Multilocus phylogeny and species delimitation within the philippinensis group (Chiroptera: Rhinolophidae)

Rhinolophids (horseshoe bats) are a widespread and diverse family. Their high level of morphological convergence has made taxonomic identification and estimation of species diversity problematic. The Rhinolophus philippinensis group, which is characterized with huge ears and low echolocation frequency relative to body size, is a specific group among all the rhinolophid groups, but the phylogeny of this group is poorly understood. In this study, we performed integrated analyses of the morphology, acoustic and genetic data and constructed the first multilocus phylogeny for the philippinensis group using four mitochondrial genes, four autosomal introns and one Y-linked intron in 95 specimens representing nine taxa. Phylogenies were constructed based on concatenated phylogenetic methods and a multilocus coalescence approach. The estimated phylogenies revealed the polyphyly of the philippinensis group. Except for R.philippinensis, all the other species in this group formed a monophyletic cluster, named herewith as R.macrotis species group. Phylogenies, genetic and phenotypic divergence, and species delimitation analyses supported the revised status of R.paradoxolophus as a subspecies of R.rex, R. cf. macrotis as a subspecies of R.macrotis, and R.huananus and R. cf. siamensis as junior synonyms of R.siamensis. Significant discordances were found between the mitochondrial and nuclear gene trees, suggesting incomplete lineage sorting or ancient introgression events within the philippinensis group. The macrotis group appeared to have undergone a rapid radiation approximately 2.57 million years ago during the early Pleistocene period due to palaeoclimatic oscillations. Reconstruction of the ancestral ranges suggested a wide distribution of the common ancestor for the philippinensis and macrotis groups.