Sample Preparation and Sequencing

We sampled 77 Chinese native sheep (O. aries) that include 21 representative breeds adapted to various local environments, such as extreme environments from Tibetan area on the Qinghai–Tibetan Plateau (defined as ‘plateau’, altitude >4,000 m), high-altitude region (altitude >1,500 m), Taklimakan Desert region (defined as ‘desert’, average annual precipitation <10 mm) and arid zone (average annual precipitation <400 mm, representing arid and semi-arid regions; Piao et al. 2010), as well as contrasting environments in Eastern China (altitude <100 m and average annual precipitation >600 mm), low-altitude region (altitude <1,300 m) and humid zone (average annual precipitation >400 mm, representing humid and semi-humid regions; Piao et al. 2010; fig. 1A and B, supplementary tables S1 and S2, Supplementary Material online). The environments encompassed here represent the typical environments that sheep inhabit. In addition, we also collected three wild species of the subfamily Caprinae, viz O. aries musimon from the Island of Sappi, Finland (descendant from the population in the Mediterranean Island of Sardinia), O. a. polii and C. ibex from Kashgar, Xinjiang, China (one animal from each species; supplementary table S1, Supplementary Material online). We sequenced genomes of the 80 samples using next-generation sequencing technology on an Illumina HiSeq 2000 platform (Illumina, San Diego, CA, USA). High-quality reads were aligned against the reference sheep genome assembly Oar_v3.1.75 using Burrows-Wheeler Aligner (BWA; Li and Durbin 2009) software. The program SAMtools v0.1.19 (Li et al. 2009) was used to identify SNPs and short insertions and deletions (indels, length <100 bp). The high-quality SNPs obtained here were subsequently regarded as the ‘called high-quality SNPs’ and used in the SNP summary, regions of homozygosity, linkage disequilibrium, selective sweep, GO and target gene analyses. The overall analysis pipeline is detailed in supplementary figure S14, Supplementary Material online.