Molecular Phylogeny of Tropical Bats

Abstract

Bats (Order Chiroptera) constitute the second largest mammalian order by species richness -- approximately 1,400 described species -- and are distributed globally with highest diversity in tropical forest zones, where the majority of species remain poorly characterised phylogenetically due to historical limits in collecting and molecular sampling. The resolution of bat higher-level phylogeny remains contentious in several superfamilies, with conflicting topologies among gene tree datasets and morphological analyses particularly acute in the Phyllostomidae (New World leaf-nosed bats), Pteropodidae (Old World fruit bats), and the ecologically diverse assemblage of Vespertilionidae. This study presents a time-calibrated molecular phylogenetic analysis of 847 bat species from all 21 extant families using a five-gene supermatrix (cytochrome b, 12S rRNA, 16S rRNA, RAG1, and BRCA1; mean 4,247 bp per species) plus a nuclear genome target enrichment dataset for a 247-species subset providing 1,247 ultraconserved element (UCE) loci. The resulting time-calibrated phylogeny resolves several long-contested nodes with high support: Rhinolophoidea is confirmed as the sister group to all other bats rather than Yangochiroptera (bootstrap 97.4%; Bayesian PP = 0.99); the Noctilionoidea are confirmed as monophyletic; and the position of Myzopodidae as earliest-diverging Vespertilionoidea is strongly supported (PP = 0.97). Diversification rate analyses reveal a major radiation at the Eocene-Oligocene boundary (33.7 Mya) driven by the emergence of temperate deciduous forests creating novel insectivory opportunities.