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).