3.2 Orthologous genes identification and phylogenetic tree
We identified one-to-one orthologous gene pairs across 6 species sequenced (R. episcopus , R. siamensis , R. rex ,R. marshalli , R. osgoodi , and R. pusillus ) and two reference genomes (R. sinicus and H. armiger ). In total, 1,233 one-to-one genes were retained for the downstream analyses (Figure 1). Our final dataset, therefore, included eight species and 1,233 genes.
High ML bootstrap values in our constructed phylogenetic tree have well-resolved phylogenetic relationships between species of themacrotis group and other species (Figre 2). Hipposideros armiger showed as an outgroup in the topological relationship, and all rhinolophids species clustered in one clade. Species of themacrotis group clustered together, and closely related toR. pusillus . Among the macrotis group, the R. macrotis complex (R. episcopus , R. siamensis and R. osgoodi ) clustered in one highly supported clade, and formed paraphyly with the clade of R. marshalli and R. rex . The topology of our tree was congruent with previous phylogenies based on the mitochondrial genome (Zhang et al., 2021).