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Genetic analyses of skeletal remains from prehistoric sites have greatly enriched our knowledge of the changes that brought sedentism and food-production, along with new people, material culture and practices, to Europe approximately 8.6 kya (kiloyears ago) through processes often described in archaeology as the “Neolithic revolution” (Childe, 1936). These processes are thought to have reached a tipping point ∼11.7 kya in Southwest Asia, where plants and animals were first domesticated (Fuller et al., 2011; Peters et al., 1999).
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Most farmers present in Continental Europe around 9 kya appear to have descended from populations inhabiting the Aegean basin and the Eastern Marmara region (Hofmanová et al., 2016), but their ultimate genetic and geographic origins are still a matter of debate.
Early Neolithic (EN) farmers from the Aegean are clearly related to Central Anatolian farmers (Kılınç et al., 2017), but they also show affinities with Pre-Pottery Neolithic farmers of the Southern Levant (Lazaridis et al., 2016). This suggests a common origin of all these populations prior to the westward spread of agriculture (Kılınç et al., 2016), potentially in the Fertile Crescent area, an archaeologically significant region that contained parts of modern-day Iran, Iraq, Israel, Palestine, Jordan, Lebanon, Syria, and Turkey.
However, research has also revealed that Aegean farmers are genetically distinct from early farming populations from the eastern wing of the Fertile Crescent, the Zagros region of Iran and northern Iraq, which may indicate parallel adoption of farming practices by genetically distant groups of HGs across Southwest Asia (Broushaki et al., 2016). Furthermore, there is some evidence of genetic continuity between Epipalaeolithic and Neolithic populations of Central Anatolia (Feldman et al., 2019), suggesting local transitions to agriculture without major gene flow. To make the picture even more complex, some Central Anatolian EFs also show genetic affinities to Caucasus HGs as represented by a 10th millennium before present (BP) genome from Kotias in Western Georgia (Jones et al., 2015; Kılınç et al., 2016; Skourtanioti et al., 2020). Caucasus HGs are themselves thought to be closely related to early Iranian Neolithic farmers (Lazaridis et al., 2016) as well as to later Pontic-Caspian steppe pastoralists (Lazaridis, 2018; Mathieson et al., 2018; Narasimhan et al., 2019).
The goal of this paper is to reconstruct the ancestry of Southwest Asian and European EFs and the processes that contributed to their differentiation from HGs. To do so, we produced 15 high-resolution genomes of early Holocene farmers and HGs distributed along a geographical and temporal transect reaching from Southwest Asia to the Rhine valley in West-Central Europe (Figure 1). DNA was extracted from skeletons recovered from some of the most important archaeological sites in early Holocene Europe and Anatolia, including the first farming villages in the Aegean basin (Barcın, Aktopraklık, Nea Nikomedeia); Mesolithic and Neolithic sites from the Iron Gates gorges and other areas of the Central Balkans (Lepenski Vir, Vlasac, Grad-Starčevo, Vinča-Belo Brdo); and the oldest cemeteries and mass grave or “massacre” sites of the Central European EN (Kleinhadersdorf, Asparn-Schletz, Essenbach-Ammerbreite, Dillingen-Steinheim, Herxheim)
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Multidimensional scaling (MDS) performed on the neutral portion of the genome (Figure 2A) of ancient individuals and modern reference populations reveals three clusters of ancient individuals: (1) European HGs, (2) western EFs, i.e., EFs from Europe and Anatolia, (3) an EF individual from Iran (WC1) and a Mesolithic HG from Caucasus (KK1). Consistent with previous analyses based on ascertained SNPs (Marcus et al., 2020; Skoglund et al., 2012), the western EFs show strongest affinities with modern Sardinians, with the exception of one English (CarsPas1) and two Northwest Anatolian EFs (Bar8 and AKT16), who are found to cluster with modern individuals from other parts of Southern Europe. In contrast, Palaeolithic and Mesolithic European HGs are genetically well differentiated from all modern Europeans. The Iranian EF and the Caucasus HG appear to be genetically close to modern populations from their sampling area, in keeping with some long-term genetic continuity in those regions. This observation is even more pronounced when performing a MDS analysis on the whole genome, including sites potentially affected by selection (Figure M1_5 from Methods S1). Generally, ancient individuals appear to be closer to modern ones, once the MDS is computed on the whole genome instead of just neutral sites. This could be explained by a slower evolution of genomic regions influenced by background selection (Pouyet et al., 2018). Another striking difference visible on the whole-genome MDS plot (Figure M1_5) is that western EFs are closer to some other Southern Europeans than to Sardinians.
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All western EFs share a remote common ancestry with Caucasus HGs
In contrast with previous studies (Lazaridis et al., 2016), we find that Caucasus HGs (represented by KK1) and western EFs are all descended from a population ancestral to the Central metapopulation. This is in line with a recent genetic study showing that KK1 was more closely related to EFs than to western European HGs (Speidel et al., 2021). This ancestral Central metapopulation received about 14% (95% CI 8–26) of its gene pool from the Western metapopulation some 14.2 kya (95% CI 13.7–19.0, Figures 3 and M1_18). Ancestors of the Iranian Neolithic population (represented by WC1) were not affected by this initial admixture: they rather diverged from the Eastern metapopulation 13.6 kya (95% CI 11–24.6) after its split from the Central metapopulation ∼15.8 kya (95% CI 14.3–25.6). Even though Caucasus HGs show closer genetic affinities with EFs from Iran (Figures 2A and 2B), our analyses suggest that they share a common ancestry with all western EFs.
Ancestors ofwestern EFs admixed twice with western HGs
We find that the ancestors of western EFs received a second pulse of gene flow (15%, 95% CI 6–17) from the Western metapopulation ∼12.9 kya (95% CI 9.4–13.9), while Caucasus HGs did not (Figure M1_20B). Models that do not include this additional admixture have a lower likelihood and are therefore rejected (Figure M1_20A). Thus, the ancestors of western EFs are the product of repeated episodes of gene flow from the Western metapopulation. These populations have then diverged from Caucasus HGs due to an intense period of genetic drift between 12.9 and 9.1 kya (Figures 3 and 4). Indeed, we find that their effective population size was reduced to 620 individuals (95% CI 72–2,150) during this relatively long period of drift, which caused them to not only diverge genetically from their ancestral population but also from Caucasus and European HGs, and from Iranian EFs (Figure 4).
Anatolian and Aegean farmers differentiation
Populations from Northwest Anatolia (the archaeological sites of Aktopraklık and Barcın) and Northern Greece (Nea Nikomedeia) appear to have diverged from one another at about the same time ∼9.1–9.3 kya (95% CI 9.1–12, Figures M1_20 and M1_22), potentially during the colonization of the wider Aegean area by EFs. In contrast, EFs from Central Anatolia (represented by a genome from Boncuklu) diverged at least 1,000 years earlier ∼10.5 kya (95% CI 10.5–11, Figure M1_24). That Anatolian and Aegean populations show varying amounts of recent gene flow from the Western metapopulation suggests different levels of interaction with surrounding HGs. Indeed, genomes from Northern Greece show a lower degree of further HG introgression (3%, 95% CI 1–11) than those of Boncuklu (10%, 95% CI 3–15), Barcın (12%, 95% CI 6–16), and especially Aktopraklık (17%, 95% CI 11–18) (Table S4). ....
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See link for more
https://www.cell.com/cell/fulltext/S...showall%3Dtrue
[...]
Most farmers present in Continental Europe around 9 kya appear to have descended from populations inhabiting the Aegean basin and the Eastern Marmara region (Hofmanová et al., 2016), but their ultimate genetic and geographic origins are still a matter of debate.
Early Neolithic (EN) farmers from the Aegean are clearly related to Central Anatolian farmers (Kılınç et al., 2017), but they also show affinities with Pre-Pottery Neolithic farmers of the Southern Levant (Lazaridis et al., 2016). This suggests a common origin of all these populations prior to the westward spread of agriculture (Kılınç et al., 2016), potentially in the Fertile Crescent area, an archaeologically significant region that contained parts of modern-day Iran, Iraq, Israel, Palestine, Jordan, Lebanon, Syria, and Turkey.
However, research has also revealed that Aegean farmers are genetically distinct from early farming populations from the eastern wing of the Fertile Crescent, the Zagros region of Iran and northern Iraq, which may indicate parallel adoption of farming practices by genetically distant groups of HGs across Southwest Asia (Broushaki et al., 2016). Furthermore, there is some evidence of genetic continuity between Epipalaeolithic and Neolithic populations of Central Anatolia (Feldman et al., 2019), suggesting local transitions to agriculture without major gene flow. To make the picture even more complex, some Central Anatolian EFs also show genetic affinities to Caucasus HGs as represented by a 10th millennium before present (BP) genome from Kotias in Western Georgia (Jones et al., 2015; Kılınç et al., 2016; Skourtanioti et al., 2020). Caucasus HGs are themselves thought to be closely related to early Iranian Neolithic farmers (Lazaridis et al., 2016) as well as to later Pontic-Caspian steppe pastoralists (Lazaridis, 2018; Mathieson et al., 2018; Narasimhan et al., 2019).
The goal of this paper is to reconstruct the ancestry of Southwest Asian and European EFs and the processes that contributed to their differentiation from HGs. To do so, we produced 15 high-resolution genomes of early Holocene farmers and HGs distributed along a geographical and temporal transect reaching from Southwest Asia to the Rhine valley in West-Central Europe (Figure 1). DNA was extracted from skeletons recovered from some of the most important archaeological sites in early Holocene Europe and Anatolia, including the first farming villages in the Aegean basin (Barcın, Aktopraklık, Nea Nikomedeia); Mesolithic and Neolithic sites from the Iron Gates gorges and other areas of the Central Balkans (Lepenski Vir, Vlasac, Grad-Starčevo, Vinča-Belo Brdo); and the oldest cemeteries and mass grave or “massacre” sites of the Central European EN (Kleinhadersdorf, Asparn-Schletz, Essenbach-Ammerbreite, Dillingen-Steinheim, Herxheim)
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| VLASA7 | LM | Vlasac | Serbia | 8,764–8,340 | 15.21 | M | U5a2a | I2 |
| VLASA32 | LM | Vlasac | Serbia | 9,741–9,468 | 12.65 | M | U5a2a | R1b1 |
| AKT16 | EN | Aktopraklık | Turkey | 8,635–8,460 | 12.25 | F | K1a3 | – |
| Bar25 | EN | Barcın | Turkey | 8,384–8,205 | 12.65 | M | N1a1a1 | G2a2b2a1 |
| Nea3 | EN | Nea Nikomedeia | Greece | 8,327–8,040 | 11.57 | F | K1a2c | – |
| Nea2 | EN | Nea Nikomedeia | Greece | 8,173–8,023 | 12.51 | F | K1a | – |
| LEPE48 | TEN | Lepenski Vir | Serbia | 8,012–7,867 | 10.92 | M | K1a1 | C1a2b |
| LEPE52 | E-MN | Lepenski Vir | Serbia | 7,931–7,693 | 12.37 | M | H3 | G2a2b2a1a1c |
| STAR1 | EN (Starčevo) | Grad-Starčevo | Serbia | 7,589–7,476 | 10.55 | F | T2e2 | – |
| VC3-2 | EN (Starčevo) | Vinča-Belo Brdo | Serbia | 7,565–7,426 | 11.22 | M | HV-16311 | G2a2a1a3 |
| Asp6 | EN (LBK) | Asparn-Schletz | Austria | 7,575–7,474 | 12.11 | M | U5a1c1 | G2a2b2a3 |
| Klein7 | EN (LBK) | Kleinhadersdorf | Austria | 7,244–7,000 | 11.30 | F | W1-119 | – |
| Dil16 | EN (LBK) | Dillingen-Steinheim | Germany | 7,235–6,998 | 10.60 | M | J1c6 | C1a2b |
| Ess7 | EN (LBK) | Essenbach-Ammerbreite | Germany | (7,050–6,900 BP) | 12.34 | M | U5b2c1 | G2a2b2a1a1 |
| Herx | EN (LBK) | Herxheim | Germany | 7,164–6,993 | 11.46 | F | K1a4a1i | – |
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All western EFs share a remote common ancestry with Caucasus HGs
In contrast with previous studies (Lazaridis et al., 2016), we find that Caucasus HGs (represented by KK1) and western EFs are all descended from a population ancestral to the Central metapopulation. This is in line with a recent genetic study showing that KK1 was more closely related to EFs than to western European HGs (Speidel et al., 2021). This ancestral Central metapopulation received about 14% (95% CI 8–26) of its gene pool from the Western metapopulation some 14.2 kya (95% CI 13.7–19.0, Figures 3 and M1_18). Ancestors of the Iranian Neolithic population (represented by WC1) were not affected by this initial admixture: they rather diverged from the Eastern metapopulation 13.6 kya (95% CI 11–24.6) after its split from the Central metapopulation ∼15.8 kya (95% CI 14.3–25.6). Even though Caucasus HGs show closer genetic affinities with EFs from Iran (Figures 2A and 2B), our analyses suggest that they share a common ancestry with all western EFs.
Ancestors ofwestern EFs admixed twice with western HGs
We find that the ancestors of western EFs received a second pulse of gene flow (15%, 95% CI 6–17) from the Western metapopulation ∼12.9 kya (95% CI 9.4–13.9), while Caucasus HGs did not (Figure M1_20B). Models that do not include this additional admixture have a lower likelihood and are therefore rejected (Figure M1_20A). Thus, the ancestors of western EFs are the product of repeated episodes of gene flow from the Western metapopulation. These populations have then diverged from Caucasus HGs due to an intense period of genetic drift between 12.9 and 9.1 kya (Figures 3 and 4). Indeed, we find that their effective population size was reduced to 620 individuals (95% CI 72–2,150) during this relatively long period of drift, which caused them to not only diverge genetically from their ancestral population but also from Caucasus and European HGs, and from Iranian EFs (Figure 4).
Anatolian and Aegean farmers differentiation
Populations from Northwest Anatolia (the archaeological sites of Aktopraklık and Barcın) and Northern Greece (Nea Nikomedeia) appear to have diverged from one another at about the same time ∼9.1–9.3 kya (95% CI 9.1–12, Figures M1_20 and M1_22), potentially during the colonization of the wider Aegean area by EFs. In contrast, EFs from Central Anatolia (represented by a genome from Boncuklu) diverged at least 1,000 years earlier ∼10.5 kya (95% CI 10.5–11, Figure M1_24). That Anatolian and Aegean populations show varying amounts of recent gene flow from the Western metapopulation suggests different levels of interaction with surrounding HGs. Indeed, genomes from Northern Greece show a lower degree of further HG introgression (3%, 95% CI 1–11) than those of Boncuklu (10%, 95% CI 3–15), Barcın (12%, 95% CI 6–16), and especially Aktopraklık (17%, 95% CI 11–18) (Table S4). ....
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See link for more
https://www.cell.com/cell/fulltext/S...showall%3Dtrue