Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.直至近期，绝大多数非人灵长类的系统发育与群体遗传学研究均依赖线粒体DNA（mitochondrial DNA）与少量核DNA标记，这类研究手段可能会限制我们对灵长类演化与种群历史的全面认知。本研究介绍了一种经济高效的简化基因组测序方法——双酶切简化基因组测序（ddRAD-seq），可用于鉴定并基因分型新世界猴类群的大量单核苷酸多态性（single nucleotide polymorphism, SNP）位点；新世界猴是一类演化辐射多样的灵长类，其共同祖先可追溯至约2000万至2600万年前。本研究还首次借助ddRAD-seq产生的SNP数据，采用最大似然法（maximum likelihood）与基于四分体的溯祖法两种分析策略，对当前已被认可的22个新世界猴属中的15个属之间的系统发育关系进行了推断。我们的系统发育分析稳健地重构出三个单系支系，分别对应现生阔鼻猴类（platyrrhines）的三个科：蛛猴科（Atelidae）、僧面猴科（Pitheciidae）与卷尾猴科（Cebidae），其中僧面猴科为该演化辐射的基部类群。在属级分类单元层面，本研究结果与此前的系统发育研究成果吻合度较高，同时为夜猴属（Aotus）在卷尾猴科中的存疑分类位置补充了新的佐证，提示我们需要进一步探究不完全谱系分选以及其他可能引发系统发育冲突的机制，包括基因渐渗（introgression）。本研究同时也是首批将下一代测序（next-generation sequencing）技术应用于古老且演化辐射多样的哺乳动物类群的系统发育历史推断的研究之一，同时彰显了ddRAD-seq数据在分子灵长类学研究中的广阔应用前景与实用价值。