Data from: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews

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.

近期快速辐射演化类群的系统发育关系往往难以解析，这一困境源于不完全谱系分选（incomplete lineage sorting）的干扰，以及研究中依赖相对于物种形成速率演化较慢的遗传标记。通过纳入数百至数千个非连锁基因座，系统发育基因组学分析（phylogenomic analyses）具备缓解此类难题的潜力。本研究尝试解析菲律宾地区8种麝鼩属（Crocidura）鼩鼱的系统发育关系——该类群的系统发育问题此前被证实无法通过基因座数量少于10的小数据集解决。我们对这些物种的数百个超保守元件（ultraconserved elements）与全线粒体基因组进行了测序，并采用串联法、汇总溯祖法与层级溯祖法估计系统发育树。串联法得到了一棵支持度最高且完全解析的系统发育树；与之相对，基于溯祖的方法虽得到了相似的拓扑结构，但各方法均存在数个支持度较低的分支节点。通过模拟分析，我们证实串联法构建的系统发育树可能存在正向误导。模拟结果还显示，我们所推断出的带有一系列短内部分支的树状结构难以解析——即便替换模型（substitution models）已知且对每个物种采样了多个个体，情况亦无改观。因此，我们基于溯祖的推断中，核心谱系关系的支持度较低，实则反映了真实且合理的不确定性。本研究结果阐明了在近期快速辐射演化类群中估计分叉型系统发育树所面临的挑战，同时为陆生动物支系跨大洋群岛扩散过程中发生的一系列近乎同时的物种形成事件提供了罕见的实证案例。