We collected blood, muscle, and skin samples of 65 wild red pandas from seven main geographic populations for whole-genome resequencing. Of the 65 individuals, 18 individuals were from the middle Himalayan Mountains (MH), 3 from the eastern Himalayan Mountains (EH), 13 from the Gaoligong Mountains (GLG), 1 from the Saluli Mountains (SLL), 12 from the Xiaoxiangling Mountains (XXL), 8 from the Liangshan Mountains (LS), and 10 from the Qionglai Mountains (QL) (Fig. 2A and table S2). For Y chromosome SNP genotyping, we first used red panda–specific sex determination primers (27) to identify the sexes of the available wild samples. As a result, 49 wild male red pandas were used, including 13 from the MH population, 2 from EH, 10 from GLG, 8 from XXL, 5 from LS, and 11 from QL (table S2). For mitochondrial genome assembly, we successfully assembled 49 complete mitochondrial genomes from the whole-genome resequencing data for 49 of 65 wild red pandas, including 13 from MH, 2 from EH, 9 from GLG, 12 from XXL, 4 from LS, and 9 from QL (table S2).

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