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

摘要

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.