Data from: Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.

Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the same molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and combined) from 60 species, and eight fossil calibration constraints, we estimated the times of origin and diversification of platyrrhines and caviomorphs via a Bayesian relaxed molecular clock approach. To account for the possible effect of an accelerated rate of evolution of the IRBP gene along the branch leading to the anthropoids, we performed the datings with and without IRBP (3768 sites and 2469 sites, respectively). The time window for the colonization of South America by primates and by rodents is demarcated by the dates of origin (upper bound) and radiation (lower bound) of platyrrhines and caviomorphs. According to this approach, platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of a concomitant arrival of primates and rodents in South America. The caviomorphs radiated soon after their arrival, before the Oligocene glaciations, and these early caviomorph lineages persisted until the present. By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification.

阔鼻下目灵长类（Platyrrhine primates）与豚鼠下目啮齿类（caviomorph rodents）均为哺乳动物演化支，它们在南美洲与其他大陆隔绝的距今1亿至300万年前（Mya）期间成功迁入南美洲大陆。迄今为止，尚无分子研究采用同一套分子数据集，探究这两个类群迁入南美洲的具体时间节点。本研究选取60个物种的3个核基因序列（ADRA2B、vWF及IRBP，分别开展单独分析与合并分析），结合8项化石校准约束，通过贝叶斯宽松分子钟方法，估算了阔鼻下目灵长类与豚鼠下目啮齿类的起源与分化时间。为考量IRBP基因沿类人猿分支的进化速率加速可能带来的分析偏差，我们分别采用包含IRBP（共计3768个位点）与不包含IRBP（共计2469个位点）的两套数据集进行年代估算。灵长类与啮齿类迁入南美洲的时间窗口，由阔鼻下目灵长类和豚鼠下目啮齿类的起源时间（时间上限）与辐射演化时间（时间下限）共同界定。基于该分析框架，阔鼻下目灵长类迁入南美洲的时间范围为37.0±3.0 Mya（不包含IRBP时为38.9±4.0 Mya）至16.8±2.3 Mya（不包含IRBP时为20.1±3.3 Mya）；豚鼠下目啮齿类的迁入时间范围为45.4±4.1 Mya（不包含IRBP时为43.7±4.8 Mya）至36.7±3.7 Mya（不包含IRBP时为35.8±4.3 Mya）。综合化石记录与本次分子年代估算结果，最受支持的演化情景为：灵长类于始新世末期或渐新世初期从非洲跨大西洋迁徙至南美洲，啮齿类则在中始新世至晚始新世期间迁入南美洲。基于我们的核DNA数据，无法排除灵长类与啮齿类同期抵达南美洲的可能性。豚鼠下目类群在抵达南美洲后很快发生辐射演化，早于渐新世冰川作用事件，且这些早期的豚鼠下目支系一直延续至现代。相较而言，渐新世的阔鼻下目灵长类化石记录极为匮乏，现生阔鼻下目类群均源自中新世早期的较晚近辐射演化。