Unraveling phylogenetic conflicts and adaptive evolution in Chiroptera using large-scale mitogenomes and nuclear genes.

The phylogenetic relationships within the order Chiroptera (bats) have long been debated. The suborder classification of Yinpterochiroptera and Yangochiroptera, based on morphology and molecular phylogenetic studies, remains controversial. The topologies of the superfamilies Noctilionoidea, Emballonuridea, and Vespertilionidea, as well as the subfamilies within Vespertiliondae and Phyllostomatidae and tribes within Vespertilionae, are unstable. Moreover, the classification of the species group within Rhinolophus remains to be clarified. To address these issues, we compiled a dataset of 219 complete mitochondrial genomes (mitogenomes) for 187 bat species, including 54 newly sequenced mitogenomes. This extensive dataset covers 13 bat families and 32% of all extant bat genera, enabling the construction of a comprehensive bat phylogeny. Furthermore, we constructed a phylogenetic tree containing 50 bat species based on 200 orthologous nuclear genes to compare with the mitogenome-based phylogeny. Our results supported the suborder classification of Yinptero- and Yangochiroptera. Bayesian dating suggests that bats originated approximately 59 Mya, with two suborders diverging at the beginning of the Eocene epoch. Our findings highly supported the superfamily Emballonuridea as the sister to Noctilionoidea and Vespertilionidea. We found that conflicts in suborder and superfamily topologies were mainly caused by incomplete lineage sorting. Furthermore, we refined the topology of subfamilies within Vespertiliondae and Phyllomatidae, and six tribes within Vespertilioninae. Our study also revealed Myotinae as a subfamily rather than a family. Additionally, we observed a decrease in C/T ratios in the family Vespertilionidae, likely related to their higher mass-specific metabolic rates. We identified a significant negative correlation between selection pressure on COX3 and migratory distance, indicating its importance in flight adaptability. This study offers novel insights into bat phylogeny and flight adaptation.