Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.
Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.
复制标题
DOI：
10.1002/ajpa.24099
复制
发表时间：
2020-09
影响因子：
2.8
通讯作者：
Malhi RS
中科院分区：
文献类型：
--
作者：
Yao L;Witt K;Li H;Rice J;Salinas NR;Martin RD;Huerta-Sánchez E;Malhi RS
长尾猕猴（Macaca fascicularis）广泛分布于东南亚大陆和岛屿，使其成为了解整个更新世海平面急剧变化所导致的复杂地理历史的有用模型。过去基于长尾猕猴博物馆标本的线粒体基因组（mitogenomes）的研究已经追踪了它们在整个群岛的殖民模式，但mitogenomes只追踪了母系历史。在这里，我们的目标是使用博物馆标本的低覆盖率核DNA（nDNA）数据来追踪长尾猕猴的地理分布模式。我们进行了人口遗传学分析和系统发育重建核单核苷酸多态性（SNP）的鸟枪测序75长尾猕猴博物馆标本从东南亚各地。我们表明，鸟枪测序博物馆标本产生足够的基因组覆盖率（平均~1.7%）重建人口关系，使用SNP数据。与预期的不同结果之间的核和线粒体基因组的女性philopatric物种，基于核SNP的地理模式被证明是非常相似的，发现使用有丝分裂基因组。特别是，群体遗传分析和系统发育重建从nDNA确定两个主要分支内M。束状肌：进化枝A包括所有来自大陆的个体沿着，以及来自北方苏门答腊的个体，而进化枝B包括其余的岛屿生活的个体，包括来自苏门答腊南部的个体。总的来说，我们证明，博物馆标本的低覆盖率nDNA测序提供了足够的数据来研究广泛的地理分布模式，虽然需要更大的基因组覆盖率和测序深度来区分非常密切相关的人群，如菲律宾各地的人群。
Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analysis and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
登录
查看更多内容
影响因子：
56.9
作者：
Frantz, Laurent A. F.;Mullin, Victoria E.;Larson, Greger
通讯作者：
Larson, Greger
影响因子：
6.5
作者：
Guschanski K;Krause J;Sawyer S;Valente LM;Bailey S;Finstermeier K;Sabin R;Gilissen E;Sonet G;Nagy ZT;Lenglet G;Mayer F;Savolainen V
通讯作者：
Savolainen V
影响因子：
56.9
作者：
Daly, Kevin G.;Delser, Pierpaolo Maisano;Bradley, Daniel G.
通讯作者：
Bradley, Daniel G.
DOI：
10.1098/rspb.1998.0267
发表时间：
1998-01-22
影响因子：
4.7
作者：
de Ruiter, JR;Geffen, E
通讯作者：
Geffen, E
DOI：
10.1073/pnas.1120774109
发表时间：
2012-03-13
影响因子：
11.1
作者：
Evans, Alistair R.;Jones, David;Uhen, Mark D.
通讯作者：
Uhen, Mark D.