SRA

The diversification of Myotis into more than 100 species in just a few million years is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial gene markers and the few studies that have used nuclear markers resulted in trees that lack resolution. The current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the true species tree. To resolve this issue, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of more than five thousand ultraconserved elements (UCEs). We explored various concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data. Of the 293 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred from the mitochondrial genomes. Several factors can drive such conflict, including incomplete lineage sorting. Quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. This suggests that Myotis genomes experienced massive amounts of incomplete lineage sorting, likely during the early stages of the radiation. Because they evolve as a single locus, mitochondrial genomes, may be susceptible to incomplete lineages sorting and may not reflect the true species tree. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving the unique nuclear, mitochondrial, and biogeographic histories.