The Date of Interbreeding between Neandertals and Modern Humans

English version České info

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

Vyšlo v časopise: The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genet 8(10): e32767. doi:10.1371/journal.pgen.1002947
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002947

Souhrn

Zdroje

1. HublinJJ (2009) Out of Africa: modern human origins special feature: the origin of Neandertals. Proceedings of the National Academy of Sciences of the United States of America 106: 16022–16027.

2. KrauseJ, OrlandoL, SerreD, ViolaB, PruferK, et al. (2007) Neanderthals in central Asia and Siberia. Nature 449: 902–904.

3. WallJD, LohmuellerKE, PlagnolV (2009) Detecting ancient admixture and estimating demographic parameters in multiple human populations. Molecular biology and evolution 26: 1823–1827.

4. CurratM, ExcoffierL (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2: e421 doi:10.1371/journal.pbio.0020421

5. BriggsAW, GoodJM, GreenRE, KrauseJ, MaricicT, et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325: 318–321.

6. KringsM (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90: 19–30.

7. OrlandoL (2006) Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence. Curr Biol 16: R400–R402.

8. OvchinnikovIV (2000) Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404: 490–493.

9. GreenRE, MalaspinasAS, KrauseJ, BriggsAW, JohnsonPL, et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416–426.

10. SerreD, LanganeyA, ChechM, Teschler-NicolaM, PaunovicM, et al. (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2: e57 doi:10.1371/journal.pbio.0020057

11. NordborgM (1998) On the probability of Neandertal ancestry. American journal of human genetics 63: 1237.

12. CurratM, ExcoffierL (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2: e421 doi:10.1371/journal.pbio.0020421

13. GreenRE, KrauseJ, BriggsAW, MaricicT, StenzelU, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.

14. ReichD, GreenRE, KircherM, KrauseJ, PattersonN, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053–1060.

15. DurandEY, PattersonN, ReichD, SlatkinM (2011) Testing for ancient admixture between closely related populations. Molecular biology and evolution 28: 2239–2252.

16. SlatkinM, PollackJL (2008) Subdivision in an ancestral species creates asymmetry in gene trees. Molecular biology and evolution 25: 2241–2246.

17. TishkoffSA, ReedFA, FriedlaenderFR, EhretC, RanciaroA, et al. (2009) The genetic structure and history of Africans and African Americans. Science 324: 1035–1044.

18. GarriganD, MobasherZ, KinganSB, WilderJA, HammerMF (2005) Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population. Genetics 170: 1849–1856.

19. BarreiroLB, PatinE, NeyrollesO, CannHM, GicquelB, et al. (2005) The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L region. American journal of human genetics 77: 869–886.

20. LabudaD, ZietkiewiczE, YotovaV (2000) Archaic lineages in the history of modern humans. Genetics 156: 799–808.

21. HarrisEE, HeyJ (1999) X chromosome evidence for ancient human histories. Proceedings of the National Academy of Sciences of the United States of America 96: 3320–3324.

22. HardingRM, McVeanG (2004) A structured ancestral population for the evolution of modern humans. Current opinion in genetics & development 14: 667–674.

23. EvansPD, Mekel-BobrovN, VallenderEJ, HudsonRR, LahnBT (2006) Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proceedings of the National Academy of Sciences of the United States of America 103: 18178–18183.

24. HayakawaT, AkiI, VarkiA, SattaY, TakahataN (2006) Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution. Genetics 172: 1139–1146.

25. PatinE, BarreiroLB, SabetiPC, AusterlitzF, LucaF, et al. (2006) Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes. American journal of human genetics 78: 423–436.

26. KimHL, SattaY (2008) Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans. Genetics 178: 1505–1515.

27. GarriganD, HammerMF (2006) Reconstructing human origins in the genomic era. Nature reviews Genetics 7: 669–680.

28. GunzP, BooksteinFL, MitteroeckerP, StadlmayrA, SeidlerH, et al. (2009) Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario. Proceedings of the National Academy of Sciences of the United States of America 106: 6094–6098.

29. Bar-Yosef O (2011) In Casting the Net Wide, essays in memory of G Isaac (Sept J and Pilbeam D (ed)) Monographs of the American School of Prehistoric Research: Oxbow (in press).

30. FalushD, StephensM, PritchardJK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.

31. MoorjaniP, PattersonN, HirschhornJN, KeinanA, HaoL, et al. (2011) The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7: e1001373 doi:10.1371/journal.pgen.1001373

32. MachadoCA, KlimanRM, MarkertJA, HeyJ (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular biology and evolution 19: 472–488.

33. PriceAL, TandonA, PattersonN, BarnesKC, RafaelsN, et al. (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5: e1000519 doi:10.1371/journal.pgen.1000519

34. PugachI, MatveyevR, WollsteinA, KayserM, StonekingM (2011) Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome biology 12: R19.

35. PlagnolV, WallJD (2006) Possible ancestral structure in human populations. PLoS Genet 2: e105 doi:10.1371/journal.pgen.0020105

36. R.C. LewontinKK (1960) The evolutionary dynamics of complex polymorphisms. Evolution 14: 458–472.

37. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073.

38. HellenthalG, StephensM (2007) msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 23: 520–521.

39. CoopG, WenX, OberC, PritchardJK, PrzeworskiM (2008) High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science 319: 1395–1398.

40. CurratM, ExcoffierL (2011) Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. Proceedings of the National Academy of Sciences of the United States of America 108: 15129–15134.

41. FennerJN (2005) Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. American journal of physical anthropology 128.

42. CaiJJ, MacphersonJM, SellaG, PetrovDA (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: e1000336 doi:10.1371/journal.pgen.0020105

43. McVickerG, GordonD, DavisC, GreenP (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471 doi:10.1371/journal.pgen.1000471

44. YangMA, MalaspinasAS, DurandEY, SlatkinM (2012) Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity. Molecular biology and evolution

45. ErikssonA, ManicaA (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences of the United States of America

46. Weir B (2010) Genetic Data Analysis III: Sinauer Associates, Inc.

47. LiH, RuanJ, DurbinR (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome research 18: 1851–1858.