Myotis rufonigerGenome Sequence and Analyses:M. rufoniger’s Genomic Feature and the Decreasing Effective Population Size ofMyotisBats

Abstract

Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has batspecific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since~30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats,Myotis*

“…Independent divergence time estimates based on whole‐genome data of four Myotis species and nine other mammals, including four bats, showed that the divergence of the group started between 29 and 15 million years ago, encompassing our results based on the Horacek's calibration (Bhak et al. ).…”

“…; Bhak et al. ). Divergence time estimates based on molecular datasets and conservative fossil calibrations suggest that Myotis sensu lato—including Submyotodon —diverged about 18 million years ago from their sister groups, the subfamilies Murininae and Kerivoulinae.…”

The Genetics of Aging: A Vertebrate Perspective

“…Several genes in the GH-IGF1 signaling pathway are under positive selection or have unique amino acid variants in long-lived animals. Long-lived bats have specific variants in GH, GHR, IGF1, and IGF1 receptor (IGF1R) (Bhak et al, 2017;Seim et al, 2013). Naked mole rats have adaptive variations in IGF1 and RHEB (a regulator of mTOR) (Sahm et al, 2018).…”

Longevity and the drift barrier: Bridging the gap between Medawar and Hamilton

“…The models considered here suggest possible empirical tests. As a preliminary and illustrative example, it is helpful to consider estimates for the parameters of equation : a small rodent‐like example (e.g., house mouse) with , , , and ; a small bat‐like species (e.g., Brandt's bat) with , , , and ; and a large whale‐like example (e.g., blue whale) with , , , and (see e.g., Roman and Palumbi 2003 for estimates of historical effective population sizes for large whales, Halligan et al 2010 for effective population size of wild mice, and Bhak et al 2017 for Myotis bats). Here, the units of b and f are years and female offspring per year, respectively.…”