Genome sequencing and population history
Whole-genome sequencing of 28 cattle with an average depth of 22.44× obtained 17.3 billion clean reads (Fig. 1a, Additional file 1: Fig. S1 and Table S1 ). In total, 45.2 million SNPs were identified and most of the SNPs were located in the intergenic (61.51%) and intron (31.75%) regions (Additional file 1: Table S2 ). Neighbor-joining trees and principal component analysis (PCA) based on the total SNPs clustered the cattle into two main groups: northern group and southern group (Fig. 1b, c ). The first principal component (PC1), representing 32.41% of the total variation, separated the samples into northern and southern cattle (Fig. 1c ). ADMIXTURE analyses with differentK -values, including K = 2, clearly indicated that cattle samples could be classified into northern and southern cattle. Linkage disequilibrium analysis showed that the southern cattle were attenuating compared with northern cattle (Fig. 1d , Additional file 1: Fig. S2 ), suggesting a higher frequency of genetic recombination in southern cattle.
The demographic history of cattle conducted by the pairwise sequentially markoyian coalescent (PSMC) [22] model showed two bottlenecks and two expansions, with population peaks at ~50 and ~700 Kya (kilo years ago) and population bottlenecks at ~30 and 400 Kya, respectively (Fig. 1f ). There were two sharp declines in population both occurred during the glacial period, consistent with the idea that environmental temperature has a determinable impact on population size. Moreover, similar historical patterns appeared in many other mammals, such as the giant panda, yak and sub-nosed monkey [23-25]. Global glaciations are the most probable cause for a sudden change in the global climate, and this extremely cold climate directly affected the decline of species populations. In addition, after the Naynayxungla Glaciation, northern cattle experienced a long-term bottleneck until 70 Kya. In contrast, the effective population size (N e) of southern cattle recovered rapidly (Fig. 1f ), which is consistent with previous studies [26-28], and might be explained by the improved living environment in the south during the glaciation [29]. At ~60 Kya, HN and YN cattle showed different trends of N e. Specifically, the N e of HN cattle increased rapidly (Fig. 1f ), probably because of the geographical location of Hainan, a small and comparatively isolated island, which lead to a better environment that, lacked of predators, thereby encouraging the survival and reproduction of HN cattle. According to mitochondrial DNA haplotypes, B. taurus (northern cattle) andB. indicus (southern cattle) are both derived from the extinct wild aurochs (Bos primigenius ) and the divergence between the two species dates back to 250,000 years ago [30].