Phylogenetic trees based on mitochondrial and nuclear markers inferred by maximum-likelihood (ML) analyses. Phylograms were obtained with the program RaxML88 based on the combined 16 s, co1, cyt and nd4 mtDNA data (left) and the bfib7, ccnb2 and rag1 nuDNA data set (right). Scutiger (S.) is followed by the species name and by locality information (Table S5 for sample IDs). An asterisk above branches indicates bootstrap support values ≥80. For clarity, branches representing individuals belonging to the same taxonomic unit were collapsed. Colour codes correspond to those of localities in Fig. 1 and Supplementary Fig. S3. #One sample (A2014-13) from Kanjiroba Himal was placed differently in the mtDNA and nDNA tree (for details text). Inconsistencies occurring between samples in mitochondrial vs. nuclear trees are explained by availability of either samples or only sequence information from previous work (for details Table S5). C-Tibet = Central Tibet; Dhaulag. N/S = Dhaulagiri North/South; DuK.E/W = Dudh Koshi River East/West; E-Nepal = East Nepal; E-Tibet = East Tibet; Liupan Mts = Liupan Mountains; Nings. = Ningshan; SX = Shaanxi.