How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

Lin, Chung Ping; Danforth, Bryan N.

doi:10.1016/s1055-7903(03)00241-0

Cited by 319 publications

(215 citation statements)

References 80 publications

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“…4C, there is much more heterogeneity in among-site rate variation in mitochondrial genes than in nuclear S7 intron 1 and intron 2, with the most heterogeneous in cyt b gene, which had the lowest a value. However, all the nuclear sequences presented lower proportion of invariable sites (Pi values), which is contrast to that of Lin and Danforth (2004), who demonstrated that the proportion of invariable sites is positively correlated with a value. These authors also showed a positive correlation between a value and CI, the consistency index, which suggests that data partitions with more heterogeneous substitution rates show a higher level of homoplasy.…”

Section: Molecular Evolution Patterns and Phylogenetic Utility Of Difcontrasting

confidence: 69%

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

Chen

Guo

Nie

2010

Molecular Phylogenetics and Evolution

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Section: Molecular Evolution Patterns and Phylogenetic Utility Of Difcontrasting

confidence: 69%

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

Chen

Guo

Nie

2010

Molecular Phylogenetics and Evolution

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“…However, the rpS7 gene fragment presented a lower proportion of invariable sites (Pi values). Lin & Danforth (2004) showed a positive correlation between a and ci, the consistency index, which suggests that data partitions with more heterogeneous substitution rates show a higher level of homoplasy. However, we did not detect this significant correlation, with the second intron of rpS7 gene having a ci value (0.7472) not significantly different from that of the 16S rRNA gene (0.7310).…”

Section: Discussionmentioning

confidence: 93%

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Guo

Zhang

2007

Hydrobiologia

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Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.

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“…When we consider our data alone this correlation is not seen because the a value of the intron is much higher than that of cyt b, whereas the Pi value of the intron is lower than that of cyt b. Lin & Danforth (2004) positive correlation between a and CI, the consistency index, which suggests that data partitions with more heterogeneous substitution rates show a higher level of homoplasy. This correlation was detected by us, with the intron having a higher CI value (0.741) than cyt b gene (0.415).…”

Section: Patterns Of Nucleotide Substitutionmentioning

confidence: 85%

“…This further supports that some sites in the intron may actually be constrained by natural selection but we were unable to detect this by the weak statistical tests we applied (Poisson goodness-of-fit test). Lin & Danforth (2004) stated in general terms that the proportion of invariable sites (Pi values) is positively correlated with a in coding regions. This may indeed be the general tendency for the exons, but it does not necessarily apply when comparing nuclear introns with mitochondrial genes (exons).…”

Section: Patterns Of Nucleotide Substitutionmentioning

confidence: 99%

Comparative evolution of the mitochondrial cytochrome b gene and nuclear S7 ribosomal protein gene intron 1 in sinipercid fishes and their relatives

Guo

Chen

2010

Hydrobiologia

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The extant sinipercids are a group of freshwater percoid fishes endemic to East Asia. A recent mitochondrial cytochrome b phylogeny of sinipercids has challenged some aspects for their traditional taxonomy and molecular phylogeny, especially for the monophyly of Sinipercidae. In this study, we analyzed mitochondrial cytochrome b and nuclear encoded S7 ribosomal protein gene intron 1 for 10 sinipercid species and 11 related species to compare the phylogenetic signal and nucleotide substitution properties of these two gene sequences. The length of S7 intron 1 ranged from 461 to 719 bp, but alignment was not difficult, and the indels, the proportion of which in the total nucleotides ranged from 3.76 to 45.83%, were phylogenetically informative. Our results indicate that: (1) the relative rate presented by cyt b is five times that of S7 intron 1; (2) the proportion of phylogenetic information is higher in S7 than in cyt b; (3) S7 intron 1 has more base composition bias, but more uniform nucleotide substitution properties; (4) the overall ratio between transitions and transversions in S7 intron 1 is lower than in cyt b. Maximum parsimony and Bayesian analyses of aligned S7 intron 1 and the combined S7 and cyt b dataset resulted in phylogenies that contained the previously identified genera Siniperca and Coreoperca, whereas the monophyly of Coreoperca cannot be corroborated by separate cyt b analysis. The monophyly of Sinipercidae is not supported in separate and combined dataset analyses, although the alternative hypothesis cannot be significantly rejected based on approximately unbiased tests and Shimodaira-Hasegawa tests. Overall, maximum parsimony analyses result in trees with a lack of phylogenetic resolution in deep nodes, and the signal from S7 intron 1 conflicts the cyt b signal in the combined dataset analyses. The reasons for the poor performance of cyt b to S7 intron 1 in the phylogeny are discussed.

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How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

Cited by 319 publications

References 80 publications

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Comparative evolution of the mitochondrial cytochrome b gene and nuclear S7 ribosomal protein gene intron 1 in sinipercid fishes and their relatives

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