Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

1. Childe VG (1957) The Dawn of European Civilization. 6th Revised edition. New York: Alfred A. Knopf Inc. 366 p.

2. Ammerman A, Cavalli-Sforza LL (1984) The Neolithic Transition and the Genetics of Populations in Europe. Princeton Univ Pr. 200 p.

3. Price TD (2000) Europe's First Farmers. Cambridge University Press. 395 p.

4. Renfrew C (1987) Archaeology and language: the puzzle of Indo-European origins. CUP Archive. 372 p.

5. Piggott S (1965) Ancient Europe. Edinburgh, United Kingdom: Edinburgh University Press. 420 p.

6. ZvelebilM (2001) The agricultural transition and the origins of Neolithic society in Europe. Documenta Praehistorica XXVIII: 1–26.

7. Cavalli-Sforza, Menozzi P, Piazza A (1994) The history and geograhpy of human genes. Princetown University Press. 1088 p.

8. SeminoO, PassarinoG, BregaA, FellousM, Santachiara-BenerecettiAS (1996) A view of the neolithic demic diffusion in Europe through two Y chromosome-specific markers. Am J Hum Genet 59: 964–968.

9. RosserZH, ZerjalT, HurlesME, AdojaanM, AlavanticD, et al. (2000) Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet 67: 1526–1543 doi:10.1086/316890

10. BalaresqueP, BowdenGR, AdamsSM, LeungH-Y, KingTE, et al. (2010) A Predominantly Neolithic Origin for European Paternal Lineages. PLoS Biol 8: e1000285 doi:10.1371/journal.pbio.1000285

11. RichardsM, Côrte-RealH, ForsterP, MacaulayV, Wilkinson-HerbotsH, et al. (1996) Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am J Hum Genet 59: 185–203.

12. RichardsM, MacaulayV, HickeyE, VegaE, SykesB, et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251–1276.

13. ZhengH-X, YanS, QinZ-D, JinL (2012) MtDNA analysis of global populations support that major population expansions began before Neolithic Time. Sci Rep 2: 745.

14. FuQ, RudanP, PääboS, KrauseJ (2012) Complete Mitochondrial Genomes Reveal Neolithic Expansion into Europe. PLoS ONE 7: e32473 doi:10.1371/journal.pone.0032473

15. DeguillouxM, LeahyR, PemongeM, RottierS (2012) European Neolithization and Ancient DNA: An Assessment. Evolutionary Anthropology: Issues, News, and Reviews 21: 24–37 doi:10.1002/evan.20341

16. RasteiroR, ChikhiL (2013) Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data. PLoS ONE 8: e60944 doi:10.1371/journal.pone.0060944

17. ZvelebilM (1998) Genetic and Cultural Diversity of Europe: A Comment on Cavalli-Sforza. Journal of Anthropological Research 54: 411–417 doi:10.2307/3630658

18. PierronD, ChangI, ArachicheA, HeiskeM, ThomasO, et al. (2011) Mutation rate switch inside Eurasian mitochondrial haplogroups: impact of selection and consequences for dating settlement in Europe. PLoS ONE 6: e21543 doi:10.1371/journal.pone.0021543

19. BrandtG, HaakW, AdlerCJ, RothC, Szecsenyi-NagyA, et al. (2013) Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342: 257–261 doi:10.1126/science.1241844

20. BollonginoR, NehlichO, RichardsMP, OrschiedtJ, ThomasMG, et al. (2013) 2000 Years of Parallel Societies in Stone Age Central Europe. Science 342: 479–481 doi:10.1126/science.1245049

21. BarbujaniG, GoldsteinDB (2004) Africans and Asians abroad: Genetic Diversity in Europe. Annual Review of Genomics and Human Genetics 5: 119–150 doi:10.1146/annurev.genom.5.061903.180021

22. ChikhiL, NicholsRA, BarbujaniG, BeaumontMA (2002) Y genetic data support the Neolithic demic diffusion model. Proc Natl Acad Sci USA 99: 11008–11013 doi:10.1073/pnas.162158799

23. BramantiB, ThomasMG, HaakW, UnterlaenderM, JoresP, et al. (2009) Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 326: 137–140 doi:10.1126/science.1176869

24. HaakW, BalanovskyO, SanchezJJ, KoshelS, ZaporozhchenkoV, et al. (2010) Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol 8: e1000536 doi:10.1371/journal.pbio.1000536

25. MalmströmH, GilbertMTP, ThomasMG, BrandströmM, StoråJ, et al. (2009) Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol 19: 1758–1762 doi:10.1016/j.cub.2009.09.017

26. SkoglundP, MalmströmH, RaghavanM, StoråJ, HallP, et al. (2012) Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science 336: 466–469 doi:10.1126/science.1216304

27. GambaC, FernándezE, TiradoM, DeguillouxMF, PemongeMH, et al. (2012) Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers. Molecular Ecology 21: 45–56 doi:10.1111/j.1365-294X.2011.05361.x

28. HervellaM, IzagirreN, AlonsoS, FregelR, AlonsoA, et al. (2012) Ancient DNA from Hunter-Gatherer and Farmer Groups from Northern Spain Supports a Random Dispersion Model for the Neolithic Expansion into Europe. PLoS ONE 7: e34417 doi:10.1371/journal.pone.0034417

29. SampietroML, LaoO, CaramelliD, LariM, PouR, et al. (2007) Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe. Proc Biol Sci 274: 2161–2167 doi:10.1098/rspb.2007.0465

30. LacanM, KeyserC, RicautF-X, BrucatoN, DuranthonF, et al. (2011) Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. Proc Natl Acad Sci USA 108: 9788–9791 doi:10.1073/pnas.1100723108

31. LacanM, KeyserC, RicautF-X, BrucatoN, TarrúsJ, et al. (2011) Ancient DNA suggests the leading role played by men in the Neolithic dissemination. Proceedings of the National Academy of Sciences 108: 18255–18259 doi:10.1073/pnas.1113061108

32. Guerrero E, Naji S, Bocquet-Appel J-P (n.d.) The Signal of the Neolithic Demographic Transition in the Levant. In: Bocquet-Appel J-P, Bar-Yosef O, editors. The Neolithic Demographic Transition and its Consequences. Dordrecht: Springer Netherlands. pp. 57–80.

33. BeharDM, MetspaluE, KivisildT, RossetS, TzurS, et al. (2008) Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS ONE 3: e2062 doi:10.1371/journal.pone.0002062

34. BrandstätterA, EgyedB, ZimmermannB, DuftnerN, PadarZ, et al. (2007) Migration rates and genetic structure of two Hungarian ethnic groups in Transylvania, Romania. Ann Hum Genet 71: 791–803 doi:10.1111/j.1469-1809.2007.00371.x

35. GreshamD, MorarB, UnderhillPA, PassarinoG, LinAA, et al. (2001) Origins and Divergence of the Roma (Gypsies). Am J Hum Genet 69: 1314–1331.

36. CooperA, PoinarHN (2000) Ancient DNA: do it right or not at all. Science 289: 1139.

37. PääboS, PoinarH, SerreD, Jaenicke-DespresV, HeblerJ, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645–679 doi:10.1146/annurev.genet.37.110801.143214

38. GilbertMTP, BandeltH-J, HofreiterM, BarnesI (2005) Assessing ancient DNA studies. Trends in Ecology & Evolution 20: 541–544 doi:10.1016/j.tree.2005.07.005

39. BollonginoR, TressetA, VigneJ-D (2008) Environment and excavation: Pre-lab impacts on ancient DNA analyses. Comptes Rendus Palevol 7: 91–98 doi:10.1016/j.crpv.2008.02.002

40. EdwardsCJ, MacHughDE, DobneyKM, MartinL, RussellN, et al. (2004) Ancient DNA analysis of 101 cattle remains: limits and prospects. Journal of Archaeological Science 31: 695–710 doi:10.1016/j.jas.2003.11.001

41. Bar-GalGK, KhalailyH, MaderO, DucosP, HorwitzLK (2002) Ancient DNA Evidence for the Transition from Wild to Domestic Status in Neolithic Goats: A Case Study from the Site of Abu Gosh, Israel. Ancient Biomolecules 4: 9–17 doi:10.1080/13586120290018482

42. SalamonM, TzurS, ArensburgB, ZiasJ, NagarY, et al. (2010) Ancient mtdna sequences and radiocarbon dating of human bones from the chalcolithic caves of wadi el-makkukh. Mediterranean Archaeology and Archaeometry 10: 1–14.

43. KuijtI, GuerreroE, MolistM, AnfrunsJ (2011) The changing Neolithic household: Household autonomy and social segmentation, Tell Halula, Syria. Journal of Anthropological Archaeology 30: 502–522 doi:10.1016/j.jaa.2011.07.001

44. FernándezE, OrtizJE, Pérez-PérezA, PratsE, TurbónD, et al. (2009) Aspartic acid racemization variability in ancient human remains: implications in the prediction of ancient DNA recovery. Journal of Archaeological Science 36: 965–972 doi:10.1016/j.jas.2008.11.009

45. SosaC, VispeE, NúñezC, BaetaM, CasalodY, et al. (2013) Association between ancient bone preservation and DNA yield: A multidisciplinary approach. Am J Phys Anthropol 151: 102–109 doi:10.1002/ajpa.22262

46. HaakW, ForsterP, BramantiB, MatsumuraS, BrandtG, et al. (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310: 1016–1018 doi:10.1126/science.1118725

47. ShlushLI, BeharDM, YudkovskyG, TempletonA, HadidY, et al. (2008) The Druze: A Population Genetic Refugium of the Near East. PLoS ONE 3: e2105 doi:10.1371/journal.pone.0002105

48. CostaMD, PereiraJB, PalaM, FernandesV, OlivieriA, et al. (2013) A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nat Commun 4: 2543.

49. SoaresP, AchilliA, SeminoO, DaviesW, MacaulayV, et al. (2010) The archaeogenetics of Europe. Curr Biol 20: R174–183 doi:10.1016/j.cub.2009.11.054

50. BrothertonP, HaakW, TempletonJ, BrandtG, SoubrierJ, et al. (2013) Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 4: 1764 doi:10.1038/ncomms2656

51. Peltenburg E, Colledge S, Croft P, Jackson A, McCartney C, et al. (2000) Agro-pastoralist colonization of Cyprus in the 10th millennium BP: initial assessments. Available: http://antiquity.ac.uk/ant/074/Ant0740844.htm. Accessed 23 May 2013.

52. VigneJ-D, BrioisF, ZazzoA, WillcoxG, CucchiT, et al. (2012) First wave of cultivators spread to Cyprus at least 10,600 y ago. PNAS 109: 8445–8449.

53. BroodbankC, StrasserT (1991) Migrant farmers and the Neolithic colonization of Crete. Antiquity 65: 233–245.

54. PerlèsC (2005) An alternate (and old fashioned) view of the Neolithisation in Greece. Documenta Praehistorica XXX: 99–113.

55. HugheyJR, PaschouP, DrineasP, MastropaoloD, LotakisDM, et al. (2013) A European population in Minoan Bronze Age Crete. Nat Commun 4: 1861 doi:10.1038/ncomms2871

56. Bocquet-AppelJ-P, NajiS, LindenMV, KozlowskiJK (2009) Detection of diffusion and contact zones of early farming in Europe from the space-time distribution of 14C dates. Journal of Archaeological Science 36: 807–820 doi:10.1016/j.jas.2008.11.004

57. Cauvin J (1997) Naissance des divinités, naissance de l'agriculture: la révolution des symboles au néolithique. 2nd ed. Paris: Editions du CNRS. 310 p.

58. Goring-Morris N, Belfer-Cohen A (2010) Different Ways of Being, Different Ways of Seeing … Changing Worldviews in the Near East. Landscapes in Transition. Oxford, UK: Council for British Research in the Levant and Oxbow Books.

59. GuilaineJ (2001) La diffusion du Néolithique en Europe. Une hypothèse arythmique. Zephyrus 53–54: 267–272.

60. Molist M (1996) Tell Halula (Siria): un yacimiento neolítico del Valle Medio de Eufrates, campañas de 1991 y 1992. Ministerio de Educación y Cultura, Dirección General de Bellas Artes y Bienes Culturales, Instituto del Patrimonio Histórico Español. 223 p.

61. Molist M (2001) Novedades de la Investigación de los orígenes de las sociedades agrícolas en el Próximo Oriente: el medio Éufrates sirio y su rol en el proceso de neolitización. De la estepa al Mediterráneo: Actas del Ier Congreso de Arqueología e Historia Antigua del Oriente Próximo. Barcelona: M Eridu, Vol. 1 . pp. 173–188.

62. MolistM, AnfrunsJ, CruellsW, ClopX, SañaM (2004) Estudio del asentamiento de Tell Halula (valle del Éufrates, Siria): aportaciones para el estudio de la emergencia de las sociedades agrícolas en el Próximo Oriente. Bienes culturales: revista del Instituto del Patrimonio Histórico Español 3: 45–62.

63. Faura JM (1996) Un conjunt ceràmic del VIII mil·leni B.P. a la Vall de l'Éufrates: Les produccions de Tell Halula (Síria) Barcelona: Universitat Autònoma de Barcelona.

64. GuerreroE, MolistM, KuijtI, AnfrunsJ (2009) Seated Memory: New Insights into Near Eastern Neolithic Mortuary Variability from Tell Halula, Syria. Current Anthropology 50: 379–391.

65. FerembachD (1970) Etude antropologique des ossements humains néolitiques de Tell Ramad (Syrie campagnes 1963–66). L'Anthropologie 74: 247–254.

66. AsoutiE, FullerDQ (2013) A contextual approach to the emergence of agriculture in southwest Asia: Reconstructing early neolithic plant-food production. Current Anthropology 54: 299–345.

67. Coqueugniot E (2000) Dja'de, Syrie: un village a la veille de la domestication. Premiers paysans du monde: naissances des agricultures: [seminaire]. Editions Errance. pp. 63–79.

68. Desmeulles V (2001) Les pratiques funéraires du PPNB ancien de Syrie, étude de cas: Dja'de El Mughara Paris: Université de Paris I Panteón-Sorbone.

69. FernándezE, ThawS, BrownTA, Arroyo-PardoE, BuxóR, et al. (2013) DNA analysis in charred grains of naked wheat from several archaeological sites in Spain. Journal of Archaeological Science 40: 659–670 doi:10.1016/j.jas.2012.07.014

70. AndrewsRM, KubackaI, ChinneryPF, LightowlersRN, TurnbullDM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147 doi:10.1038/13779

71. Kloss-BrandstätterA, PacherD, SchönherrS, WeissensteinerH, BinnaR, et al. (2011) HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Human Mutation 32: 25–32 doi:10.1002/humu.21382

72. Van OvenM, KayserM (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386–394 doi:10.1002/humu.20921

73. 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 doi:10.1016/j.cub.2012.06.005

74. HandtO, KringsM, WardRH, PääboS (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59: 368–376.

75. FregelR, DelgadoS (2011) HaploSearch: a tool for haplotype-sequence two-way transformation. Mitochondrion 11: 366–367 doi:10.1016/j.mito.2010.11.001

76. IBM Corp. (2012) IBM SPSS Statistics for Windows, Version 21.0. Armonk, NY: IBM Corp: IBM Corp. p.

77. ExcoffierL, LischerHEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564–567 doi:10.1111/j.1755-0998.2010.02847.x

78. ReynoldsJ, WeirBS, CockerhamCC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767–779.

79. SlatkinM (1995) A Measure of Population Subdivision Based on Microsatellite Allele Frequencies. Genetics 139: 457–462.

80. BenjaminiY, HochbergY (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society, Series B (Methodological) 57: 289–300.

81. R Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. p. Available:http://www.R-project.org/.

82. WardJH (1963) Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association 58: 236–244.

83. Lebart L, Morineau A, Warwick K (1984) Multivariate Descriptive Statistical Analysis. New York: Wiley. p.