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
豚科（Caviidae）是一类物种多样性丰富的豚形啮齿类，广泛分布于南美洲，现生类群分为三个分化程度极高的支系：豚鼠亚科（Caviinae，豚鼠）、长耳豚鼠亚科（Dolichotinae，马拉豚鼠）以及水豚亚科（Hydrochoerinae，水豚）。豚科的化石记录仅在晚中新世以来才变得丰富多样。
豚科隶属于严格意义豚总科（Cavioidea sensu stricto，简称Cavioidea s.s.），该类群还包含从南美洲晚渐新世至中中新世地层中发现的多种已灭绝类群（即"eocardiids"，始豚类）。

## 研究结果
本研究开展了一项结合形态学与分子数据的系统发育分析，基于化石类群校准的系统发育树，并运用宽松分子钟模型，评估了选定演化节点的分化时间。
该分析揭示了严格意义豚总科演化历史中的三个主要分化阶段：前两个阶段为晚渐新世至早中新世期间发生的两次连续的已灭绝支系辐射演化事件；第三个阶段为豚科的分化。
基于化石记录，豚科的初始分化时间被定为中中新世。尽管宽松贝叶斯分子钟估算的平均分化年龄比该时间早3.5至7百万年，但该化石定年结果落在宽松贝叶斯分子钟估算的95%高概率置信区间内。
豚科初始分化之后，存在一段化石记录匮乏的模糊时段（本文称之为"Mayoan gap"，梅奥间断），随后出现了高度分化的现生豚科支系。综合化石记录与分子钟估算结果表明，该支系出现的时间为晚中新世。

## 研究结论
本研究采用的整合分析方法，使我们得以厘清豚总科演化重大事件时间节点上化石记录与分子钟估算结果的一致性与分歧，揭示了仅依靠单一分子数据或古生物数据无法获取的演化模式。