Abstract Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.

中文翻译：

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重建新世界猴（Platyrrhini）的系统发育：来自多个非编码基因座的证据

摘要在哺乳动物系统发育中，那些以快速辐射为特征的系统发育尤其成问题。新世界猴（NWMs，Platyrrhini）由3个科7个亚科组成，在相对较短的时间内辐射。因此，它们的系统发育关系仍然存在很大争议。在本研究中，来自代表 18 个物种的 20 个 NWM 个体的 56 个核非编码位点，包括 33 个内含子 (IN) 和 23 个基因间区域 (IG)，用于研究科和亚科之间的系统发育关系。在 56 个基因座中，有 43 个未用于以前的 NWM 系统发育。我们应用了串联和合并树推理方法，以及最近提出的针对特定问题的方法来解决 NWM 系统发育问题。我们的结果表明 IN 和 IG 数据集的串联和合并方法之间存在不一致。然而，尽管具有不同程度的统计支持，但通过对组合 IN 和 IG 的所有分析以及使用串联和合并方法对特定问题位点的所有分析，通过单一树拓扑达成了共识。详细地，我们的结果表明了 Atelidae 和 Pitheciidae 科之间以及 Cebidae 中 Aotinae 和 Callithrichinae 亚科之间的姐妹群关系。我们的研究从多个非编码基因座和各种树推断方法的角度提供了对 NWM 家族和亚家族之间有争议的系统发育关系的见解。然而，目前的系统发育框架需要通过添加更多独立的序列数据和更深入的分类抽样来进一步评估。总的来说，我们的工作对处理快速辐射的系统发育研究具有重要意义。