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 53 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 5 0.042 Levant_N and 0.516 5 0.042 Iran_ChL. 

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 53 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 5 0.042 Levant_N and 0.516 5 0.042 Iran_ChL. 

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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 unc...

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... In the later Chalcolithic period, evidence of distinctive cultural practices and associated population movements highlight the dynamic history of the region, especially in the Southern Levant 7,8 . Further, genomic studies from the Bronze to Iron Ages in the Levant also report admixture and population movements, suggesting some degree of continuity with modern populations 6,[9][10][11] . On a more recent timescale, studies from the medieval period 12 and modern populations 13,14 describe genetic structure and the role played by culture and religion in the formation of these structures. ...
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... Instead, Sidonian marriages might have occurred between families within the region, and inter-regional connections were forged in other ways. Analysis of dental non-metric traits between the warrior burials did not highlight Burial 23 as genetically distinct from the group , although this fits with genomic analysis of the wider region which found that the people of the ancient Near East shared common genetic connections (Haber et al., 2017 Regarding comparative isotopic studies of mobility, the only other MBA assemblage within the same cultural sphere as Sidon is the city of Avaris (the site of Tell el-Dab'a) in the northeastern Nile Delta (Bietak, 2010;Bietak, 2013). Strontium analysis of the assemblage at this site revealed that most (40/75 or 53%) originated from outside the Nile Delta (Stantis, Kharobi, et al., 2020). ...
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... This contrast is noteworthy since it starts after the end of the Last Glacial Maximum and becomes prominent during the Neolithic, when agriculture developed in the Fertile Crescent and led to settled societies supporting larger populations. Following the Neolithic, and with the start of the aridification of Arabia around 6 kya, Arabian populations experienced a ll OPEN ACCESS The choice of a 4-way admixture derives from previous knowledge on the region with Levant_N and GanjDareh_N contributing significant ancestry to ancient Near Easterners (Lazaridis et al., 2016), EHG/Steppe ancestry penetrating the region after Bronze Age (Haber et al., 2017(Haber et al., , 2020, and African ancestry (represented by Mota; Gallego Llorente et al., 2015) found today in most Levantines and Arabians (Moorjani et al., 2011;Haber et al., 2013 Article bottleneck while Levantines continued to increase in size. The expansion in Levantines then plateaus and their population size decreases around the 4.2 kiloyear aridification event (Weiss et al., 1993). ...
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... This restricts the degree to which hypotheses regarding mobility can be effectively tested, although isotopic work done in 2 nd millennium BC Middle and Late Bronze Age contexts in Egypt [27], modern Sudan [28,29], Crete [30,31], Greece [32,33], Anatolia [34,35], and Arabia [36] have indicated differing levels of individual mobility ranging from populations composed primarily of local individuals to those with very high levels of non-locals. Ancient DNA (aDNA) analysis has also begun to illuminate these issues in recent years, with work in the southern Levant [37][38][39][40][41][42][43], Iran [42,44], Anatolia [42,[45][46][47][48][49][50][51], and the Aegean [52,53] stretching across large transects of both time and space. Two recent studies have independently detected gene flow during the 2 nd millennium BC from the northeast into the northern [49] and southern Levant [37] that seems to have ultimately originated from the Caucasus and/or Zagros regions. ...
... Ebla and Alalakh) are more closely related to Iranian Neolithic individuals and/or Caucasus Hunter Gatherer individuals (test) than are the earlier Tell Kurdu and Barcın individuals [49]. A similar genetic shift towards Iranian/Caucasus-related populations was detected for the contemporary Southern Levant [37][38][39]. This means that in the period between 5000-2000 BC, gene flow from populations harboring Iranian/Caucasus-like ancestries, which also includes populations that are genetically similar to these but have not yet been sampled, and are thus unknown, affected southern Anatolia and the entire Levant, including the Amuq Valley. ...
... The genome-wide data from the new individuals were combined with previously published ancient and modern data [39,42,45,46,49,162,. For readability, we kept most of the group labels used in Skourtanioti et al. [49], most importantly "Alalakh_MLBA", "ALA019" (genetic outlier) (n = 1), "Ebla_EMBA" (n = 9), "K.Kalehöyük_MLBA" (Kaman-Kalehöyük, n = 5), and "TellKurdu_EC" (n = 5), but dubbed individuals from Sidon with the label "Sidon_MBA" (instead of "Levant_MBA"; n = 5). ...
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... Comparative analyses ruled out that the Chalcolithic group could have been a direct ancestor of the EBA individuals studied to date (Lazaridis et al. 2016;Harney et al. 2018). However, a related group to the Chalcolithic one might have genetically contributed to Middle BA (MBA) inhabitants of the ancient city of Sidon in today's Lebanon (Haber et al. 2017;Harney et al. 2018). ...
... The MBA individuals from the central Levantine city of Sidon showed a high genetic similarity to the southern Levantine EBA ones from Jordan. This similarity is remarkable given the distance between the two sites (ca 180 km) and in light of the major cultural distinctions and temporal gap of around a millennium separating the two groups (Haber et al. 2017). Furthermore, southern Levantine MBA to LBA groups from present-day Israel showed a high level of genetic continuity with the earlier Levantine genomes Agranat-Tamir et al. 2020). ...
Article
Context The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent’s surrounding regions. Objective We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age. Methods We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe. Results We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data. Conclusion In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.
... The initial low absolute number of people bearing haplogroup J1a1a1-P58, as we see through our demographic analysis (Fig. 4), further complicates our possibility to find them in the early Holocene assemblages. Ne was increasing starting from the Chalcolithic and the Bronze Age periods (Fig. 4), the time when haplogroup J1a1a1-P58 appeared in the archaeological record of the Levant 22,46,61,62 . These are the oldest haplogroup J1a1a1-P58 members found so far in the world, further supporting its origin in the southern regions of West Asia. ...
... But we argue that in West Asia the distribution of haplogroup J1-M267 was already shaped before the spread of Islam. This conclusion aligns with aDNA studies, reporting J1a1a1-P58 at least before ~ 2.5 kya in a wide area encompassing Syria in the north and Egypt in the south 22,46,61,62,72 . ...
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Human Y chromosome haplogroup J1-M267 is a common male lineage in West Asia. One high-frequency region—encompassing the Arabian Peninsula, southern Mesopotamia, and the southern Levant—resides ~ 2000 km away from the other one found in the Caucasus. The region between them, although has a lower frequency, nevertheless demonstrates high genetic diversity. Studies associate this haplogroup with the spread of farming from the Fertile Crescent to Europe, the spread of mobile pastoralism in the desert regions of the Arabian Peninsula, the history of the Jews, and the spread of Islam. Here, we study past human male demography in West Asia with 172 high-coverage whole Y chromosome sequences and 889 genotyped samples of haplogroup J1-M267. We show that this haplogroup evolved ~ 20,000 years ago somewhere in northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. The major branch—J1a1a1-P58—evolved during the early Holocene ~ 9500 years ago somewhere in the Arabian Peninsula, the Levant, and southern Mesopotamia. Haplogroup J1-M267 expanded during the Chalcolithic, the Bronze Age, and the Iron Age. Most probably, the spread of Afro-Asiatic languages, the spread of mobile pastoralism in the arid zones, or both of these events together explain the distribution of haplogroup J1-M267 we see today in the southern regions of West Asia.
... Of the models we tested, one seems to have a good fit to the data (worst f-statistics Z < |3|). The best fit (worst f-statistic Z = -2.9, Figure 3.9), shows Lebanese forming from the Bronze Age Sidon (89%) population, with an additional contribution of Steppe-like ancestry (11%), consistent with the literature (Haber et al., 2017). While Emirati.core, instead, form from a Natufian-like (25%) and Sidon-like population (75%). ...
Thesis
Despite the progress in sampling many populations, human genomics research is still not fully reflective of the diversity found globally. Understudied populations limit our knowledge of genetic variation and population history, and their inclusion is needed to ensure they benefit from future developments in genomic medicine. In this thesis, I describe extending our understanding of global genetic diversity and population history by two main projects. The first is focused on structural variation in a diverse set of 54 human populations which are part of the Human Genome Diversity Project (HGDP-CEPH) panel. Using whole-genome sequences previously produced at the Wellcome Sanger Institute, I generated a comprehensive catalogue of structural variation identifying a total of 126,018 variants, of which 78% are novel. Some reach high frequency and are private to continental groups or even individual populations, including regionally-restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, I discovered 1643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference genome, highlighting the limitation of a single human reference genome. In the second project I collected and analysed a dataset of 137 high-coverage physically-phased genome sequences from eight Middle Eastern populations using linked-read sequencing. Focusing on the population history using single nucleotide variants, I found no genetic traces of archeologically documented early expansions out-of-Africa in present-day populations in the region. I show that Arabian populations have the lowest Neanderthal ancestry of all non-African populations tested, which is explained by them having elevated Basal Eurasian ancestry. By comparing Levantines and Arabian historical population sizes, I find a divergence that starts before the Neolithic era, when Levantines expanded while Arabians maintained small populations that could have derived ancestry from local epipaleolithic hunter-gatherers. All populations suffered a bottleneck overlapping the archaeologically-documented aridification events, with Arabians decreasing in size with the onset of the desert climate in Arabia ~6 kya while the Levantine bottleneck overlaps the 4.2 kiloyear aridification event. I also identify an ancestry that is associated with the spread of Semitic languages across the region during the Bronze Age. Finally, I identify novel variants that show evidence of selection, including signals of polygenic selection. This thesis fills an important gap in the study of diverse human populations, although further work is needed to sequence and characterize additional genetically underrepresented groups.