Amaral AJ, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, Ramos-Onsins SE, et al. Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA. PLoS One. 2011;6(4):e14782.
Article
PubMed Central
CAS
PubMed
Google Scholar
Akey JM, Ruhe AL, Akey DT, Wong AK, Connelly CF, Madeoy J, et al. Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci U S A. 2010;107(3):1160–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, et al. Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A. 2012;109(48):19529–36.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilkinson S, Lu ZH, Megens HJ, Archibald AL, Haley C, Jackson IJ, et al. Signatures of diversifying selection in European pig breeds. PLoS Genet. 2013;9(4):e1003453.
Article
PubMed Central
CAS
PubMed
Google Scholar
Purugganan MD, Fuller DQ. The nature of selection during plant domestication. Nature. 2009;457(7231):843–8.
Article
CAS
PubMed
Google Scholar
Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet. 2004;5(3):202–12.
Article
CAS
PubMed
Google Scholar
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012;491(7424):393–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, et al. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude. Science. 2010;329(5987):75–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sabeti PC. Positive Natural Selection in the Human Lineage. Science. 2006;312(5780):1614–20.
Article
CAS
PubMed
Google Scholar
Lewontin RC, Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics. 1973;74(1):175–95.
PubMed Central
CAS
PubMed
Google Scholar
Akey JM. Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res. 2009;19(5):711–22.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maynard-Smith J, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974;23(1):23–35.
Article
Google Scholar
Giuffra E, Kijas JM, Amarger V, Carlborg O, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics. 2000;154(4):1785–91.
PubMed Central
CAS
PubMed
Google Scholar
Larson G, Dobney K, Albarella U, Fang M, Matisoo-Smith E, Robins J, et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science. 2005;307(5715):1618–21.
Article
CAS
PubMed
Google Scholar
Wu GS, Yao YG, Qu KX, Ding ZL, Li H, Palanichamy MG, et al. Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol. 2007;8(11):R245.
Article
PubMed Central
PubMed
Google Scholar
Amaral AJ, Megens HJ, Crooijmans RPMA, Heuven HCM, Groenen MAM. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics. 2008;179(1):569–79.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bosse M, Megens HJ, Frantz LAF, Madsen O, Larson G, Paudel Y, et al. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat Commun. 2014;5:4392.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jones G. Genetic aspects of domestication, common breeds and their origin. In The Genetics of the Pig. Edited by Rothschild MF, Ruvinsky A. CAB International, Wallingford, UK; 1998:17-50.
Darwin C. The variation of animals and plants under domestication. John Murray, London. 1868.
Wiener P, Wilkinson S. Deciphering the genetic basis of animal domestication. Proc Biol Sci Royal Soc. 2011;278(1722):3161–70.
Article
Google Scholar
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007;449(7164):913–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Innan H, Kim Y. Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics. 2008;179(3):1713–20.
Article
PubMed Central
PubMed
Google Scholar
Kim Y, Gulisija D. Signatures of recent directional selection under different models of population expansion during colonization of new selective environments. Genetics. 2010;184(2):571–85.
Article
PubMed Central
CAS
PubMed
Google Scholar
Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol. 2006;4(3):e72.
Article
PubMed Central
PubMed
Google Scholar
Kim TH, Kim KS, Choi BH, Yoon DH, Jang GW, Lee KT, et al. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci. 2005;83(10):2255–63.
CAS
PubMed
Google Scholar
Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464(7288):587–91.
Article
CAS
PubMed
Google Scholar
Qanbari S, Pausch H, Jansen S, Somel M, Strom TM, Fries R, et al. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet. 2014;10(2):e1004148.
Article
PubMed Central
PubMed
Google Scholar
Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495(7441):360–4.
Article
CAS
PubMed
Google Scholar
Alexander DH, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics. 2011;12:246.
Article
PubMed Central
PubMed
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75.
Article
PubMed Central
CAS
PubMed
Google Scholar
Moltke I, Albrechtsen A. RelateAdmix: a software tool for estimating relatedness between admixed individuals. Bioinformatics. 2014;30(7):1027–8.
Article
CAS
PubMed
Google Scholar
Ottoni C, Flink LG, Evin A, Georg C, De Cupere B, Van Neer W, et al. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol. 2013;30(4):824–32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, et al. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 2012;10(2):e1001258.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hu ZL, Park CA, Wu XL, Reecy JM. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 2013;41(Database issue):D871–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Niswender CM, Conn PJ. Metabotropic glutamate receptors: physiology, pharmacology, and disease. Annu Rev Pharmacol Toxicol. 2010;50:295–322.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013;45(12):1431–8.
Article
CAS
PubMed
Google Scholar
Knott SA, Marklund L, Haley CS, Andersson K, Davies W, Ellegren H, et al. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics. 1998;149(2):1069–80.
PubMed Central
CAS
PubMed
Google Scholar
da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
Gratacos M, Escaramis G, Bustamante M, Saus E, Aguera Z, Bayes M, et al. Role of the neurotrophin network in eating disorders’ subphenotypes: body mass index and age at onset of the disease. J Psychiatr Res. 2010;44(13):834–40.
Article
PubMed
Google Scholar
Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, et al. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One. 2009;4(8):e6524.
Article
PubMed Central
PubMed
Google Scholar
Ai H, Huang L, Ren J. Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers. PLoS One. 2013;8(2):e56001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang GD, Zhai W, Yang HC, Fan RX, Cao X, Zhong L, et al. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun. 2013;4:1860.
Article
PubMed
Google Scholar
O’Connor RM, Thakker DR, Schmutz M, van der Putten H, Hoyer D, Flor PJ, et al. Adult siRNA-induced knockdown of mGlu7 receptors reduces anxiety in the mouse. Neuropharmacology. 2013;72:66–73.
Article
PubMed
Google Scholar
Sinisalo A, Niemi JK, Heinonen M, Valros A. Tail biting and production performance in fattening pigs. Livest Sci. 2012;143(2):220–5.
Article
Google Scholar
Meruvu S, Hugendubler L, Mueller E. Regulation of adipocyte differentiation by the zinc finger protein ZNF638. J Biol Chem. 2011;286(30):26516–23.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed Central
PubMed
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One. 2012;7(7):e37558.
Article
PubMed Central
CAS
PubMed
Google Scholar
Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81(5):1084–97.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009;5(10):e1000695.
Article
PubMed Central
PubMed
Google Scholar
Hudson RR. Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337–8.
Article
CAS
PubMed
Google Scholar
Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992;132(2):583–9.
PubMed Central
CAS
PubMed
Google Scholar
Cavalli-Sforza L. Human diversity. In: Proceedings of the 12th International Congress of Genetics: 1969; Tokyo. 1969. p. 405–16.
Google Scholar
Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature. 2002;419(6909):832–7.
Article
CAS
PubMed
Google Scholar
Gautier M, Vitalis R. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics. 2012;28(8):1176–7.
Article
CAS
PubMed
Google Scholar