An index of substitution saturation and its application

Xia, Xuhua; Xie, Zhoujie; Salemi, Marco; Chen, Lu; Wang, Yong

doi:10.1016/s1055-7903(02)00326-3

Cited by 1,358 publications

(991 citation statements)

References 27 publications

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“…In addition, another index (I ss ) suggested by Xia et al (2003) also being used to measure substitution saturation of these COI sequences of species.…”

Section: Discussionmentioning

confidence: 99%

MitochondrialCOIGene Sequence Variation and Taxonomic Status of ThreeMacrobrachiumSpecies

Zhang

Cheng²,

Guan

2010

Zoological Research

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Freshwater prawns (Decapoda: Caridea: Macrobrachium) play an important role in domestic fishery resources. Culturing M. rosenbergii and M. nipponense brings great economic benefits, as the two species were widely farmed in China. M. qilianensis, a native species with natural distribution limited in Gansu province, was classified into genus Macrobrachium based on external morphological characters. In order to understand the molecular genetic differences among the three species of Macrobrachium, i.e., M. rosenbergii, M. nipponense, and M. qilianensis, we analyzed sequences of mitochondrial cytochrome oxidase subunit I (COI) of them. It would provide theoretical basis of exploiting and utilizing Macrobrachium resources rationally. A total of 30 individuals (10 individuals of each species) were collected from Gansu and Zhejiang province. Samples of M. qilianensis were wild, however, that of M. rosenbergii and M. nipponense were cultured. Their mitochondrial COI gene segment sequences were obtained by using the method of PCR amplification and sequencing. After alignment, 649 bp consensus sequences of COI were obtained. One hundred and sixty-nine variable sites were detected in all 30 individuals, accounting for 26.04% of total sequence. A total of seven haplotypes were also detected. Nucleotide diversity was 0.411% within M. rosenbergii, 0.092% within M. nipponense, and 0.031% within M. qilianensis. Genetic diversity of wild M. qilianensis was much lower than that of cultured M. rosenbergii and M. nipponense. Genetic distances between different haplotypes of the three prawns ranged from 19.87% to 23.84%. It suggested that the three species were valid species, because genetic distances among them were quite great. To further determine the taxonomic status of the three prawns in family Palaemonoidae, we downloaded the corresponding COI sequences of Palaemonoidae prawns from Genbank and analyzed the phylogenetic relationships of them. Phylogenetic tree (NJ)

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“…In addition, another index (I ss ) suggested by Xia et al (2003) also being used to measure substitution saturation of these COI sequences of species.…”

Section: Discussionmentioning

confidence: 99%

MitochondrialCOIGene Sequence Variation and Taxonomic Status of ThreeMacrobrachiumSpecies

Zhang

Cheng²,

Guan

2010

Zoological Research

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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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“…Regions with ambiguous positions that could not be aligned were difficult to identify manually and were removed using Gblocks (Castresana, 2000), with the 37, 95, 102-104, 165-176, 182, 206, 211-262, 268-84, 298, 325-328, 366, 382, 397, 421, 530, 551, 741-1008, 1022-1023, 1045, 1121-1124, 1128, 1170-1171, 1189-1191, 1293, 1395, 1719-1923, 2254-2264, 2272-2273, 2284-2286. Substitution saturation was measured using Xia's test (Xia et al, 2003;Xia and Lemey, 2009) implemented in DAMBE (Xia and Xie, 2001). No saturation was detected in the 16S alignment (321 sites) from which gaps and ambiguous regions had been removed (Iss significantly < Iss.c).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling

Dayrat

Conrad

Balayan

et al. 2011

Molecular Phylogenetics and Evolution

143

182

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An index of substitution saturation and its application

Cited by 1,358 publications

References 27 publications

Mitochondrial<I>COI</I>Gene Sequence Variation and Taxonomic Status of Three<I>Macrobrachium</I>Species

Mitochondrial<I>COI</I>Gene Sequence Variation and Taxonomic Status of Three<I>Macrobrachium</I>Species

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

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling

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