Phylogenetic Model Evaluation

Jermiin, Lars S.; Jayaswal, Vivek; Ababneh, Faisal; Robinson, John

doi:10.1007/978-1-60327-159-2_16

Cited by 71 publications

(52 citation statements)

References 122 publications

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“…Evidence of evolution under conditions more complex than that assumed by commonly applied models (i.e., stationary, reversible, and homogeneous conditions) was inferred if the scatter of dots in the tetrahedral plots was widely dispersed and if x% of the matched-pairs tests of symmetry produced p values greater than or equal to x; this procedure is consistent with that advocated by Jermiin et al (2008). Substitution saturation was tested by inspecting a new entropy-based index as implemented in DAMBE (Xia and Xie 2001).…”

Section: Sequence Alignment and Analysessupporting

confidence: 63%

Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences

Yang

Guo

et al. 2010

Parasitol Res

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Leishmaniasis is a geographically widespread disease, caused by protozoan flagellates of the genus Leishmania. This disease still remains endemic in China, especially in the west and northwest frontier regions. To date, the phylogenetic relationships among Chinese Leishmania isolates are still unclear, and the possible taxonomic diversity remains to be established. In this study, the ITS1-5.8S fragments of ten isolates collected from different foci in China were determined. To infer the phylogenetic relationships among them, seven sequences of Chinese Leishmania isolates retrieved from GenBank were also included. Both parsimony and Bayesian analyses reveal an unexpected but strongly supported clade comprising eight newly determined isolates, which is sister to other members of subgenus Leishmania. In combination with genetic distance analysis, this provides evidence of the occurrence of an undescribed species of Leishmania. Our results also suggest that (1) the isolate IPHL

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Section: Sequence Alignment and Analysessupporting

confidence: 63%

Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences

Yang

Guo

et al. 2010

Parasitol Res

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“…Kim et al (1994) a Inferred from ITS1 sequence analysis (Yang et al 2010) b Named previously on the basis of zymodeme analysis (Xu et al 1984) c Identified as L. donovani according to the zymodeme, LON41, whereas recent analysis have shown that it is L. infantum (Ibrahim and Barker 2001) Compositional heterogeneity was evaluated using Chisquare (# 2 ) tests implemented in PAUP* 4.0b10 (Swofford 2002) and assessed using the software SeqVis v.1.5 (Ho et al 2006) to visualize and to conduct matched-pairs test of symmetry (Ababneh et al 2006). Evidence of evolution under conditions more complex than that assumed by commonly applied models (i.e., stationary, reversible, and homogeneous conditions) was inferred if the scatter of dots in the tetrahedral plots was widely dispersed and if x% of the matched-pairs test of symmetry produced p values greater than or equal to x; this procedure is consistent with that advocated by Jermiin et al (2008). Substitution saturation was tested by inspecting a new entropy-based index as implemented in DAMBE v.5.2.11 (Xia and Xie 2001).…”

Section: Sequence Alignment and Analysessupporting

confidence: 52%

Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences

et al. 2011

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Leishmaniasis is a geographically widespread disease caused by protozoan parasites belonging to the genus Leishmania and transmitted by certain species of sand fly. This disease still remains endemic in China, especially in the west and northwest frontier regions. A recent ITS1 phylogeny of Chinese Leishmania isolates has challenged some aspects for their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within Chinese Leishmania isolates highlights the need for additional data and analyses. Here, we test the phylogenetic relationships among Chinese isolates and their relatives by analyzing kinetoplast cytochrome oxidase II (COII) gene sequences, including 14 Chinese isolates and three isolates from other countries plus 17 sequences retrieved from GenBank. The COII gene might have experienced little substitution saturation, and its evolutionary process was likely to have been stationary, reversible, and homogeneous. Both neighbor-joining and Bayesian analyses reveal a moderately supported group comprising ten newly determined isolates, which is closely related to Leishmania tarentolae and Endotrypanum monterogeii. In combination with genetic distance analysis as well as Bayesian hypothesis testing, this further corroborates the occurrence of an undescribed species of Leishmania. Our results also suggest that (1) isolate MHOM/CN/93/GS7 and isolate IPHL/CN/77/XJ771 are Leishmania donovani; (2) isolate MHOM/CN/84/JS1 is Leishmania tropica; (3) the status referring to an isolate MRHO/CN/62/GS-GER20 from a great gerbil in Gansu, China, as Leishmania gerbilli, formerly based on multilocus enzyme electrophoresis, is recognized; and (4) E. monterogeii is nested within the genus Leishmania, resulting in a paraphyletic Leishmania. In addition, the results of this study enrich our understanding of the heterogeneity and relationships of Chinese Leishmania isolates.

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“…Evidence of evolution under conditions more complex than that assumed by commonly applied models (i. e., stationary, reversible and homogeneous conditions) was inferred if the scatter of dots in the tetrahedral plots was widely dispersed and if a proportion X of the matched-pairs tests of symmetry rejected symmetry with P-values less than or equal to X. This procedure is consistent with that advocated by Jermiin et al (2008Jermiin et al ( , 2009. If the matched-pairs tests yield a larger than expected proportion of probabilities ≤ 0.05 (i. e., with > 5% of the tests producing probabilities ≤ 0.05), then the conclusion is that the sequences have not evolved under stationary, reversible and homogeneous conditions.…”

Section: Sequence Alignment and Analysessupporting

confidence: 67%

Phylogeography of the Phrynocephalus vlangalii Species Complex in the Upper Reaches of the Yellow River Inferred from mtDNAND4-tRNALEU Segments

Guo¹,

Li²,

Wang³

2012

AHR

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especially in the context of Quaternary and Holocene histories of regional biotas (Hewitt, 2001). The dramatic geological and climatic history and striking habitat diversity of the Qinghai-Tibetan Plateau (QTP), ranging from broad plantation surfaces, basins to mountain ranges, have made it a geographic focus of many phylogeographic studies Qu et al., 2010;Xu et al., 2010;Zhan et al., 2011). As reviewed by Yang et al. (2009), the geomorphic and climatic changes on the plateau during the Quaternary have a remarkable influence on regional and adjacent biogeographic patterns.The Quaternary glaciations in the QTP and the bordering mountains were the consequence of a combination between climate and local tectonic uplift. The diversification of P. putjatia may be triggered by the tectonic movement in the Huangshui River valley during the C phase of Qingzang Movement. Subsequently, the glacial climate throughout the Pleistocene may have continued to impede the gene flow of P. putjatia, eventually resulting in the genetic divergence of P. putjatia in the allopatric regions. Demographic estimates revealed weak population expansion in one lineage of P. vlangalii (A2, the Qaidam Basin lineage) and one lineage of P. putjatia (B2, the north Qinghai Lake lineage) after approximately 42 000 years before present. However, constant population size through time was inferred for two lineages (A1 and B1), the source of Yellow River lineage of P. vlangalii and the southeast of Qinghai Lake lineage of P. putjatia, possibly due to stable populations persisting in areas unaffected by glacial advances. Our results also suggest: 1) at least four differentiated lineages of P. vlangalii complex may have evolved allopatrically in different regions during the Pleistocene glaciation events; 2) in support of several recent studies, P. putjatia is a valid species, having a more wide distribution than previously considered; and 3) a hypothesis referring to P. v. hongyuanensis, inhabiting in the source region of the Yellow River, being synonymous with P. v. pylozwi is supported.

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Phylogenetic Model Evaluation

Cited by 71 publications

References 122 publications

Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences

Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences

Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences

Phylogeography of the Phrynocephalus vlangalii Species Complex in the Upper Reaches of the Yellow River Inferred from mtDNAND4-tRNALEU Segments

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