Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks

BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). RESULTS: A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. CONCLUSIONS: The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.

背景：豚鼠科（Caviidae）是一类广泛分布于南美洲的多样豚鼠型啮齿类（caviomorph rodents），现生支系可划分为三个高度分化的类群：豚鼠亚科（Caviinae，俗称豚鼠）、长耳豚鼠亚科（Dolichotinae，俗称长耳豚鼠）以及水豚亚科（Hydrochoerinae，俗称水豚）。豚鼠科的化石记录仅自晚中新世（late Miocene）起才变得丰富且多样。豚鼠科隶属于严格意义上的豚鼠总科（Cavioidea sensu stricto, Cavioidea s.s.），该总科还包含一类从南美洲渐新世晚期（late Oligocene）至中中新世（middle Miocene）地层中记录的多样灭绝类群——“始豚鼠类（"eocardiids"）”。结果：本文整合形态学与分子数据开展系统发育分析，基于化石类群校准系统发育树并运用宽松分子钟（relaxed molecular clocks），评估了选定支系的分化时间。分析结果显示，严格意义上的豚鼠总科的演化历史存在三个主要分化阶段：前两个阶段为渐新世晚期与早中新世（early Miocene）先后发生的两波灭绝支系适应性辐射；第三个阶段则为豚鼠科的分化。根据化石记录，豚鼠科的初始分化时间被定为中中新世，该时间落在宽松贝叶斯分子钟估算得到的95%高概率区间内，不过其平均估算年龄比化石记录结果早3.5至7百万年。豚鼠科初始分化之后，存在一段化石记录匮乏的模糊时期（本文称之为“梅奥期缺失（"Mayoan gap"）”），随后便出现了高度分化的豚鼠科现生支系；结合化石记录与分子钟估算结果可知，这一过程发生于晚中新世。结论：本文采用的整合分析方法，得以厘清古生物化石记录与分子钟估算在豚鼠总科演化重大事件时间节点上的一致性与分歧，揭示了仅依靠分子数据或古生物学数据无法获取的演化模式。