.2020 Jul 2;107(1):149-157.

doi: 10.1016/j.ajhg.2020.05.008. Epub 2020 May 28.

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

Marc Haber¹, Joyce Nassar², Mohamed A Almarri³, Tina Saupe⁴, Lehti Saag⁵, Samuel J Griffith⁵, Claude Doumet-Serhal⁶, Julien Chanteau⁷, Muntaha Saghieh-Beydoun⁸, Yali Xue³, Christiana L Scheib⁵, Chris Tyler-Smith⁹

Affiliations

¹ Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: m.haber@bham.ac.uk.
² Institut Français du Proche-Orient, BP 11-1424, Beirut, Lebanon.
³ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
⁴ Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia.
⁵ Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
⁶ The Sidon Excavation, Saida, Lebanon.
⁷ Département des Antiquités Orientales, Musée du Louvre, France.
⁸ Université Libanaise, Rectorat, BP 14-6573, Place du Musée, Beirut, Lebanon.
⁹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: cts@sanger.ac.uk.

PMID:32470374
PMCID: PMC7332655
DOI: 10.1016/j.ajhg.2020.05.008

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

Marc Haber et al. Am J Hum Genet.2020.

.2020 Jul 2;107(1):149-157.

doi: 10.1016/j.ajhg.2020.05.008. Epub 2020 May 28.

Authors

Affiliations

¹ Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: m.haber@bham.ac.uk.
² Institut Français du Proche-Orient, BP 11-1424, Beirut, Lebanon.
³ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
⁴ Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia; Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu 51010, Estonia.
⁵ Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
⁶ The Sidon Excavation, Saida, Lebanon.
⁷ Département des Antiquités Orientales, Musée du Louvre, France.
⁸ Université Libanaise, Rectorat, BP 14-6573, Place du Musée, Beirut, Lebanon.
⁹ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address: cts@sanger.ac.uk.

PMID:32470374
PMCID: PMC7332655
DOI: 10.1016/j.ajhg.2020.05.008

Abstract

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world's great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

Keywords: Beirut, Bronze Age; Classical Antiquity; Iron Age; Lebanon; culture; migration, admixture; population genetics; whole-genome sequences.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Figure 1**
Principal Components Analysis of West, Central, and South Eurasians Eigenvectors were inferred with present-day populations (light-colored points in the background of the plot), and the ancient samples (colored solid shapes in the foreground of the plot) were projected onto the plot.

**Figure 2**
Admixture in Ancient Lebanon (A) Historical context of the studied samples. Horizontal lines indicate the time period of a sampled population, and the blue lozenges represent newly sequenced samples. (B and C) Locations of the source populations we used inqpAdm to test for admixture at the Iron Age (B) and the Hellenistic/early Roman period (C). The black lozenge on each map shows Lebanon’s location. Points represent modern populations in the dataset, whereas triangles represent ancient populations. Increased intensity of the red color indicates a higher p value for the model involving the source population (this should not be interpreted as an indication of the best model). We set the p values of the models that can be rejected to zero. (D) A DyStruct run with 166,693 transversions found in set 1 across nine time points. We show the plot of K = 6, which reveals an ancestral component (red) related to the Bronze Age Steppe population appearing in the Near East after the Bronze Age. (E) Haplotype segments shared between the ancient Lebanese and global modern populations. The heatmap is based on ChromoPainter’s co-ancestry matrix, and we averaged values from the modern populations over all individuals in the population. We scaled the heatmap by row to highlight the differences between the ancient individuals. Two Hellenistic individuals and one early Roman individual showed excess haplotype sharing with Central and South Asian populations compared with that of other ancient Lebanese individuals, whereas individuals SFI-43 and SFI-44 shared more segments with Africans and Egyptians. We counted between 19,073 (blue) and 19,659 (red) shared haplotype chunks in the dataset.

**Figure 3**
An Admixture Graph Model for Ancient Lebanon A graph model that fits our data showing the relationship between the ancient Lebanon populations and the admixture events that contributed to the population until modern times. Worstf4-statistics, Iran_N,Levant_N;EHG,Qed_LRoman;Z score = 3.0. See Figure S13 for alternative graph models.

See this image and copyright information in PMC

References

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A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

Affiliations

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous