S1 File -

The UPGMA phylogenetic tree show that the 490 sequences of 15 Tibetan sheep populations (Fig A). The UPGMA phylogenetic tree show that the 64 sequences of 12 Tibetan sheep populations (Fig B). The UPGMA phylogenetic tree show that the 81 sequences of 14 Tibetan sheep populations (Fig C). Median-joining networks for the mtDNA D-loop in the control region show that 636 sequences of 15 Tibetan sheep populations and six reference breeds fall into five distinct cluster haplogroup A, haplogroup B, haplogroup C, haplogroup D and haplogroup E, respectively. The majorities of the 490 individuals were grouped in haplogroup A, followed by haplogroup B (64) and C (81); however, only one animal from LZ03 belonged to haplogroup D. The AW population was composed of one haplogroup, the DM population was composed of two haplogroups, and the remaining 13 Tibetan sheep populations were composed of three haplogroups (Fig D). The mismatch distribution of the complete dataset of the mtDNA types of Tibetan sheep of the four lineages on the Qinghai-Tibetan Plateau areas showed that there were two major peaks, with maximum values at 4 and 27 pairwise differences and two smaller peaks at 45 and 51 pairwise differences (Fig E). Mitochondrial genomes of the 6 reference breeds included in the phylogenetic analyses in this study (Table A). The length of the complete mtDNA D-loop sequence in fifteen Tibetan sheep populations (Table B). Base pair composition of mtDNA D-loop of fifteen Tibetan sheep populations (Table C). Gene flow (Nm) of the sequence (above the diagonals) and Nm of the haplotype (below the diagonals) between fifteen Tibetan sheep populations (Table D). Dxy (the average number of nuc. subs. per site between populations) (above the diagonals) and Da (the number of net nuc. subs. per site between populations) (below the diagonals) of the difference in the number of nucleotides per site differences between fifteen Tibetan sheep populations (Table E). Hierarchical analysis of the molecular variance (AMOVA) of the D-loop region of mtDNA for fifteen Tibetan sheep populations (Table F). Neutrality tests for fifteen Tibetan sheep populations (Table G).
(XLSX)