Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

被引:44
作者
Bjork, Adam [1 ]
Liu, Weimin [2 ]
Wertheim, Joel O. [1 ]
Hahn, Beatrice H. [2 ,3 ]
Worobey, Michael [1 ]
机构
[1] Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA
[2] Univ Alabama Birmingham, Dept Med, Birmingham, AL USA
[3] Univ Alabama Birmingham, Dept Microbiol, Birmingham, AL USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
evolution; chimpanzee; phylogeny; relaxed molecular clock; Yule; coalescent; DIVERGENCE TIMES; NUCLEOTIDE DIVERSITY; DNA; POPULATIONS; INFECTION;
D O I
10.1093/molbev/msq227
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Investigations into the evolutionary history of the common chimpanzee, Pan troglodytes, have produced inconsistent results due to differences in the types of molecular data considered, the model assumptions employed, and the quantity and geographical range of samples used. We amplified and sequenced 24 complete P. troglodytes mitochondrial genomes from fecal samples collected at multiple study sites throughout sub-Saharan Africa. Using a "relaxed molecular clock," fossil calibrations, and 12 additional complete primate mitochondrial genomes, we analyzed the pattern and timing of primate diversification in a Bayesian framework. Our results support the recognition of four chimpanzee subspecies. Within P. troglodytes, we report a mean (95% highest posterior density [HPD]) time since most recent common ancestor (tMRCA) of 1.026 (0.811-1.263) Ma for the four proposed subspecies, with two major lineages. One of these lineages (tMRCA = 0.510 [0.387-0.650] Ma) contains P. t. verus (tMRCA = 0.155 [0.101-0.213] Ma) and P. t. ellioti (formerly P. t. vellerosus; tMRCA = 0.157 [0.102-0.215] Ma), both of which are monophyletic. The other major lineage contains P. t. schweinfurthii (tMRCA = 0.111 [0.077-0.146] Ma), a monophyletic clade nested within the P. t. troglodytes lineage (tMRCA = 0.380 [0.296-0.476] Ma). We utilized two analysis techniques that may be of widespread interest. First, we implemented a Yule speciation prior across the entire primate tree with separate coalescent priors on each of the chimpanzee subspecies. The validity of this approach was confirmed by estimates based on more traditional techniques. We also suggest that accurate tMRCA estimates from large computationally difficult sequence alignments may be obtained by implementing our novel method of bootstrapping smaller randomly subsampled alignments.
引用
收藏
页码:615 / 623
页数:9
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