Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.

线粒体DNA仍然是分子生态学的基石，特别是对于那些难以轻易获取高质量组织样本的研究物种而言。使用线粒体标记的方法通常依赖于参考数据库，但这些数据库往往不完整。此外，现有的线粒体基因组往往缺乏关键的元数据，比如采样地点，这限制了它们在许多分析中的用途。在此，我们为阔鼻猴类灵长目动物组装了205个新的线粒体基因组，其中大多数来自亚马逊地区且采样地点已知。我们基于这些样本以及其他已发表的阔鼻猴类线粒体基因组呈现了一个有年代的线粒体基因组系统发育树，并利用它来评估对长期存在的河流屏障假说（RBH）的支持，该假说提出河流的形成是亚马逊灵长类动物物种形成的主要驱动力。沿着亚马逊河、内格罗河和马德拉河，我们发现对RBH的支持情况不一。虽然我们确定了与河流屏障相吻合的分化，但只有一些是同步发生的，并且也与河流形成的推测时间重叠。最有力的证据是亚马逊河可能推动了髭长尾猴（Chiropotes属）以及现存最小的阔鼻猴类——狨猴和绢毛猴的物种形成。然而，我们还发现，即使是大河似乎也不是一些灵长类动物的屏障，包括吼猴（Alouatta属）、秃猴（Cacajao属）、僧面猴（Pithecia属）和粗壮卷尾猴（Sapajus属）。我们的研究结果支持河流屏障具有更细致、类群特异性的影响，并表明除了RBH和异域物种形成之外，其他进化机制可能在阔鼻猴类的多样化过程中发挥了重要作用。