Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

English version České info

The DNA of domesticated plants and animals contains information about how species were domesticated, exported, and bred by early farmers. Modern breeds were developed by lengthy and complex processes; however, our use of 134 breeds and new analytical models enabled us to reveal some of the processes that created modern cattle diversity. In Asia, Africa, North and South America, humpless (Bos t. taurus or taurine) and humped (Bos t. indicus or indicine) cattle were crossbred to produce hybrids adapted to the environment and local production systems. The history of Asian cattle involves the domestication and admixture of several species whereas African taurines arose through the introduction of domesticated Fertile Crescent taurines and their hybridization with wild African aurochs. African taurine genetic background is commonly observed among European Mediterranean breeds. The absence of indicine introgression within most European taurine breeds, but presence within three Italian breeds is consistent with at least two separate migration waves of cattle to Europe, one from the Middle East which captured taurines in which indicine introgression had already occurred and the second from western Africa into Spain with no indicine introgression. This second group seems to have radiated from Spain into the Mediterranean resulting in a cline of African taurine introgression into European taurines.

Vyšlo v časopise: Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle. PLoS Genet 10(3): e32767. doi:10.1371/journal.pgen.1004254
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004254

Souhrn

Zdroje

1. NovembreJ, RamachandranS (2011) Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 12: 245–274 Available: http://www.ncbi.nlm.nih.gov/pubmed/21801023.

2. GibbsRA, TaylorJF, Van TassellCP, BarendseW, EversoleKA, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattlebreeds. Science (80-) 324: 528–532 Available: http://www.ncbi.nlm.nih.gov/pubmed/19390050.

3. DeckerJE, PiresJC, ConantGC, McKaySD, HeatonMP, et al. (2009) Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci U S A 106: 18644–18649 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2765454&tool=pmcentrez&rendertype=abstract. Accessed 13 August 2013.

4. GautierM, LaloëD, Moazami-GoudarziK (2010) Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS One 5: e13038 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2948016&tool=pmcentrez&rendertype=abstract. Accessed 13 September 2013.

5. KijasJW, TownleyD, DalrympleBP, HeatonMP, MaddoxJF, et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One 4: e4668 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2652362&tool=pmcentrez&rendertype=abstract. Accessed 29 February 2012.

6. VonholdtBM, PollingerJP, LohmuellerKE, HanE, ParkerHG, et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898–902 Available: http://www.ncbi.nlm.nih.gov/pubmed/20237475. Accessed 2 March 2012.

7. McCueME, BannaschDL, PetersenJL, GurrJ, BaileyE, et al. (2012) A high density SNP array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 8: e1002451 Available: http://dx.plos.org/10.1371/journal.pgen.1002451. Accessed 16 January 2012.

8. SchachererJ, ShapiroJA, RuderferDM, KruglyakL (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342–345 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2782482&tool=pmcentrez&rendertype=abstract. Accessed 31 July 2013.

9. YangH, WangJR, DidionJP, BuusRJ, BellTA, et al. (2011) Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 43: 648–655 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3125408&tool=pmcentrez&rendertype=abstract.

10. StaubachF, LorencA, MesserPW, TangK, PetrovDA, et al. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet 8: e1002891 Available: http://dx.plos.org/10.1371/journal.pgen.1002891. Accessed 31 July 2013.

11. McNallyKL, ChildsKL, BohnertR, DavidsonRM, ZhaoK, et al. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106: 12273–12278 Available: http://www.pnas.org/cgi/content/long/106/30/12273. Accessed 31 July 2013.

12. ZhaoK, WrightM, KimballJ, EizengaG, McClungA, et al. (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5: e10780 Available: http://dx.plos.org/10.1371/journal.pone.0010780. Accessed 31 July 2013.

13. YanJ, ShahT, WarburtonML, BucklerES, McMullenMD, et al. (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One 4: e8451 Available: http://dx.plos.org/10.1371/journal.pone.0008451. Accessed 31 July 2013.

14. Van HeerwaardenJ, DoebleyJ, BriggsWH, GlaubitzJC, GoodmanMM, et al. (2011) Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci U S A 108: 1088–1092 Available: http://www.pnas.org/cgi/content/long/1013011108v1. Accessed 4 December 2012.

15. Van HeerwaardenJ, HuffordMB, Ross-IbarraJ (2012) Historical genomics of North American maize. Proc Natl Acad Sci U S A 109: 12420–12425 Available: http://www.pnas.org/cgi/content/long/109/31/12420. Accessed 31 July 2013.

16. HuffordMB, LubinksyP, PyhäjärviT, DevengenzoMT, EllstrandNC, et al. (2013) The genomic signature of crop-wild introgression in maize. PLoS Genet 9: e1003477 Available: http://dx.plos.org/10.1371/journal.pgen.1003477. Accessed 31 July 2013.

17. MylesS, BoykoAR, OwensCL, BrownPJ, GrassiF, et al. (2011) Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 108: 3530–3535 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3048109&tool=pmcentrez&rendertype=abstract. Accessed 14 March 2012.

18. CavanaghCR, ChaoS, WangS, HuangBE, StephenS, et al. (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci U S A 110: 8057–8062 Available: http://www.pnas.org/cgi/content/long/110/20/8057. Accessed 31 July 2013.

19. PattersonNJ, PriceAL, ReichD (2006) Population structure and eigenanalysis. PLoS Genet 2: e190 Available: http://www.ncbi.nlm.nih.gov/pubmed/17194218. Accessed 12 March 2012.

20. PickrellJK, PritchardJK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967 Available: http://dx.plos.org/10.1371/journal.pgen.1002967. Accessed 16 November 2012.

21. AlexanderDH, NovembreJ, LangeK (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655–1664 Available: http://www.ncbi.nlm.nih.gov/pubmed/19648217.

22. LoftusRT, MacHughDE, BradleyDG, SharpPM, CunninghamP (1994) Evidence for two independent domestications of cattle. Proc Natl Acad Sci U S A 91: 2757–2761 Available: http://www.ncbi.nlm.nih.gov/pubmed/8146187.

23. McVeanG (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5: e1000686 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2757795&tool=pmcentrez&rendertype=abstract. Accessed 11 July 2011.

24. DiamondJ (2002) Evolution, consequences and future of plant and animal domestication. Nature 418: 700–707 Available: http://www.ncbi.nlm.nih.gov/pubmed/12167878.

25. Felius M (1995) Cattle breeds - an encyclopedia. Doetinchem, Netherlands: Misset.

26. EvannoG, RegnautS, GoudetJ (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620 Available: http://www.ncbi.nlm.nih.gov/pubmed/15969739. Accessed 3 October 2012.

27. ReichD, ThangarajK, PattersonNJ, PriceAL, SinghL (2009) Reconstructing Indian population history. Nature 461: 489–494 Available: http://www.ncbi.nlm.nih.gov/pubmed/19779445.

28. LoftusRT, ErtugrulO, HarbaAH, El-BarodyMA, MacHughDE, et al. (1999) A microsatellite survey of cattle from a centre of origin: the Near East. Mol Ecol 8: 2015–2022 Available: http://www.ncbi.nlm.nih.gov/pubmed/10632853. Accessed 5 September 2013.

29. ChristianD (2000) Silk roads or steppe roads? The silk roads in world history. J World Hist 11: 1–26 Available: http://muse.jhu.edu/journals/jwh/summary/v011/11.1christian.html. Accessed 6 January 2014.

30. StockF, Gifford-GonzalezD (2013) Genetics and African Cattle Domestication. African Archaeol Rev 30: 51–72 Available: http://link.springer.com/10.1007/s10437-013-9131-6.

31. LinseeleV (2004) Size and size change of the African aurochs during the Pleistocene and Holocene. J African Archaeol 2: 165–185 Available: http://www.african-archaeology.de/index.php?page_id=154&journal_id=6&pdf_id=96. Accessed 10 December 2013.

32. TroyCS, MacHughDE, BaileyJF, MageeDA, LoftusRT, et al. (2001) Genetic evidence for Near-Eastern origins of European cattle. Nature 410: 1088–1091 Available: http://www.ncbi.nlm.nih.gov/pubmed/11323670.

33. BradleyDG, MacHughDE, CunninghamP, LoftusRT (1996) Mitochondrial diversity and the origins of African and European cattle. Proc Natl Acad Sci U S A 93: 5131–5135 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=39419&tool=pmcentrez&rendertype=abstract.

34. HanotteO, BradleyDG, OchiengJW, VerjeeY, HillEW, et al. (2002) African pastoralism: genetic imprints of origins and migrations. Science (80-) 296: 336–339 Available: http://www.ncbi.nlm.nih.gov/pubmed/11951043.

35. MarshallF, WeissbrodL (2011) Domestication Processes and Morphological Change. Curr Anthropol 52: S397–S413 Available: http://www.jstor.org/stable/info/10.1086/658389. Accessed 24 August 2013.

36. Pérez-PardalL, RoyoLJ, Beja-Pereiraa, ChenS, CantetRJC, et al. (2010) Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites. Heredity (Edinb) 105: 511–519 Available: http://www.ncbi.nlm.nih.gov/pubmed/20332805. Accessed 11 September 2013.

37. FalushD, StephensM, PritchardJK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1462648&tool=pmcentrez&rendertype=abstract.

38. LarsonG, BurgerJ (2013) A population genetics view of animal domestication. Trends Genet 29: 197–205 Available: http://www.ncbi.nlm.nih.gov/pubmed/23415592. Accessed 22 May 2013.

39. BonfiglioS, GinjaC, De GaetanoA, AchilliA, OlivieriA, et al. (2012) Origin and spread of Bos taurus: new clues from mitochondrial genomes belonging to haplogroup T1. PLoS One 7: e38601 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3369859&tool=pmcentrez&rendertype=abstract. Accessed 9 August 2012.

40. LarsonG, AlbarellaU, DobneyK, Rowley-ConwyP, SchiblerJ, et al. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc Natl Acad Sci U S A 104: 15276–15281 Available: http://www.pnas.org/content/104/39/15276.short. Accessed 28 August 2013.

41. OttoniC, FlinkLG, EvinA, GeörgC, De CupereB, et al. (2013) Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol 30: 824–832 Available: http://www.ncbi.nlm.nih.gov/pubmed/23180578. Accessed 13 September 2013.

42. LarsonG, CucchiT, FujitaM, Matisoo-SmithE, RobinsJ, et al. (2007) Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania. Proc Natl Acad Sci U S A 104: 4834–4839 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1829225&tool=pmcentrez&rendertype=abstract.

43. ErikssonJ, LarsonG, GunnarssonU, Bed'homB, Tixier-BoichardM, et al. (2008) Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4: e1000010 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2265484&tool=pmcentrez&rendertype=abstract. Accessed 22 May 2013.

44. StewartJL (1951) The West African Shorthorn cattle. Their value to Africa as trypanosomiasis-resistant animals. Vet Rec 63: 454.

45. Abi-RachedL, JobinMJ, KulkarniS, McWhinnieA, DalvaK, et al. (2011) The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334: 89–94 Available: http://www.ncbi.nlm.nih.gov/pubmed/21868630. Accessed 6 August 2013.

46. DowningT, LynnDJ, ConnellS, LloydAT, Bhuiyan aK, et al. (2009) Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus. BMC Evol Biol 9: 136 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3224688&tool=pmcentrez&rendertype=abstract. Accessed 6 September 2013.

47. MacHughDE, ShriverMD, LoftusRT, CunninghamP, BradleyDG (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146: 1071–1086 Available: http://www.genetics.org/cgi/content/abstract/146/3/1071.

48. Ajmone-MarsanP, GarciaJF, LenstraJA (2010) On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol Issues, News, Rev 19: 148–157 Available: http://doi.wiley.com/10.1002/evan.20267. Accessed 5 September 2013.

49. Cockrill WR (1974) The husbandry and health of the domestic buffalo. Cockrill WR, editor Rome: Food and Agriculture Organization of the United Nations.

50. CymbronT, LoftusRT, MalheiroMI, BradleyDG (1999) Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Proc Biol Sci 266: 597–603 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1689806&tool=pmcentrez&rendertype=abstract. Accessed 23 July 2013.

51. CymbronT, FreemanAR, Isabel MalheiroM, VigneJ-D, BradleyDG (2005) Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Proc Biol Sci 272: 1837–1843 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1559860&tool=pmcentrez&rendertype=abstract. Accessed 31 December 2012.

52. MirolPM, GiovambattistaG, LirónJP, DuloutFN (2003) African and European mitochondrial haplotypes in South American Creole cattle. Heredity (Edinb) 91: 248–254 Available: http://www.ncbi.nlm.nih.gov/pubmed/12939625.

53. LirónJP, BraviCM, MirolPM, Peral-GarcíaP, GiovambattistaG (2006) African matrilineages in American Creole cattle: evidence of two independent continental sources. Anim Genet 37: 379–382 Available: http://www.ncbi.nlm.nih.gov/pubmed/16879351. Accessed 5 September 2013.

54. PattersonN, MoorjaniP, LuoY, MallickS, RohlandN, et al. (2012) Ancient admixture in human history. Genetics 192: 1065–1093 Available: http://www.ncbi.nlm.nih.gov/pubmed/22960212. Accessed 13 September 2013.

55. McTavishEJ, DeckerJE, SchnabelRD, TaylorJF, HillisDM (2013) New World cattle show ancestry from multiple independent domestication events. Proc Natl Acad Sci U S A 110: E1398–406 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3625352&tool=pmcentrez&rendertype=abstract. Accessed 21 May 2013.

56. MatukumalliLK, LawleyCT, SchnabelRD, TaylorJF, AllanMF, et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4: e5350 Available: http://www.ncbi.nlm.nih.gov/pubmed/19390634.

57. ZiminAV, DelcherAL, FloreaL, KelleyDR, SchatzMC, et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10: R42 Available: http://www.ncbi.nlm.nih.gov/pubmed/19393038. Accessed 5 March 2012.

58. PurcellSM, NealeB, Todd-BrownK, ThomasL, FerreiraMAR, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559–575 Available: http://pngu.mgh.harvard.edu/purcell/plink/. Accessed 1 March 2012.

59. Purcell SM (2009) PLINK. Available: http://pngu.mgh.harvard.edu/purcell/plink/.

60. DeckerJE, McKaySD, RolfMM, KimJ, AlcaláAM, et al. (2013) Data from: Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle. Dryad Digit Repos doi:10.5061/dryad.th092

61. ReichD, ThangarajK, PattersonN, PriceAL, SinghL (2009) Reconstructing Indian population history. Nature 461: 489–494 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2842210&tool=pmcentrez&rendertype=abstract. Accessed 2 March 2013.