title: Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.
abstract: BACKGROUND
  The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds.
  
  
  RESULTS
  Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals.
  
  
  CONCLUSIONS
  Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.
authors.forename: Huashui
authors.initials: H
authors.lastname: Ai
authors.forename: Bin
authors.initials: B
authors.lastname: Yang
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Xianhua
authors.initials: X
authors.lastname: Xie
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, P, R China. renjunjxau@hotmail.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000531:Altitude; D000626:Aminopeptidases / Q000235:genetics; D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D005075:Biological Evolution; D056426:Genetic Loci; D005828:Genetics, Population; D016678:Genome; D005838:Genotype; D064799:Hypoxia-Inducible Factor-Proline Dioxygenases / Q000235:genetics; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D016194:Receptors, N-Methyl-D-Aspartate / Q000235:genetics; D012641:Selection, Genetic; D013552:Swine; D018609:Tibet
chemical_list: D000626:Aminopeptidases; D051792:Basic Helix-Loop-Helix Proteins; D064799:Hypoxia-Inducible Factor-Proline Dioxygenases; D016194:Receptors, N-Methyl-D-Aspartate