Sampling, morphological data and species tree. (a) Map showing the sampling localities of Rhinolophus affinis used in this study (modified from Mao et al. 2013 ). Populations are presented as circles in which individuals are coloured based on the subspecies membership (R. a. himalayanus: blue; R. a. macrurus: orange; R. a. hainanus: green); (b) Plot showing echolocation call frequency (kHz) and forearm (mm) data for a subset of bats from the three subspecies (R. a. himalayanus, n = 43; R. a. macrurus, n = 39; R. a. hainanus, n = 32). Downward and upward triangles correspond to male and female bats, respectively. Full details are provided in Additional file 3: Table S3; (c) Species tree based on all nuclear markers using BEST.