Assessing substitution saturation with DAMBE

Xia, Xuhua; Lemey, Philippe

doi:10.1017/cbo9780511819049.022

Cited by 401 publications

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“…Nucleotide variation and substitution patterns were examined using MEGA v. 5.0 (Tamura et al, 2011). To evaluate the occurrence of substitution saturation in the sequences, the index of substitution saturation (Iss) described by Xia et al (2003) and Xia, Lemey (2009) in DAMBE 5.3.48 (Xia 2013 was estimated.…”

Section: Methodsmentioning

confidence: 99%

Molecular phylogeny and biogeographic history of the Neotropical tribe Glandulocaudini (Characiformes: Characidae: Stevardiinae)

et al. 2018

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Although former studies on systematics and biogeography represent a progress on the knowledge of the tribe Glandulocaudini, none was grounded on molecular evidence. Thus, the first hypothesis of relationships for the tribe based on a multilocus analysis is presented, including all genera and most of the valid species. DNA sequences of Glandulocauda caerulea and Mimagoniates sylvicola were analyzed for the first time. A molecular clock analysis was used to estimate the origin of the Glandulocaudini and the approximate timing of cladogenetic events within the group. Glandulocaudini was recovered as monophyletic. No hypothesis recovered Glandulocauda as monophyletic, since G. melanopleura is sister to Lophiobrycon weitzmani while G. caerulea is closely related to Mimagoniates. The relationships within the latter genus were resolved. The molecular clock results indicate the origin of the Glandulocaudini during the Miocene with diversification in the group occurring from Neogene to Pleistocene. These results corroborated the hypothesis that its origin took place on the Brazilian crystalline shield with the subsequent occupation of the Atlantic Coastal drainages. Apparently, Pleistocene sea-level fluctuations might have shaped the distribution pattern of some species in Glandulocaudini.Keywords: Brazilian Crystalline Shield, Coastal Drainages, Molecular Clock, Molecular Systematics, Multilocus Analysis.Embora estudos prévios sobre sistemática e biogeografia representam um avanço no conhecimento da tribo Glandulocaudini, nenhum foi baseado em evidência molecular. Assim, a primeira hipótese de relações para a tribo com base em uma análise multilocus é apresentada, incluindo todos os gêneros e a maioria das espécies válidas. Sequências de DNA de Glandulocauda caerulea e Mimagoniates sylvicola foram analisadas pela primeira vez. Uma análise de relógio molecular foi utilizada para estimar a origem de Glandulocaudini e datas aproximadas de eventos cladogenéticos dentro do grupo. Glandulocaudini foi recuperada como monofilética. Nenhuma hipótese recuperou Glandulocauda como monofilético, uma vez que G. melanopleura é irmã de Lophiobrycon weitzmani e G. caerulea está proximamente relacionada a Mimagoniates. As relações dentro deste último gênero foram resolvidas. Os resultados do relógio molecular indicam que Glandulocaudini originouse durante o Mioceno, com diversificação dentro do grupo ocorrendo desde o Neogeno até o Pleistoceno. Estes resultados corroboram a hipótese da sua origem no escudo cristalino brasileiro, com a subsequente ocupação das drenagens costeiras atlânticas. Aparentemente, as flutuações pleistocênicas do nível do mar podem ter moldado o padrão de distribuição de algumas espécies em Glandulocaudini. Palavras-chave:

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Section: Methodsmentioning

confidence: 99%

Molecular phylogeny and biogeographic history of the Neotropical tribe Glandulocaudini (Characiformes: Characidae: Stevardiinae)

et al. 2018

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“…To test for the possible saturation of substitution types, DAMBE was used to plot the number of transitions (Ti) and transversions (Tv) against the uncorrected pairwise distances for each marker (Xia and Lemey, 2009). …”

Section: Sequence Alignment and Analysesmentioning

confidence: 99%

Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

Zheng

Yang

2012

Current Zoology

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The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals (representing 24 genera and 73 species) of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine , a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia [Current Zoology 58 (6) Keywords Phylogeny, Character evolution, Biogeography, LabeoninaeThe Labeoninae is a group of fishes with small to medium sized and inferior mouths within a clade of the Cyprinidae (Order Cypriniformes). The labeonine fishes are adapted to swift currents and mostly scrape algae off the benthic substrate. These fishes display the greatest diversity in lip morphology and other structures associated with the mouth among the Cyprinidae (Zhang et al., 2000). Diverse morphology of the mouth and associated structures distinguishes labeonines from other cyprinid fishes and also serves as the main basis of generic taxonomy and phylogenetic analyses. Consequently, several new genera have been successively erected according to special oromandibular morphology (e.g. Cophecheilus Zhu et al., 2011, Hongshuia Zhang et al., 2008, and Qianlabeo Zhang and Chen, 2004. Several morphology-based phylogenetic studies about the labeonines have been undertaken, but the phylogenetic results based on different data sets have been inconsistent. This incongruence may be the result of insufficient or different sampling, but these morphology-based phylogenetic studies were mainly based on the characters of the mouth and associated structures (Zhang, 1994;Zhang, 1998;Su, 2001;Zhang, 2005;Li et al., 2005).As molecular techniques provided a new perspective in phylogenetic studies, the morphological phylogeny of the Labeoninae has been challenged. A few earlier molecular studies did not resolve the phylogeny of the labeonines due to insufficient samples (e.g. Li et al., 2005). Two recent studies present relatively detailed phy...

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“…Genomics of the Methanomicrobiales predicts adaptations P Browne et al protein clusters data set, we omitted all clusters that at any point of our analyses had more than one copy per genome and filtered out clusters whose corresponding nucleotide codon alignment showed evidence of substitution saturation (Xia and Lemey, 2009). The remaining 437 protein clusters (Supplementary Data 1) were aligned and concatenated for analyses.…”

Section: Phylogenetic Inferencementioning

confidence: 99%

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

et al. 2016

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Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H 2 -CO 2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H + rather than Na + transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na + and H + chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

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Assessing substitution saturation with DAMBE

Cited by 401 publications

References 0 publications

Molecular phylogeny and biogeographic history of the Neotropical tribe Glandulocaudini (Characiformes: Characidae: Stevardiinae)

Molecular phylogeny and biogeographic history of the Neotropical tribe Glandulocaudini (Characiformes: Characidae: Stevardiinae)

Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

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