coleoptera: Elateroidea) in southern and central Brazil.

Science.gov (United States)

Amaral, D T; Arnoldi, F G C; Rosa, S P; Viviani, V R

2014-08-01

Bioluminescence in beetles is found mainly in the Elateroidea superfamily (Elateridae, Lampyridae and Phengodidae). The Neotropical region accounts for the richest diversity of bioluminescent species in the world with about 500 described species, most occurring in the Amazon, Atlantic rainforest and Cerrado (savanna) ecosystems in Brazil. The origin and evolution of bioluminescence, as well as the taxonomic status of several Neotropical taxa in these families remains unclear. In order to contribute to a better understanding of the phylogeny and evolution of bioluminescent Elateroidea we sequenced and analyzed sequences of mitochondrial NADH2 and the nuclear 28S genes and of the cloned luciferase sequences of Brazilian species belonging to the following genera: (Lampyridae) Macrolampis, Photuris, Amydetes, Bicellonycha, Aspisoma, Lucidota, Cratomorphus; (Elateridae) Conoderus, Pyrophorus, Hapsodrilus, Pyrearinus, Fulgeochlizus; and (Phengodidae) Pseudophengodes, Phrixothrix, Euryopa and Brasilocerus. Our study supports a closer phylogenetic relationship between Elateridae and Phengodidae as other molecular studies, in contrast with previous morphologic and molecular studies that clustered Lampyridae/Phengodidae. Molecular data also supported division of the Phengodinae subfamily into the tribes Phengodini and Mastinocerini. The position of the genus Amydetes supports the status of the Amydetinae as a subfamily. The genus Euryopa is included in the Mastinocerini tribe within the Phengodinae/Phengodidae. Copyright © 2013 John Wiley & Sons, Ltd.

Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

Science.gov (United States)

Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae

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Francisco Perfectti

2017-10-01

Full Text Available Background The phylogeny of tribe Brassiceae (Brassicaceae has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established. Methods Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region. We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca. Results The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis. Discussion We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic

Phylogeny and Evolution of Bracts and Bracteoles in Tacca (Dioscoreaceae)

Institute of Scientific and Technical Information of China (English)

Ling Zhang; Hong-Tao Li; Lian-Ming Gao; Jun-Bo Yang; De-Zhu Li; Charles H. Cannon; Jin Chen; Qing-Jun Li

2011-01-01

Most species in the genus Tacca (Dioscoreaceae) feature green to black purple,conspicuous inflorescence involucral bracts with variable shapes,motile filiform appendages (bracteoles),and diverse types of inflorescence morphology.To infer the evolution of these inflorescence traits,we reconstructed the molecular phylogeny of the genus,using DNA sequences from one nuclear,one mitochondrial,and three plastid loci (Internal Transcribed Spacer (ITS),atpA,rbcL,trnL-F,and trnH-psbA).Involucres and bracteoles characters were mapped onto the phylogeny to analyze the sequence of inflorescence trait evolution.In all analyses,species with showy involucres and bracteoles formed the most derived clade,while ancestral Tacca had small and plain involucres and short bracteoles,namely less conspicuous inflorescence structures.Two of the species with the most elaborate inflorescence morphologies (T.chantrieri in southeast China and T.integrifolia in Tibet),are predominantly self-pollinated,indicating that these conspicuous floral displays have other functions rather than pollinator attraction.We hypothesize that the motile bracteoles and involucres may facilitate selfing; display photosynthesis in the dim understory,and protect flowers from herbivory.

Identification and phylogeny of the tomato receptor-like proteins family

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Ermis Yanes-Paz

2017-03-01

Full Text Available The receptor-like proteins (RLPs play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L. using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between related proteins of different species. Indeed, the functionally characterized CLAVATA2 (CLV2, the maize ortholog FASCIATED EAR2 (FEA2 and a putative tomato CLV2 described in Uniprot clustered together, which validates the approach. Using this approach Solyc12g042760.1.1 was identified as the putative tomato homologue of TOO MANY MOUTHS (TMM. It was shown that proteins in the same cluster of the phylogenetic tree share functional relations since several clusters of functionally related proteins i.e. the Ve cluster, the Cf cluster, and the Eix clade were formed.   Keywords: phylogeny, receptors, RLP, tomato

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

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Turmel Monique

2007-01-01

Full Text Available Abstract Background The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. Results The 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology

Complete chloroplast genome sequences of Drimys, Liriodendron, andPiper: Implications for the phylogeny of magnoliids and the evolution ofGC content

Energy Technology Data Exchange (ETDEWEB)

Zhengqiu, C.; Penaflor, C.; Kuehl, J.V.; Leebens-Mack, J.; Carlson, J.; dePamphilis, C.W.; Boore, J.L.; Jansen, R.K.

2006-06-01

The magnoliids represent the largest basal angiosperm clade with four orders, 19 families and 8,500 species. Although several recent angiosperm molecular phylogenies have supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence has resulted in phylogenies supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. This is one of the most important remaining issues concerning relationships among basal angiosperms. We sequenced the chloroplast genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other completed angiosperm chloroplast genomes to assess phylogenetic relationships among magnoliids. The Drimys and Piper chloroplast genomes are nearly identical in size at 160,606 and 160,624 bp, respectively. The genomes include a pair of inverted repeats of 26,649 bp (Drimys) and 27,039 (Piper), separated by a small single copy region of 18,621 (Drimys) and 18,878 (Piper) and a large single copy region of 88,685 bp (Drimys) and 87,666 bp (Piper). The gene order of both taxa is nearly identical to many other unrearranged angiosperm chloroplast genomes, including Calycanthus, the other published magnoliid genome. Comparisons of angiosperm chloroplast genomes indicate that GC content is not uniformly distributed across the genome. Overall GC content ranges from 34-39%, and coding regions have a substantially higher GC content than non-coding regions (both intergenic spacers and introns). Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Across the genome, GC content is highest in

Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

Science.gov (United States)

The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

Leukemia and ionizing radiation revisited

Energy Technology Data Exchange (ETDEWEB)

Cuttler, J.M. [Cuttler & Associates Inc., Vaughan, Ontario (Canada); Welsh, J.S. [Loyola University-Chicago, Dept. or Radiation Oncology, Stritch School of Medicine, Maywood, Illinois (United States)

2016-03-15

A world-wide radiation health scare was created in the late 19508 to stop the testing of atomic bombs and block the development of nuclear energy. In spite of the large amount of evidence that contradicts the cancer predictions, this fear continues. It impairs the use of low radiation doses in medical diagnostic imaging and radiation therapy. This brief article revisits the second of two key studies, which revolutionized radiation protection, and identifies a serious error that was missed. This error in analyzing the leukemia incidence among the 195,000 survivors, in the combined exposed populations of Hiroshima and Nagasaki, invalidates use of the LNT model for assessing the risk of cancer from ionizing radiation. The threshold acute dose for radiation-induced leukemia, based on about 96,800 humans, is identified to be about 50 rem, or 0.5 Sv. It is reasonable to expect that the thresholds for other cancer types are higher than this level. No predictions or hints of excess cancer risk (or any other health risk) should be made for an acute exposure below this value until there is scientific evidence to support the LNT hypothesis. (author)

Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

Science.gov (United States)

Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

2017-03-01

Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Revisiting Hansen Solubility Parameters by Including Thermodynamics

NARCIS (Netherlands)

Louwerse, Manuel J; Fernández-Maldonado, Ana María; Rousseau, Simon; Moreau-Masselon, Chloe; Roux, Bernard; Rothenberg, Gadi

2017-01-01

The Hansen solubility parameter approach is revisited by implementing the thermodynamics of dissolution and mixing. Hansen's pragmatic approach has earned its spurs in predicting solvents for polymer solutions, but for molecular solutes improvements are needed. By going into the details of entropy

Bottomonium spectrum revisited

CERN Document Server

Segovia, Jorge; Entem, David R.; Fernández, Francisco

2016-01-01

We revisit the bottomonium spectrum motivated by the recently exciting experimental progress in the observation of new bottomonium states, both conventional and unconventional. Our framework is a nonrelativistic constituent quark model which has been applied to a wide range of hadronic observables from the light to the heavy quark sector and thus the model parameters are completely constrained. Beyond the spectrum, we provide a large number of electromagnetic, strong and hadronic decays in order to discuss the quark content of the bottomonium states and give more insights about the better way to determine their properties experimentally.

[Molecular phylogeny of Turbellaria, based on data from comparing the nucleotide sequences of 18S ribosomal RNA genes].

Science.gov (United States)

Kuznedelov, K D; Timoshkin, O A

1995-01-01

Polymerase chain reaction and direct sequencing of the 5'-end region of the 18S ribosomal RNA gene were used to infer phylogenetic relationship among turbellarian flatworms from Lake Baikal. Representatives of 5 orders (Tricladida--10 spp., Lecithoepitheliata--5 spp., Prolecithophora--3 spp., Proseriata and Kalyptorhynchia one for each) were studied; nucleotide sequence of more than 340 nucleotides was determined for each species. Consensus sequence for each order having more than one representative species was determined. Distance matrix and maximum parsimony approaches were applied to infer phylogenies. Bootstrap procedure was used to estimate confidence limits, at the 100% level by bootstrapping, the group of three orders: Kalyptorhynchia, Proseriata and Lecithoepitheliata was found to be monophyletic. However, subsets inside the group had no significant support to be preferred or rejected. Our data do not support traditional systematics which joins two suborders Tricladida and Proseriata into the single order Seriata, and also do not support comparative anatomical data which show close relationship of Lecithoepitheliata and lower Prolecithophora.

Hospital revisit rate after a diagnosis of conversion disorder.

Science.gov (United States)

Merkler, Alexander E; Parikh, Neal S; Chaudhry, Simriti; Chait, Alanna; Allen, Nicole C; Navi, Babak B; Kamel, Hooman

2016-04-01

To estimate the hospital revisit rate of patients diagnosed with conversion disorder (CD). Using administrative data, we identified all patients discharged from California, Florida and New York emergency departments (EDs) and acute care hospitals between 2005 and 2011 with a primary discharge diagnosis of CD. Patients discharged with a primary diagnosis of seizure or transient global amnesia (TGA) served as control groups. Our primary outcome was the rate of repeat ED visits and hospital admissions after initial presentation. Poisson regression was used to compare rates between diagnosis groups while adjusting for demographic characteristics. We identified 7946 patients discharged with a primary diagnosis of CD. During a mean follow-up of 3.0 (±1.6) years, patients with CD had a median of three (IQR, 1-9) ED or inpatient revisits, compared with 0 (IQR, 0-2) in patients with TGA and 3 (IQR, 1-7) in those with seizures. Revisit rates were 18.25 (95% CI, 18.10 to 18.40) visits per 100 patients per month in those with CD, 3.90 (95% CI, 3.84 to 3.95) in those with TGA and 17.78 (95% CI, 17.75 to 17.81) in those with seizures. As compared to CD, the incidence rate ratio for repeat ED visits or hospitalisations was 0.89 (95% CI, 0.86 to 0.93) for seizure disorder and 0.32 (95% CI 0.31 to 0.34) for TGA. CD is associated with a substantial hospital revisit rate. Our findings suggest that CD is not an acute, time-limited response to stress, but rather that CD is a manifestation of a broader pattern of chronic neuropsychiatric disease. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A multi gene sequence-based phylogeny of the Musaceae (banana) family

Czech Academy of Sciences Publication Activity Database

Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; De Langhe, E.; Doležel, Jaroslav

2011-01-01

Roč. 11, č. 103 (2011), s. 1-13 ISSN 1471-2148 R&D Projects: GA AV ČR IAA600380703 Institutional research plan: CEZ:AV0Z50380511 Keywords : MOLECULAR PHYLOGENY * FLOWERING PLANTS * RIBOSOMAL DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.521, year: 2011

Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

NARCIS (Netherlands)

Bokma, Folmer

2006-01-01

Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because. recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process,

The Future of Engineering Education--Revisited

Science.gov (United States)

Wankat, Phillip C.; Bullard, Lisa G.

2016-01-01

This paper revisits the landmark CEE series, "The Future of Engineering Education," published in 2000 (available free in the CEE archives on the internet) to examine the predictions made in the original paper as well as the tools and approaches documented. Most of the advice offered in the original series remains current. Despite new…

Effects of phylogeny, leaf traits, and the altitudinal distribution of host plants on herbivore assemblages on congeneric Acer species.

Science.gov (United States)

Nakadai, Ryosuke; Murakami, Masashi; Hirao, Toshihide

2014-08-01

Historical, niche-based, and stochastic processes have been proposed as the mechanisms that drive community assembly. In plant-herbivore systems, these processes can correspond to phylogeny, leaf traits, and the distribution of host plants, respectively. Although patterns of herbivore assemblages among plant species have been repeatedly examined, the effects of these factors among co-occurring congeneric host plant species have rarely been studied. Our aim was to reveal the process of community assembly for herbivores by investigating the effects of phylogeny, leaf traits, and the altitudinal distribution of closely related host plants of the genus Acer. We sampled leaf functional traits for 30 Acer species in Japan. Using a newly constructed phylogeny, we determined that three of the six measured leaf traits (leaf thickness, C/N ratio, and condensed tannin content) showed a phylogenetic signal. In a field study, we sampled herbivore communities on 14 Acer species within an elevation gradient and examined relationships between herbivore assemblages and host plants. We found that herbivore assemblages were significantly correlated with phylogeny, leaf traits, phylogenetic signals, and the altitudinal distribution of host plants. Our results indicate that the interaction between historical and current ecological processes shapes herbivore community assemblages.

A molecular phylogeny of nephilid spiders: evolutionary history of a model lineage.

Science.gov (United States)

Kuntner, Matjaž; Arnedo, Miquel A; Trontelj, Peter; Lokovšek, Tjaša; Agnarsson, Ingi

2013-12-01

The pantropical orb web spider family Nephilidae is known for the most extreme sexual size dimorphism among terrestrial animals. Numerous studies have made Nephilidae, particularly Nephila, a model lineage in evolutionary research. However, a poorly understood phylogeny of this lineage, relying only on morphology, has prevented thorough evolutionary syntheses of nephilid biology. We here use three nuclear and five mitochondrial genes for 28 out of 40 nephilid species to provide a more robust nephilid phylogeny and infer clade ages in a fossil-calibrated Bayesian framework. We complement the molecular analyses with total evidence analysis including morphology. All analyses find strong support for nephilid monophyly and exclusivity and the monophyly of the genera Herennia and Clitaetra. The inferred phylogenetic structure within Nephilidae is novel and conflicts with morphological phylogeny and traditional taxonomy. Nephilengys species fall into two clades, one with Australasian species (true Nephilengys) as sister to Herennia, and another with Afrotropical species (Nephilingis Kuntner new genus) as sister to a clade containing Clitaetra plus most currently described Nephila. Surprisingly, Nephila is also diphyletic, with true Nephila containing N. pilipes+N. constricta, and the second clade with all other species sister to Clitaetra; this "Nephila" clade is further split into an Australasian clade that also contains the South American N. sexpunctata and the Eurasian N. clavata, and an African clade that also contains the Panamerican N. clavipes. An approximately unbiased test constraining the monophyly of Nephilengys, Nephila, and Nephilinae (Nephila, Nephilengys, Herennia), respectively, rejected Nephilengys monophyly, but not that of Nephila and Nephilinae. Further data are therefore necessary to robustly test these two new, but inconclusive findings, and also to further test the precise placement of Nephilidae within the Araneoidea. For divergence date estimation

Mixed integer linear programming for maximum-parsimony phylogeny inference.

Science.gov (United States)

Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell

2008-01-01

Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats

DEFF Research Database (Denmark)

Fabre, Pierre-Henri; Upham, Nathan S.; Emmons, Louise H.

2017-01-01

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorina...... Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes....

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

Science.gov (United States)

Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

2003-01-01

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

Revisiting Weak Simulation for Substochastic Markov Chains

DEFF Research Database (Denmark)

Jansen, David N.; Song, Lei; Zhang, Lijun

2013-01-01

of the logic PCTL\\x, and its completeness was conjectured. We revisit this result and show that soundness does not hold in general, but only for Markov chains without divergence. It is refuted for some systems with substochastic distributions. Moreover, we provide a counterexample to completeness...

A novel phylogeny of the Gelidiales (Rhodophyta) based on five genes including the nuclear CesA, with descriptions of Orthogonacladia gen. nov. and Orthogonacladiaceae fam. nov.

Science.gov (United States)

Boo, Ga Hun; Le Gall, Line; Miller, Kathy Ann; Freshwater, D Wilson; Wernberg, Thomas; Terada, Ryuta; Yoon, Kyung Ju; Boo, Sung Min

2016-08-01

Although the Gelidiales are economically important marine red algae producing agar and agarose, the phylogeny of this order remains poorly resolved. The present study provides a molecular phylogeny based on a novel marker, nuclear-encoded CesA, plus plastid-encoded psaA, psbA, rbcL, and mitochondria-encoded cox1 from subsets of 107 species from all ten genera within the Gelidiales. Analyses of individual and combined datasets support the monophyly of three currently recognized families, and reveal a new clade. On the basis of these results, the new family Orthogonacladiaceae is described to accommodate Aphanta and a new genus Orthogonacladia that includes species previously classified as Gelidium madagascariense and Pterocladia rectangularis. Acanthopeltis is merged with Gelidium, which has nomenclatural priority. Nuclear-encoded CesA was found to be useful for improving the resolution of phylogenetic relationships within the Gelidiales and is likely to be valuable for the inference of phylogenetic relationship among other red algal taxa. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

Science.gov (United States)

Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

2014-11-01

The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

Evaluation of support loss in micro-beam resonators: A revisit

Science.gov (United States)

Chen, S. Y.; Liu, J. Z.; Guo, F. L.

2017-12-01

This paper presents an analytical study on evaluation of support loss in micromechanical resonators undergoing in-plane flexural vibrations. Two-dimensional elastic wave theory is used to determine the energy transmission from the vibrating resonator to the support. Fourier transform and Green's function technique are adopted to solve the problem of wave motions on the surface of the support excited by the forces transmitted by the resonator onto the support. Analytical expressions of support loss in terms of quality factor, taking into account distributed normal stress and shear stress in the attachment region, and coupling between the normal stress and shear stress as well as material disparity between the support and the resonator, have been derived. Effects of geometry of micro-beam resonators, and material dissimilarity between support and resonator on support loss are examined. Numerical results show that 'harder resonator' and 'softer support' combination leads to larger support loss. In addition, the Perfectly Matched Layer (PML) numerical simulation technique is employed for validation of the proposed analytical model. Comparing with results of quality factor obtained by PML technique, we find that the present model agrees well with the results of PML technique and the pure-shear model overestimates support loss noticeably, especially for resonators with small aspect ratio and large material dissimilarity between the support and resonator.

Revisiting the formal foundation of Probabilistic Databases

NARCIS (Netherlands)

Wanders, B.; van Keulen, Maurice

2015-01-01

One of the core problems in soft computing is dealing with uncertainty in data. In this paper, we revisit the formal foundation of a class of probabilistic databases with the purpose to (1) obtain data model independence, (2) separate metadata on uncertainty and probabilities from the raw data, (3)

A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota: new species, new combination and infrageneric classification

Directory of Open Access Journals (Sweden)

Zai-Wei Ge

2018-03-01

Full Text Available Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS, the partial large subunit nuclear ribosomal DNA (nrLSU, the second largest subunit of RNA polymerase II (rpb2 and translation elongation factor 1-α (tef1 sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum.

Phylogeny of the Gondwanan beetle family Ulodidae (Tenebrionoidea).

Science.gov (United States)

Leschen, Richard A B; Escalona, Hermes E; Elgueta, Mario

2016-07-18

Ulodidae is a small family of saproxylic and fungus feeding beetles restricted to New Zealand, Australia, Chile and New Caledonia. The phylogeny of this family is presented for the first time, based on a cladistic analysis of 53 adult characters from 16 ulodid genera, rooted with Parahelops Waterhouse (Promecheilidae). The topology shows Arthopus Sharp at the base of the tree and confirms the placement of Meryx Latreille as a member of Ulodidae and closely related to the Chilean genus Trachyderas Philippi & Philippi. The extinct New Zealand genus Waitomophylax Leschen & Rhode was placed among a clade consisting of Brouniphylax Strand, Exohadrus Broun, and Pteroderes Germain. Two new genera and two new species are described: Ulobostrichus gen. n. (type species: Ulobostrichus monteithi sp. n.) and Ulocyphaleus gen. n. (type species: Cyphaleus valdivianus Philippi & Philippi, 1864, now U. valdivianus (Philippi & Philippi) n. comb.; U. laetus sp. n.). Dipsaconia pyritosa Pascoe is designated as the type species of Dipsaconia Pascoe and a lectotype was designated for C. valdivianus. A fully illustrated key to the genera and a checklist of the 16 genera and 42 species is included. Based on the phylogeny, the following characters are derived in the family: tuberculate body surface and the presence of scales and /or encrustations. The presence of pore-fields in the abdominal cuticle has evolved at least three times in Meryx Latreille (Australia), Syrphetodes Pascoe (New Zealand) and Trachyderastes Kaszab (New Caledonia).

Revisiting Mutual Fund Performance Evaluation

OpenAIRE

Angelidis, Timotheos; Giamouridis, Daniel; Tessaromatis, Nikolaos

2012-01-01

Mutual fund manager excess performance should be measured relative to their self-reported benchmark rather than the return of a passive portfolio with the same risk characteristics. Ignoring the self-reported benchmark introduces biases in the measurement of stock selection and timing components of excess performance. We revisit baseline empirical evidence in mutual fund performance evaluation utilizing stock selection and timing measures that address these biases. We introduce a new factor e...

Phylogeny and evolution of life-history strategies in the Sycophaginae non-pollinating fig wasps (Hymenoptera, Chalcidoidea

Directory of Open Access Journals (Sweden)

Farache Fernando HA

2011-06-01

Full Text Available Abstract Background Non-pollinating Sycophaginae (Hymenoptera, Chalcidoidea form small communities within Urostigma and Sycomorus fig trees. The species show differences in galling habits and exhibit apterous, winged or dimorphic males. The large gall inducers oviposit early in syconium development and lay few eggs; the small gall inducers lay more eggs soon after pollination; the ostiolar gall-inducers enter the syconium to oviposit and the cleptoparasites oviposit in galls induced by other fig wasps. The systematics of the group remains unclear and only one phylogeny based on limited sampling has been published to date. Here we present an expanded phylogeny for sycophagine fig wasps including about 1.5 times the number of described species. We sequenced mitochondrial and nuclear markers (4.2 kb on 73 species and 145 individuals and conducted maximum likelihood and Bayesian phylogenetic analyses. We then used this phylogeny to reconstruct the evolution of Sycophaginae life-history strategies and test if the presence of winged males and small brood size may be correlated. Results The resulting trees are well resolved and strongly supported. With the exception of Apocrytophagus, which is paraphyletic with respect to Sycophaga, all genera are monophyletic. The Sycophaginae are divided into three clades: (i Eukoebelea; (ii Pseudidarnes, Anidarnes and Conidarnes and (iii Apocryptophagus, Sycophaga and Idarnes. The ancestral states for galling habits and male morphology remain ambiguous and our reconstructions show that the two traits are evolutionary labile. Conclusions The three main clades could be considered as tribes and we list some morphological characters that define them. The same biologies re-evolved several times independently, which make Sycophaginae an interesting model to test predictions on what factors will canalize the evolution of a particular biology. The ostiolar gall-inducers are the only monophyletic group. In 15 Myr, they

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Science.gov (United States)

Hale, Vanessa L; Tan, Chia L; Niu, Kefeng; Yang, Yeqin; Knight, Rob; Zhang, Qikun; Cui, Duoying; Amato, Katherine R

2018-02-01

Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.

Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny.

Science.gov (United States)

Zhang, Junxia; Maddison, Wayne P

2015-03-27

Morphological traits of euophryine jumping spiders were studied to clarify generic limits in the Euophryinae and to permit phylogenetic classification of genera lacking molecular data. One hundred and eight genera are recognized within the subfamily. Euophryine generic groups and the delimitation of some genera are reviewed in detail. In order to explore the effect of adding formal morphological data to previous molecular phylogenetic studies, and to find morphological synapomorphies, eighty-two morphological characters were scored for 203 euophryine species and seven outgroup species. The morphological dataset does not perform as well as the molecular dataset (genes 28S, Actin 5C; 16S-ND1, COI) in resolving the phylogeny of Euophryinae, probably because of frequent convergence and reversal. The formal morphological data were mapped on the phylogeny in order to seek synapomorphies, in hopes of extending the phylogeny to include taxa for which molecular data are not available. Because of homoplasy, few globally-applicable morphological synapomorphies for euophryine clades were found. However, synapomorphies that are unique locally in subclades still help to delimit euophryine generic groups and genera. The following synonyms of euophryine genera are proposed: Maeotella with Anasaitis; Dinattus with Corythalia; Paradecta with Compsodecta; Cobanus, Chloridusa and Wallaba with Sidusa; Tariona with Mopiopia; Nebridia with Amphidraus; Asaphobelis and Siloca with Coryphasia; Ocnotelus with Semnolius; Palpelius with Pristobaeus; Junxattus with Laufeia; Donoessus with Colyttus; Nicylla, Pselcis and Thianitara with Thiania. The new genus Saphrys is erected for misplaced species from southern South America.

Deterministic Graphical Games Revisited

DEFF Research Database (Denmark)

Andersson, Klas Olof Daniel; Hansen, Kristoffer Arnsfelt; Miltersen, Peter Bro

2012-01-01

Starting from Zermelo’s classical formal treatment of chess, we trace through history the analysis of two-player win/lose/draw games with perfect information and potentially infinite play. Such chess-like games have appeared in many different research communities, and methods for solving them......, such as retrograde analysis, have been rediscovered independently. We then revisit Washburn’s deterministic graphical games (DGGs), a natural generalization of chess-like games to arbitrary zero-sum payoffs. We study the complexity of solving DGGs and obtain an almost-linear time comparison-based algorithm...

Metamorphosis in Craniiformea revisited

DEFF Research Database (Denmark)

Altenburger, Andreas; Wanninger, Andreas; Holmer, Lars E.

2013-01-01

We revisited the brachiopod fold hypothesis and investigated metamorphosis in the craniiform brachiopod Novocrania anomala. Larval development is lecithotrophic and the dorsal (brachial) valve is secreted by dorsal epithelia. We found that the juvenile ventral valve, which consists only of a thin...... brachiopods during metamorphosis to cement their pedicle to the substrate. N. anomala is therefore not initially attached by a valve but by material corresponding to pedicle cuticle. This is different to previous descriptions, which had led to speculations about a folding event in the evolution of Brachiopoda...

The co phylogeny reconstruction problem is NP-complete.

Science.gov (United States)

Ovadia, Y; Fielder, D; Conow, C; Libeskind-Hadas, R

2011-01-01

The co phylogeny reconstruction problem is that of finding minimum cost explanations of differences between historical associations. The problem arises in parasitology, molecular systematics, and biogeography. Existing software tools for this problem either have worst-case exponential time or use heuristics that do not guarantee optimal solutions. To date, no polynomial time optimal algorithms have been found for this problem. In this article, we prove that the problem is NP-complete, suggesting that future research on algorithms for this problem should seek better polynomial-time approximation algorithms and heuristics rather than optimal solutions.

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).

Science.gov (United States)

Young, Andrew Donovan; Lemmon, Alan R; Skevington, Jeffrey H; Mengual, Ximo; Ståhls, Gunilla; Reemer, Menno; Jordaens, Kurt; Kelso, Scott; Lemmon, Emily Moriarty; Hauser, Martin; De Meyer, Marc; Misof, Bernhard; Wiegmann, Brian M

2016-06-29

Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported

Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

Directory of Open Access Journals (Sweden)

Michelle Klein Sercundes

2016-03-01

Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

Phylogeny of European bat Lyssavirus 1 in Eptesicus isabellinus bats, Spain.

Science.gov (United States)

Vázquez-Moron, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M; Echevarria, Juan E

2011-03-01

To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

Phylogeny of European Bat Lyssavirus 1 in Eptesicus isabellinus Bats, Spain

OpenAIRE

Vázquez-Morón, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M.; Echevarría, Juan E.

2011-01-01

To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

Phylogeny and diversification of mountain vipers (Montivipera, Nilson et al., 2001) triggered by multiple Plio-Pleistocene refugia and high-mountain topography in the Near and Middle East.

Science.gov (United States)

Stümpel, Nikolaus; Rajabizadeh, Mehdi; Avcı, Aziz; Wüster, Wolfgang; Joger, Ulrich

2016-08-01

The Near and Middle East is a hotspot of biodiversity, but the region remains underexplored at the level of genetic biodiversity. Here, we present an extensive molecular phylogeny of the viperid snake genus Montivipera, including all known taxa. Based on nuclear and mitochondrial data, we present novel insights into the phylogeny of the genus and review the status of its constituent species. Maximum likelihood methods revealed a montane origin of Montivipera at 12.3Mya. We then analyzed factors of mountain viper diversity. Our data support substantial changes in effective population size through Plio-Pleistocene periods. We conclude that climatic oscillations were drivers of allopatric speciation, and that mountain systems of the Near and Middle East have strongly influenced the evolution and survival of taxa, because climatic and topographical heterogeneities induced by mountains have played a crucial role as filters for dispersal and as multiple refugia. The wide diversity of montane microhabitats enabled mountain vipers to retain their ecological niche during climatic pessima. In consequence the varied geological and topographical conditions between refugia favoured genetic isolation and created patterns of species richness resulting in the formation of neoendemic taxa. Our data support high concordance between geographic distributions of Montivipera haplotypes with putative plant refugia. Copyright © 2016. Published by Elsevier Inc.

The hard-core model on random graphs revisited

International Nuclear Information System (INIS)

Barbier, Jean; Krzakala, Florent; Zhang, Pan; Zdeborová, Lenka

2013-01-01

We revisit the classical hard-core model, also known as independent set and dual to vertex cover problem, where one puts particles with a first-neighbor hard-core repulsion on the vertices of a random graph. Although the case of random graphs with small and very large average degrees respectively are quite well understood, they yield qualitatively different results and our aim here is to reconciliate these two cases. We revisit results that can be obtained using the (heuristic) cavity method and show that it provides a closed-form conjecture for the exact density of the densest packing on random regular graphs with degree K ≥ 20, and that for K > 16 the nature of the phase transition is the same as for large K. This also shows that the hard-code model is the simplest mean-field lattice model for structural glasses and jamming

A synthetic phylogeny of freshwater crayfish: insights for conservation

Science.gov (United States)

Owen, Christopher L.; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A.

2015-01-01

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

Freud e a filogenia anímica Freud and the animic phylogeny

Directory of Open Access Journals (Sweden)

Monah Winograd

2007-01-01

Full Text Available Este ensaio investiga a presença, na obra de Freud, da idéia de uma filogenia anímica paralela, concomitante e dependente da filogenia somática descrita pelos teóricos da evolução. Objetivamos mostrar como se forma esta vizinhança da psicanálise com a biologia evolutiva, sublinhando que na filogenia esboçada por Freud, formas psíquicas típicas se sucedem na história da espécie humana, sendo repetidas por cada indivíduo em sua ontogenia singular. Tal como ocorre no plano somático, tempo e forma se associam intimamente na espécie e nos indivíduos. A presença desta idéia no pensamento freudiano abriu um debate sobre sua filiação lamarckista ou darwinista.This essay investigates the presence, in Freud´s work, of the idea of an animic phylogeny parallel, concomitant and dependent of the somatic phylogeny that the theoreticians of evolution describe. Our objective is to show how this neighborhood between psychoanalysis and evolutionary theory is formed. To do so, we stress that, in the phylogeny theory that Freud sketches, typical psychic forms occurs in the history of the human kind in a way that each individual repeats it in its singular ontogeny. As it happens in the somatic level, time and form are intimately associated in the species and in the individuals. The presence of that idea in Freud´s work has opened a debate about his Darwinist or Lamarckist inspiration.

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

Science.gov (United States)

2013-01-01

Background Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set H of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of distinct haplotypes hi,hj∈H, the sum of the edge weights belonging to the path from hi to hj in T∗ is not smaller than the observed number of changes between hi and hj. Finding the most parsimonious phylogeny for H involves solving an optimization problem, called the Most Parsimonious Phylogeny Estimation Problem (MPPEP), which is NP-hard in many of its versions. Results In this article we investigate a recent version of the MPPEP that arises when input data consist of single nucleotide polymorphism haplotypes extracted from a population of individuals on a common genomic region. Specifically, we explore the prospects for improving on the implicit enumeration strategy of implicit enumeration strategy used in previous work using a novel problem formulation and a series of strengthening valid inequalities and preliminary symmetry breaking constraints to more precisely bound the solution space and accelerate implicit enumeration of possible optimal phylogenies. We present the basic formulation and then introduce a series of provable valid constraints to reduce the solution space. We then prove

Adipokinetic hormones provide inference for the phylogeny of Odonata

Czech Academy of Sciences Publication Activity Database

Gäde, G.; Šimek, Petr; Fescemyer, H. W.

2011-01-01

Roč. 57, č. 1 (2011), s. 174-178 ISSN 0022-1910 R&D Projects: GA ČR GA203/09/2014 Grant - others:University of Cape Town for a Block grant(ZA) IFR 2008071500048; National Research Foundation, Pretoria(ZA) FA 2007021300002; USDA, ARS Specific Cooperative Agreement(US) 58-6402-5-066; US National Science Foundation(US) EF-0412651 Institutional research plan: CEZ:AV0Z50070508 Keywords : phylogeny of Odonata * Libellulidae * Corduliidae Subject RIV: ED - Physiology Impact factor: 2.236, year: 2011

Towards improving searches for optimal phylogenies.

Science.gov (United States)

Ford, Eric; St John, Katherine; Wheeler, Ward C

2015-01-01

Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be "tree-like" and focusing on the maximum-parsimony optimality criterion. This has led to much work on using heuristic tree searches to find approximate solutions. We present an approach for finding exact optimal solutions that employs and complements the current heuristic methods for finding optimal trees. Given a set of taxa and a set of aligned sequences of characters, there may be subsets of characters that are compatible, and for each such subset there is an associated (possibly partially resolved) phylogeny with edges corresponding to each character state change. These perfect phylogenies serve as anchor trees for our constrained search space. We show that, for sequences with compatible sites, the parsimony score of any tree [Formula: see text] is at least the parsimony score of the anchor trees plus the number of inferred changes between [Formula: see text] and the anchor trees. As the maximum-parsimony optimality score is additive, the sum of the lower bounds on compatible character partitions provides a lower bound on the complete alignment of characters. This yields a region in the space of trees within which the best tree is guaranteed to be found; limiting the search for the optimal tree to this region can significantly reduce the number of trees that must be examined in a search of the space of trees. We analyze this method empirically using four different biological data sets as well as surveying 400 data sets from the TreeBASE repository, demonstrating the effectiveness of our technique in reducing the number of steps in exact heuristic searches for trees under the maximum-parsimony optimality criterion. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

Directory of Open Access Journals (Sweden)

Zhou Kaiya

2009-01-01

Full Text Available Abstract Background The phylogeny of Cetacea (whales is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages. Results The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins and Lipotidae (Yangtze River dolphins. The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins and Stenella (spotted dolphins. Conclusion Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy

KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

Science.gov (United States)

Wang, Dapeng; Xu, Jiayue; Yu, Jun

2015-09-16

The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

Bayesian, maximum parsimony and UPGMA models for inferring the phylogenies of antelopes using mitochondrial markers.

Science.gov (United States)

Khan, Haseeb A; Arif, Ibrahim A; Bahkali, Ali H; Al Farhan, Ahmad H; Al Homaidan, Ali A

2008-10-06

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.

The Impact of Information on Death Penalty Support, Revisited

Science.gov (United States)

Lambert, Eric G.; Camp, Scott D.; Clarke, Alan; Jiang, Shanhe

2011-01-01

In 1972, former Supreme Court Justice Marshall postulated that the public was uninformed about the death penalty and information would change their support for it. There is some indication that information about the death penalty may change people's level of support. This study re-examines data used by Lambert and Clarke (2001). Using multivariate…

Towards a consensus Y-chromosomal phylogeny and Y-SNP set in forensics in the next-generation sequencing era.

Science.gov (United States)

Larmuseau, Maarten H D; Van Geystelen, Anneleen; Kayser, Manfred; van Oven, Mannis; Decorte, Ronny

2015-03-01

Currently, several different Y-chromosomal phylogenies and haplogroup nomenclatures are presented in scientific literature and at conferences demonstrating the present diversity in Y-chromosomal phylogenetic trees and Y-SNP sets used within forensic and anthropological research. This situation can be ascribed to the exponential growth of the number of Y-SNPs discovered due to mostly next-generation sequencing (NGS) studies. As Y-SNPs and their respective phylogenetic positions are important in forensics, such as for male lineage characterization and paternal bio-geographic ancestry inference, there is a need for forensic geneticists to know how to deal with these newly identified Y-SNPs and phylogenies, especially since these phylogenies are often created with other aims than to carry out forensic genetic research. Therefore, we give here an overview of four categories of currently used Y-chromosomal phylogenies and the associated Y-SNP sets in scientific research in the current NGS era. We compare these categories based on the construction method, their advantages and disadvantages, the disciplines wherein the phylogenetic tree can be used, and their specific relevance for forensic geneticists. Based on this overview, it is clear that an up-to-date reduced tree with a consensus Y-SNP set and a stable nomenclature will be the most appropriate reference resource for forensic research. Initiatives to reach such an international consensus are therefore highly recommended. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes).

Science.gov (United States)

Fan, X L; Barreto, R W; Groenewald, J Z; Bezerra, J D P; Pereira, O L; Cheewangkoon, R; Mostert, L; Tian, C M; Crous, P W

2017-06-01

Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë -host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë . Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma . A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.

Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes

Directory of Open Access Journals (Sweden)

X.L. Fan

2017-06-01

Full Text Available Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë-host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë. Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma. A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage.

Science.gov (United States)

Teske, Peter R; Hamilton, Healy; Matthee, Conrad A; Barker, Nigel P

2007-08-15

The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns. Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to diverge. This suggests that their

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage

Directory of Open Access Journals (Sweden)

Matthee Conrad A

2007-08-01

Full Text Available Abstract Background The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses, as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns. Results Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to

A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach.

Science.gov (United States)

Faurby, Søren; Svenning, Jens-Christian

2015-03-01

Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups. Copyright © 2014 Elsevier Inc. All rights reserved.

Phylogeny and micro-habitats utilized by lizards determine the composition of their endoparasites in the semiarid Caatinga of Northeast Brazil.

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Brito, S V; Corso, G; Almeida, A M; Ferreira, F S; Almeida, W O; Anjos, L A; Mesquita, D O; Vasconcellos, A

2014-11-01

Trophic networks can have architectonic configurations influenced by historical and ecological factors. The objective of this study was to analyze the architecture of networks between lizards, their endoparasites, diet, and micro-habitat, aiming to understand which factors exert an influence on the composition of the species of parasites. All networks showed a compartmentalized pattern. There was a positive relation between diet and the diversity of endoparasites. Our analyses also demonstrated that phylogeny and the use of micro-habitat influenced the composition of species of endoparasites and diet pattern of lizards. The principal factor that explained the modularity of the network was the foraging strategy, with segregation between the "active foragers" and "sit-and-wait" lizards. Our analyses also demonstrated that historical (phylogeny) and ecological factors (use of micro-habitat by the lizards) influenced the composition of parasite communities. These results corroborate other studies with ectoparasites, which indicate phylogeny and micro-habitat as determinants in the composition of parasitic fauna. The influence of phylogeny can be the result of coevolution between parasites and lizards in the Caatinga, and the influence of micro-habitat should be a result of adaptations of species of parasites to occupy the same categories of micro-habitats as hosts, thus favoring contagion.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

Science.gov (United States)

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

Coccolithophorids in polar waters: Wigwamma spp. revisited

DEFF Research Database (Denmark)

Thomsen, Helge Abildhauge; Østergaard, Jette B.; Heldal, Mikal

2013-01-01

A contingent of weakly calcified coccolithophorid genera and species were described from polar regions almost 40 years ago. In the interim period a few additional findings have been reported enlarging the realm of some of the species. The genus Wigwamma is revisited here with the purpose of provi...... appearance of the coccolith armour of the cell...

The significance test controversy revisited the fiducial Bayesian alternative

CERN Document Server

Lecoutre, Bruno

2014-01-01

The purpose of this book is not only to revisit the “significance test controversy,”but also to provide a conceptually sounder alternative. As such, it presents a Bayesian framework for a new approach to analyzing and interpreting experimental data. It also prepares students and researchers for reporting on experimental results. Normative aspects: The main views of statistical tests are revisited and the philosophies of Fisher, Neyman-Pearson and Jeffrey are discussed in detail. Descriptive aspects: The misuses of Null Hypothesis Significance Tests are reconsidered in light of Jeffreys’ Bayesian conceptions concerning the role of statistical inference in experimental investigations. Prescriptive aspects: The current effect size and confidence interval reporting practices are presented and seriously questioned. Methodological aspects are carefully discussed and fiducial Bayesian methods are proposed as a more suitable alternative for reporting on experimental results. In closing, basic routine procedures...

Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes, Cobitidae)

Czech Academy of Sciences Publication Activity Database

Bohlen, Jörg; Šlechtová, Vendula; Tan, H. H.; Britz, R.

2011-01-01

Roč. 61, č. 3 (2011), s. 854-865 ISSN 1055-7903 R&D Projects: GA ČR GA206/05/2556; GA ČR GA206/08/0637; GA AV ČR IAA600450508; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : pangio * eel loaches * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.609, year: 2011

Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (lepidoptera: papilionoidea: nymphalidae).

Science.gov (United States)

Shi, Qing-Hui; Sun, Xiao-Yan; Wang, Yun-Liang; Hao, Jia-Sheng; Yang, Qun

2015-01-01

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).

Satellite failures revisited

Science.gov (United States)

Balcerak, Ernie

2012-12-01

In January 1994, the two geostationary satellites known as Anik-E1 and Anik-E2, operated by Telesat Canada, failed one after the other within 9 hours, leaving many northern Canadian communities without television and data services. The outage, which shut down much of the country's broadcast television for hours and cost Telesat Canada more than $15 million, generated significant media attention. Lam et al. used publicly available records to revisit the event; they looked at failure details, media coverage, recovery effort, and cost. They also used satellite and ground data to determine the precise causes of those satellite failures. The researchers traced the entire space weather event from conditions on the Sun through the interplanetary medium to the particle environment in geostationary orbit.

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea).

Science.gov (United States)

Tkach, Vasyl V; Kudlai, Olena; Kostadinova, Aneta

2016-03-01

The Echinostomatoidea is a large, cosmopolitan group of digeneans currently including nine families and 105 genera, the vast majority parasitic, as adults, in birds with relatively few taxa parasitising mammals, reptiles and, exceptionally, fish. Despite the complex structure, diverse content and substantial species richness of the group, almost no attempt has been made to elucidate its phylogenetic relationships at the suprageneric level based on molecules due to the lack of data. Herein, we evaluate the consistency of the present morphology-based classification system of the Echinostomatoidea with the phylogenetic relationships of its members based on partial sequences of the nuclear lsrRNA gene for a broad diversity of taxa (80 species, representing eight families and 40 genera), including representatives of five subfamilies of the Echinostomatidae, which currently exhibits the most complex taxonomic structure within the superfamily. This first comprehensive phylogeny for the Echinostomatoidea challenged the current systematic framework based on comparative morphology. A morphology-based evaluation of this new molecular framework resulted in a number of systematic and nomenclatural changes consistent with the phylogenetic estimates of the generic and suprageneric boundaries and a new phylogeny-based classification of the Echinostomatoidea. In the current systematic treatment: (i) the rank of two family level lineages, the former Himasthlinae and Echinochasminae, is elevated to full family status; (ii) Caballerotrema is distinguished at the family level; (iii) the content and diagnosis of the Echinostomatidae (sensu stricto) (s. str.) are revised to reflect its phylogeny, resulting in the abolition of the Nephrostominae and Chaunocephalinae as synonyms of the Echinostomatidae (s. str.); (iv) Artyfechinostomum, Cathaemasia, Rhopalias and Ribeiroia are re-allocated within the Echinostomatidae (s. str.), resulting in the abolition of the Cathaemasiidae, Rhopaliidae

Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea

Directory of Open Access Journals (Sweden)

von Döhren Jörn

2009-08-01

Full Text Available Abstract Background The new animal phylogeny established several taxa which were not identified by morphological analyses, most prominently the Ecdysozoa (arthropods, roundworms, priapulids and others and Lophotrochozoa (molluscs, annelids, brachiopods and others. Lophotrochozoan interrelationships are under discussion, e.g. regarding the position of Nemertea (ribbon worms, which were discussed to be sister group to e.g. Mollusca, Brachiozoa or Platyhelminthes. Mitochondrial genomes contributed well with sequence data and gene order characters to the deep metazoan phylogeny debate. Results In this study we present the first complete mitochondrial genome record for a member of the Nemertea, Lineus viridis. Except two trnP and trnT, all genes are located on the same strand. While gene order is most similar to that of the brachiopod Terebratulina retusa, sequence based analyses of mitochondrial genes place nemerteans close to molluscs, phoronids and entoprocts without clear preference for one of these taxa as sister group. Conclusion Almost all recent analyses with large datasets show good support for a taxon comprising Annelida, Mollusca, Brachiopoda, Phoronida and Nemertea. But the relationships among these taxa vary between different studies. The analysis of gene order differences gives evidence for a multiple independent occurrence of a large inversion in the mitochondrial genome of Lophotrochozoa and a re-inversion of the same part in gastropods. We hypothesize that some regions of the genome have a higher chance for intramolecular recombination than others and gene order data have to be analysed carefully to detect convergent rearrangement events.

Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

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Tellier Laurent C

2010-03-01

Full Text Available Abstract Background Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae. Results We identified 347 single nucleotide polymorphisms (SNPs in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication. Conclusions We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.

Pockets of Participation: Revisiting Child-Centred Participation Research

Science.gov (United States)

Franks, Myfanwy

2011-01-01

This article revisits the theme of the clash of interests and power relations at work in participatory research which is prescribed from above. It offers a possible route toward solving conflict between adult-led research carried out by young researchers, funding requirements and organisational constraints. The article explores issues of…

Faraday effect revisited: sum rules and convergence issues

DEFF Research Database (Denmark)

Cornean, Horia; Nenciu, Gheorghe

2010-01-01

This is the third paper of a series revisiting the Faraday effect. The question of the absolute convergence of the sums over the band indices entering the Verdet constant is considered. In general, sum rules and traces per unit volume play an important role in solid-state physics, and they give...

Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram.

Science.gov (United States)

Liu, Qing; Triplett, Jimmy K; Wen, Jun; Peterson, Paul M

2011-11-01

Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa. Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method. The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica-E. tristachya clade, which is considered a source of maternal parents for allotetraploids. Two homoeologous loci are isolated from three tetraploid species in the Pepc4 phylogeny, and the maternal parents receive further support. The A-type EF-1α sequences possess three characters, i.e. a large number of variations of intron 2; clade E-A distantly diverged from clade E-B and other diploid species; and seven deletions in intron 2, implying a possible derivation through a gene duplication event. The crown age of Eleusine and the allotetraploid lineage are 3·89 million years ago (mya) and 1·40 mya, respectively. The molecular data support independent allotetraploid origins for E. kigeziensis and the E. africana-E. coracana clade. Both events may have involved diploids E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The habitat-specific hypothesis is proposed to explain the divergence of Eleusine and its allotetraploid lineage.

Identification and phylogeny of the tomato receptor-like proteins family

OpenAIRE

Ermis Yanes-Paz; Gioser María Ramos-Echazábal; Glay Chinea; Yanelis Capdesuñer Ruiz; Ramón Santos Bermúdez

2017-01-01

The receptor-like proteins (RLPs) play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L.) using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between...

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

Science.gov (United States)

Sims, Gregory E.; Kim, Sung-Hou

2011-01-01

A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (∼8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (∼0.56 million features), which account for ∼69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup. PMID:21536867

Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.

Science.gov (United States)

Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S

2014-01-01

The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids.

A molecular phylogeny of the Australian huntsman spiders (Sparassidae, Deleninae): implications for taxonomy and social behaviour.

Science.gov (United States)

Agnarsson, Ingi; Rayor, Linda S

2013-12-01

Huntsman spiders (Sparassidae) are a diverse group with a worldwide distribution, yet are poorly known both taxonomically and phylogenetically. They are particularly diverse in Australia where an endemic lineage, Deleninae, has diversified to form nearly 100 species. One unusual species, Delena cancerides, has been believed to be the sole group-living sparassid. Unlike all of the other subsocial and social spiders which are capture-web based or live in silken tunnels, D. cancerides are non-web building spiders that live in large matrilineal colonies of a single adult female and her offspring from multiple clutches of under the bark of dead trees. Here we report the discovery of two additional prolonged subsocial sparassid species, currently in Eodelena but here formally proposed as a synonomy of Delena (new synonoymy), Delena (Eodelena) lapidicola and D. (E.) melanochelis. We briefly describe their social demographics, behavior, and habitat use. In order to understand the evolutionary relationships among these species, and thus origin of sociality and other traits in this group, we also offer the first molecular phylogeny of Deleninae and relatives. We employ model based phylogenetic analyses on two mtDNA and three nuDNA loci using maximum likelihood and Bayesian methods, including both 'classical' concatenation approach as well as coalescent-based analysis of species trees from gene trees. Our results support the hypothesis that the delenine huntsman spiders are a monophyletic Australian radiation, approximately 23 million year old, and indicate that the current ten genera should be merged to six genera in four clades. Our findings are inconsistent with some relatively recent changes in the taxonomy of Deleninae. The three known group-living delenine species are related and likely represent a single origin of sociality with a single reversal to solitary life-styles. Our results provide strong support for the classical Isopeda, but not for the recent splitting of

A mitochondrial DNA phylogeny of the endangered vipers of the Vipera ursinii complex

Czech Academy of Sciences Publication Activity Database

Gvoždík, Václav; Jandzik, D.; Cordos, B.; Řehák, I.; Kotlík, Petr

2012-01-01

Roč. 62, č. 3 (2012), s. 1019-1024 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : Conservation * Meadow viper * Phylogeny * Steppe viper * Systematics * Vipera ursinii complex Subject RIV: EH - Ecology, Behaviour Impact factor: 4.066, year: 2012

Failure by Design? Revisiting Tanzania′s Flagship Wildlife Management Area Burunge

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Francis Moyo

2016-01-01

Full Text Available In this paper, we revisit the on-the-ground reality of Burunge Wildlife Management Area (WMA that is celebrated as one of Tanzania's best examples of community-based conservation (CBC. We find Burunge WMA rife with conflict and contestation over grievances that remained unsettled since its establishment a decade ago. These grievances have been accentuated by growing land pressure resulting from increasing human, livestock, and elephant populations, in combination with infrastructure improvements and support for agriculture-led development. The WMA governance regime has little to offer the residents and village leaders of Burunge member villages who appear hostages in a situation where interests in human development and conservation are pitted against each other, making a mockery of the notions of CBC. By re-examining this exemplary WMA case and compare our findings with the way it is being portrayed by supporting agencies, we pinpoint the tendency of the actors promoting conservation in Tanzania to misrepresent or ignore the realities on the ground that defy official policy promises. In doing this, we hope to call upon the many empathetic and hard-working individuals to end the collective failure to address this detrimental discrepancy between reality and representation, and start supporting affected residents in their struggles for self-determination.

Short or Long End of the Lever? Associations between Provider Communication of the "Asthma-Action Plan" and Outpatient Revisits for Pediatric Asthma.

Science.gov (United States)

Rangachari, Pavani; Mehta, Renuka; Rethemeyer, R Karl; Ferrang, Carole; Dennis, Clifton; Redd, Vickie

2015-10-01

At the Children's Hospital of Georgia (CHOG), we found that outpatient revisits for pediatric asthma were significantly above national norms. According to the NIH, costly hospital revisits for asthma can be prevented through guidelines-based self-management of asthma, central to which, is the use of a written Asthma-Action Plan (AAP). The asthma services literature has emphasized the role of the healthcare provider in promoting asthma self-management using the AAP, to prevent hospital revisits. On the other hand, the asthma policy literature has emphasized the need for community-based interventions to promote asthma self-management. A gap remains in understanding the extent of leverage that healthcare providers may have in preventing hospital revisits for asthma, through effective communication of AAP in the outpatient setting. Our study sought to address this gap. We conducted a 6-month intervention to implement "patient-and-family-centered communication of the AAP" in CHOG outpatient clinics, based on the "change-management" theoretical framework. Provider communication of AAP was assessed through a survey of "Parent Understanding of the Child's AAP." A quasi-experimental approach was used to measure outpatient revisits for pediatric asthma, pre- and post-intervention. Survey results showed that provider communication of the AAP was unanimously perceived highly positively by parents of pediatric asthma patients, across various metrics of patient-centered care. However, there were no statistically significant differences in outpatient "revisit behavior" for pediatric asthma between pre- and post-intervention periods after controlling for several demographic variables. Additionally, revisits remained significantly above national norms. Results suggest limited potential of "effective provider communication of AAP," in reducing outpatient revisits for pediatric asthma; and indicate need for broader community-based interventions to address patient life variables

Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.

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Qiu, Dajun; Huang, Liangmin; Liu, Sheng; Zhang, Huan; Lin, Senjie

2013-01-01

Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.

Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.

Directory of Open Access Journals (Sweden)

Dajun Qiu

Full Text Available Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium. Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.

Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae and phylogenetic support

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Amanda Ciprandi Pires

2011-03-01

Full Text Available Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae and phylogenetic support. The distributional pattern of the genus Thecomyia Perty, 1833 was defined using panbiogeographic tools, and analyzed based on the phylogeny of the group. This study sought to establish biogeographical homologies in the Neotropical region between different species of the genus, based on their distribution pattern and later corroboration through its phylogeny. Eight individual tracks and 16 generalized tracks were identified, established along nearly the entire swath of the Neotropics. Individual tracks are the basic units of a panbiogeographic study, and correspond to the hypothesis of minimum distribution of the organisms involved. The generalized tracks, obtained from the spatial congruence between two or more individual tracks, are important in the identification of smaller areas of endemism. Thus, we found evidence from the generalized tracks in support of previous classification for the Neotropical region. The Amazon domain is indicated as an area of outstanding importance in the diversification of the group, by the confluence of generalized tracks and biogeographic nodes in the region. Most of the generalized tracks and biogeographical nodes were congruent with the phylogenetic hypothesis of the genus, indicating support of the primary biogeographical homologies originally defined by the track analysis.

Additively homomorphic encryption with a double decryption mechanism, revisited

NARCIS (Netherlands)

Peter, Andreas; Kronberg, M.; Trei, W.; Katzenbeisser, S.

We revisit the notion of additively homomorphic encryption with a double decryption mechanism (DD-PKE), which allows for additions in the encrypted domain while having a master decryption procedure that can decrypt all properly formed ciphertexts by using a special master secret. This type of

Moral Judgment Development across Cultures: Revisiting Kohlberg's Universality Claims

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Gibbs, John C.; Basinger, Karen S.; Grime, Rebecca L.; Snarey, John R.

2007-01-01

This article revisits Kohlberg's cognitive developmental claims that stages of moral judgment, facilitative processes of social perspective-taking, and moral values are commonly identifiable across cultures. Snarey [Snarey, J. (1985). "The cross-cultural universality of social-moral development: A critical review of Kohlbergian research."…

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms.

Science.gov (United States)

Chavda, Kalyan D; Chen, Liang; Fouts, Derrick E; Sutton, Granger; Brinkac, Lauren; Jenkins, Stephen G; Bonomo, Robert A; Adams, Mark D; Kreiswirth, Barry N

2016-12-13

genus. Enterobacter spp., especially carbapenemase-producing Enterobacter spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of Enterobacter strains because of ambiguous typing methods and imprecise taxonomy. In this study, we used a whole-genome-based comparative phylogenetic approach to (i) revisit and redefine the genus Enterobacter and (ii) unravel the emergence and evolution of the Klebsiella pneumoniae carbapenemase-harboring Enterobacter spp. Using genomic analysis of 447 sequenced strains, we developed an improved understanding of the species designations within this complex genus and identified the diverse mechanisms driving the molecular evolution of carbapenem resistance. The findings in this study provide a solid genomic framework that will serve as an important resource in the future development of molecular diagnostics and in supporting drug discovery programs. Copyright © 2016 Chavda et al.

High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses

NARCIS (Netherlands)

Barry, A.F.; Durães-Carvalho, R.; Oliveira-Filho, Edmilson F.; Alfieri, A.; Poel, Van der W.H.M.

2017-01-01

The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses

Phylogeny and resistance profiles of HIV-1 POL sequences from rectal biopsies and blood

DEFF Research Database (Denmark)

Katzenstein, Terese Lea; Petersen, A B; Storgaard, M

2010-01-01

The phylogeny and resistance profiles of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) sequences were compared among six patients with HIV-1 who had received numerous treatments. RNA and DNA fractions were obtained from concurrent blood and rectal biopsy...

Radiative corrections to double-Dalitz decays revisited

Science.gov (United States)

Kampf, Karol; Novotný, Jiři; Sanchez-Puertas, Pablo

2018-03-01

In this study, we revisit and complete the full next-to-leading order corrections to pseudoscalar double-Dalitz decays within the soft-photon approximation. Comparing to the previous study, we find small differences, which are nevertheless relevant for extracting information about the pseudoscalar transition form factors. Concerning the latter, these processes could offer the opportunity to test them—for the first time—in their double-virtual regime.

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.

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Chen, Meng-Yun; Liang, Dan; Zhang, Peng

2015-11-01

Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes. © 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.

A Feminist Revisit to the First-Year Curriculum.

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Bernstein, Anita

1996-01-01

A seminar at Chicago-Kent College of Law (Illinois) that reviews six first-year law school courses by focusing on feminist issues in course content and structure is described. The seminar functions as both a review and a shift in perspective. Courses revisited include civil procedure, contracts, criminal law, justice and the legal system,…

Quantum duel revisited

International Nuclear Information System (INIS)

Schmidt, Alexandre G M; Paiva, Milena M

2012-01-01

We revisit the quantum two-person duel. In this problem, both Alice and Bob each possess a spin-1/2 particle which models dead and alive states for each player. We review the Abbott and Flitney result—now considering non-zero α 1 and α 2 in order to decide if it is better for Alice to shoot or not the second time—and we also consider a duel where players do not necessarily start alive. This simple assumption allows us to explore several interesting special cases, namely how a dead player can win the duel shooting just once, or how can Bob revive Alice after one shot, and the better strategy for Alice—being either alive or in a superposition of alive and dead states—fighting a dead opponent. (paper)

Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin's stag beetle.

Science.gov (United States)

Kim, Sang Il; Farrell, Brian D

2015-05-01

Stag beetles (family Lucanidae Latreille, 1804) are one of the earliest branching lineages of scarab beetles that are characterized by the striking development of the male mandibles. Despite stag beetles' popularity among traditional taxonomists and amateur collectors, there has been almost no study of lucanid relationships and evolution. Entomologists, including Jeannel (1942), have long recognized resemblance between the austral stag beetles of the tribes Chiasognathini, Colophonini, Lamprimini, Pholidotini, Rhyssonotini, and Streptocerini, but this hypothesis of their close relationship across the continents has never been tested. To gain further insight into lucanid phylogeny and biogeography, we reconstructed the first molecular phylogeny of world stag beetles using DNA sequences from mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and the nuclear protein-coding (NPC) gene wingless for 93 lucanid species representing all extant subfamilies and 24 out of the 27 tribes, together with 14 representative samples of other early branching scarabaeoid families and two staphyliniform beetle families as outgroups. Both Bayesian inference (BI) and maximum likelihood inference (MLI) strongly supported the monophyly of Lucanidae sensu lato that includes Diphyllostomatidae. Within Lucanidae sensu stricto, the subfamilies Lucaninae and Lampriminae appeared monophyletic under both methods of phylogenetic inferences; however, Aesalinae and Syndesinae were found to be polyphyletic. A time-calibrated phylogeny based on five fossil data estimated the origin of crown group Lucanidae as circa 160 million years ago (MYA). Divergence between the Neotropical and Australasian groups of the Chiasognathini was estimated to be circa 47MYA, with the South African Colophonini branching off from the ancient Chiasognathini lineage around 87MYA. Another Gondwanan relationship was recovered between the Australasian Eucarteria and the Neotropical Casignetus, which diverged circa 58MYA. Lastly

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

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Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

2016-01-01

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

The Importance of Being a Complement: CED Effects Revisited

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Jurka, Johannes

2010-01-01

This dissertation revisits subject island effects (Ross 1967, Chomsky 1973) cross-linguistically. Controlled acceptability judgment studies in German, English, Japanese and Serbian show that extraction out of specifiers is consistently degraded compared to extraction out of complements, indicating that the Condition on Extraction domains (CED,…

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae).

Science.gov (United States)

Yamaguchi, M; Miya, M; Okiyama, M; Nishida, M

2000-04-01

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution. Copyright 2000 Academic Press.

The Effect of Brand Equity and Perceived Value on Customer Revisit Intention: A Study in Quick-Service Restaurants in Vietnam

Directory of Open Access Journals (Sweden)

Ly Thi Minh Pham

2016-10-01

Full Text Available The purpose of this study is to examine how brand equity, from a customer point of view, influences quick-service restaurant revisit intention. The authors propose a conceptual framework in which three dimensions of brand equity including brand associations combined with brand awareness, perceived quality, brand loyalty and perceived value are related to revisit intention. Data from 570 customers who had visited four quick-service restaurants in Ho Chi Minh City were used for the structural equation modelling (SEM analysis. The results show that strong brand equity is significantly correlated with revisit intention. Additionally, the effect of brand equity on revisit intention was mediated by perceived value, among others. Overall, this study emphasizes the importance of perceived value in lodging in the customer’s mind. Finally, managerial implications are presented based on the study results.

Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity.

Science.gov (United States)

Marx, Felix G; Fordyce, R Ewan

2015-04-01

A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36-30 Ma), a shift towards bulk filter-feeding (30-23 Ma) and a climate-driven diversity loss around 3 Ma. Evolutionary rates and disparity were high following the origin of mysticetes around 38 Ma, coincident with global cooling, abrupt Southern Ocean eutrophication and the development of the Antarctic Circumpolar Current (ACC). Subsequently, evolutionary rates and disparity fell, becoming nearly constant after approximately 23 Ma as the ACC reached its full strength. By contrast, species diversity rose until 15 Ma and then remained stable, before dropping sharply with the onset of Northern Hemisphere glaciation. This decline coincided with the final establishment of modern mysticete gigantism and may be linked to glacially driven variability in the distribution of shallow habitats or an increased need for long-distance migration related to iron-mediated changes in glacial marine productivity.

Literary Origins of the Term "School Psychologist" Revisited

Science.gov (United States)

Fagan, Thomas K.

2005-01-01

Previous research on the literary origins of the term "school psychologist" is revisited, and conclusions are revised in light of new evidence. It appears that the origin of the term in the American literature occurred as early as 1898 in an article by Hugo Munsterberg, predating the usage by Wilhelm Stern in 1911. The early references to the…

A Multi-Level Model of Moral Functioning Revisited

Science.gov (United States)

Reed, Don Collins

2009-01-01

The model of moral functioning scaffolded in the 2008 "JME" Special Issue is here revisited in response to three papers criticising that volume. As guest editor of that Special Issue I have formulated the main body of this response, concerning the dynamic systems approach to moral development, the problem of moral relativism and the role of…

Haemoprotozoa: Making biological sense of molecular phylogenies

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Peter O'Donoghue

2017-12-01

Full Text Available A range of protistan parasites occur in the blood of vertebrates and are transmitted by haematophagous invertebrate vectors. Some 48 genera are recognized in bood primarily on the basis of parasite morphology and host specificity; including extracellular kinetoplastids (trypanosomatids and intracellular apicomplexa (haemogregarines, haemococcidia, haemosporidia and piroplasms. Gene sequences are available for a growing number of species and molecular phylogenies often link parasite and host or vector evolution. This review endeavours to reconcile molecular clades with biological characters. Four major trypanosomatid clades have been associated with site of development in the vector: salivarian or stercorarian for Trypanosoma, and supra- or peri-pylorian for Leishmania. Four haemogregarine clades have been associated with acarine vectors (Hepatozoon A and B, Karyolysus, Hemolivia and another two with leeches (Dactylosoma, Haemogregarina sensu stricto. Two haemococcidian clades (Lankesterella, Schellackia using leeches and mosquitoes (as paratenic hosts! were paraphyletic with monoxenous enteric coccidia. Two major haemosporidian clades have been associated with mosquito vectors (Plasmodium from mammals, Plasmodium from birds and lizards, two with midges (Hepatocystis from bats, Parahaemoproteus from birds and two with louse-flies and black-flies (Haemoproteus and Leucocytozoon from birds. Three major piroplasm clades were recognized: one associated with transovarian transmission in ticks (Babesia sensu stricto; one with pre-erythrocytic schizogony in vertebrates (Theileria/Cytauxzoon; and one with neither (Babesia sensu lato. Broad comparative studies with allied groups suggest that trypanosomatids and haemogregarines evolved first in aquatic and then terrestrial environments, as evidenced by extant lineages in invertebrates and their radiation in vertebrates. In contrast, haemosporidia and haemococcidia are thought to have evolved first in

MOLECULAR PHYLOGENY OF THREE SPECIES OF LAND SNAILS (STYLOMMATOPHORA AND ACHATINIDAE, ARCHACHATINA MARGINATA (SWAINSON, 1821, ACHATINA ACHATINA (LINNAEUS, 1758, AND ACHATINA FULICA (BOWDICH, 1822 IN SOME SOUTHERN STATES AND NORTH CENTRAL STATES IN NIGERIA

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Michael Olufemi AWODIRAN

2015-12-01

Full Text Available Partial sequences of mitochondrial gene cytochrome oxidase sub unit 1 (CO1 and ribosomal RNA 18S nuclear encoding gene of 43 individuals belonging to two genera in order Stylommatophora and the family Achatinidae (Archachatina and Achatina were obtained to investigate molecular phylogeny in the family. The CO1 was found to be highly variable while the 18S was found to be highly conserved yielding invariable sequences. Several primers were also tested both for the mitochondrial and nuclear genomes but CO1 produced the best results giving single and clear bands. Four main genetic phylogroups/clades were identified within the Bayesian tree constructed and all the four clades were supported by bootstrap values of 100% and also were supported by bootstrap values above 79% in the NJ. Two unidentified species used in the analysis were found in the basal clade which may mean that they were of ancient origin. This study provides preliminary and novel insights on the molecular phylogeny of the snails’ species, though there is still a need to collect samples of other species in this family to provide a more robust phylogenetic relationship of achatinid snails in Nigeria.

BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

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Lin Kui

2007-07-01

Full Text Available Abstract Background Overlapping genes (OGs in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest. Description BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ and Unweighted Pair-Group Method using Arithmetic averages (UPGMA. Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint. Conclusion BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by

A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation.

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Russello, Michael A; Amato, George

2004-02-01

Amazon parrots (Genus Amazona) are among the most recognizable and imperiled of all birds. Several hypotheses regarding the evolutionary history of Amazona are investigated using a combined phylogenetic analysis of DNA sequence data from six partitions including mitochondrial (COI, 12S, and 16S) and nuclear (beta-fibint7, RP40, and TROP) regions. The results demonstrate that Amazona is not monophyletic with respect to the placement of the Yellow-faced parrot (Amazona xanthops), as first implied by. In addition, the analysis corroborates previous studies suggesting a Neotropical short-tailed parrot genus as sister to Amazona. At a finer level, the phylogeny resolves the Greater Antillean endemic species as constituting a monophyletic group, including the Central American Amazona albifrons, while further revealing a paraphyletic history for the extant Amazon species of the Lesser Antilles. The reconstructed phylogeny provides further insights into the mainland sources of the Antillean Amazona, reveals areas of taxonomic uncertainty within the genus, and presents historical information that may be included in conservation priority-setting for Amazon parrots.

Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach.

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Borner, Janus; Pick, Christian; Thiede, Jenny; Kolawole, Olatunji Matthew; Kingsley, Manchang Tanyi; Schulze, Jana; Cottontail, Veronika M; Wellinghausen, Nele; Schmidt-Chanasit, Jonas; Bruchhaus, Iris; Burmester, Thorsten

2016-01-01

The apicomplexan order Haemosporida is a clade of unicellular blood parasites that infect a variety of reptilian, avian and mammalian hosts. Among them are the agents of human malaria, parasites of the genus Plasmodium, which pose a major threat to human health. Illuminating the evolutionary history of Haemosporida may help us in understanding their enormous biological diversity, as well as tracing the multiple host switches and associated acquisitions of novel life-history traits. However, the deep-level phylogenetic relationships among major haemosporidian clades have remained enigmatic because the datasets employed in phylogenetic analyses were severely limited in either gene coverage or taxon sampling. Using a PCR-based approach that employs a novel set of primers, we sequenced fragments of 21 nuclear genes from seven haemosporidian parasites of the genera Leucocytozoon, Haemoproteus, Parahaemoproteus, Polychromophilus and Plasmodium. After addition of genomic data from 25 apicomplexan species, the unreduced alignment comprised 20,580 bp from 32 species. Phylogenetic analyses were performed based on nucleotide, codon and amino acid data employing Bayesian inference, maximum likelihood and maximum parsimony. All analyses resulted in highly congruent topologies. We found consistent support for a basal position of Leucocytozoon within Haemosporida. In contrast to all previous studies, we recovered a sister group relationship between the genera Polychromophilus and Plasmodium. Within Plasmodium, the sauropsid and mammal-infecting lineages were recovered as sister clades. Support for these relationships was high in nearly all trees, revealing a novel phylogeny of Haemosporida, which is robust to the choice of the outgroup and the method of tree inference. Copyright © 2015 Elsevier Inc. All rights reserved.

Short or Long End of the Lever? Associations between Provider Communication of the “Asthma-Action Plan” and Outpatient Revisits for Pediatric Asthma

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Rangachari, Pavani; Mehta, Renuka; Rethemeyer, R. Karl; Ferrang, Carole; Dennis, Clifton; Redd, Vickie

2017-01-01

Background At the Children’s Hospital of Georgia (CHOG), we found that outpatient revisits for pediatric asthma were significantly above national norms. According to the NIH, costly hospital revisits for asthma can be prevented through guidelines-based self-management of asthma, central to which, is the use of a written Asthma-Action Plan (AAP). Purpose The asthma services literature has emphasized the role of the healthcare provider in promoting asthma self-management using the AAP, to prevent hospital revisits. On the other hand, the asthma policy literature has emphasized the need for community-based interventions to promote asthma self-management. A gap remains in understanding the extent of leverage that healthcare providers may have in preventing hospital revisits for asthma, through effective communication of AAP in the outpatient setting. Our study sought to address this gap. Methods We conducted a 6-month intervention to implement “patient-and-family-centered communication of the AAP” in CHOG outpatient clinics, based on the “change-management” theoretical framework. Provider communication of AAP was assessed through a survey of “Parent Understanding of the Child’s AAP.” A quasi-experimental approach was used to measure outpatient revisits for pediatric asthma, pre- and post-intervention. Results Survey results showed that provider communication of the AAP was unanimously perceived highly positively by parents of pediatric asthma patients, across various metrics of patient-centered care. However, there were no statistically significant differences in outpatient “revisit behavior” for pediatric asthma between pre- and post-intervention periods after controlling for several demographic variables. Additionally, revisits remained significantly above national norms. Conclusions Results suggest limited potential of “effective provider communication of AAP,” in reducing outpatient revisits for pediatric asthma; and indicate need for

Reframing in dentistry: Revisited

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Sivakumar Nuvvula

2013-01-01

Full Text Available The successful practice of dentistry involves a good combination of technical skills and soft skills. Soft skills or communication skills are not taught extensively in dental schools and it can be challenging to learn and at times in treating dental patients. Guiding the child′s behavior in the dental operatory is one of the preliminary steps to be taken by the pediatric dentist and one who can successfully modify the behavior can definitely pave the way for a life time comprehensive oral care. This article is an attempt to revisit a simple behavior guidance technique, reframing and explain the possible psychological perspectives behind it for better use in the clinical practice.

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

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Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

2017-04-01

Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

On the ionospheric perturbation for the 1995 Kobe earthquake: revisited

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Masashi Hayakawa

2016-01-01

Full Text Available The presence of seismo-lower ionospheric perturbation for the Kobe earthquake (EQ has been revisited with a relatively new phenomenon of ULF (ultra-low-frequency magnetic field depression effect. By using the ULF data in Japan only at Kakioka belonging to Japan Meteorological Agency (because data from Memambetsu and Kanoya were not available, we have found that a very clear ULF depression was observed at Kakioka on 14 January 1995. A comparison with our former result on subionospheric VLF (very low frequency propagation anomaly indicates that the occurrence of ULF depression exhibits a temporal coincidence (synchronization with that of subionospheric VLF anomaly. This may be acceptable because the ULF depression can be explained in terms of enhanced absorption of magnetospheric ULF waves through the disturbed lower ionosphere prior to an EQ. The result of ULF magnetic field depression in this paper is likely to provide a further support to the presence of the lower ionospheric perturbation before the Kobe EQ.

Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

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Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

2015-10-30

Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

Towards a comprehensive phylogeny of the large temperate genus Pedicularis (Orobanchaceae), with an emphasis on species from the Himalaya-Hengduan Mountains.

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Yu, Wen-Bin; Liu, Min-Lu; Wang, Hong; Mill, Robert R; Ree, Richard H; Yang, Jun-Bo; Li, De-Zhu

2015-07-11

Striking interspecific variations in floral traits of the large temperate genus Pedicularis have given rise to controversies concerning infra-generic classifications. To date, phylogenetic relationships within the genus have not been well resolved. The main goal of this study is to construct a backbone phylogeny of Pedicularis, with extensive sampling of species from the Himalaya-Hengduan Mountains. Phylogenetic analyses included 257 species, representing all 13 informal groups and 104 out of 130 series in the classification system of Tsoong, using sequences of the nuclear ribosomal internal transcribed spacer (nrITS) and three plastid regions (matK, rbcL and trnL-F). Bayesian inference and maximum likelihood methods were applied in separate and combined analyses of these datasets. Thirteen major clades are resolved with strong support, although the backbone of the tree is poorly resolved. There is little consensus between the phylogenetic tree and Tsoong's classification of Pedicularis. Only two of the 13 groups (15.4 %), and 19 of the 56 series (33.9 %) with more than one sampled species were found to be strictly monophyletic. Most opposite-/whorled-leaved species fall into a single clade, i.e. clade 1, while alternate leaves species occur in the remaining 12 clades. Excluding the widespread P. verticillata in clade 1, species from Europe and North America fall into clades 6-8. Our results suggest that combinations of morphological and geographic characters associated with strongly supported clades are needed to elucidate a comprehensive global phylogeny of Pedicularis. Alternate leaves are inferred to be plesiomorphic in Pedicularis, with multiple transitions to opposite/whorled phyllotaxy. Alternate-leaved species show high diversity in plant habit and floral forms. In the Himalaya-Hengduan Mountains, geographical barriers may have facilitated diversification of species with long corolla tubes, and the reproductive advantages of beakless galeas in opposite

Chromosome phylogenies of man, great apes, and Old World monkeys.

Science.gov (United States)

De Grouchy, J

1987-08-31

The karyotypes of man and of the closely related Pongidae--chimpanzee, gorilla, and orangutan--differ by a small number of well known rearrangements, mainly pericentric inversions and one fusion which reduced the chromosome number from 48 in the Pongidae to 46 in man. Dutrillaux et al. (1973, 1975, 1979) reconstructed the chromosomal phylogeny of the entire primate order. More and more distantly related species were compared thus moving backward in evolution to the common ancestors of the Pongidae, of the Cercopithecoidae, the Catarrhini, the Platyrrhini, the Prosimians, and finally the common ancestor of all primates. Descending the pyramid it becomes possible to assign the rearrangements that occurred in each phylum, and the one that led to man in particular. The main conclusions are that this phylogeny is compatible with the occurrence during evolution of simple chromosome rearrangements--inversions, fusions, reciprocal translocation, acquisition or loss of heterochromatin--and that it is entirely consistent with the known primate phylogeny based on physical morphology and molecular evolution. If heterochromatin is not taken into account, man has in common with the other primates practically all of his chromosomal material as determined by chromosome banding. However, it is arranged differently, according to species, on account of chromosome rearrangements. This interpretation has been confirmed by comparative gene mapping, which established that the same chromosome segments, identified by banding, carry the same genes (Finaz et al., 1973; Human Gene Mapping 8, 1985). A remarkable observation made by Dutrillaux is that different primate phyla seem to have adopted different chromosome rearrangements in the course of evolution: inversions for the Pongidae, Robertsonian fusions for the lemurs, etc. This observation may raise many questions, among which is that of an organized evolution. Also, the breakpoints of chromosomal rearrangements observed during evolution

Revisiting Jack Goody to Rethink Determinisms in Literacy Studies

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Collin, Ross

2013-01-01

This article revisits Goody's arguments about literacy's influence on social arrangements, culture, cognition, economics, and other domains of existence. Whereas some of his arguments tend toward technological determinism (i.e., literacy causes change in the world), other of his arguments construe literacy as a force that shapes and is shaped by…

A control center design revisited: learning from users’ appropriation

DEFF Research Database (Denmark)

Souza da Conceição, Carolina; Cordeiro, Cláudia

2014-01-01

This paper aims to present the lessons learned during a control center design project by revisiting another control center from the same company designed two and a half years before by the same project team. In light of the experience with the first project and its analysis, the designers and res...

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

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Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further

Data partitions, Bayesian analysis and phylogeny of the zygomycetous fungal family Mortierellaceae, inferred from nuclear ribosomal DNA sequences.

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Tamás Petkovits

Full Text Available Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values, implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.

PENGARUH GUIDE PERFORMANCE DAN QUALITY TOURISM SERVICE TERHADAP REVISIT INTENTION DI KEBUN RAYA BOGOR

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Rian Andriani

2016-11-01

ABSTRACT Bogor Botanical Gardens is one of tourist destination in Bogor City, West Java, which the geographical in a strategic location between two big cities, Jakarta and Bandung. This location factor is can become an opportunity for Bogor Botanical Gardens to become a favorite tourist destination in Bogor City. Guide Performance and Quality Tourism Service is one of part of the tourism, so the researcher focus to Guide Performance and Quality Tourism Service To Revisit Intention in Bogor Botanical Gardens. In this research, the researcher used quantitative methode with descriptive verificative. The researcher used 100 respondent for a sample. In this research, the researcher used multiple linier regresion analysis with hypotesis test used determination coefficient test and F test. The classical assumption of this research is used normality test, multicollinearity test, heteroskedastisitas test and auto correlation test. In this research, the Guide Performance and Quality Tourism Service factors has an influence 33,2% of Revisit Intention in Bogor Botanical Garden. Keywords: Guide Performance, Quality Tourism Service and Revisit Intention

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae.

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C Haris Saslis-Lagoudakis

Full Text Available The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae. We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae).

Science.gov (United States)

Saslis-Lagoudakis, C Haris; Klitgaard, Bente B; Forest, Félix; Francis, Louise; Savolainen, Vincent; Williamson, Elizabeth M; Hawkins, Julie A

2011-01-01

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce. In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships. This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into

Revisiting the Political Economy of Communication

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Nicholas Garnham

2014-02-01

The task of the paper and the seminar was to revisit some of Nicholas Garnham’s ideas, writings and contributions to the study of the Political Economy of Communication and to reflect on the concepts, history, current status and perspectives of this field and the broader study of political economy today. The topics covered include Raymond Williams’ cultural materialism, Pierre Bourdieu’s sociology of culture, the debate between Political Economy and Cultural Studies, information society theory, Karl Marx’s theory and the critique of capitalism.

Molecular phylogeny of Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae).

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Wells, J D; Sperling, F A

1999-05-01

Mitochondrial DNA was used to infer the phylogeny and genetic divergences of Chrysomya albiceps (Wiedemann) and C. rufifacies (Maquart) specimens from widely separated localities in the Old and New World. Analyses based on a 2.3-kb region including the genes for cytochrome oxidase subunits I and II indicated that the 2 species were separate monophyletic lineages that have been separated for > 1 million years. Analysis of DNA, in the form of either sequence or restriction fragment-length polymorphism (RFLP) data, will permit the identification of problematic specimens.

What do we know about the phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha)?

DEFF Research Database (Denmark)

Damgaard, Jakob

2012-01-01

The present study summarizes knowledge about phylogenetic relationships of the heteropteran infraorder Gerromorpha. A phylogeny for all families and subfamilies, and for all genera but those assigned to the two most diverse families, Veliidae and Gerridae, is compiled from the many studies by the...

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

Science.gov (United States)

Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

2002-07-01

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Mammals on the EDGE: conservation priorities based on threat and phylogeny.

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Nick J B Isaac

2007-03-01

Full Text Available Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.

The vacuum structure, special relativity theory and quantum mechanics revisited: a field theory-no-geometry approach

International Nuclear Information System (INIS)

Bogolubov, N.N. Jr.; Prykarpatsky, A.K.; Ufuk Taneri

2008-07-01

The main fundamental principles characterizing the vacuum field structure are formulated and the modeling of the related vacuum medium and charged point particle dynamics by means of de- vised field theoretic tools are analyzed. The Maxwell electrodynamic theory is revisited and newly derived from the suggested vacuum field structure principles and the classical special relativity theory relationship between the energy and the corresponding point particle mass is revisited and newly obtained. The Lorentz force expression with respect to arbitrary non-inertial reference frames is revisited and discussed in detail, and some new interpretations of relations between the special relativity theory and quantum mechanics are presented. The famous quantum-mechanical Schroedinger type equations for a relativistic point particle in the external potential and magnetic fields within the quasiclassical approximation as the Planck constant (h/2π) → 0 and the light velocity c → ∞ are obtained. (author)

K Mbugua The Problem of Hell Revisited pp93-103

African Journals Online (AJOL)

K Mbugua

The Problem of Hell Revisited: Towards a Gentler Theology of Hell 93 ... One who, after He has killed, has authority to cast into hell; yes, I tell you, fear. Him! .... Suppose your spouse or parent or child goes to hell and you go to heaven.

The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis

Czech Academy of Sciences Publication Activity Database

Fiala, Ivan

2006-01-01

Roč. 36, č. 14 (2006), s. 1521-1534 ISSN 0020-7519 R&D Projects: GA MŠk LC522 Grant - others:Grantová agentura Jihočeské univerzity(CZ) 58/2002//P-BF Institutional research plan: CEZ:AV0Z60220518 Keywords : Myxosporea * SSU rDNA * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.337, year: 2006

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers.

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Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters' approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

What matters to infrequent customers: a pragmatic approach to understanding perceived value and intention to revisit trendy coffee café.

Science.gov (United States)

Ting, Hiram; Thurasamy, Ramayah

2016-01-01

Notwithstanding the rise of trendy coffee café, little is done to investigate revisit intention towards the café in the context of developing markets. In particular, there is a lack of study which provides theoretical and practical explanation to the perceptions and behaviours of infrequent customers. Hence, the study aims to look into the subject matter by using the theory of reasoned action and social exchange theory as the underpinning basis. The framework proposed by Pine and Gilmore (Strat Leadersh 28:18-23, 2000), which asserts the importance of product quality, service quality and experience quality in a progressive manner, is used to decompose perceived value in the model so as to determine their effects on intention to revisit the café. Given the importance to gain practical insights into revisit intention of infrequent customers, pragmatism stance is assumed. Explanatory sequential mixed-method design is thus adopted whereby qualitative approach is used to confirm and complement quantitative findings. Self-administered questionnaire-based survey is first administered before personal interview is carried out at various cafés. Partial least squares structural equation modelling and content analysis are appropriated successively. In the quantitative findings, although product quality, service quality and experience quality are found to have positive effect on perceived value and revisit intention towards trendy coffee café, experience quality is found to have the greater effect than the others among the infrequent customers. The qualitative findings not only confirm their importance, but most importantly explain the favourable impressions they have at trendy coffee café based on their last in-store experience. While product and service quality might not necessary stimulate them to revisit trendy coffee café, experience quality driven by purposes of visit would likely affect their intention to revisit. As retaining customers is of utmost importance to

Molecular phylogeny of Duvenhage virus

Directory of Open Access Journals (Sweden)

Louis H. Nel

2011-11-01

Full Text Available The Duvenhage virus (DUVV constitutes one of the 11 species in the Lyssavirus genus and causes fatal rabies encephalitis. The virus is associated with insectivorous bat species and three human cases have been reported, all of which were linked to contact with bats. Few of these isolates have been studied and thus little is known about the phylogeny and epidemiology of this lyssavirus. Until 2007, when an isolate was made from the East African country of Kenya, all isolations of this virus had been from southern Africa. This discovery led to many questions regarding the spread and diversity of this lyssavirus. Phylogenetic analysis indicated that the DUVV isolates constitute two different lineages, in which the southern African isolates group together to form one lineage and the more recent isolate from Kenya constitutes a new, second lineage. We found that the new isolate has a genetic variation that has not yet been seen for DUVV. Not only is our lack of knowledge regarding the geographical distribution of this uniquely African virus emphasised, but we have also demonstrated the potential diversity within this genotype.

Radiative corrections to neutrino deep inelastic scattering revisited

International Nuclear Information System (INIS)

Arbuzov, Andrej B.; Bardin, Dmitry Yu.; Kalinovskaya, Lidia V.

2005-01-01

Radiative corrections to neutrino deep inelastic scattering are revisited. One-loop electroweak corrections are re-calculated within the automatic SANC system. Terms with mass singularities are treated including higher order leading logarithmic corrections. Scheme dependence of corrections due to weak interactions is investigated. The results are implemented into the data analysis of the NOMAD experiment. The present theoretical accuracy in description of the process is discussed

Doppler Processing with Ultra-Wideband (UWB) Radar Revisited

Science.gov (United States)

2018-01-01

REPORT TYPE Technical Note 3. DATES COVERED (From - To) December 2017 4. TITLE AND SUBTITLE Doppler Processing with Ultra-Wideband (UWB) Radar...unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT This technical note revisits previous work performed at the US Army Research Laboratory related to...target considered previously is proportional to a delayed version of the transmitted signal, up to a complex constant factor. We write the received

Pipe failure probability - the Thomas paper revisited

International Nuclear Information System (INIS)

Lydell, B.O.Y.

2000-01-01

Almost twenty years ago, in Volume 2 of Reliability Engineering (the predecessor of Reliability Engineering and System Safety), a paper by H. M. Thomas of Rolls Royce and Associates Ltd. presented a generalized approach to the estimation of piping and vessel failure probability. The 'Thomas-approach' used insights from actual failure statistics to calculate the probability of leakage and conditional probability of rupture given leakage. It was intended for practitioners without access to data on the service experience with piping and piping system components. This article revisits the Thomas paper by drawing on insights from development of a new database on piping failures in commercial nuclear power plants worldwide (SKI-PIPE). Partially sponsored by the Swedish Nuclear Power Inspectorate (SKI), the R and D leading up to this note was performed during 1994-1999. Motivated by data requirements of reliability analysis and probabilistic safety assessment (PSA), the new database supports statistical analysis of piping failure data. Against the background of this database development program, the article reviews the applicability of the 'Thomas approach' in applied risk and reliability analysis. It addresses the question whether a new and expanded database on the service experience with piping systems would alter the original piping reliability correlation as suggested by H. M. Thomas

Dynamics of Shape Fluctuations of Quasi-spherical Vesicles Revisited

DEFF Research Database (Denmark)

Miao, L.; Lomholt, Michael Andersen; Kleis, J.

2002-01-01

In this paper, the dynamics of spontaneous shape fluctuations of a single, giant quasi-spherical vesicle formed from a single lipid species is revisited theoretically. A coherent physical theory for the dynamics is developed based on a number of fundamental principles and considerations, and a sy......In this paper, the dynamics of spontaneous shape fluctuations of a single, giant quasi-spherical vesicle formed from a single lipid species is revisited theoretically. A coherent physical theory for the dynamics is developed based on a number of fundamental principles and considerations...... of the phenomenological constants in a canonical continuum description of fluid lipid-bilayer membranes and shown the consequences of this new interpretation in terms of the characteristics of the dynamics of vesicle shape fluctuations. Moreover, we have used the systematic formulation of our theory as a framework...... against which we have discussed the previously existing theories and their discrepancies. Finally, we have made a systematic prediction about the system-dependent characteristics of the relaxation dynamics of shape fluctuations of quasi-spherical vesicles with a view of experimental studies...

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

Czech Academy of Sciences Publication Activity Database

Musilová, Zuzana; Říčan, Oldřich; Janko, Karel; Novák, J.

2008-01-01

Roč. 46, - (2008), s. 659-672 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Grant - others:GA UK(CZ) 182/2004/B-BIO; GA UK(CZ) 139407 Institutional research plan: CEZ:AV0Z50450515 Keywords : molecular phylogeny * Cichlids * south America Subject RIV: EG - Zoology Impact factor: 3.871, year: 2008

Revisiting Constructivist Teaching Methods in Ontario Colleges Preparing for Accreditation

Science.gov (United States)

Schultz, Rachel A.

2015-01-01

At the time of writing, the first community colleges in Ontario were preparing for transition to an accreditation model from an audit system. This paper revisits constructivist literature, arguing that a more pragmatic definition of constructivism effectively blends positivist and interactionist philosophies to achieve both student centred…

Thorbecke Revisited : The Role of Doctrinaire Liberalism in Dutch Politics

NARCIS (Netherlands)

Drentje, Jan

2011-01-01

Thorbecke Revisited: The Role of Doctrinaire Liberalism in Dutch Politics In the political history of the nineteenth century Thorbecke played a crucial role. As the architect of the 1848 liberal constitutional reform he led three cabinets. In many ways he dominated the political discourse during the

The anatomy and ontogeny of the head, neck, pectoral, and upper limb muscles of Lemur catta and Propithecus coquereli (primates): discussion on the parallelism between ontogeny and phylogeny and implications for evolutionary and developmental biology.

Science.gov (United States)

Diogo, Rui; Molnar, Julia L; Smith, Timothy D

2014-08-01

Most anatomical studies of primates focus on skeletal tissues, but muscular anatomy can provide valuable information about phylogeny, functional specializations, and evolution. Herein, we present the first detailed description of the head, neck, pectoral, and upper limb muscles of the fetal lemuriforms Lemur catta (Lemuridae) and Propithecus coquereli (Indriidae). These two species belong to the suborder Strepsirrhini, which is often presumed to possess some plesiomorphic anatomical features within primates. We compare the muscular anatomy of the fetuses with that of infants and adults and discuss the evolutionary and developmental implications. The fetal anatomy reflects a phylogenetically more plesiomorphic condition in nine of the muscles we studied and a more derived condition in only two, supporting a parallel between ontogeny and phylogeny. The derived exceptions concern muscles with additional insertions in the fetus which are lost in adults of the same species, that is, flexor carpi radialis inserts on metacarpal III and levator claviculae inserts on the clavicle. Interestingly, these two muscles are involved in movements of the pectoral girdle and upper limb, which are mainly important for activities in later stages of life, such as locomotion and prey capture, rather than activities in fetal life. Accordingly, our findings suggest that some exceptions to the "ontogeny parallels phylogeny" rule are probably driven more by ontogenetic constraints than by adaptive plasticity. © 2014 Wiley Periodicals, Inc.

Revisiting Cementoblastoma with a Rare Case Presentation

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Vijayanirmala Subramani

2017-01-01

Full Text Available Cementoblastoma is a rare benign odontogenic neoplasm which is characterized by the proliferation of cellular cementum. Diagnosis of cementoblastoma is challenging because of its protracted clinical, radiographic features, and bland histological appearance; most often cementoblastoma is often confused with other cementum and bone originated lesions. The aim of this article is to overview/revisit, approach the diagnosis of cementoblastoma, and also present a unique radiographic appearance of a cementoblastoma lesion associated with an impacted tooth.

Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa.

Science.gov (United States)

Li, Lin-Feng; Häkkinen, Markku; Yuan, Yong-Ming; Hao, Gang; Ge, Xue-Jun

2010-10-01

Musaceae is a small paleotropical family. Three genera have been recognised within this family although the generic delimitations remain controversial. Most species of the family (around 65 species) have been placed under the genus Musa and its infrageneric classification has long been disputed. In this study, we obtained nuclear ribosomal ITS and chloroplast (atpB-rbcL, rps16, and trnL-F) DNA sequences of 36 species (42 accessions of ingroups representing three genera) together with 10 accessions of ingroups retrieved from GenBank database and 4 accessions of outgroups, to construct the phylogeny of the family, with a special reference to the infrageneric classification of the genus Musa. Our phylogenetic analyses elaborated previous results in supporting the monophyly of the family and suggested that Musella and Ensete may be congeneric or at least closely related, but refuted the previous infrageneric classification of Musa. None of the five sections of Musa previously defined based on morphology was recovered as monophyletic group in the molecular phylogeny. Two infrageneric clades were identified, which corresponded well to the basic chromosome numbers of x=11 and 10/9/7, respectively: the former clade comprises species from the sections Musa and Rhodochlamys while the latter contains sections of Callimusa, Australimusa, and Ingentimusa. Copyright 2010 Elsevier Inc. All rights reserved.

DNA variation within Juncaceae: Comparison of impact of organelle regions on phylogeny

Czech Academy of Sciences Publication Activity Database

Záveská Drábková, Lenka; Vlček, Čestmír

2009-01-01

Roč. 278, č. 3 (2009), s. 169-186 ISSN 0378-2697 R&D Projects: GA ČR GP206/07/P147; GA MŠk(CZ) 1M0520 Grant - others:EU(XE) SYNTHESYS DK-TAF 1295; EU(XE) SYNTHESYS GB-TAF 2052 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50520514 Keywords : molecular phylogeny * Juncaceae * mtDNA Subject RIV: EF - Botanics Impact factor: 1.410, year: 2009

Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data

Czech Academy of Sciences Publication Activity Database

Ogden, T. H.; Gattolliat, J. L.; Sartori, M.; Staniczek, A. H.; Soldán, Tomáš; Whiting, M. F.

2009-01-01

Roč. 34, č. 4 (2009), s. 616-634 ISSN 0307-6970 R&D Projects: GA AV ČR 1QS500070505 Institutional research plan: CEZ:AV0Z50070508 Keywords : Ephemeroptera * phylogeny * morfological a molecular data Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.467, year: 2009

Dynamic Topography Revisited

Science.gov (United States)

Moresi, Louis

2015-04-01

Dynamic Topography Revisited Dynamic topography is usually considered to be one of the trinity of contributing causes to the Earth's non-hydrostatic topography along with the long-term elastic strength of the lithosphere and isostatic responses to density anomalies within the lithosphere. Dynamic topography, thought of this way, is what is left over when other sources of support have been eliminated. An alternate and explicit definition of dynamic topography is that deflection of the surface which is attributable to creeping viscous flow. The problem with the first definition of dynamic topography is 1) that the lithosphere is almost certainly a visco-elastic / brittle layer with no absolute boundary between flowing and static regions, and 2) the lithosphere is, a thermal / compositional boundary layer in which some buoyancy is attributable to immutable, intrinsic density variations and some is due to thermal anomalies which are coupled to the flow. In each case, it is difficult to draw a sharp line between each contribution to the overall topography. The second definition of dynamic topography does seem cleaner / more precise but it suffers from the problem that it is not measurable in practice. On the other hand, this approach has resulted in a rich literature concerning the analysis of large scale geoid and topography and the relation to buoyancy and mechanical properties of the Earth [e.g. refs 1,2,3] In convection models with viscous, elastic, brittle rheology and compositional buoyancy, however, it is possible to examine how the surface topography (and geoid) are supported and how different ways of interpreting the "observable" fields introduce different biases. This is what we will do. References (a.k.a. homework) [1] Hager, B. H., R. W. Clayton, M. A. Richards, R. P. Comer, and A. M. Dziewonski (1985), Lower mantle heterogeneity, dynamic topography and the geoid, Nature, 313(6003), 541-545, doi:10.1038/313541a0. [2] Parsons, B., and S. Daly (1983), The

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers

Science.gov (United States)

Thuillard, Marc; Fraix-Burnet, Didier

2015-01-01

This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters’ approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers. PMID:26508826

Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels

Czech Academy of Sciences Publication Activity Database

Liu, H.-Z.; Zhu, Y.-R.; Smith, C.; Reichard, Martin

2006-01-01

Roč. 45, č. 3 (2006), s. 428-434 ISSN 1021-5506 Grant - others:NSFC(CN) 30470237; NSFC(CN) 40432003; Innovation Program of the Chinese Academy of Sciences(CN) KZCX3-SW-126 Institutional research plan: CEZ:AV0Z60930519 Keywords : bitterling * host specificity * coevolution * phylogeny Subject RIV: EG - Zoology Impact factor: 0.943, year: 2006 http://zoolstud.sinica.edu.tw/Journals/45.3/428.pdf

Microsporidia in aquatic microcrustacea: the copepod microsporidium Marssoniella elegans Lemmermann, 1900 revisited

Czech Academy of Sciences Publication Activity Database

Vávra, Jiří; Hyliš, M.; Oborník, Miroslav; Vossbrinck, C. R.

2005-01-01

Roč. 52, 1/2 (2005), s. 163-172 ISSN 0015-5683 Institutional research plan: CEZ:AV0Z60220518 Keywords : Microsporidia * Marssoniella elegans * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.138, year: 2005

The role of glycans in immune evasion: the human fetoembryonic defence system hypothesis revisited.

Science.gov (United States)

Clark, Gary F

2014-03-01

Emerging data suggest that mechanisms to evade the human immune system may be shared by the conceptus, tumour cells, persistent pathogens and viruses. It is therefore timely to revisit the human fetoembryonic defense system (Hu-FEDS) hypothesis that was proposed in two papers in the 1990s. The initial paper suggested that glycoconjugates expressed in the human reproductive system inhibited immune responses directed against gametes and the developing human by employing their carbohydrate sequences as functional groups. These glycoconjugates were proposed to block specific binding interactions and interact with lectins linked to signal transduction pathways that modulated immune cell functions. The second article suggested that aggressive tumour cells and persistent pathogens (HIV, H. pylori, schistosomes) either mimicked or acquired the same carbohydrate functional groups employed in this system to evade immune responses. This subterfuge enabled these pathogens and tumour cells to couple their survival to the human reproductive imperative. The Hu-FEDS model has been repeatedly tested since its inception. Data relevant to this model have also been obtained in other studies. Herein, the Hu-FEDS hypothesis is revisited in the context of these more recent findings. Far more supportive evidence for this model now exists than when it was first proposed, and many of the original predictions have been validated. This type of subterfuge by pathogens and tumour cells likely applies to all sexually reproducing metazoans that must protect their gametes from immune responses. Intervention in these pathological states will likely remain problematic until this system of immune evasion is fully understood and appreciated.

Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

Science.gov (United States)

Li, Pengbo; Liu, Fang; Wang, Yumei; Xu, Qin; Shang, Mingzhao; Zhou, Zhongli; Cai, Xiaoyan; Wang, Xingxing; Wendel, Jonathan F.; Wang, Kunbo

2016-01-01

The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium. PMID:27309527

Increased 30-Day Emergency Department Revisits Among Homeless Patients with Mental Health Conditions

Directory of Open Access Journals (Sweden)

Chun Nok Lam

2016-09-01

Full Text Available Introduction: Patients with mental health conditions frequently use emergency medical services. Many suffer from substance use and homelessness. If they use the emergency department (ED as their primary source of care, potentially preventable frequent ED revisits and hospital readmissions can worsen an already crowded healthcare system. However, the magnitude to which homelessness affects health service utilization among patients with mental health conditions remains unclear in the medical community. This study assessed the impact of homelessness on 30-day ED revisits and hospital readmissions among patients presenting with mental health conditions in an urban, safety-net hospital. Methods: We conducted a secondary analysis of administrative data on all adult ED visits in 2012 in an urban safety-net hospital. Patient demographics, mental health status, homelessness, insurance coverage, level of acuity, and ED disposition per ED visit were analyzed using multilevel modeling to control for multiple visits nested within patients. We performed multivariate logistic regressions to evaluate if homelessness moderated the likelihood of mental health patients’ 30-day ED revisits and hospital readmissions. Results: Study included 139,414 adult ED visits from 92,307 unique patients (43.5±15.1 years, 51.3% male, 68.2% Hispanic/Latino. Nearly 8% of patients presented with mental health conditions, while 4.6% were homeless at any time during the study period. Among patients with mental health conditions, being homeless contributed to an additional 28.0% increase in likelihood (4.28 to 5.48 odds of 30-day ED revisits and 38.2% increase in likelihood (2.04 to 2.82 odds of hospital readmission, compared to non-homeless, non-mental health (NHNM patients as the base category. Adjusted predicted probabilities showed that homeless patients presenting with mental health conditions have a 31.1% chance of returning to the ED within 30-day post discharge and a 3

Coloration mechanisms and phylogeny of Morpho butterflies.

Science.gov (United States)

Giraldo, M A; Yoshioka, S; Liu, C; Stavenga, D G

2016-12-15

Morpho butterflies are universally admired for their iridescent blue coloration, which is due to nanostructured wing scales. We performed a comparative study on the coloration of 16 Morpho species, investigating the morphological, spectral and spatial scattering properties of the differently organized wing scales. In numerous previous studies, the bright blue Morpho coloration has been fully attributed to the multi-layered ridges of the cover scales' upper laminae, but we found that the lower laminae of the cover and ground scales play an important additional role, by acting as optical thin film reflectors. We conclude that Morpho coloration is a subtle combination of overlapping pigmented and/or unpigmented scales, multilayer systems, optical thin films and sometimes undulated scale surfaces. Based on the scales' architecture and their organization, five main groups can be distinguished within the genus Morpho, largely agreeing with the accepted phylogeny. © 2016. Published by The Company of Biologists Ltd.

Phylogeny of Gobioidei and the origin of European gobies

Directory of Open Access Journals (Sweden)

Ainhoa Agorreta

2015-11-01

Full Text Available The percomorph order Gobioidei comprises over 2200 species worldwide distributed that occupy most freshwater, brackish and marine environments, and show a spectacular variety in morphology, ecology, and behaviour. However, phylogenetic relationships among many gobioid groups still remain poorly understood. Such is the case of Gobiidae, a rapidly radiating lineage that encompass an unusually high diversity of species (nearly 2000, including the largely endemic European species whose origin and ancestry remain uncertain. The resolution and accuracy of previous molecular phylogenetic studies has been limited due to the use of only a few (generally mitochondrial molecular markers and/or the absence of representatives of several key lineages. Our study (built on Agorreta et al. 2013 is the first to include multiple nuclear and mitochondrial genes for nearly 300 terminal taxa representing the vast diversity of gobioid lineages. We have used this information to reconstruct a robust phylogeny of Gobioidei, and we are now investigating the historical biogeography and diversification times of European gobies with a time-calibrated molecular phylogeny. Robustness of the inferred phylogenetic trees is significantly higher than that of previous studies, hence providing the most compelling molecular phylogenetic hypotheses for Gobioidei thus far. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade followed by the Butidae as the sister-group of the Gobiidae. Several monophyletic groups are identified within the two major Gobiidae subclades, the gobionelline-like and the gobiine-like gobiids. The European gobies cluster in three distinct lineages (Pomatoschistus-, Aphia-, and Gobius-lineages, each with different affinities with gobiids from the Indo-Pacific and perhaps the New World. Our ongoing more-detailed study on European gobies will reveal whether their origin is related to vicariant events linked to the

Novel intron markers to study the phylogeny of closely related mammalian species

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Castresana Jose

2010-11-01

Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae)

Czech Academy of Sciences Publication Activity Database

Fehrer, Judith; Gemeinholzer, B.; Chrtek, Jindřich; Bräutigam, S.

2007-01-01

Roč. 42, - (2007), s. 347-361 ISSN 1055-7903 R&D Projects: GA MŽP SE/610/3/00 Institutional research plan: CEZ:AV0Z60050516 Keywords : molecular phylogeny * Hieracium * chloroplast capture Subject RIV: EF - Botanics Impact factor: 3.994, year: 2007

Blastocystis phylogeny among various isolates from humans to insects.

Science.gov (United States)

Yoshikawa, Hisao; Koyama, Yukiko; Tsuchiya, Erika; Takami, Kazutoshi

2016-12-01

Blastocystis is a common unicellular eukaryotic parasite found not only in humans, but also in various kinds of animal species worldwide. Since Blastocystis isolates are morphologically indistinguishable, many molecular biological approaches have been applied to classify these isolates. The complete or partial sequences of the small subunit rRNA gene (SSU rDNA) are mainly used for comparisons and phylogenetic analyses among Blastocystis isolates. However, various lengths of the partial SSU rDNA sequence have been used for phylogenetic inference among genetically different isolates. Based on the complete SSU rDNA sequences, consensus terminology of nine subtypes (STs) of Blastocystis sp. that were supported by phylogenetically monophyletic nine clades was proposed in 2007. Thereafter, eight additional kinds of STs comprising non-human mammalian Blastocystis isolates have been reported based on the phylogeny of SSU rDNA sequences, while STs 11 and 12 were only proposed on the base of partial sequences. Although many sequence data from mammalian and avian Blastocystis are registered in GenBank, only limited data on SSU rDNA are available for poikilotherm-derived Blastocystis isolates. Therefore, the phylogenetic positions of the reptilian/amphibian Blastocystis clades are unstable. The phylogenetic inference of various STs comprising mammalian and/or avian Blastocystis isolates was verified herein based on comparisons between partial and complete SSU rDNA sequences, and the phylogenetic positions of reptilian and amphibian Blastocystis isolates were also investigated using 14 new Blastocystis isolates from reptiles with all known isolates from other reptilians, amphibians, and insects registered in GenBank. Copyright © 2016. Published by Elsevier Ireland Ltd.

Slowdowns in diversification rates from real phylogenies may not be real.

Science.gov (United States)

Cusimano, Natalie; Renner, Susanne S

2010-07-01

Studies of diversification patterns often find a slowing in lineage accumulation toward the present. This seemingly pervasive pattern of rate downturns has been taken as evidence for adaptive radiations, density-dependent regulation, and metacommunity species interactions. The significance of rate downturns is evaluated with statistical tests (the gamma statistic and Monte Carlo constant rates (MCCR) test; birth-death likelihood models and Akaike Information Criterion [AIC] scores) that rely on null distributions, which assume that the included species are a random sample of the entire clade. Sampling in real phylogenies, however, often is nonrandom because systematists try to include early-diverging species or representatives of previous intrataxon classifications. We studied the effects of biased sampling, structured sampling, and random sampling by experimentally pruning simulated trees (60 and 150 species) as well as a completely sampled empirical tree (58 species) and then applying the gamma statistic/MCCR test and birth-death likelihood models/AIC scores to assess rate changes. For trees with random species sampling, the true model (i.e., the one fitting the complete phylogenies) could be inferred in most cases. Oversampling deep nodes, however, strongly biases inferences toward downturns, with simulations of structured and biased sampling suggesting that this occurs when sampling percentages drop below 80%. The magnitude of the effect and the sensitivity of diversification rate models is such that a useful rule of thumb may be not to infer rate downturns from real trees unless they have >80% species sampling.

Surface tension in soap films: revisiting a classic demonstration

International Nuclear Information System (INIS)

Behroozi, F

2010-01-01

We revisit a classic demonstration for surface tension in soap films and introduce a more striking variation of it. The demonstration shows how the film, pulling uniformly and normally on a loose string, transforms it into a circular arc under tension. The relationship between the surface tension and the string tension is analysed and presented in a useful graphical form. (letters and comments)

The Neutrosophic Logic View to Schrodinger's Cat Paradox, Revisited

Directory of Open Access Journals (Sweden)

Florentin Smarandache

2008-07-01

Full Text Available The present article discusses Neutrosophic logic view to Schrodinger's cat paradox. We argue that this paradox involves some degree of indeterminacy (unknown which Neutrosophic logic can take into consideration, whereas other methods including Fuzzy logic cannot. To make this proposition clear, we revisit our previous paper by offering an illustration using modified coin tossing problem, known as Parrondo's game.

Surface tension in soap films: revisiting a classic demonstration

Energy Technology Data Exchange (ETDEWEB)

Behroozi, F [Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614 (United States)], E-mail: behroozi@uni.edu

2010-01-15

We revisit a classic demonstration for surface tension in soap films and introduce a more striking variation of it. The demonstration shows how the film, pulling uniformly and normally on a loose string, transforms it into a circular arc under tension. The relationship between the surface tension and the string tension is analysed and presented in a useful graphical form. (letters and comments)

Revisiting the quantum harmonic oscillator via unilateral Fourier transforms

International Nuclear Information System (INIS)

Nogueira, Pedro H F; Castro, Antonio S de

2016-01-01

The literature on the exponential Fourier approach to the one-dimensional quantum harmonic oscillator problem is revised and criticized. It is shown that the solution of this problem has been built on faulty premises. The problem is revisited via the Fourier sine and cosine transform method and the stationary states are properly determined by requiring definite parity and square-integrable eigenfunctions. (paper)

Transport benchmarks for one-dimensional binary Markovian mixtures revisited

International Nuclear Information System (INIS)

Malvagi, F.

2013-01-01

The classic benchmarks for transport through a binary Markovian mixture are revisited to look at the probability distribution function of the chosen 'results': reflection, transmission and scalar flux. We argue that the knowledge of the ensemble averaged results is not sufficient for reliable predictions: a measure of the dispersion must also be obtained. An algorithm to estimate this dispersion is tested. (author)

Resolution of Reflection Seismic Data Revisited

DEFF Research Database (Denmark)

Hansen, Thomas Mejer; Mosegaard, Klaus; Zunino, Andrea

The Rayleigh Principle states that the minimum separation between two reflectors that allows them to be visually separated is the separation where the wavelet maxima from the two superimposed reflections combine into one maximum. This happens around Δtres = λb/8, where λb is the predominant...... lower vertical resolution of reflection seismic data. In the following we will revisit think layer model and demonstrate that there is in practice no limit to the vertical resolution using the parameterization of Widess (1973), and that the vertical resolution is limited by the noise in the data...

Spider mite (Acari: Tetranychidae) mitochondrial COI phylogeny reviewed: host plant relationships, phylogeography, reproductive parasites and barcoding

NARCIS (Netherlands)

Ros, V.I.D.; Breeuwer, J.A.J.

2007-01-01

The past 15 years have witnessed a number of molecular studies that aimed to resolve issues of species delineation and phylogeny of mites in the family Tetranychidae. The central part of the mitochondrial COI region has frequently been used for investigating intra- and interspecific variation. All

Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes.

Science.gov (United States)

Höhna, Sebastian

2013-06-01

Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth-death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit. In the present article, I consider as the model a global time-dependent birth-death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth-death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae). The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/). Supplementary data are available at Bioinformatics online.

Correlating molecular phylogeny with venom apparatus occurrence in Panamic auger snails (Terebridae.

Directory of Open Access Journals (Sweden)

Mandë Holford

2009-11-01

Full Text Available Central to the discovery of neuroactive compounds produced by predatory marine snails of the superfamily Conoidea (cone snails, terebrids, and turrids is identifying those species with a venom apparatus. Previous analyses of western Pacific terebrid specimens has shown that some Terebridae groups have secondarily lost their venom apparatus. In order to efficiently characterize terebrid toxins, it is essential to devise a key for identifying which species have a venom apparatus. The findings presented here integrate molecular phylogeny and the evolution of character traits to infer the presence or absence of the venom apparatus in the Terebridae. Using a combined dataset of 156 western and 33 eastern Pacific terebrid samples, a phylogenetic tree was constructed based on analyses of 16S, COI and 12S mitochondrial genes. The 33 eastern Pacific specimens analyzed represent four different species: Acus strigatus, Terebra argyosia, T. ornata, and T. cf. formosa. Anatomical analysis was congruent with molecular characters, confirming that species included in the clade Acus do not have a venom apparatus, while those in the clade Terebra do. Discovery of the association between terebrid molecular phylogeny and the occurrence of a venom apparatus provides a useful tool for effectively identifying the terebrid lineages that may be investigated for novel pharmacological active neurotoxins, enhancing conservation of this important resource, while providing supplementary information towards understanding terebrid evolutionary diversification.

Morphology, morphogenesis, and phylogeny of an Anteholosticha intermedia (Ciliophora, Urostylida) population from the United States.

Science.gov (United States)

Chen, Lingyun; Wu, Weining; El-Serehy, Hamed A; Hu, Xiaozhong; Clamp, John C

2018-04-30

A distinct population of Anteholosticha intermedia was isolated from soil in the Great Smoky Mountains of North Carolina, USA, and its morphology, morphogenesis and molecular phylogeny investigated by microscopic observations of live and protargol-prepared specimens and analyses of the sequence of small subunit (SSU) rDNA. Our population closely resembles the populations from Austria and Korea. Members of the genus Anteholosticha have been regarded as ontogenetically diverse, which is confirmed by the present work. The most noteworthy ontogenetic feature of the American population of A. intermedia is that the oral primordium in the proter appears apokinetally at the posterior end of the undulating membranes anlage at the beginning of division and then dedifferentiates midway through morphogenesis. Molecular phylogenetic analyses demonstrate, with high support, that the American population of A. intermedia is clearly distinct from congeners and branches as part of a sister lineage to the Bakuella-Urostyla clade that belongs to the major clade comprising the order Urostylida. Copyright © 2018 Elsevier GmbH. All rights reserved.

The Effects of Korean Medical Service Quality and Satisfaction on Revisit Intention of the United Arab Emirates Government Sponsored Patients

Directory of Open Access Journals (Sweden)

Seoyoung Lee, RN, MSN

2017-06-01

Conclusions: There are needs for physicians to communicate with patients while ensuring sufficient consultation time based on excellent medical skills and nurses to respond immediately for the patients' needs through an empathic encounter in order to improve medical service quality and patient satisfaction so that to increase the revisit intention of the United Arab Emirates government sponsored patients. Further, it is necessary for the hospitals to have support plans for providing country specialized services in consideration of the UAE culture to ensure that physicians' and nurses' competencies are not undervalued by non-medical service elements such as interpreters and meals.

Sloan Digital Sky Survey Photometric Calibration Revisited

International Nuclear Information System (INIS)

Marriner, John

2012-01-01

The Sloan Digital Sky Survey calibration is revisited to obtain the most accurate photometric calibration. A small but significant error is found in the flat-fielding of the Photometric telescope used for calibration. Two SDSS star catalogs are compared and the average difference in magnitude as a function of right ascension and declination exhibits small systematic errors in relative calibration. The photometric transformation from the SDSS Photometric Telescope to the 2.5 m telescope is recomputed and compared to synthetic magnitudes computed from measured filter bandpasses.

REVISITING A CLASSIC: THE PARKER–MOFFATT PROBLEM

International Nuclear Information System (INIS)

Pezzi, O.; Servidio, S.; Valentini, F.; Malara, F.; Veltri, P.; Parashar, T. N.; Yang, Y.; Matthaeus, W. H.; Vásconez, C. L.

2017-01-01

The interaction of two colliding Alfvén wave packets is described here by means of magnetohydrodynamics (MHD) and hybrid kinetic numerical simulations. The MHD evolution revisits the theoretical insights described by Moffatt, Parker, Kraichnan, Chandrasekhar, and Elsässer in which the oppositely propagating large-amplitude wave packets interact for a finite time, initiating turbulence. However, the extension to include compressive and kinetic effects, while maintaining the gross characteristics of the simpler classic formulation, also reveals intriguing features that go beyond the pure MHD treatment.

REVISITING A CLASSIC: THE PARKER–MOFFATT PROBLEM

Energy Technology Data Exchange (ETDEWEB)

Pezzi, O.; Servidio, S.; Valentini, F.; Malara, F.; Veltri, P. [Dipartimento di Fisica, Università della Calabria, 87036 Rende (CS) (Italy); Parashar, T. N.; Yang, Y.; Matthaeus, W. H. [Department of Physics and Astronomy, University of Delaware, DE 19716 (United States); Vásconez, C. L. [Departamento de Física, Escuela Politécnica Nacional, Quito (Ecuador)

2017-01-10

The interaction of two colliding Alfvén wave packets is described here by means of magnetohydrodynamics (MHD) and hybrid kinetic numerical simulations. The MHD evolution revisits the theoretical insights described by Moffatt, Parker, Kraichnan, Chandrasekhar, and Elsässer in which the oppositely propagating large-amplitude wave packets interact for a finite time, initiating turbulence. However, the extension to include compressive and kinetic effects, while maintaining the gross characteristics of the simpler classic formulation, also reveals intriguing features that go beyond the pure MHD treatment.

Sloan Digital Sky Survey Photometric Calibration Revisited

Energy Technology Data Exchange (ETDEWEB)

Marriner, John; /Fermilab

2012-06-29

The Sloan Digital Sky Survey calibration is revisited to obtain the most accurate photometric calibration. A small but significant error is found in the flat-fielding of the Photometric telescope used for calibration. Two SDSS star catalogs are compared and the average difference in magnitude as a function of right ascension and declination exhibits small systematic errors in relative calibration. The photometric transformation from the SDSS Photometric Telescope to the 2.5 m telescope is recomputed and compared to synthetic magnitudes computed from measured filter bandpasses.

18S rDNA phylogeny of lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa.

Directory of Open Access Journals (Sweden)

Anna Maria Fiore-Donno

Full Text Available The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (~600 bases of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species.

A mitogenomic re-evaluation of the bdelloid phylogeny and relationships among the Syndermata.

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Erica Lasek-Nesselquist

Full Text Available Molecular and morphological data regarding the relationships among the three classes of Rotifera (Bdelloidea, Seisonidea, and Monogononta and the phylum Acanthocephala are inconclusive. In particular, Bdelloidea lacks molecular-based phylogenetic appraisal. I obtained coding sequences from the mitochondrial genomes of twelve bdelloids and two monogononts to explore the molecular phylogeny of Bdelloidea and provide insight into the relationships among lineages of Syndermata (Rotifera + Acanthocephala. With additional sequences taken from previously published mitochondrial genomes, the total dataset included nine species of bdelloids, three species of monogononts, and two species of acanthocephalans. A supermatrix of these 10-12 mitochondrial proteins consistently recovered a bdelloid phylogeny that questions the validity of a generally accepted classification scheme despite different methods of inference and various parameter adjustments. Specifically, results showed that neither the family Philodinidae nor the order Philodinida are monophyletic as currently defined. The application of a similar analytical strategy to assess syndermate relationships recovered either a tree with Bdelloidea and Monogononta as sister taxa (Eurotatoria or Bdelloidea and Acanthocephala as sister taxa (Lemniscea. Both outgroup choice and method of inference affected the topological outcome emphasizing the need for sequences from more closely related outgroups and more sophisticated methods of analysis that can account for the complexity of the data.

Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding.

Science.gov (United States)

Liu, Jun; Li, Qi; Kong, Lingfeng; Yu, Hong; Zheng, Xiaodong

2011-09-01

Oysters (family Ostreidae), with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. As a useful tool for molecular species identification, DNA barcoding might offer significant potential for oyster identification and taxonomy. This study used two mitochondrial fragments, cytochrome c oxidase I (COI) and the large ribosomal subunit (16S rDNA), to assess whether oyster species could be identified by phylogeny and distance-based DNA barcoding techniques. Relationships among species were estimated by the phylogenetic analyses of both genes, and then pairwise inter- and intraspecific genetic divergences were assessed. Species forming well-differentiated clades in the molecular phylogenies were identical for both genes even when the closely related species were included. Intraspecific variability of 16S rDNA overlapped with interspecific divergence. However, average intra- and interspecific genetic divergences for COI were 0-1.4% (maximum 2.2%) and 2.6-32.2% (minimum 2.2%), respectively, indicating the existence of a barcoding gap. These results confirm the efficacy of species identification in oysters via DNA barcodes and phylogenetic analysis. © 2011 Blackwell Publishing Ltd.

Revisiting deforestation in Africa (1990–2010): One more lost ...

African Journals Online (AJOL)

This spotlight revisits the dynamics and prognosis outlined in the late 1980's published in Déforestation en Afrique. This book on deforestation in Africa utilized available statistical data from the 1980's and was a pioneering self - styled attempt to provide a holistic viewpoint of the ongoing trends pertaining to deforestation in ...

Revisiting Individual Creativity Assessment: Triangulation in Subjective and Objective Assessment Methods

Science.gov (United States)

Park, Namgyoo K.; Chun, Monica Youngshin; Lee, Jinju

2016-01-01

Compared to the significant development of creativity studies, individual creativity research has not reached a meaningful consensus regarding the most valid and reliable method for assessing individual creativity. This study revisited 2 of the most popular methods for assessing individual creativity: subjective and objective methods. This study…

Are characiform fishes Gondwanan in origin? Insights from a time-scaled molecular phylogeny of the Citharinoidei (Ostariophysi: Characiformes.

Directory of Open Access Journals (Sweden)

Jairo Arroyave

Full Text Available Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary

Data supporting a molecular phylogeny of the hyper-diverse genus Brueelia

Directory of Open Access Journals (Sweden)

Sarah E. Bush

2015-12-01

Full Text Available Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015 [1]. Presented data include the voucher information and molecular data (GenBank accession numbers of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequences for Brueelia-complex species and outgroup taxa.

Logistics Innovation Process Revisited

DEFF Research Database (Denmark)

Gammelgaard, Britta; Su, Shong-Iee Ivan; Yang, Su-Lan

2011-01-01

Purpose – The purpose of this paper is to learn more about logistics innovation processes and their implications for the focal organization as well as the supply chain, especially suppliers. Design/methodology/approach – The empirical basis of the study is a longitudinal action research project...... that was triggered by the practical needs of new ways of handling material flows of a hospital. This approach made it possible to revisit theory on logistics innovation process. Findings – Apart from the tangible benefits reported to the case hospital, five findings can be extracted from this study: the logistics...... innovation process model may include not just customers but also suppliers; logistics innovation in buyer-supplier relations may serve as an alternative to outsourcing; logistics innovation processes are dynamic and may improve supplier partnerships; logistics innovations in the supply chain are as dependent...

Life quality index revisited

DEFF Research Database (Denmark)

Ditlevsen, Ove Dalager

2004-01-01

The derivation of the life quality index (LQI) is revisited for a revision. This revision takes into account the unpaid but necessary work time needed to stay alive in clean and healthy conditions to be fit for effective wealth producing work and to enjoyable free time. Dimension analysis...... at birth should not vary between countries. Finally the distributional assumptions are relaxed as compared to the assumptions made in an earlier work by the author. These assumptions concern the calculation of the life expectancy change due to the removal of an accident source. Moreover a simple public...... consistency problems with the standard power function expression of the LQI are pointed out. It is emphasized that the combination coefficient in the convex differential combination between the relative differential of the gross domestic product per capita and the relative differential of the expected life...

Revisiting support policies for RES-E adulthood: Towards market compatible schemes

International Nuclear Information System (INIS)

Huntington, Samuel C.; Rodilla, Pablo; Herrero, Ignacio; Batlle, Carlos

2017-01-01

The past two decades of growth in renewable energy sources of electricity (RES-E) have been largely driven by out-of-market support policies. These schemes were designed to drive deployment on the basis of specific subsidies sustained in time to allow for the larger costs as well as to limit investor risk. While these policies have proven to be effective, the way they have been designed to date has led to costly market distortions that are becoming more difficult to ignore as penetrations reach unpreceded levels. In the context of this growing concern, we provide a critical analysis of the design elements of RES-E support schemes, focusing on how they affect this trade-off between promoting and efficiently integrating RES-E. The emphasis is on the structure of the incentive payment, which in the end turns to be the cornerstone for an efficient integration. We conclude that, while needed, a well-designed and further developed capacity-based support mechanism complemented with ex-post compensations defined for reference benchmark plants, such as the mechanism currently implemented in Spain, is an alternative with good properties if the major goal is truly market integration. The approach is robust to future developments in technology cost, performance and market penetration of RES-E. - Highlights: • Market distortions due to RES support mechanisms are becoming difficult to ignore. • This paper provides a critical analysis of the design elements of RES support schemes. • The emphasis is on the structure of the incentive, key for an efficient integration. • We argue in favor of a further developed capacity-based support mechanism. • The incentive should be combined with the design of a set of reference plants.

Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley, (1975) 1976 ssrDNA

Czech Academy of Sciences Publication Activity Database

Šlapeta, Jan Roger; Kyselová, Iveta; Richardson, A. O.; Modrý, David; Lukeš, Julius

2002-01-01

Roč. 88, č. 9 (2002), s. 810-815 ISSN 0932-0113 R&D Projects: GA ČR GA524/00/P015; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Sarcocystis * phylogeny * ssrDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.046, year: 2002

Growth trajectories in the cave bear and its extant relatives: an examination of ontogenetic patterns in phylogeny.

Science.gov (United States)

Fuchs, Manuela; Geiger, Madeleine; Stange, Madlen; Sánchez-Villagra, Marcelo R

2015-11-02

The study of postnatal ontogeny can provide insights into evolution by offering an understanding of how growth trajectories have evolved resulting in adult morphological disparity. The Ursus lineage is a good subject for studying cranial and mandibular shape and size variation in relation to postnatal ontogeny and phylogeny because it is at the same time not diverse but the species exhibit different feeding ecologies. Cranial and mandibular shapes of Ursus arctos (brown bear), U. maritimus (polar bear), U. americanus (American black bear), and the extinct U. spelaeus (cave bear) were examined, using a three-dimensional geometric morphometric approach. Additionally, ontogenetic series of crania and mandibles of U. arctos and U. spelaeus ranging from newborns to senile age were sampled. The distribution of specimens in morphospace allowed to distinguish species and age classes and the ontogenetic trajectories U. arctos and U. spelaeus were found to be more similar than expected by chance. Cranial shape changes during ontogeny are largely size related whereas the evolution of cranial shape disparity in this clade appears to be more influenced by dietary adaptation than by size and phylogeny. The different feeding ecologies are reflected in different cranial and mandibular shapes among species. The cranial and mandibular shape disparity in the Ursus lineage appears to be more influenced by adaptation to diet than by size or phylogeny. In contrast, the cranial and mandibular shape changes during postnatal ontogeny in U. arctos and U. spelaeus are probably largely size related. The patterns of morphospace occupation of the cranium and the mandible in adults and through ontogeny are different.

Rereading Albert B. Lord's The Singer of Tales . Revisiting the ...

African Journals Online (AJOL)

Access to a fresh set of video-recordings of Sesotho praise-poetry made in the year 2000 enabled the author to revisit his adaptation of Albert Lord's definition of the formula as a dynamic compositional device that the oral poet utilizes during delivery. The basic adaptation made in 1983 pertains to heroic praises (dithoko tsa ...

Re-Visit to the School Nurse and Adolescents' Medicine Use

Science.gov (United States)

Borup, Ina K.; Andersen, Anette; Holstein, Bjorn E.

2011-01-01

Objective: To examine if students who re-visit the school nurse use medicines differently than other students when exposed to aches and psychological problems. Methods: The study includes all 11-, 13- and 15-year-old students from a random sample of schools in Denmark, response rate 87 per cent, n = 5,205. The data collection followed the…

The relative roles of local climate adaptation and phylogeny in determining leaf-out timing of temperate tree species

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Elsa Desnoues

2017-12-01

Full Text Available Background Leaf out times of temperate forest trees are a prominent determinant of global carbon dynamics throughout the year. Abiotic cues of leaf emergence are well studied but investigation of the relative roles of shared evolutionary history (phylogeny and local adaptation to climate in determining the species-level responses to these cues is needed to better apprehend the effect of global change on leaf emergence. We explored the relative importance of phylogeny and climate in determining the innate leaf out phenology across the temperate biome. Methods We used an extensive dataset of leaf-out dates of 1126 temperate woody species grown in eight Northern Hemisphere common gardens. For these species, information on the native climate and phylogenetic position was collected. Using linear regression analyses, we examine the relative effect of climate variables and phylogeny on leaf out variation among species. Results Climate variables explained twice as much variation in leaf out timing as phylogenetic information, a process that was driven primarily by the complex interactive effects of multiple climate variables. Although the primary climate factors explaining species-level variation in leaf-out timing varied drastically across different families, our analyses reveal that local adaptation plays a stronger role than common evolutionary history in determining tree phenology across the temperate biome. Conclusions In the long-term, the direct effects of physiological adaptation to abiotic effects of climate change on forest phenology are likely to outweigh the indirect effects mediated through changes in tree species composition.

Molecular phylogeny of the Oriental butterfly genus Arhopala (Lycaenidae, Theclinae) inferred from mitochondrial and nuclear genes

NARCIS (Netherlands)

Megens, H.J.W.C.; Nes, Van W.J.; Moorsel, van C.H.M.; Pierce, N.E.; Jong, de R.

2004-01-01

We present a phylogeny for a selection of species of the butterfly genus Arhopala Boisduval, 1832 based on molecular characters. We sequenced 1778 bases of the mitochondrial genes Cytochrome Oxidase 1 and 2 including tRNALeu, and a 393-bp fragment of the nuclear wingless gene for a total of 42

An analytic algorithm for global coverage of the revisiting orbit and its application to the CFOSAT satellite

Science.gov (United States)

Xu, Ming; Huang, Li

2014-08-01

This paper addresses a new analytic algorithm for global coverage of the revisiting orbit and its application to the mission revisiting the Earth within long periods of time, such as Chinese-French Oceanic Satellite (abbr., CFOSAT). In the first, it is presented that the traditional design methodology of the revisiting orbit for some imaging satellites only on the single (ascending or descending) pass, and the repeating orbit is employed to perform the global coverage within short periods of time. However, the selection of the repeating orbit is essentially to yield the suboptimum from the rare measure of rational numbers of passes per day, which will lose lots of available revisiting orbits. Thus, an innovative design scheme is proposed to check both rational and irrational passes per day to acquire the relationship between the coverage percentage and the altitude. To improve the traditional imaging only on the single pass, the proposed algorithm is mapping every pass into its ascending and descending nodes on the specified latitude circle, and then is accumulating the projected width on the circle by the field of view of the satellite. The ergodic geometry of coverage percentage produced from the algorithm is affecting the final scheme, such as the optimal one owning the largest percentage, and the balance one possessing the less gradient in its vicinity, and is guiding to heuristic design for the station-keeping control strategies. The application of CFOSAT validates the feasibility of the algorithm.

The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?

Science.gov (United States)

Murray, Gemma G. R.; Weinert, Lucy A.; Rhule, Emma L.; Welch, John J.

2016-01-01

Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives. PMID:26559010

New insights into the systematics and phylogeny of the genus Jattaea and similar fungi of the Calosphaeriales

Czech Academy of Sciences Publication Activity Database

Réblová, Martina

2011-01-01

Roč. 49, č. 1 (2011), s. 167-198 ISSN 1560-2745 R&D Projects: GA ČR GA206/09/0547 Institutional research plan: CEZ:AV0Z60050516 Keywords : Wegelina * Calosphaeria * phylogeny Subject RIV: EF - Botanics Impact factor: 4.769, year: 2011

Revisiting the roles and responsibilities of speech-language therapists in South African schools.

Science.gov (United States)

Wium, A M; Louw, B

2013-12-01

The role of speech-language therapists (SLTs) in schools in South Africa needs to be revisited based on the changing educational needs in the country. This article builds on a paper by Kathard et al. (2011), which discussed the changing needs of the country with regard to the role of SLTs working in schools. South African policy changes indicated a shift from supporting the child to supporting the teacher, but also place more emphasis on the support of all learners in literacy in an effort to address past inequities. This paper addresses several of the questions that emerged from Kathard et al. and explores the collaborative roles played by SLTs on four levels in the education context. Collaboration at the learner level (level 1) focuses on prevention and support, whereas collaboration at the teacher level (level 2) is described in terms of training, mentoring, monitoring and consultation. Collaboration can also occur at the district level (level 3), where the focus is mainly on the development and implementation of support programmes for teachers in areas of literacy and numeracy. Collaboration at the level of national and provincial education (level 4) is key to all other roles, as it impacts on policy. This last level is the platform to advocate for the employment of SLTs in schools. Such new roles and responsibilities have important implications for the preparation of future SLTs. Suggestions for curricular review and professional development are discussed. It is proposed that SASLHA responds to the changes by developing a position statement on the roles and responsibilities of SLTs in schools.

Phylogeny is a powerful tool for predicting plant biomass responses to nitrogen enrichment.

Science.gov (United States)

Wooliver, Rachel C; Marion, Zachary H; Peterson, Christopher R; Potts, Brad M; Senior, John K; Bailey, Joseph K; Schweitzer, Jennifer A

2017-08-01

Increasing rates of anthropogenic nitrogen (N) enrichment to soils often lead to the dominance of nitrophilic plant species and reduce plant diversity in natural ecosystems. Yet, we lack a framework to predict which species will be winners or losers in soil N enrichment scenarios, a framework that current literature suggests should integrate plant phylogeny, functional tradeoffs, and nutrient co-limitation. Using a controlled fertilization experiment, we quantified biomass responses to N enrichment for 23 forest tree species within the genus Eucalyptus that are native to Tasmania, Australia. Based on previous work with these species' responses to global change factors and theory on the evolution of plant resource-use strategies, we hypothesized that (1) growth responses to N enrichment are phylogenetically structured, (2) species with more resource-acquisitive functional traits have greater growth responses to N enrichment, and (3) phosphorus (P) limits growth responses to N enrichment differentially across species, wherein P enrichment increases growth responses to N enrichment more in some species than others. We built a hierarchical Bayesian model estimating effects of functional traits (specific leaf area, specific stem density, and specific root length) and P fertilization on species' biomass responses to N, which we then compared between lineages to determine whether phylogeny explains variation in responses to N. In concordance with literature on N limitation, a majority of species responded strongly and positively to N enrichment. Mean responses ranged three-fold, from 6.21 (E. pulchella) to 16.87 (E. delegatensis) percent increases in biomass per g N·m -2 ·yr -1 added. We identified a strong difference in responses to N between two phylogenetic lineages in the Eucalyptus subgenus Symphyomyrtus, suggesting that shared ancestry explains variation in N limitation. However, our model indicated that after controlling for phylogenetic non

Biogeography and Phylogeny of Wood-feeding Cockroaches in the Genus Cryptocercus

Directory of Open Access Journals (Sweden)

Kiyoto Maekawa

2011-07-01

Full Text Available Subsocial, xylophagous cockroaches of the genus Cryptocercus exhibit a disjunct distribution, with representatives in mature montane forests of North America, China, Korea and the Russian Far East. All described species are wingless and dependent on rotting wood for food and shelter at all stages of their life cycle; consequently, their distribution is tied to that of forests and strongly influenced by palaeogeographical events. Asian and American lineages form distinct monophyletic groups, comprised of populations with complex geographic substructuring. We review the phylogeny and distribution of Cryptocercus, and discuss splitting events inferred from molecular data.

The Peter Effect Revisited: Reading Habits and Attitudes of College Students

Science.gov (United States)

Applegate, Anthony J.; Applegate, Mary DeKonty; Mercantini, Martha A.; McGeehan, Catherine M.; Cobb, Jeanne B.; DeBoy, Joanne R.; Modla, Virginia B.; Lewinski, Kimberly E.

2014-01-01

Certainly a primary goal of literacy education is the creation of avid, enthusiastic, and highly motivated readers. However, in this article revisiting the Peter Effect (Applegate & Applegate, 2004), researchers surveyed more than 1,000 college sophomores and found strikingly low levels of enthusiasm for reading. Only 46.6% of surveyed…

Ambulatory thyroidectomy: A multistate study of revisits and complications

OpenAIRE

Orosco, RK; Lin, HW; Bhattacharyya, N

2015-01-01

© 2015 American Academy of Otolaryngology - Head and Neck Surgery Foundation. Objective. Determine rates and reasons for revisits after ambulatory adult thyroidectomy. Study Design. Cross-sectional analysis of multistate ambulatory surgery and hospital databases. Setting. Ambulatory surgery data from the State Ambulatory Surgery Databases of California, Florida, Iowa, and New York for calendar years 2010 and 2011. Subjects and Methods. Ambulatory thyroidectomy cases were linked to state ambul...

Molecular phylogeny of selected species of the order Dinophysiales (Dinophyceae) - testing the hypothesis of a Dinophysioid radiation

DEFF Research Database (Denmark)

Jensen, Maria Hastrup; Daugbjerg, Niels

2009-01-01

additional information on morphology and ecology to these evolutionary lineages. We have for the first time combined morphological information with molecular phylogenies to test the dinophysioid radiation hypothesis in a modern context. Nuclear-encoded LSU rDNA sequences including domains D1-D6 from 27...

Myrteae phylogeny, calibration, biogeography and diversification patterns: Increased understanding in the most species rich tribe of Myrtaceae.

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Vasconcelos, Thais N C; Proença, Carol E B; Ahmad, Berhaman; Aguilar, Daniel S; Aguilar, Reinaldo; Amorim, Bruno S; Campbell, Keron; Costa, Itayguara R; De-Carvalho, Plauto S; Faria, Jair E Q; Giaretta, Augusto; Kooij, Pepijn W; Lima, Duane F; Mazine, Fiorella F; Peguero, Brigido; Prenner, Gerhard; Santos, Matheus F; Soewarto, Julia; Wingler, Astrid; Lucas, Eve J

2017-04-01

Myrteae (c. 2500 species; 51 genera) is the largest tribe of Myrtaceae and an ecologically important groups of angiosperms in the Neotropics. Systematic relationships in Myrteae are complex, hindering conservation initiatives and jeopardizing evolutionary modelling. A well-supported and robust phylogenetic hypothesis was here targeted towards a comprehensive understanding of the relationships within the tribe. The resultant topology was used as a base for key evolutionary analyses such as age estimation, historical biogeography and diversification rate patterns. One nuclear (ITS) and seven chloroplast (psbA-trnH, matK, ndhF, trnl-trnF, trnQ-rps16, rpl16 and rpl32-trnL) DNA regions for 115 taxa representing 46 out of the 51 genera in the tribe were accessed and analysed using maximum likelihood and Bayesian inference tools for phylogenetic reconstruction. Dates of diversification events were estimated and contrasted using two distinct fossil sets (macro and pollen) in BEAST. The subsequent dated phylogenies were compared and analysed for biogeographical patterns using BioGeoBEARS and diversification rates using BAMM. Myrteae phylogeny presents strong statistical support for three major clades within the tribe: Australasian group, Myrtus group and Main Neotropical Lineage. Dating results from calibration using macrofossil are an average of 20 million years older and show an early Paleocene origin of Myrteae, against a mid-Eocene one from the pollen fossil calibration. Biogeographic analysis shows the origin of Myrteae in Zealandia in both calibration approaches, followed by a widespread distribution throughout the still-linked Gondwana continents and diversification of Neotropical endemic lineages by later vicariance. Best configuration shift indicates three points of acceleration in diversification rates, all of them occurring in the Main Neotropical Lineage. Based on the reconstructed topology, several new taxonomic placements were recovered, including: the

Taï chimpanzees anticipate revisiting high-valued fruit trees from further distances.

Science.gov (United States)

Ban, Simone D; Boesch, Christophe; Janmaat, Karline R L

2014-11-01

The use of spatio-temporal memory has been argued to increase food-finding efficiency in rainforest primates. However, the exact content of this memory is poorly known to date. This study investigated what specific information from previous feeding visits chimpanzees (Pan troglodytes verus), in Taï National Park, Côte d'Ivoire, take into account when they revisit the same feeding trees. By following five adult females for many consecutive days, we tested from what distance the females directed their travels towards previously visited feeding trees and how previous feeding experiences and fruit tree properties influenced this distance. To exclude the influence of sensory cues, the females' approach distance was measured from their last significant change in travel direction until the moment they entered the tree's maximum detection field. We found that chimpanzees travelled longer distances to trees at which they had previously made food grunts and had rejected fewer fruits compared to other trees. In addition, the results suggest that the chimpanzees were able to anticipate the amount of fruit that they would find in the trees. Overall, our findings are consistent with the hypothesis that chimpanzees act upon a retrieved memory of their last feeding experiences long before they revisit feeding trees, which would indicate a daily use of long-term prospective memory. Further, the results are consistent with the possibility that positive emotional experiences help to trigger prospective memory retrieval in forest areas that are further away and have fewer cues associated with revisited feeding trees.

Biodiversity, Phylogeny, and Antifungal Functions of Endophytic Fungi Associated with Zanthoxylum bungeanum

Directory of Open Access Journals (Sweden)

Peiqin Li

2016-09-01

Full Text Available This study investigated the biodiversity, phylogeny, and antifungal activity of endophytic fungi isolated from Zanthoxylum bungeanum. A total of 940 isolates obtained were grouped into 93 morphotypes, 43 species, and 23 genera, which were authenticated by molecular identification based on rDNA internal transcribed spacer (ITS sequence analysis. A high diversity of endophytic fungi from Z. bungeanum are observed with high species richness S (43, Margalef index D′ (6.1351, Shannon–Wiener index H′ (3.2743, Simpson diversity index Ds (0.9476, PIE index (0.9486, and evenness Pielou index J (0.8705 but a low dominant index λ (0.0524. Significant tissue specificity of the endophytic fungi was observed in Z. bungeanum, and the highest species richness and diversity indexes were obtained in the stem. Phylogenetic analyses of the 93 endophytic isolates were carried out by the neighbor-joining (NJ method to demonstrate their evolutionary processes. Antifungal activities of endophytic fungi were assayed and eight endophytic isolates showed strong and long-lasting inhibition against host pathogenic fungi Fusarium sambucinum and Pseudocercospora zanthoxyli. Here, for the first time, we systematically demonstrate the biodiversity, phylogeny, and antifungal activity of endophytic fungi associated with Z. bungeanum and reveal the value of sampling different tissues of a given plant to obtain the greatest endophyte species diversity, which might offer a framework for further investigation and utilization of endophytic fungi as aunique source of interesting and useful bioactive compounds.

ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.

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Yan, Dong-Hui; Gao, Qian; Sun, Xiaoming; Song, Xiaoyu; Li, Hongchang

2018-04-01

For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny

Science.gov (United States)

Longdon, Ben; Obbard, Darren J.; Jiggins, Francis M.

2010-01-01

The sigma virus (DMelSV), which is a natural pathogen of Drosophila melanogaster, is the only Drosophila-specific rhabdovirus that has been described. We have discovered two new rhabdoviruses, D. obscura and D. affinis, which we have named DObsSV and DAffSV, respectively. We sequenced the complete genomes of DObsSV and DMelSV, and the L gene from DAffSV. Combining these data with sequences from a wide range of other rhabdoviruses, we found that the three sigma viruses form a distinct clade which is a sister group to the Dimarhabdovirus supergroup, and the high levels of divergence between these viruses suggest that they deserve to be recognized as a new genus. Furthermore, our analysis produced the most robustly supported phylogeny of the Rhabdoviridae to date, allowing us to reconstruct the major transitions that have occurred during the evolution of the family. Our data suggest that the bias towards research into plants and vertebrates means that much of the diversity of rhabdoviruses has been missed, and rhabdoviruses may be common pathogens of insects. PMID:19812076

High precision mass measurements in Ψ and Υ families revisited

International Nuclear Information System (INIS)

Artamonov, A.S.; Baru, S.E.; Blinov, A.E.

2000-01-01

High precision mass measurements in Ψ and Υ families performed in 1980-1984 at the VEPP-4 collider with OLYA and MD-1 detectors are revisited. The corrections for the new value of the electron mass are presented. The effect of the updated radiative corrections has been calculated for the J/Ψ(1S) and Ψ(2S) mass measurements [ru

[Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

Science.gov (United States)

Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

2014-10-01

Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.