Local molecular clocks in three nuclear genes: Divergence times for rodents and other mammals and incompatibility among fossil calibrations
Local molecular clocks in three nuclear genes: Divergence times for rodents and other mammals and incompatibility among fossil calibrations
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DOI：
10.1007/s00239-003-0028-x
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发表时间：
2003-01-01
影响因子：
3.9
通讯作者：
Huchon, D
中科院分区：
文献类型：
--
作者：
Douzery, EJP;Delsuc, F;Huchon, D
重建哺乳动物进化的年表是一个基于分子和化石的推论之间争论不休的问题。分子生物学的一个方法学局限是不同谱系之间的进化速率差异，这就排除了全球分子钟的应用。我们考虑了2422个第一和第二密码子位置的组合ADRA 2B，IRBP，和vWF核基因的一组有据可查的胎盘，包括一个广泛的啮齿类动物的采样。使用7个独立的校准点和最大似然框架，我们评估了是否分子和古生物学估计的哺乳动物分歧日期可以调和的本地分子钟的方法，允许本地恒定的替代率在较大的系统发育尺度的变化。为了解决在各种谱系的所有可能速率分配中进行选择的困难，局部分子钟基于分支长度和两簇测试的结果。广泛的谱系特异性变化的进化速率被检测到，甚至在啮齿类动物。交叉校准表明，不同的古生物学参考的分歧日期之间的一些不兼容性。为了减少单个校准点的影响，对仅显示轻微倒数不相容性的独立校准得出的估计值进行平均。小鼠和大鼠之间的分歧日期推断（类似于13 -19百万年）比以前发表的分子估计更年轻。啮齿类、灵长类和啮齿类、北方真兽目和胎盘类最近的共同祖先估计分别为6000万年、7000万年、7500万年和7800万年。全球时钟，当地时钟和四重测年分析表明，晚白垩世起源的冠胎盘分支，其次是第三纪辐射的一些胎盘订单，如啮齿动物。
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 (similar to13-19 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, similar to60, 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.