Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum
Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum
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DOI：
10.1093/molbev/msr227
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发表时间：
2012-02-01
影响因子：
10.7
通讯作者：
Carpenter, Kent E.
中科院分区：
文献类型：
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作者：
Crandall, Eric D.;Sbrocco, Elizabeth J.;Carpenter, Kent E.
DNA的变化率是理解分子进化的一个重要参数，因此也是从生物地理学和生物遗传学研究中得出推论的一个重要参数。大多数海洋物种线粒体编码区的速率校准都是从化石和年龄超过1-2 My的替代事件的分歧测年中进行的，通常是每百万年每个谱系0.5-2%。最近，用来自较年轻日期的古代DNA（aDNA）进行的校准产生了更快的速率，这表明对分子变化速率的估计取决于校准的时间，从瞬时突变率衰减到系统发育取代率。最近校准的aDNA方法不适用于大多数海洋分类群，因此我们使用辐射测量日期来测量末次冰期最大期（始于18，000年前）之后巽他大陆架的海平面上升，这导致了海洋物种的大规模人口扩张。而不是分歧约会，我们使用两个时代的结合模型的逻辑人口增长之前，一个恒定的人口规模来推断这些扩张事件的开始突变单位的时间。这个模型相比，更简单的合并模型的人口规模不变，指数或逻辑增长，是远远更精确的估计从错配分布。用这种方法估计的三种无脊椎动物线粒体编码基因的平均速率与较老的校准点相比有所升高（每百万年每谱系2.3-6.6%），为分子速率的校准时间依赖性的假设提供了额外的支持。
The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting similar to 18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.