Excerpts from the study:
https://www.nature.com/articles/s41467-018-05649-9
"(...) The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel.
These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.
"Based on this uniquely fitting qpAdm model
we infer the ancestry of Levant_ChL to be the result of a three-way admixture of populations related to Levant_N (57%), Iran_ChL (17%), and Anatolia_N (26%).
It was striking to us that previously published Bronze Age Levantine samples from the sites of 'Ain Ghazal in present-day Jordan (Levant_BA_South) and Sidon in present-day Lebanon (Levant_BA_North) can be modeled as two-way admixtures, without the Anatolia_N contribution that is required to model the Levant_ChL population24,26. This suggests that the Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry.
In what follows, we treat Levant_BA_South and Levant_BA_North as separate populations for analysis, since the symmetry statistic f4(Levant_BA_North, Levant_BA_South; A, Chimp) is significant for a number test populations A (|Z| ≥ 3) (Supplementary Data 5), consistent with the different estimated proportions of Levant_N and Iran_ChL ancestry reported in24,26.
(...)
We observe a qualitatively different pattern in the Levant_BA_North samples from Sidon, Lebanon, where models including Levant_ChL paired with either Iran_N, Iran_LN, or Iran_HotuIIIb populations appear to be a significantly better fit than those including Levant_N + Iran_ChL. We largely confirm this result using the “Right” population outgroups defined in26. (abb. Haber: Ust_Ishim, Kostenki14, MA1, Han, Papuan, Ami, Chuckhi, Karitiana, Mbuti, Switzerland_HG, EHG, WHG, and CHG), although we find that the specific model involving Iran_HotuIIIb no longer works with this “Right” set of populations.
Investigating this further, we find that the addition of Anatolia_N in the “Right” outgroup set excludes the model of Levant_N + Iran_ChL favored by26. These results imply that a population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.
We obtained additional insight by running qpAdm with Levant_BA_South as a target of two-way admixture between Levant_N and Iran_ChL, but now adding Levant_ChL and Anatolia_N to the basic 09NW “Right” set of 11 outgroups.
The addition of the Levant_ChL causes the model to fail, indicating that Levant_BA_South and Levant_ChL share ancestry following the separation of both of them from the ancestors of Levant_N and Iran_ChL. Thus, in the past there existed an unsampled population that contributed both to Levant_ChL and to Levant_BA_South, even though Levant_ChL cannot be the direct ancestor of Levant_BA_South because, as described above, it harbors Anatolia_N-related ancestry not present in Levant_BA_South.
(...)
Our finding that the Levant_ChL population can be well-modeled as a three-way admixture between Levant_N (57%), Anatolia_N (26%), and Iran_ChL (17%), while the Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry, can only be explained by multiple episodes of population movement. The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region. We additionally find that the Levant_ChL population does not serve as a likely source of the Levantine-related ancestry in present-day East African populations (see Supplementary Note 4)24.
These genetic results have striking correlates to material culture changes in the archaeological record. The archaeological finds at Peqi’in Cave share distinctive characteristics with other Chalcolithic sites, both to the north and south, including secondary burial in ossuaries with iconographic and geometric designs. It has been suggested that some Late Chalcolithic burial customs, artifacts and motifs may have had their origin in earlier Neolithic traditions in Anatolia and northern Mesopotamia8,13,47. Some of the artistic expressions have been related to finds and ideas and to later religious concepts such as the gods Inanna and Dumuzi from these more northern regions6,8,47,48,49,50. The knowledge and resources required to produce metallurgical artifacts in the Levant have also been hypothesized to come from the north11,51.
Our finding of genetic discontinuity between the Chalcolithic and Early Bronze Age periods also resonates with aspects of the archeological record marked by dramatic changes in settlement patterns43, large-scale abandonment of sites52,53,54,55, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries56,57,58,59. This supports the view that profound cultural upheaval, leading to the extinction of populations, was associated with the collapse of the Chalcolithic culture in this region18,60,61,62,63,64. (...)"
PCA graph: