Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing

Abstract

Recent genomic studies show that introgression can occur at a genome-wide scale among recently diverged lineages. However, introgression is difficult to distinguish from incomplete lineage sorting (ILS), and these processes are expected to occur together. Moreover, ncDNA introgression is less easily detected than mtDNA introgression, and as such its prevalence is less well understood. The Chinese horseshoe bat (Rhinolophus sinicus) occurs as three distinct forms on mainland China: the subspecies R. s. septentrionalis and two parapatric clades of R. s. sinicus (Central and East R. s. sinicus). Previous work suggested widespread mtDNA introgression between these subspecies, however, no ncDNA introgression was detected. In this new study we sampled the coding genomes of all three forms of R. sinicus in order to perform a more sensitive test for ncDNA introgression against an expected background of incomplete lineage sorting. We assembled 3548 nuclear protein-coding genes from these and three congeneric species, and built a high confidence species tree using Maximum Likelihood and Bayesian concordance methods. Phylogenetic analysis suggested a mosaic genome for Central R. s. sinicus derived from R. s. septentrionalis and East R. s. sinicus. Nuclear DNA introgression between Central R. s. sinicus and R. s. septentrionalis was supported by three different tests, whereas ILS could not be ruled out completely. Our findings, in line with other recent results, indicate that recently diverged taxa undergo large scale secondary introgression, and that this process likely operates alongside incomplete lineage sorting to give rise to phylogenomic discordances or even mosaic genomes.

Diversification and introgression in four chromosomal taxa of the Pearson’s horseshoe bat (Rhinolophus pearsoni) group

“…This analysis was conducted with the GTRGAMMA model and bootstrap support was estimated based on 1000 pseudoreplicate searches. In this analysis, we included sequences of the 13 MPC genes from R. ferrumequinum, R. sinicus and R. rex, obtained from Mao et al (2017) as outgroups.…”