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 genetic markers that evolve slowly relative to the rate of speciation. By incorporating hundreds to thousands of unlinked loci, phylogenomic analyses may 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) datasets. We sequenced hundreds of ultraconserved elements (UCEs) and whole mitochondrial genomes in these species and estimated phylogenies using concatenation, summary coalescent, and hierarchical coalescent methods. The concatenated approach recovered a well-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, with its complete support for all nodes, may be positively misleading. Our simulations show that the tree shape we tend to infer, which involves a series of short internode 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 reflect a real and appropriate lack of certainty. Our results illuminate the challenges of estimating bifurcating trees in a rapid and recent radiation and provide a rare empirical example of a nearly simultaneous series of speciation events that occurred in a terrestrial animal lineage as it spread across an oceanic archipelago.