Lobon Irene, Tucci Serena, de Manuel Marc, Ghirotto Silvia, Benazzo Andrea, Prado-Martinez Javier, Lorente-Galdos Belen, Nam Kiwoong, Dabad Marc, Hernandez-Rodriguez Jessica, Comas David, Navarro Arcadi, Schierup Mikkel H, Andres Aida M, Barbujani Guido, Hvilsom Christina, Marques-Bonet Tomas
Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
Genome Biol Evol. 2016 Jul 3;8(6):2020-30. doi: 10.1093/gbe/evw124.
The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.
黑猩猩属是与我们人类亲缘关系最近的属，它包含两个物种，即倭黑猩猩（Pan paniscus）和黑猩猩（Pan troglodytes）。后者由四个亚种组成，均处于高度濒危状态。由于亚种之间复杂的关系以及所分析样本数量或基因组标记数量减少带来的统计限制，对黑猩猩属的研究一直不断复杂化。在这里，我们提出了一种从全基因组鸟枪法（WGS）数据集中重建完整线粒体基因组（线粒体基因组）的新方法——mtArchitect，结果表明其重建高度准确且与长距离PCR线粒体基因组一致。我们使用这种方法构建了20个新测序样本的线粒体基因组，这些样本与现有基因组一起，使我们能够分析迄今为止最完整的黑猩猩线粒体基因组数据集，其中包括156只黑猩猩和44只倭黑猩猩个体，且所有黑猩猩亚种都有相应比例的样本。我们估计黑猩猩和倭黑猩猩的分化时间约在115万年前（Mya）[0.81 - 1.49]。此外，我们发现，在最可能的系统发育模型下，黑猩猩的两个分支，即西部 + 尼日利亚 - 喀麦隆分支和中部 + 东部分支，分别在0.59 Mya [0.41 - 0.78]时分化，内部进一步分化时间分别为0.32 Mya [0.22 - 0.43]和0.16 Mya [0.17 - 0.34]。最后，对于我们样本中的一个子集，我们比较了核基因组与线粒体基因组，发现黑猩猩亚种的核多样性和线粒体多样性模式不同，这可能是影响线粒体基因组的过程（如搭便车或背景选择）导致的结果，也可能是种群动态的结果。
