title: Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA.
abstract: The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.
authors.affiliation: State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. greger.larson@durham.ac.uk
authors.forename: Greger
authors.initials: G
authors.lastname: Larson
authors.forename: Ranran
authors.initials: R
authors.lastname: Liu
authors.forename: Xingbo
authors.initials: X
authors.lastname: Zhao
authors.forename: Jing
authors.initials: J
authors.lastname: Yuan
authors.forename: Dorian
authors.initials: D
authors.lastname: Fuller
authors.forename: Loukas
authors.initials: L
authors.lastname: Barton
authors.forename: Keith
authors.initials: K
authors.lastname: Dobney
authors.forename: Qipeng
authors.initials: Q
authors.lastname: Fan
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Gu
authors.forename: Xiao-Hui
authors.initials: XH
authors.lastname: Liu
authors.forename: Yunbing
authors.initials: Y
authors.lastname: Luo
authors.forename: Peng
authors.initials: P
authors.lastname: Lv
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
authors.forename: Ning
authors.initials: N
authors.lastname: Li
mesh_terms: D000383:Agriculture / Q000266:history*; D025041:Animal Migration; D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D004272:DNA, Mitochondrial / Q000235:genetics*; D003710:Demography; D019143:Evolution, Molecular; D005202:Asia, Eastern; D005580:Fossils; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D049690:History, Ancient; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D034421:Sus scrofa
chemical_list: D004272:DNA, Mitochondrial
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12963-8
references.pmid: 15317936
references.citation: Mol Biol Evol. 1999 Jan;16(1):37-48
references.pmid: 10331250
references.citation: Trends Genet. 2006 Mar;22(3):139-55
references.pmid: 16458995
references.citation: Genetics. 2000 Apr;154(4):1785-91
references.pmid: 10747069
references.citation: Anim Genet. 2007 Oct;38(5):499-505
references.pmid: 17894564
references.citation: Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15276-81
references.pmid: 17855556
references.citation: BMC Evol Biol. 2006 Sep 22;6:73
references.pmid: 16995938
references.citation: Bioinformatics. 1998;14(9):817-8
references.pmid: 9918953
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Science. 2003 Apr 25;300(5619):597-603
references.pmid: 12714734
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):4834-9
references.pmid: 17360400
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5523-8
references.pmid: 19307567
references.citation: Genet Sel Evol. 2008 Jan-Feb;40(1):103-28
references.pmid: 18096118
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5123-8
references.pmid: 18347332
references.citation: Mol Phylogenet Evol. 2010 Mar;54(3):680-6
references.pmid: 19900568
references.citation: Biol Lett. 2008 Dec 23;4(6):752-4
references.pmid: 18713712
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7367-72
references.pmid: 19383791
references.citation: Mol Phylogenet Evol. 2006 Jan;38(1):12-9
references.pmid: 16275023
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10308-13
references.pmid: 18663216
references.citation: Science. 2005 Mar 11;307(5715):1618-21
references.pmid: 15761152
references.citation: Genome Biol. 2007;8(11):R245
references.pmid: 18021448
references.citation: Zoolog Sci. 2002 Nov;19(11):1329-35
references.pmid: 12499677
references.citation: Science. 2009 Mar 20;323(5921):1607-10
references.pmid: 19299619