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.

研究背景：
豚鼠科（Caviidae）是一类物种丰富的豚鼠型啮齿类（caviomorph rodents），广泛分布于南美洲，现生类群分为三个高度分化的支系：豚鼠亚科（Caviinae，豚鼠类cavies）、长耳豚鼠亚科（Dolichotinae，长耳豚鼠maras）以及水豚亚科（Hydrochoerinae，水豚capybaras）。豚鼠科的化石记录仅在晚中新世之后才变得丰富多样。豚鼠类隶属于狭义豚鼠总科（Cavioidea sensu stricto，简称Cavioidea s.s.），该总科还包含一类从南美洲渐新世晚期至中新世中期产出的多样已灭绝类群（始豚鼠类 eocardiids）。
研究结果：
本文开展了整合形态学与分子数据的系统发育分析，基于以化石类群校准的系统发育树，并结合松弛分子钟（relaxed molecular clocks）方法，对选定关键节点的分化时间进行了估算。本分析揭示了狭义豚鼠总科演化历史中的三个主要分化阶段：前两个阶段为渐新世晚期与中新世早期相继发生的两波已灭绝支系辐射演化；第三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新世中期，该时间落在松弛贝叶斯分子钟（Bayesian molecular clock）估算得到的95%高概率分布区间内，不过其平均估算年龄比化石定年老3.5至7百万年。豚鼠科的初始分化之后，存在一段化石记录匮乏的模糊时期（本文将其称为梅奥安间断 Mayoan gap），随后出现了高度分化的现代豚鼠科支系，该事件的发生时间为晚中新世，这一结论得到了化石记录与分子钟估算的共同佐证。
结论：
本研究采用的整合研究方法，使我们得以厘清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差异，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。