Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal.
Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal.
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类人猿Y染色体和线粒体DNA的同源性反映了亚种的结构以及交配和扩散的模式。
DOI：
10.1101/gr.198754.115
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发表时间：
2016-04
期刊：
影响因子：
7
通讯作者：
Jobling MA
中科院分区：
文献类型：
--
作者：
Hallast P;Maisano Delser P;Batini C;Zadik D;Rocchi M;Schempp W;Tyler-Smith C;Jobling MA
类人猿物种遗传多样性的分布很可能受到扩散和交配模式的影响。这以前已经通过测序常染色体和线粒体DNA（mtDNA）进行了研究，但尚未进行Y染色体（MSY）男性特异性区域的大规模序列分析。在这里，我们使用人类MSY参考序列作为19只雄性类人猿的序列捕获和读取映射的基础，将数据与从24只其他雄性的已发表的全基因组中提取的序列相结合，以产生19只黑猩猩，4只倭黑猩猩，14只大猩猩和6只猩猩的总样本，其中可解释的MSY序列范围为2.61至3.80 Mb。该分析揭示了数千种新的MSY变体，并定义了无偏遗传。我们将这些与相同个体中基于mtDNA的树进行比较，估计两种情况下关键节点的最近共同祖先（TMRCA）时间。这两个位点表现出高度的拓扑一致性，并与公认的（子）种的定义是一致的，但时间深度不同的位点和（子）种之间的巨大差异，可能反映了不同的传播和交配模式。大猩猩和黑猩猩/倭黑猩猩目前普遍低和高MSY多样性，分别反映了一夫多妻制与多雌多雌交配。然而，黑猩猩亚种之间存在着特别显著的差异：西部黑猩猩的MSY遗传的TMRCA只有13.2（10.8-15.8）千年，但中部黑猩猩的TMRCA超过100万年。在一个单一的MSY系统发育的跨物种比较强调低的人类多样性，并揭示物种特异性的分支长度的变化，可能反映了长期世代时间的差异。
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.