Genomic Signatures of Decline and Recovery in an Endangered Bat

Abstract Tremendous population declines may result in the loss of genetic diversity, which can in turn lead to reduced phenotypic health, reduced adaptive potential, and further population declines. In other words, a severe demographic decline may ultimately lead to an extinction vortex. Therefore, understanding genetic diversity is vital for assessing the health of species that have undergone declines, and can even reflect the effectiveness of management actions. We investigated signatures of genetic bottlenecks in a species that has been the subject of focused management efforts since its 1976 listing as endangered in the US, the gray bat ( Myotis grisescens) . We used whole genome sequencing to calculate genetic diversity metrics, including inbreeding coefficients, Tajima’s D, and heterozygosity, and to infer effective population size and structuring. We found a loss of rare alleles and heterozygosity excess, in line with strong declines in relative abundance of the census population. However, we did not detect inbreeding, erasure of population substructure, or low effective population size. Despite an apparent bottleneck, the gray bat appears to have avoided detrimental genetic consequences associated with population declines, likely due to the conservation of connected populations of adequate effective size. Our findings highlight the importance and effectiveness of timely conservation interventions for preserving the genetic health of species. Strong declines in relative abundance (i.e., based on percentage of the initial population) do not necessarily lead to inbreeding when there is still adequate absolute abundance (i.e., number of individuals).