A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America
A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America
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DOI：
10.1016/j.ympev.2018.02.023
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发表时间：
2018-07-01
影响因子：
4.1
通讯作者：
Alfaro, Jessica W. Lynch
中科院分区：
文献类型：
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作者：
Lima, Marcela G. M.;de Sousa e Silva-Junior, Jose;Alfaro, Jessica W. Lynch
粗壮的卷尾猴(Sapajus属)之间的系统发育关系尚不清楚。基于形态的分类学已经识别了从1到12个不同的物种。目前的IUCN(2017)分类列出了8种粗壮的卷尾猴：黄腹鱼、黑腹卷尾鱼、粗壮卷尾鱼、黄氏卷尾鱼、利比迪诺斯卷尾鱼、凯氏卷尾鱼、阿佩拉卷尾鱼和大头卷尾鱼。在这里，我们使用超保守元件(UCES)组装了第一个Sapajus的系统基因组数据集，以重建卷尾猴的系统发育。所有的系统发育分析都有力地支持了卷尾猴中Sapajus和Cebus分支的深度分化，并支持Sapajus nigritus、S.robustus和S.xanthosternos作为不同的物种。然而，UCE的系统发育将推测的种S.cay、S.libitinosus、S.apella、S.maccephalus和S.Flavius集中在一起，作为一个单一的分布广泛的谱系。根据UCE数据构建的SNP系统发育被更好地解析和恢复为姐妹种；然而，在亚马逊东北部和西南部的两个地理分支中发现了S-apella、S-maccephalus和S-cay个体，而不是根据目前定义的形态种进行聚类。种群聚集性的结构分析表明，在亚马逊地区，甚至在塞拉多和大西洋森林中，Sapajus种群之间存在着广泛的混杂。很难通过形态来指定物种，这可能是由于粗壮的卷尾猴频繁地在主要河流甚至生态系统中迁徙，促进了广泛的种群混合。
Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.