|
Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 33, No. 4, 2012, pp. E47-E56
|
Bioline Code: zr12056
Full paper language: English
Document type: Report
Document available free of charge
|
|
Zoological Research, Vol. 33, No. 4, 2012, pp. E47-E56
en |
Preliminary analysis of the mitochondrial genome evolutionary pattern in primates
ZHAO, Liang; ZHANG, Xingtao; TAO, Xingkui; WANG, Weiwei & LI, Ming
Abstract
Since the birth of molecular evolutionary analysis, primates have been a central focus of study and mitochondrial DNA is
well suited to these endeavors because of its unique features. Surprisingly, to date no comprehensive evaluation of the nucleotide
substitution patterns has been conducted on the mitochondrial genome of primates. Here, we analyzed the evolutionary patterns and
evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank. The results
revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons. Likewise, an obvious decline in primate
nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes. Within 13 protein-coding
genes, the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence, while synonymous changes
differed only for individual genes, indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites.
Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes, and supported the idea
that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias.
Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for
any gene, consistent with near neutrality. Recombination tests based on the pairwise homoplasy test statistic supported complete
linkage even for much older divergent primate species. Thus, with the exception of rate heterogeneity among mitochondrial genes,
evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic
analysis seems unnecessary.
Keywords
Mitochondrial genome; Evolutionary pattern; Codon usage bias; Complete linkage; Evolution neutrality; Primates
|
|
© Copyright 2012 - Kunming Institute of Zoology, the Chinese Academy of Sciences Alternative site location: http://www.zoores.ac.cn/
|
|