Investigating the genomic differentiation landscape of the large mouse-eared bats

Abstract

Interspecific gene flow, through shaping the evolution of species over time, plays a pivotal role in evolutionary biology. Often complex and multifaceted, this process presents a rich area to explore the intricate dynamics that drive the evolution of species. The large mouse-eared bats, specifically Myotis myotis and M. blythii, present a particularly intriguing species complex for studying interspecific gene flow. Myotis myotis and M. blythii have substantially overlapping ranges across Europe and Anatolia. These species also exhibit evidence of gene flow, identified in the previous studies. Their shared mitochondrial lineage suggests past hybridization events. Additionally, nuclear marker based analyses identified evidence of recent gene flow events. Despite their sympatric distribution coupled with past and present hybridization events, the mechanism underlying the maintenance of separate gene pools remains an intriguing question. This study aims to contribute in the understanding of the evolutionary history of the large Myotis bats through a whole-genome approach. In this regard, genomic differentiation landscapes were considered within and between Large Myotis bats. For the genomic analysis, whole-genome shotgun sequencing data was generated from a total of thirty-four samples, representing M. myotis, M. blythii, and their closely related species, M. punicus. To assess the population structures and differentiation levels, Principal Component and Admixture analyses were conducted. Both analyses identified three distinct clusters in accordance with the three large Myotis taxa. Within M. blythii, a further split separating the individuals from Kyrgyzstan and Mongolia from the rest was present. Genomic landscapes of differentiation were explored through Manhattan plots of fixation index, nucleotide diversity and genomic divergence. The genomic differentiation assessments supported the nuclear divergence of M. myotis and M. blythii. Within M. blythii, East and West populations exhibited a significant divergence, although not to a level comparable to the divergence seen between two different species. Potentially introgressed genomic regions were investigated. Although a slightly increased gene flow signal was observed across the entire genome between M. myotis and Eastern M. blythii, localized introgression regions that would indicate recent hybridization could not be detected. Further exploration of introgressed genomic regions may reveal the genomic basis for species differentiation. This study contributes to future studies on large Myotis bats and other cryptic species complexes, while also demonstrating the power of whole-genome data in unraveling the complex processes that shape the evolution of species.