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].