Giarla Thomas C, Esselstyn Jacob A
Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Syst Biol. 2015 Sep;64(5):727-40. doi: 10.1093/sysbio/syv029. Epub 2015 May 14.
Phylogenetic relationships in recent, rapid radiations can be difficult to resolve due to incomplete lineage sorting and reliance on genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses have the potential to mitigate these difficulties. Here, we attempt to resolve phylogenetic relationships among eight shrew species (genus Crocidura) from the Philippines, a phylogenetic problem that has proven intractable with small (< 10 loci) data sets. We sequenced hundreds of ultraconserved elements and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a maximally supported and fully resolved tree. In contrast, the coalescent-based approaches produced similar topologies, but each had several poorly supported nodes. Using simulations, we demonstrate that the concatenated tree could be positively misleading. Our simulations also show that the tree shape we tend to infer, which involves a series of short internal branches, is difficult to resolve, even if substitution models are known and multiple individuals per species are sampled. As such, the low support we obtained for backbone relationships in our coalescent-based inferences reflects a real and appropriate lack of certainty. Our results illuminate the challenges of estimating a bifurcating tree in a rapid and recent radiation, providing a rare empirical example of a nearly simultaneous series of speciation events in a terrestrial animal lineage as it spreads across an oceanic archipelago.
由于不完全谱系分选以及依赖相对于物种形成速率而言进化缓慢的遗传标记，近期快速辐射中的系统发育关系可能难以解析。通过纳入数百到数千个不连锁的基因座，系统发育基因组学分析有潜力缓解这些困难。在此，我们试图解析来自菲律宾的八种鼩鼱物种（麝鼩属）之间的系统发育关系，这一系统发育问题已证明使用小数据集（< 10个基因座）难以解决。我们对这些物种中的数百个超保守元件和整个线粒体基因组进行了测序，并使用串联法、总结合并法和分层合并法估计系统发育。串联法得到了一个支持度最高且完全解析的树。相比之下，基于合并的方法产生了相似的拓扑结构，但每个都有几个支持度较差的节点。通过模拟，我们证明串联树可能会产生正向误导。我们的模拟还表明，我们倾向于推断的树形状，涉及一系列短的内部分支，即使知道替换模型且每个物种采样多个个体，也难以解析。因此，我们在基于合并的推断中对主干关系获得的低支持度反映了真实且恰当的不确定性。我们的结果揭示了在近期快速辐射中估计二叉树的挑战，提供了一个罕见的实证例子，展示了陆地动物谱系在跨越海洋群岛扩散时几乎同时发生的一系列物种形成事件。
