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.哺乳动物演化年代学的重构，是基于分子证据与基于化石证据的推断之间长期存在的争议性问题。分子研究存在一项方法学局限：不同演化支系间的演化速率存在差异，这使得全局分子钟(global molecular clock)的应用受到限制。本研究选取了ADRA2B、IRBP与vWF这三个核基因(nuclear genes)的2422个第一及第二密码子位点(codon positions)，针对一组记录详实的胎盘类哺乳动物类群（包含大量啮齿类(rodents)采样）展开分析。本研究采用7个独立校准点与最大似然(maximum-likelihood)分析框架，旨在验证：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与古生物学估计值——该方法允许替换速率在局部保持恒定，而在更大的系统发育尺度上存在速率变异。为解决不同演化支系间所有可能的速率分配方案难以抉择的问题，本研究的局部分子钟分析基于分支长度(branch-length)与双簇测试(two-cluster tests)的结果。研究检测到广泛存在的演化支系特异性速率变异，即便在啮齿类内部亦不例外。交叉校准分析显示，基于不同古生物学参照的分化时间估计值之间存在一定的不相容性。为降低单个校准点的影响，本研究对仅存在轻微相互不相容性的独立校准所得的估计值进行了平均加权整合。本研究推断的小鼠与大鼠分化时间（约1300万至1900万年前），较此前已发表的分子估计结果更为年轻。啮齿类、灵长类、北方真兽类(boreoeutherians)以及胎盘类的最近共同祖先时间，经估计分别约为6000万、7000万、7500万以及7800万年前。全局分子钟、局部分子钟以及四元组定年(quartet dating)分析均显示：冠群胎盘类支系(crown placental clades)起源于白垩纪晚期，随后部分胎盘类类群（如啮齿类）在第三纪发生辐射演化。