Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

English version České info

The analysis of the genome of the Tyrolean Iceman, a 5,300 year old mummy from Central Europe, revealed a surprising recent common ancestry with modern Sardinians for this ancient genome. However, this study was limited both by the availability of data from Sardinians and by a lack of genomic data from other ancient European samples. Here, we use genomic data from modern Sardinians and from ancient European individuals from different geographic regions and cultural contexts, to demonstrate that this ancestry component is shared among individuals associated with the onset of agriculture in Europe. Our results thus suggest that the Iceman's Sardinian ancestry actually reflects a more widespread genetic component related to the migration of people during the Neolithic transition in Central Europe.

Vyšlo v časopise: Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe. PLoS Genet 10(5): e32767. doi:10.1371/journal.pgen.1004353
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004353

Souhrn

Zdroje

1. SeidlerH, BernhardW, Teschler-NicolaM, PlatzerW, zurNedden D, et al. (1992) Some anthropological aspects of the prehistoric Tyrolean ice man. Science 258: 455–457.

2. MurphyWA, zurNedden D, GostnerP, KnappR, RecheisW, et al. (2003) The Iceman: Discovery and Imaging. Radiology 226: 614–629.

3. Kutschera W, Golser R, Priller A, Rom W, Steier P, et al.. (2000) Radiocarbon dating of equipment from the Iceman. In: Bortenschlager U-PMDS, Oeggl U-PDK, editors. The Iceman and his Natural Environment: Palaeobotanical Results (The Man in the Ice). Vienna: Springer. pp. 1–9.

4. RolloF, UbaldiM, ErminiL, MarotaI (2002) Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proc Natl Acad Sci U S A 99: 12594–12599.

5. KellerA, GraefenA, BallM, MatzasM, BoisguerinV, et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nature Communications 3: 698.

6. MüllerW, FrickeH, HallidayAN, McCullochMT, WarthoJ-A (2003) Origin and Migration of the Alpine Iceman. Science 302: 862–866.

7. BramantiB, ThomasMG, HaakW, UnterlaenderM, JoresP, et al. (2009) Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers. Science 326: 137–140.

8. HaakW, BalanovskyO, SanchezJJ, KoshelS, ZaporozhchenkoV, et al. (2010) Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities. PLoS Biol 8: e1000536.

9. LacanM, KeyserC, RicautF-X, BrucatoN, DuranthonF, et al. (2011) Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. Proc Natl Acad Sci U S A 108: 9788–9791.

10. Der SarkissianC, BalanovskyO, BrandtG, KhartanovichV, BuzhilovaA, et al. (2013) Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. PLoS Genet 9: e1003296.

11. BrothertonP, HaakW, TempletonJ, BrandtG, SoubrierJ, et al. (2013) Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 4: 1764.

12. FuQ, RudanP, PääboS, KrauseJ (2012) Complete Mitochondrial Genomes Reveal Neolithic Expansion into Europe. PLoS ONE 7: e32473.

13. SkoglundP, MalmströmH, RaghavanM, StoråJ, HallP, et al. (2012) Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science 336: 466–469.

14. Sánchez-QuintoF, SchroederH, RamirezO, Ávila-ArcosMC, PybusM, et al. (2012) Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Current Biology 22: 1494–1499.

15. CarpenterML, BuenrostroJD, ValdioseraC, SchroederH, AllentoftME, et al. (2013) Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. The American Journal of Human Genetics 93: 852–864.

16. AlexanderDH, NovembreJ, LangeK (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655–1664.

17. DurandEY, PattersonN, ReichD, SlatkinM (2011) Testing for Ancient Admixture between Closely Related Populations. Molecular Biology and Evolution 28: 2239–2252.

18. PattersonN, MoorjaniP, LuoY, MallickS, RohlandN, et al. (2012) Ancient Admixture in Human History. Genetics 192: 1065–1093.

19. PickrellJK, PritchardJK (2012) Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. PLoS Genet 8: e1002967.

20. FuQ, MeyerM, GaoX, StenzelU, BurbanoHA, et al. (2013) DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci U S A 110: 2223–2227.

21. SkoglundP, GötherströmA, JakobssonM (2011) Estimation of Population Divergence Times from Non-Overlapping Genomic Sequences: Examples from Dogs and Wolves. Mol Biol Evol 28: 1505–1517.

22. GravelS, HennBM, GutenkunstRN, IndapAR, MarthGT, et al. (2011) Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A 108: 11983–11988.

23. GronauI, HubiszMJ, GulkoB, DankoCG, SiepelA (2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet 43: 1031–1034.

24. RalphP, CoopG (2013) The Geography of Recent Genetic Ancestry across Europe. PLoS Biol 11: e1001555.

25. BotiguéLR, HennBM, GravelS, MaplesBK, GignouxCR, et al. (2013) Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc Natl Acad Sci U S A 110: 11791–11796.

26. MoorjaniP, PattersonN, HirschhornJN, KeinanA, HaoL, et al. (2011) The History of African Gene Flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7: e1001373.

27. DerenkoM, MalyarchukB, DenisovaG, WozniakM, GrzybowskiT, et al. (2007) Y-chromosome haplogroup N dispersals from south Siberia to Europe. J Hum Genet 52: 763–770.

28. SalmelaE, LappalainenT, FranssonI, AndersenPM, Dahlman-WrightK, et al. (2008) Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe. PLoS ONE 3: e3519.

29. The International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52–58.

30. HennBM, GignouxCR, JobinM, GrankaJM, MacphersonJM, et al. (2011) Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci U S A 108: 5154–5162.

31. WallJD, YangMA, JayF, KimSK, DurandEY, et al. (2013) Higher Levels of Neanderthal Ancestry in East Asians than in Europeans. Genetics 194: 199–209.

32. NovembreJ, JohnsonT, BrycK, KutalikZ, BoykoAR, et al. (2008) Genes mirror geography within Europe. Nature 456: 98–101.

33. LaoO, LuTT, NothnagelM, JungeO, Freitag-WolfS, et al. (2008) Correlation between Genetic and Geographic Structure in Europe. Current Biology 18: 1241–1248.

34. JayF, SjödinP, JakobssonM, BlumMGB (2013) Anisotropic Isolation by Distance: The Main Orientations of Human Genetic Differentiation. Mol Biol Evol 30: 513–525.

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

36. GreenRE, KrauseJ, BriggsAW, MaricicT, StenzelU, et al. (2010) A Draft Sequence of the Neandertal Genome. Science 328: 710–722.

37. Cavalli-SforzaLL, PiazzaA (1993) Human genomic diversity in Europe: a summary of recent research and prospects for the future. Eur J Hum Genet 1: 3–18.

38. D'AmoreG, Di MarcoS, FlorisG, PaccianiE, SannaE (2010) Craniofacial morphometric variation and the biological history of the peopling of Sardinia. HOMO - Journal of Comparative Human Biology 61: 385–412.

39. CaramelliD, VernesiC, SannaS, SampietroL, LariM, et al. (2007) Genetic variation in prehistoric Sardinia. Hum Genet 122: 327–336.

40. GhirottoS, MonaS, BenazzoA, PaparazzoF, CaramelliD, et al. (2010) Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA Variation in Sardinia. Mol Biol Evol 27: 875–886.

41. BrandtG, HaakW, AdlerCJ, RothC, Szécsényi-NagyA, et al. (2013) Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342: 257–261.

42. PinhasiR, ThomasMG, HofreiterM, CurratM, BurgerJ (2012) The genetic history of Europeans. Trends in Genetics 28: 496–505.

43. Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, et al.. (2013) Ancient human genomes suggest three ancestral populations for present-day Europeans. bioRxiv. Available: http://biorxiv.org/content/early/2013/12/23/001552. Accesed 14 April 2014.

44. RasmussenM, GuoX, WangY, LohmuellerKE, RasmussenS, et al. (2011) An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 334: 94–98.

45. YangDY, EngB, WayeJS, DudarJC, SaundersSR (1998) Improved DNA extraction from ancient bones using silica-based spin columns. American Journal of Physical Anthropology 105: 539–543.

46. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079.

47. LiH, DurbinR (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25: 1754–1760.

48. KiddJM, GravelS, ByrnesJ, Moreno-EstradaA, MusharoffS, et al. (2012) Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation. The American Journal of Human Genetics 91: 660–671.

49. FrancalacciP, MorelliL, AngiusA, BeruttiR, ReinierF, et al. (2013) Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science 341: 565–569.

50. OrrùV, SteriM, SoleG, SidoreC, VirdisF, et al. (2013) Genetic Variants Regulating Immune Cell Levels in Health and Disease. Cell 155: 242–256.