Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.重建哺乳动物演化的年代学，是基于分子的推断与基于化石的推断之间长期存在的争议议题。分子推断方法存在一项方法论局限：不同演化支间的进化速率存在变异，这使得全球分子钟（global molecular clock）的应用受到限制。我们针对一组记录完备的胎盘类哺乳动物（包含大量啮齿类采样样本），分析了ADRA2B、IRBP与vWF这三个核基因的2422个第一和第二密码子位点。本研究采用7个独立校准点，并基于最大似然（maximum-likelihood）框架，评估通过局部分子钟（local molecular clock）方法是否能够调和哺乳动物分化时间的分子推断与古生物学推断——该方法允许替换率在局部保持恒定，而在更大的系统发育尺度上存在变异。为解决不同演化支的速率分配选择难题，本研究的局部分子钟分析基于分支长度（branch-length）与双簇检验（two-cluster tests）的结果。研究检测到广泛的演化支特异性进化速率变异，即便在啮齿类内部亦是如此。交叉校准结果显示，基于不同古生物学参照标准得到的分化时间存在一定不相容性。为降低单一校准点的影响，我们对仅存在轻微相互不相容性的独立校准所得到的推断结果进行了平均化处理。小鼠与大鼠的分化时间推断结果约为1300万至1900万年前，早于此前已发表的分子推断结果。啮齿类、灵长类、北方真兽类（boreoeutherians）与胎盘类哺乳动物的最近共同祖先，其推断年代分别约为6000万、7000万、7500万与7800万年前。全球分子钟、局部分子钟以及四元组定年分析（quartet dating analyses）均显示，冠群胎盘类演化支（crown placental clades）起源于白垩纪晚期，随后在第三纪发生了啮齿类等部分胎盘类目级类群的辐射演化。