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, 101 (2), 274-282

Continuity and Admixture in the Last Five Millennia of Levantine History From Ancient Canaanite and Present-Day Lebanese Genome Sequences

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Continuity and Admixture in the Last Five Millennia of Levantine History From Ancient Canaanite and Present-Day Lebanese Genome Sequences

Marc Haber et al. Am J Hum Genet.

Abstract

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.

Keywords: Bronze Age; Lebanon; Near East; Phoenicians; Sidon; aDNA; population genetic history; whole-genome sequences.

Figures

Figure 1
Figure 1
Population Locations and Genetic Structure (A) The map shows the location of the newly sequenced Bronze Age Sidon samples (pink triangle labeled with red text), as well as the locations of published ancient samples used as comparative data in this study. (B) PCA of ancient Eurasian samples (colored shapes) projected using eigenvectors from present-day Eurasian populations (gray points).
Figure 2
Figure 2
Admixture in Bronze Age Levantine Populations (A) The statistic f4(Levant_N, Sidon_BA; Ancient Eurasian, Chimpanzee) is most negative for ancient populations from the Caucasus and Iran, suggesting an increase in ancestry related to these populations in Sidon after the Neolithic period. The plot shows the estimated statistic value and ±3 standard errors. (B) Modeling Sidon as mixture between Neolithic Levant and an ancient Eurasian population shows that Chalcolithic Iran fits the model best when using a large number of outgroups: Ust_Ishim, Kostenki14, MA1, Han, Papuan, Ami, Chukchi, Karitiana, Mbuti, Switzerland_HG, EHG, WHG, and CHG. Sidon_BA can then be modeled using qpAdm as 0.484 ± 0.042 Levant_N and 0.516 ± 0.042 Iran_ChL.
Figure 3
Figure 3
Admixture in Present-Day Levantine Populations (A) Supervised ADMIXTURE using Levant_N, Iran_N, EHG, and WHG as reference populations. A Eurasian ancestry found in Eastern hunter-gatherers and the steppe Bronze Age appears in present-day Levantines after the Bronze Age. (B) The statistic f4(Sidon_BA, Lebanese; Ancient Eurasian, Chimpanzee) confirms the ADMIXTURE results and is most negative for populations from the steppe and Eurasian hunter-gatherers. We show the estimated statistic value and ±3 standard errors. (C) Present-day Lebanese can be modeled as mixture between Bronze Age Sidon and a steppe population. The model with mix proportions 0.932 ± 0.016 Sidon_BA and 0.068 ± 0.016 steppe_EMBA for Lebanese is supported with the lowest SE.
Figure 4
Figure 4
Genetic History of the Levant (A) A model of population relationships which fits the qpAdm results from Lazaridis et al. (solid arrows) and this study (dotted arrows). Percentages on arrows are the inferred admixture proportions. (B) Levant timeline of historical events with genetically inferred admixture dates shown as colored double-ended arrows with length representing the SE.

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