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.