PDF(Pubmed)
Abstract：
BACKGROUND: There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.
RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.
CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.
RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.
CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.
摘要：
背景：关于家养牦牛（Bosgrunniens）的起源尚无共识。以往对牦牛线粒体的研究主要集中在线粒体置换环(D-loop),系统发育分辨率低的区域。这里,我们分析了509头牦牛的整个线粒体基因组，以获得更高的系统发育分辨率和地理多样性的全面图片。
结果：在来自21个牦牛品种的509头牦牛中，共定义了278个单倍型。其中,不同品种共有28种单倍型，250个单倍型是特定品种特有的。牦牛总体单倍型多样性和核苷酸多样性分别为0.979±0.0039和0.00237±0.00076。系统发育树和网络分析显示，牦牛有3个高度分化的遗传分支，支持率高。进化枝Ⅰ和进化枝Ⅱ的分化时间约为0.4328Ma,进化枝(Ⅰ和Ⅱ)和Ⅲ的分化时间为0.5654Ma。玉树牦牛是所有单倍群共有的。大部分（94.70%）的遗传变异发生在种群内，只有5.30%的遗传变异发生在种群之间。分类显示牦牛和野牦牛首先聚集在一起,牦牛与整个美国野牛聚集在一起。海拔对牦牛分布的影响最大。
结论：牦牛具有较高的遗传多样性，牦牛种群数量扩张，缺乏明显的系统地理结构。在冰川期,牦牛至少有三个或更多的冰川避难所。
结果：在来自21个牦牛品种的509头牦牛中，共定义了278个单倍型。其中,不同品种共有28种单倍型，250个单倍型是特定品种特有的。牦牛总体单倍型多样性和核苷酸多样性分别为0.979±0.0039和0.00237±0.00076。系统发育树和网络分析显示，牦牛有3个高度分化的遗传分支，支持率高。进化枝Ⅰ和进化枝Ⅱ的分化时间约为0.4328Ma,进化枝(Ⅰ和Ⅱ)和Ⅲ的分化时间为0.5654Ma。玉树牦牛是所有单倍群共有的。大部分（94.70%）的遗传变异发生在种群内，只有5.30%的遗传变异发生在种群之间。分类显示牦牛和野牦牛首先聚集在一起,牦牛与整个美国野牛聚集在一起。海拔对牦牛分布的影响最大。
结论：牦牛具有较高的遗传多样性，牦牛种群数量扩张，缺乏明显的系统地理结构。在冰川期,牦牛至少有三个或更多的冰川避难所。
