Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes
Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes
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DOI：
10.1093/molbev/msq227
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发表时间：
2011-01-01
影响因子：
10.7
通讯作者：
Worobey, Michael
中科院分区：
文献类型：
--
作者：
Bjork, Adam;Liu, Weimin;Worobey, Michael
由于所考虑的分子数据的类型、所采用的模型假设以及所使用的样本的数量和地理范围的不同，对常见的黑猩猩--泛黑猩猩的进化史的研究产生了不一致的结果。我们从撒哈拉以南非洲多个研究地点收集的粪便样本中扩增并测序了24个完整的轮虫线粒体基因组。利用一个“松弛的分子钟”、化石校准和另外12个完整的灵长类动物线粒体基因组，我们在贝叶斯框架下分析了灵长类物种多样化的模式和时间。我们的结果支持对四个黑猩猩亚种的识别。在美洲斑潜蝇中，我们报告了四个亚种自最近共同祖先以来的平均时间(最高后验密度[HPD])为1.026(0.811-1.263)Ma，有两个主要谱系。其中一个谱系(tMRCA=0.510[0.387-0.650]Ma)包括P.T.verus(tMRCA=0.155[0.101-0.213]Ma)和P.T.ellioti(前P.T.vellerosus；tMRCA=0.157[0.102-0.215]Ma)，两者都是单系。另一个主要谱系包括P.T.schweinFurthii(tMRCA=0.111[0.077-0.146]Ma)，这是一个嵌套在P.T.轮虫谱系(tMRCA=0.380[0.296-0.476]Ma)中的单系支系。我们使用了两种可能会引起广泛兴趣的分析技术。首先，我们在整个灵长类动物树上实现了Yule优先物种形成，每个黑猩猩亚种都有单独的合并优先物种。基于更传统技术的估计结果证实了该方法的有效性。我们还建议，通过实现我们的新方法来自举较小的随机下采样比对，可以从大的计算困难的序列比对中获得准确的tMRCA估计。
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.