Untangling the hybrid nature of modern pig genomes: A mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

Molecular Ecology

Volumn 23, Issue 16, 2014, Pages 4089-4102

  Bosse, Mirte ^a   Megens, Hendrik Jan ^a   Madsen, Ole ^a   Frantz, Laurent A F ^a   Paudel, Yogesh ^a   Crooijmans, Richard P M A ^a   Groenen, Martien A M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

conservation genetics; domestication; hybridization; identity by descent; introgression; Sus scrofa

Indexed keywords

MYA; SUIDAE; SUS SCROFA;

ANIMAL; ASIA; DNA SEQUENCE; EUROPE; GENETIC VARIATION; GENETICS; GENOME; HAPLOTYPE; HYBRIDIZATION; PHYLOGENY; PIG; POPULATION GENETICS;

ANIMALS; ASIA; EUROPE; GENETIC VARIATION; GENETICS, POPULATION; GENOME; HAPLOTYPES; HYBRIDIZATION, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SUS SCROFA;

EID: 84905494162     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12807     Document Type: Article

References (52)

1. Abi-Rached L, Jobin MJ, Kulkarni S, et al,. (2011) The shaping of modern human immune systems by multiregional admixture with archaic humans. Science, 334, 89-94.
2. Aguilar A, Roemer G, Debenham S, et al,. (2004) High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. Proceedings of the National Academy of Sciences USA, 101, 3490-3494.
3. Alexander DH, Novembre J, Lange K, (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655-1664.
4. Alves PC, Pinheiro I, Godinho R, et al,. (2010) Genetic diversity of wild boar populations and domestic pig breeds (Sus scrofa) in South-western Europe. Biological Journal of the Linnean Society, 101, 797-822.
5. Begun DJ, Aquadro CF, (1992) Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature, 356, 519-520.
6. Bosse M, Megens H-J, Madsen O, et al,. (2012) Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genetics, 8, e1003100.
7. Browning BL, Browning SR, (2011) A fast, powerful method for detecting identity by descent. American Journal of Human Genetics, 88, 173-182.
8. Castric V, Bechsgaard J, Schierup MH, Vekemans X, (2008) Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genetics, 4, e1000168.
9. Charbonnel N, Pemberton J, (2005) A long-term genetic survey of an ungulate population reveals balancing selection acting on MHC through spatial and temporal fluctuations in selection. Heredity, 95, 377-388.
10. Fang MY, Andersson L, (2006) Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication. Proceedings of the Royal Society B-Biological Sciences, 273, 1803-1810.
11. Fang M, Berg F, Ducos A, Andersson L, (2006) Mitochondrial haplotypes of European wild boars with 2n=36 are closely related to those of European domestic pigs with 2n=38. Animal Genetics, 37, 459-464.
12. Fang L, Ye J, Li N, et al,. (2008) Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome. Chinese Science Bulletin, 53, 746-750.
13. Felsenstein J,. (2005). PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
14. Frantz L, Schraiber J, Madsen O, et al,. (2013) Genomic sequencing provides fine scale inference of evolutionary history. Genome Biology, 14, R107.
15. Genov PV, (1999) A review of the cranial characteristics of the wild boar (Sus scrofa Linnaeus, 1758), with systematic conclusions. Mammal Review, 29, 205-238.
16. Giuffra E, Kijas JM, Amarger V, et al,. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 154, 1785-1791.
17. Goedbloed D, Megens H, van Hooft P, et al,. (2013) Genome-wide SNP analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations. Molecular Ecology, 22, 856-866.
18. Groenen MAM, Archibald AL, Uenishi H, et al,. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398.
19. Groves C,. (2008) Current views on the taxonomy and zoogeography of the genus Sus. In Pigs and Humans: 10,000 Years of Interaction (eds, Albarella U, Dobney K, Ervynck A, Rowley-Conwy P,), pp. 15-29. Oxford University Press: Oxford, UK.
20. Harris K, Nielsen R, (2013) Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genetics, 9, e1003521.
21. Hedrick PW, (2013) Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Molecular Ecology, 22, 4606-4618.
22. Henn BM, Botigue LR, Gravel S, et al,. (2012) Genomic ancestry of north Africans supports back-to-Africa migrations. PLoS Genetics, 8, e1002397.
23. Herrero-Medrano JM, Megens HJ, Crooijmans RP, et al,. (2013a) Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed. Animal Genetics, 44, 259-266.
24. Herrero-Medrano JM, Megens HJ, Groenen MAM, et al,. (2013b) Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genetics, 14, 106.
25. Jeong C, Alkorta-Aranburu G, Basnyat B, et al,. (2014) Admixture facilitates genetic adaptations to high altitude in Tibet. Nature Communications, 5, 3281.
26. Jimenez JA, Hughes KA, Alaks G, et al,. (1994) An experimental study of inbreeding depression in a natural habitat. Science, 266, 271-273.
27. Keller LF, Waller DM, (2002) Inbreeding effects in wild populations. Trends in Ecology and Evolution, 17, 230-241.
28. Kijas JMH, Andersson L, (2001) A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. Journal Molecular Evolution, 52, 302-308.
29. Lacy RC, Alaks G, Walsh A, (1996) Hierarchical analysis of inbreeding depression in Peromyscus polionotus. Evolution, 50, 2187-2200.
30. Larson G, Dobney K, Albarella U, et al,. (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science, 307, 1618-1621.
31. Larson G, Albarella U, Dobney K, et al,. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences USA, 104, 15276-15281.
32. Lercher MJ, Hurst LD, (2002) Human SNP variability and mutation rate are higher in regions of high recombination. Trends in Genetics., 18, 337-340.
33. Li H, Durbin R, (2011) Inference of human population history from individual whole-genome sequences. Nature, 475, 493-496.
34. Li H, Handsaker B, Wysoker A, et al,. (2009) The sequence alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
35. Megens HJ, Groenen MAM, (2012) Domesticated species form a treasure-trove for molecular characterization of Mendelian traits by exploiting the specific genetic structure of these species in across-breed genome wide association studies. Heredity, 109, 1-3.
36. Megens HJ, Crooijmans R, Cristobal MS, et al,. (2008) Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genetics Selection Evolution, 40, 103-128.
37. Meijaard E, d'Huart JP, Oliver WLR, (2011). In Handbook of the Mammals of the World Vol 2 (eds, Wilson DE, Mittermeier RA,), pp. 248-291. Lynx Edicions, Barcelona, Spain.
38. Merks JWM, Mathur PK, Knol EF, (2012) New phenotypes for new breeding goals in pigs. Animal, 6, 535-543.
39. Miller W, Schuster S, Welch A, et al,. (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences USA, 109, E2382-E2390.
40. Ottoni C, Girland Flink L, Evin A, et al,. (2013) Pig domestication and human-mediated dispersal in western eurasia revealed through ancient DNA and geometric morphometrics. Molecular Biology Evolution, 30, 824-832.
41. Palamara PF, Lencz T, Darvasi A, Pe'er I, (2012) Length distributions of identity by descent reveal fine-scale demographic history. American Journal of Human Genetics, 91, 809-822.
42. Porter V, (1993) Pigs-a Handbook to the Breeds of the World. Helm Information, Mountfield, East Sussex, UK. 256 pp.
43. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure usingmultilocus genotype data. Genetics, 155, 945-959.
44. Purcell S, Neale B, Todd-Brown K, et al,. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559-575.
45. Ralph P, Coop G, (2013) The geography of recent genetic ancestry across Europe. PLoS Biology, 11, e1001555.
46. Ramirez O, Ojeda A, Tomas A, et al,. (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Molecular Biology Evolution, 26, 2061-2072.
47. Rousset F, (2008) Genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.
48. Song Y, Endepols S, Klemann N, et al,. (2011) Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice. Current Biology, 21, 1296-1301.
49. Staubach F, Lorenc A, Messer PW, et al,. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genetics, 8, e1002891.
50. Tortereau F, Servin B, Frantz LAF, et al,. (2012) A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics, 13, 586.
51. Weir BS, Cockerham CC, (1984) Estimating f-statistics for the analysis of population structure. Evolution, 38, 1358.
52. White S, (2011) From globalized pig breeds to capitalist pigs: a study in animals cultures and evolutionary history. Environmental History, 16, 94-120.