title: Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.
abstract: Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Huashui
authors.initials: H
authors.lastname: Ai
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Huang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Likai
authors.initials: L
authors.lastname: Mao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Leilei
authors.initials: L
authors.lastname: Cui
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Yao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Lisheng
authors.initials: L
authors.lastname: Zhou
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Han
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Silong
authors.initials: S
authors.lastname: Sun
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Xianhua
authors.initials: X
authors.lastname: Xie
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Boxian
authors.initials: B
authors.lastname: Lai
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Su
authors.affiliation: BGI-Tech, BGI-Shenzhen, Shenzhen, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Yang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Wenjiang
authors.initials: W
authors.lastname: Deng
authors.affiliation: 1] BGI-Tech, BGI-Shenzhen, Shenzhen, China. [2] Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
mesh_terms: D000064:Acclimatization / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D002681:China; D004777:Environment; D019143:Evolution, Molecular; D005260:Female; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D005828:Genetics, Population / Q000379:methods; D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods; D006239:Haplotypes; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017386:Sequence Homology, Amino Acid; D013552:Swine; D014960:X Chromosome