Yao Lu, Li Hongjie, Martin Robert D, Moreau Corrie S, Malhi Ripan S
Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA.
Mol Phylogenet Evol. 2017 Nov;116:227-238. doi: 10.1016/j.ympev.2017.08.006. Epub 2017 Aug 31.
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
由于整个更新世期间陆桥的不断出现和消失，东南亚的生物地理历史十分复杂。在此，我们以长尾猕猴（食蟹猴）作为研究对象，它们广泛分布于东南亚大陆和岛屿，以此更好地理解这个地理环境复杂地区的生物地理多样化模式。为了追溯该地区的亲缘关系以及殖民模式和时间，需要一个可靠的种内系统发育树，涵盖来自海洋岛屿、大陆岛屿和大陆各地的个体。我们运用高通量测序技术，对世界各地自然历史博物馆收藏的95个东南亚食蟹猴标本的线粒体基因组（线粒体基因组）进行测序。为了获得全面的情况，我们将食蟹猴线粒体基因组样本量比之前的研究增加了两倍多，并且首次纳入了来自菲律宾和印度尼西亚几个小岛的有记录样本。新构建的135个标本的系统发育树证实了先前关于食蟹猴种内系统发育的结果，将样本分为两个主要分支：A分支包括来自大陆的单倍型以及一些来自苏门答腊北部的单倍型，而B分支包括所有岛屿单倍型以及来自苏门答腊南部的谱系。这项研究通过揭示苏门答腊猕猴起源的间断性解决了先前的一个差异，两个主要分支中各自独立起源的谱系表明至少有两次主要的迁移进入苏门答腊。然而，我们的定年系统发育树显示，这两个主要分支在约188万年前分裂，这比之前发表的系统发育树更早。我们的新数据表明，大多数菲律宾猕猴谱系在过去约0.06 - 0.43百万年内从婆罗洲种群分化而来。最后，我们的研究为跨博物馆成功进行DNA测序以及将DNA标本鸟枪法测序作为一种线粒体基因组测序方法提供了见解。
