Analysis of genomic data leads to an improved understanding of the phylogeny and biogeography of yellow bats

Abstract Improvements in genomic data collection, phylogenetic methods, and biogeographical modeling can provide a better understanding of the evolutionary history of taxa that have historically been difficult to resolve. One group that would benefit from a comprehensive reassessment using genomic data is the yellow bats (Lasiurus ega, L. insularis, L. intermedius, and L. xanthinus). Yellow bats are foliage-roosting and widely distributed in tropical and subtropical regions of North and South America. Previous molecular investigations into the evolutionary history of yellow bats were limited to few genetic loci. Here, we analyzed thousands of genomic loci with broad geographic sampling to resolve the phylogeny, assess population genetic structure, and reconstruct the biogeographic history of yellow bats. We inferred a phylogeny with species relationships consistent with recent previous work and distinct lineages that correspond to proposed subspecies of L. intermedius and L. ega. Analysis of the genomic data produced estimates of divergence dates more recent than previously reported, and together with ancestral niche reconstruction, suggest that yellow bats primarily diversified in southern North America, Central America, and the Caribbean during Pleistocene climate cycles. Our results provide an improved understanding of the evolutionary history of yellow bats and indicate a need for rigorous assessment of species limits within the clade.