Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences
2017; Elsevier BV; Volume: 101; Issue: 2 Linguagem: Inglês
10.1016/j.ajhg.2017.06.013
ISSN1537-6605
AutoresMarc Haber, Claude Doumet‐Serhal, Christiana L. Scheib, Yali Xue, Petr Danecek, Massimo Mezzavilla, Sonia Youhanna, Rui Martiniano, Javier Prado-Martinez, Michał Szpak, Elizabeth Matisoo‐Smith, Holger Schutkowski, Richard Mikulski, Pierre Zalloua, Toomas Kivisild, Chris Tyler‐Smith,
Tópico(s)Archaeology and ancient environmental studies
ResumoThe Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600–3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750–2,170 years ago during a period of successive conquests by distant populations. The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600–3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750–2,170 years ago during a period of successive conquests by distant populations. The Near East, including the Levant, has been central to human prehistory and history from the expansion out of Africa 50–60 thousand years ago (kya),1Pagani L. Schiffels S. Gurdasani D. Danecek P. Scally A. Chen Y. Xue Y. Haber M. Ekong R. Oljira T. et al.Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.Am. J. Hum. Genet. 2015; 96: 986-991Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar through post-glacial expansions2Platt D.E. Haber M. Dagher-Kharrat M.B. Douaihy B. Khazen G. Ashrafian Bonab M. Salloum A. Mouzaya F. Luiselli D. Tyler-Smith C. et al.Mapping post-glacial expansions: the peopling of Southwest Asia.Sci. Rep. 2017; 7: 40338Crossref PubMed Scopus (20) Google Scholar and the Neolithic transition 10 kya, to the historical period when Ancient Egyptians, Greeks, Phoenicians, Assyrians, Babylonians, Persians, Romans, and many others left their impact on the region.3Hitti P.K. Lebanon in History: From the Earliest Times to the Present. Macmillan, London1967Google Scholar Aspects of the genetic history of the Levant have been inferred from present-day DNA,4Haber M. Gauguier D. Youhanna S. Patterson N. Moorjani P. Botigué L.R. Platt D.E. Matisoo-Smith E. Soria-Hernanz D.F. Wells R.S. et al.Genome-wide diversity in the levant reveals recent structuring by culture.PLoS Genet. 2013; 9: e1003316Crossref PubMed Scopus (57) Google Scholar, 5Zalloua P.A. Platt D.E. El Sibai M. Khalife J. Makhoul N. Haber M. Xue Y. Izaabel H. Bosch E. Adams S.M. et al.Genographic ConsortiumIdentifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean.Am. J. Hum. Genet. 2008; 83: 633-642Abstract Full Text Full Text PDF PubMed Scopus (105) Google Scholar but the more comprehensive analyses performed in Europe6Allentoft M.E. Sikora M. Sjögren K.G. Rasmussen S. Rasmussen M. Stenderup J. Damgaard P.B. Schroeder H. Ahlström T. Vinner L. et al.Population genomics of Bronze Age Eurasia.Nature. 2015; 522: 167-172Crossref PubMed Scopus (837) Google Scholar, 7Günther T. Valdiosera C. Malmström H. Ureña I. Rodriguez-Varela R. Sverrisdóttir O.O. Daskalaki E.A. Skoglund P. Naidoo T. Svensson E.M. et al.Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.Proc. Natl. Acad. Sci. USA. 2015; 112: 11917-11922Crossref PubMed Scopus (142) Google Scholar, 8Haak W. Lazaridis I. Patterson N. Rohland N. Mallick S. Llamas B. Brandt G. Nordenfelt S. Harney E. Stewardson K. et al.Massive migration from the steppe was a source for Indo-European languages in Europe.Nature. 2015; 522: 207-211Crossref PubMed Scopus (975) Google Scholar, 9Lazaridis I. Patterson N. Mittnik A. Renaud G. Mallick S. Kirsanow K. Sudmant P.H. Schraiber J.G. Castellano S. Lipson M. et al.Ancient human genomes suggest three ancestral populations for present-day Europeans.Nature. 2014; 513: 409-413Crossref PubMed Scopus (750) Google Scholar, 10Mathieson I. Lazaridis I. Rohland N. Mallick S. Patterson N. Roodenberg S.A. Harney E. Stewardson K. Fernandes D. Novak M. et al.Genome-wide patterns of selection in 230 ancient Eurasians.Nature. 2015; 528: 499-503Crossref PubMed Scopus (735) Google Scholar, 11Olalde I. Schroeder H. Sandoval-Velasco M. Vinner L. Lobón I. Ramirez O. Civit S. García Borja P. Salazar-García D.C. Talamo S. et al.A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures.Mol. Biol. Evol. 2015; 32: 3132-3142PubMed Google Scholar have shown the limitations of relying on present-day information alone and highlighted the power of ancient DNA (aDNA) for addressing questions about population histories.12Haber M. Mezzavilla M. Xue Y. Tyler-Smith C. Ancient DNA and the rewriting of human history: be sparing with Occam's razor.Genome Biol. 2016; 17: 1Crossref PubMed Scopus (42) Google Scholar Unfortunately, although the few aDNA results from the Levant available so far are sufficient to reveal how much its history differs from that of Europe,13Lazaridis I. Nadel D. Rollefson G. Merrett D.C. Rohland N. Mallick S. Fernandes D. Novak M. Gamarra B. Sirak K. et al.Genomic insights into the origin of farming in the ancient Near East.Nature. 2016; 536: 419-424Crossref PubMed Scopus (474) Google Scholar more work is needed to establish a thorough understanding of Levantine genetic history. Such work is hindered by the hot and sometimes wet environment,12Haber M. Mezzavilla M. Xue Y. Tyler-Smith C. Ancient DNA and the rewriting of human history: be sparing with Occam's razor.Genome Biol. 2016; 17: 1Crossref PubMed Scopus (42) Google Scholar, 13Lazaridis I. Nadel D. Rollefson G. Merrett D.C. Rohland N. Mallick S. Fernandes D. Novak M. Gamarra B. Sirak K. et al.Genomic insights into the origin of farming in the ancient Near East.Nature. 2016; 536: 419-424Crossref PubMed Scopus (474) Google Scholar but improved aDNA technologies including use of the petrous bone as a source of DNA14Gamba C. Jones E.R. Teasdale M.D. McLaughlin R.L. Gonzalez-Fortes G. Mattiangeli V. Domboróczki L. Kővári I. Pap I. Anders A. et al.Genome flux and stasis in a five millennium transect of European prehistory.Nat. Commun. 2014; 5: 5257Crossref PubMed Scopus (391) Google Scholar and the rich archaeological remains available encouraged us to further explore the potential of aDNA in this region. Here, we present genome sequences from five Bronze Age Lebanese samples and show how they improve our understanding of the Levant's history over the last five millennia. During the Bronze Age in the Levant, around 3–4 kya, a distinctive culture emerged as a Semitic-speaking people known as the Canaanites. The Canaanites inhabited an area bounded by Anatolia to the north, Mesopotamia to the east, and Egypt to the south, with access to Cyprus and the Aegean through the Mediterranean. Thus the Canaanites were at the center of emerging Bronze Age civilizations and became politically and culturally influential.15Tubb J.N. Canaanites. Published for the Trustees of the British Museum by British Museum Press, London1998Google Scholar They were later known to the ancient Greeks as the Phoenicians who, 2.3–3.5 kya, colonized territories throughout the Mediterranean reaching as far as the Iberian Peninsula.16Markoe G. Phoenicians. British Museum Press, London2000Google Scholar However, for uncertain reasons but perhaps related to the use of papyrus instead of clay for documentation, few textual records have survived from the Canaanites themselves and most of their history known today has been reconstructed from ancient Egyptian and Greek records, the Hebrew Bible, and archaeological excavations.15Tubb J.N. Canaanites. Published for the Trustees of the British Museum by British Museum Press, London1998Google Scholar Many uncertainties still surround the origin of the Canaanites. Ancient Greek historians believed their homeland was located in the region of the Persian Gulf,16Markoe G. Phoenicians. British Museum Press, London2000Google Scholar, 17Al Khalifa H.A.S. Rice M. Bahrain through the Ages: The Archaeology. KPI, London1986Google Scholar but modern researchers tend to reject this hypothesis because of archaeological and historical evidence of population continuity through successive millennia in the Levant. The Canaanite culture is alternatively thought to have developed from local Chalcolithic people who were themselves derived from people who settled in farming villages 9–10 kya during the Neolithic period.15Tubb J.N. Canaanites. Published for the Trustees of the British Museum by British Museum Press, London1998Google Scholar Uncertainties also surround the fate of the Canaanites: the Bible reports the destruction of the Canaanite cities and the annihilation of its people; if true, the Canaanites could not have directly contributed genetically to present-day populations. 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We obtained a genomic coverage of 0.4–2.3× and a mitochondrial DNA (mtDNA) genome coverage of 53–164× (Table 1). Y chromosome genotypes were jointly called across males from the 1000 Genomes Project, present-day Lebanese, and two identified Canaanite males using FreeBayes v.0.9.18.23Garrison, E., and Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv. arXiv:1207.3907 [q-bio.GN]. https://arxiv.org/abs/1207.3907.Google Scholar A maximum likelihood phylogeny was inferred using RAxML v.8.2.1024Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics. 2014; 30: 1312-1313Crossref PubMed Scopus (19427) Google Scholar and visualized using iTOL v.3.5.3.25Letunic I. Bork P. 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We merged the low-coverage Lebanese data with four high-coverage (30×) Lebanese samples,31Haber M. Mezzavilla M. Bergström A. Prado-Martinez J. Hallast P. Saif-Ali R. Al-Habori M. Dedoussis G. Zeggini E. Blue-Smith J. et al.Chad genetic diversity reveals an African history marked by multiple Holocene eurasian migrations.Am. J. Hum. Genet. 2016; 99: 1316-1324Abstract Full Text Full Text PDF PubMed Scopus (24) Google Scholar 1000 Genomes Project phase 3 CEU, YRI, and CHB populations,32The 1000 Genomes Project ConsortiumA global reference for human genetic variation.Nature. 2015; 526: 68-74Crossref PubMed Scopus (8504) Google Scholar and sequence data previously published from regional populations (Egyptians, Ethiopians, and Greeks).1Pagani L. Schiffels S. Gurdasani D. Danecek P. Scally A. Chen Y. Xue Y. Haber M. Ekong R. Oljira T. et al.Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.Am. J. Hum. 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Wells R.S. et al.Genome-wide diversity in the levant reveals recent structuring by culture.PLoS Genet. 2013; 9: e1003316Crossref PubMed Scopus (57) Google Scholar A principal component analysis (PCA) using the 99 sequenced present-day individuals show that they capture the previously described genetic diversity with distinct clusters reflecting the different cultural groups in Lebanon today (Figure S5). We combined our ancient and modern samples with previously published ancient data6Allentoft M.E. Sikora M. Sjögren K.G. Rasmussen S. Rasmussen M. Stenderup J. Damgaard P.B. Schroeder H. Ahlström T. Vinner L. et al.Population genomics of Bronze Age Eurasia.Nature. 2015; 522: 167-172Crossref PubMed Scopus (837) Google Scholar, 7Günther T. Valdiosera C. Malmström H. Ureña I. Rodriguez-Varela R. Sverrisdóttir O.O. Daskalaki E.A. Skoglund P. Naidoo T. Svensson E.M. et al.Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.Proc. Natl. Acad. Sci. 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Sirak K. et al.Genomic insights into the origin of farming in the ancient Near East.Nature. 2016; 536: 419-424Crossref PubMed Scopus (474) Google Scholar on the basis of archaeological culture, chronology, and genetic clustering. We used this dataset to shed light on the genetic history of the Canaanites, resolving their relationship to other ancient populations and assessing their genetic contribution to present-day populations. We first explored our dataset using PCA40Patterson N. Price A.L. Reich D. Population structure and eigenanalysis.PLoS Genet. 2006; 2: e190Crossref PubMed Scopus (3070) Google Scholar on present-day West Eurasian (including Levantine) populations and projected the ancient samples onto this plot (Figures 1B and S6). The Bronze Age Sidon samples (Sidon_BA) overlap with present-day Levantines and were positioned between the ancient Levantines (Natufians/Neolithic) and ancient Iranians (Neolithic/Chalcolithic). The overlap between the Bronze Age and present-day Levantines suggests a degree of genetic continuity in the region. We explored this further by computing the statistic f4(Lebanese, present-day Near Easterner; Sidon_BA, Chimpanzee) using qpDstat39Patterson N. Moorjani P. Luo Y. Mallick S. Rohland N. Zhan Y. Genschoreck T. Webster T. Reich D. Ancient admixture in human history.Genetics. 2012; 192: 1065-1093Crossref PubMed Scopus (1190) Google Scholar (with parameter f4mode: YES) and found that Sidon_BA shared more alleles with the Lebanese than with most other present-day Levantines (Figure S7), supporting local population continuity as observed in Sidon's archaeological records. When we substituted present-day Near Easterners with a panel of 150 present-day populations available in the Human Origins dataset, we found that only Sardinians and Italian_North shared significantly more alleles with Sidon_BA compared with the Lebanese (Figure S8). Sardinians are known to have retained a large proportion of ancestry from Early European farmers (EEFs) and therefore the increased affinity to Sidon_BA could be related to a shared Neolithic ancestry. We computed f4(Lebanese, Sardinian/Italian_North; Sidon_BA, Levant_N) and found no evidence of increased affinity of Sardinians or Italian_North to Sidon_BA after the Neolithic (both Z-scores are positive). We next wanted to explore whether the increased affinity of Sidon_BA to the Lebanese could also be observed when analyzing functionally important regions of the genome that are less susceptible to genetic drift. Our sequence data allowed us to scan loci linked to phenotypic traits and loci previously identified as functional variants in the Lebanese and other Levantines.41Nakouzi G. Kreidieh K. Yazbek S. A review of the diverse genetic disorders in the Lebanese population: highlighting the urgency for community genetic services.J. 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ANGSD: Analysis of Next Generation Sequencing Data.BMC Bioinformatics. 2014; 15: 356Crossref PubMed Scopus (1129) Google Scholar based on a method from Li et al.44Li Y. Vinckenbosch N. Tian G. Huerta-Sanchez E. Jiang T. Jiang H. Albrechtsen A. Andersen G. Cao H. Korneliussen T. et al.Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants.Nat. Genet. 2010; 42: 969-972Crossref PubMed Scopus (260) Google Scholar and calculated Pearson pairwise correlation coefficients between AF in Sidon_BA and AF in Africans, Europeans, Asians,32The 1000 Genomes Project ConsortiumA global reference for human genetic variation.Nature. 2015; 526: 68-74Crossref PubMed Scopus (8504) Google Scholar and Lebanese. We found a high significant correlation between Sidon_BA and the Lebanese (r = 0.74; 95% CI = 0.63–0.82; p value = 8.168 × 10−16) and lower correlations between Sidon_BA and Europeans (r = 0.56), Africans (r = 0.55), and Asians (r = 0.53) (Figure S9). These results support population continuity in the region and suggest that several present-day genetic disorders might stem from risk alleles that were already present in the Bronze Age population. In addition, SNPs associated with phenotypic traits show that Sidon_BA and the Lebanese had comparable skin, hair, and eye colors (in general: light intermediate skin pigmentation, brown eyes, and dark hair) with similar frequencies of the underlying causal variants in SLC24A5 and HERC2, but with Sidon_BA probably having darker skin than Lebanese today from variants in SLC45A2 resulting in darker pigmenta
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