Diversification And Introgression In Four Chromosomal Taxa Of The Pearson’s Horseshoe Bat(Rhinolophus Pearsoni) Group

Chromosomal variations among closely related taxa are common in both plants and animals.They can reduce the occurrence of introgression and promote reproduction isolation and speciation.However,in mammals,studies relating gene flow to chromosomal variations have tended to focus on a few model systems and typically characterized levels of introgression among chromosomal taxa using small numbers of loci.Here we focus on closely related,but chromosomally distinct members of the Rhinolophus pearsoni group,which possess four chromosomal taxa(2n=42,44,46,and 60),corresponding to R.p.chinensis,R.p.pearsoni,R.yunanensis,and R.thailandensis,respectively.Among the four chromosomal taxa of this group,Robertsonian changes(fusions or fissions)are major forms of chromosomal rearrangement.Using a sequence capture approach,we obtained orthologous loci for thousands of nuclear loci,as well as mitogenomes from 83 individuals.Subsequently,phylogenetic,population structure and introgression analysis were performed based on the single nucleotide polymorphism(SNP)dataset and nucleotide sequence dataset.We aimed to examine the levels of diversification and introgression between the four chromosomal taxa.Our main results are shown below:1)Results of phylogenetic and population structure analyses both supported that R.thailandensis with 2n = 60 was the first to diverge in this group.However,the relationships among the three other taxa(R.p.chinensis,R.p.pearsoni and R.yunanensis)showed discordance across our different analyses.The results of population structure analyses indicated that R.yunanensis(2n=46)had a closer relationship with R.p.pearsoni(2n=44).Instead,phylogenetic analysis supported a sister relationship between the R.p.chinensis(2n=42)and R.p.pearsoni(2n=44).The later was also supported by Tree Mix and PhyloNet analysis.In addition,R.p.pearsoni exhibited high genetic differentiation and it further diverged into three clades.(clade1,clade2 and clade 3).2)Using different methods of introgression analysis,we have discovered multiple events of ancient introgression between four chromosomal taxa.Firstly,the ABBA-BABA test,Tree Mix and PhyloNet analyses all supported introgression between R.p.chinensis and R.p.pearsoni clade 2;Secondly,the ABBA-BABA test also found evidence of past introgression between R.yunanensis and each of the three clade of R.p.pearsoni.Finaly,we found unexpected evidence of introgression between R.thailandensis and R.yunanensis using ADMIXTURE,the ABBA-BABA test and PhyloNet analysis.Despite this,we found no evidence of recent and/or ongoing introgression between four chromosomal taxa.In conclusion,our current results indicate that the effects of Robertsonian changes(fusions or fissions)on introgression are complicated and they may contribute to reproductive isolation and speciation in concert with other factors(e.g.phenotypic and genic divergence).In the future,to further test the role of chromosomal rearrangements in reproductive isolation and speciation,chromosomelevel sequence alignments will be applied to identify whether other chromosomal changes(e.g.inversion)have occured between four chromosomal taxa here,in particular the two closely related R.pearsoni subspecies(R.p.chinensis and R.p.pearsoni),apart from Robertsonian changes.