Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Evolution. 2011 Jan;65(1):184-202. doi: 10.1111/j.1558-5646.2010.01097.x.
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation in these jays coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's rule could account for some differences in timing estimates between mitochondrial DNA and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
估计分歧的时间对于检验物种形成的潜在原因至关重要。放松分子钟和化石校准提高了这些估计值；然而，这些进展是在基因树的背景下实施的，基因树可能会高估分歧时间。在这里，我们将最近用于确定物种形成事件时间的创新方法与物种树的分析能力相结合，在这种方法中，多基因数据在合并背景下进行考虑。我们在 Aphelocoma 鸟属中估计分歧时间，以检验这些松鸦的物种形成是否与山脉抬升或冰川周期同时发生。基因树和物种树普遍一致地表明，这些鸟类的多样化始于中新世，当时山脉抬升。然而，来自多基因物种树的日期更新近，主要发生在更新世，这与理论一致，即基于基因树的方法不纠正在物种形成之前发生的遗传分歧，可能会大大高估分歧时间。除了合并随机性之外，Haldane 规则可以解释线粒体 DNA 和核基因之间时间估计的一些差异。通过将适用于物种树的化石校准以及基因谱系合并过程结合起来，目前的方法为确定物种形成事件提供了一个更具生物学现实性的框架，从而为检验多样化与特定生物地理和地质事件之间的联系提供了基础。
