Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analyzed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks....确定物种分化时间并解析物种形成过程，是生物进化历史研究的核心议题，但该领域的研究素来极具挑战性。这类研究的难点主要源于祖先种群大小的差异，或是不同基因座（locus）间的谱系演化变异。为阐明台湾特有3种单系草蜥属（Takydromus）物种的物种形成过程与分化历史，我们对20个核基因座（nuclear locus）进行了测序，并整合GenBank中已发表的1个线粒体基因座（mitochondrial locus）数据。我们采用贝叶斯框架（Bayesian framework）下的多物种溯祖分析法（multispecies coalescent approach）对上述数据开展分析。基于基因树法（gene tree approach）的分化时间估算结果显示，不同基因座的估算值存在显著异质性，且该方法得到的分化时间早于物种树法（species tree approach）的估算结果。为验证祖先种群大小的差异是否是造成上述估算差异的主要原因，我们采用隔离迁移（isolation-with-migration, IM）模型与近似贝叶斯计算（approximate Bayesian computation, ABC）框架开展了计算机推演分析。