Migrations in the Levant region during the Chalcolithic, also marked by distinct Y-DNA


Open access Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation, by Harney et al. Nature Communications (2018).

Interesting excerpts (emphasis mine, reference numbers deleted for clarity):


The material culture of the Late Chalcolithic period in the southern Levant contrasts qualitatively with that of earlier and later periods in the same region. The Late Chalcolithic in the Levant is characterized by increases in the density of settlements, introduction of sanctuaries, utilization of ossuaries in secondary burials, and expansion of public ritual practices as well as an efflorescence of symbolic motifs sculpted and painted on artifacts made of pottery, basalt, copper, and ivory. The period’s impressive metal artifacts, which reflect the first known use of the “lost wax” technique for casting of copper, attest to the extraordinary technical skill of the people of this period.

The distinctive cultural characteristics of the Late Chalcolithic period in the Levant (often related to the Ghassulian culture, although this term is not in practice applied to the Galilee region where this study is based) have few stylistic links to the earlier or later material cultures of the region, which has led to extensive debate about the origins of the people who made this material culture. One hypothesis is that the Chalcolithic culture in the region was spread in part by immigrants from the north (i.e., northern Mesopotamia), based on similarities in artistic designs. Others have suggested that the local populations of the Levant were entirely responsible for developing this culture, and that any similarities to material cultures to the north are due to borrowing of ideas and not to movements of people.

Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today. By the Bronze Age, however, expansion of different Near Eastern agriculturalist populations — Anatolian, Iranian, and Levantine — in all directions and admixture with each other substantially homogenized populations across the region, thereby contributing to the relatively low genetic differentiation that prevails today. Showed that the Levant Bronze Age population from the site of ‘Ain Ghazal, Jordan (2490–2300 BCE) could be fit statistically as a mixture of around 56% ancestry from a group related to Levantine Pre-Pottery Neolithic agriculturalists (represented by ancient DNA from Motza, Israel and ‘Ain Ghazal, Jordan; 8300–6700 BCE) and 44% related to populations of the Iranian Chalcolithic (Seh Gabi, Iran; 4680–3662 calBCE). Suggested that the Canaanite Levant Bronze Age population from the site of Sidon, Lebanon (~1700 BCE) could be modeled as a mixture of the same two groups albeit in different proportions (48% Levant Neolithic-related and 52% Iran Chalcolithic-related). However, the Neolithic and Bronze Age sites analyzed so far in the Levant are separated in time by more than three thousand years, making the study of samples that fill in this gap, such as those from Peqi’in, of critical importance.

This procedure produced genome-wide data from 22 ancient individuals from Peqi’in Cave (4500–3900 calBCE) (…)


We find that the individuals buried in Peqi’in Cave represent a relatively genetically homogenous population. This homogeneity is evident not only in the genome-wide analyses but also in the fact that most of the male individuals (nine out of ten) belong to the Y-chromosome haplogroup T, a lineage thought to have diversified in the Near East. This finding contrasts with both earlier (Neolithic and Epipaleolithic) Levantine populations, which were dominated by haplogroup E, and later Bronze Age individuals, all of whom belonged to haplogroup J.

Detailed sample background data for each of the 22 samples from which we successfully obtained ancient DNA. Additionally, background information for all samples from Peqi’in that were screened is included in Supplementary Data 1. *Indicates that Y-chromosome haplogroup call should be interpreted with caution, due to low coverage data.

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.

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 Mesopotamia. 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 regions. The knowledge and resources required to produce metallurgical artifacts in the Levant have also been hypothesized to come from the north.

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 patterns, large-scale abandonment of sites, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries. 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 region.

Genetic structure of analyzed individuals. a Principal component analysis of 984 present-day West Eurasians (shown in gray) with 306 ancient samples projected onto the first two principal component axes and labeled by culture. b ADMIXTURE analysis of 984 and 306 ancient samples with K = 11
ancestral components. Only ancient samples are shown


I think the most interesting aspect of this paper is – as usual – the expansion of peoples associated with a single Y-DNA haplogroup. Given that the expansion of Semitic languages in the Middle East – like that of Anatolian languages from the north – must have happened after ca. 3100 BC, coinciding with the collapse of the Uruk period, these Chalcolithic north Levant peoples are probably not related to the posterior Semitic expansion in the region. This can be said to be supported by their lack of relationship with posterior Levantine migrations into Africa. The replacement of haplogroup E before the arrival of haplogroup J suggests still more clearly that Natufians and their main haplogroup were not related to the Afroasiatic expansions.

Distribution of Semitic languages. From Wikipedia.

On the other hand, while their ancestry points to neighbouring regional origins, their haplogroup T1a1a (probably T1a1a1b2) may be closely related to that of other Semitic peoples to the south, as found in east Africa and Arabia. This may be due either to a northern migration of these Chalcolithic Levantine peoples from southern regions in the 5th millennium BC, or maybe to a posterior migration of Semitic peoples from the Levant to the south, coupled with the expansion of this haplogroup, but associated with a distinct population. As we know, ancestry can change within certain generations of intense admixture, while Y-DNA haplogroups are not commonly admixed in prehistoric population expansions.

Without more data from ancient DNA, it is difficult to say. Haplogroup T1a1 is found in Morocco (ca. 3780-3650 calBC), which could point to a recent expansion of a Berbero-Semitic branch; but also in a sample from Balkans Neolithic ca. 5800-5400 calBCE, which could suggest an Anatolian origin of the specific subclades encountered here. In any case, a potential origin of Proto-Semitic anywhere near this wide Near Eastern region ca. 4500-3500 BC cannot be discarded, knowing that their ancestors came probably from Africa.

Distribution of haplogroup T of Y-chromosome. From Wikipedia.

Interesting from this paper is also that we are yet to find a single prehistoric population expansion not associated with a reduction of variability and expansion of Y-DNA haplogroups. It seems that the supposedly mixed Yamna community remains the only (hypothetical) example in history where expanding patrilineal clans will not share Y-DNA haplogroup…


Expansion of domesticated goat echoes expansion of early farmers


New paper (behind paywall) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, by Daly et al. Science (2018) 361(6397):85-88.

Interesting excerpts (emphasis mine):

Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).

PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.

Maximumlikelihood phylogeny and geographical distributions of ancient mtDNA haplogroups. (A) A phylogeny placing ancient whole mtDNA sequences in the context of known haplogroups. Symbols denoting individuals are colored by clade membership; shape indicates archaeological period (see key). Unlabeled nodes are modern bezoar and outgroup sequence (Nubian ibex) added for reference.We define haplogroup T as the sister branch to the West Caucasian tur (9). (B and C) Geographical distributions of haplogroups show early highly structured diversity in the Neolithic period (B) followed by collapse of structure in succeeding periods (C).We delineate the tiled maps at 7250 to 6950 BP, a period >bracketing both our earliest Chalcolithic sequence (24, Mianroud) and latest Neolithic (6, Aşağı Pınar). Numbered archaeological sites also include Direkli Cave (8), Abu Ghosh (9), ‘Ain Ghazal (10), and Hovk-1 Cave (11) (table S1) (9).

Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.


Kura-Araxes implicated in the transformation of regional trade in the Near East


Craft production at Köhne Shahar, a Kura-Araxes settlement in Iranian Azerbaijan, by Alizadeh et al. J Anthropol Arch (2018) 51:127-143.

Interesting excerpts (emphasis mine):


Kura-Araxes communities first emerged throughout the southern Caucasus in the mid-4th millennium BC (Sagona, 1984; Rothman, 2005; Kohl, 2009) or possibly earlier in Nakhchivan (Marro et al., 2014; Palumbi and Chataigner, 2014: 250; Marro et al., 2015; Palumbi and Chataigner, 2015). By the late 4th-early 3rd millennium BC, their characteristic material culture, particularly hand-made black burnished pottery, spread throughout much of Southwest Asia after 2900 BCE (Fig. 1). The widespread dissemination of this material culture, along with the small size of most sites, the ephemeral nature of their architectural remains in these smaller sites, and their presence in both fertile lowlands and seasonally-inhospitable highlands, have been used to portray Kura-Araxes communities as small, egalitarian communities of mobile pastoralists or sedentary agriculturalists; economically undifferentiated and socially non-hierarchical (Smith, 2005: 258; Frangipane and Palumbi, 2007; Kohl, 2007: 113; 2009: 250). Limited evidence for craft production and trade among Kura-Araxes communities has further strengthened the argument that Kura-Araxes economies were dominated by domestic and subsistence-related activities (Palumbi, 2008: 53). With some rare exceptions (Marro et al., 2010; Stöllner, 2014; Simonyan and Rothman, 2015), Kura-Araxes settlements lack any evidence of craft production, mining, or resource extraction.

Distribution of Kura-Araxes material culture in the Near East (modified from Wikimedia).

Kura-Araxes communities, however, are also implicated in the evolution and transformation of regional trade in the Near East. Cause and effect of the spread of Kura-Araxes material culture beyond the Caucasus “homeland” and the establishment of diaspora is hotly debated. Among proponents of emigration, the strongest arguments for movement out of the Caucasus include the presence of strong pull factors, notably productive activities like meat and wool production, viticulture, and metals and metallurgy (Rothman, 2003). Kura-Araxes populations primarily inhabited mountains and intermontane valleys of the highland zone surrounding Mesopotamia. Kura-Araxes communities had access to metals, precious and semi-precious stones, stones for tool making, wood, and animal products; resources that were abundant in the mountain zone, yet critical to the evolution of Mesopotamian societies. The frequent appearance of simple bronze and copper objects at temporary camps of Kura-Araxes herders suggests that mobile agropastoralists engaged in metallurgy and trade in metals, especially with societies of the Upper Euphrates (Frangipane et al., 2001; Hauptmann et al., 2002; Rothman, 2003; Connor and Sagona, 2007; Frangipane, 2014). Wool and textiles products from sheep herded by mountainous communities may have been major exports of the mountain zone to Mesopotamia (Anthony, 2007: 284; Nosch et al., 2013; Breniquet and Michel, 2014).

It is argued that by the second half of the 4th millennium BC (Surenhagen, 1986; Algaze, 1989, 2004, 2007), Uruk polities of southern Mesopotamia established colonies across northern Mesopotamia, southern Anatolia, and western Iran to better control regional trade. Although the nature of these colonies and local developments is still debated (Stein, 2002, 2014), co-occurrence of the sudden abandonment of these colonies and regional expansion of Kura-Araxes communities by the end of the 4th millennium BC has led some scholars to argue that Kura-Araxes communities were emergent competitors of Mesopotamia whose economic activities possibly contributed to the decline and eventual collapse of the Uruk system (Algaze, 2001: 76; Kohl, 2007: 97–98; Lamberg-Karlovsky, 2008: 10).

Major Kura-Araxes sites in the Caucasus region and location of Köhne Shahar (modified map from wikimedia.org).


The abundant evidence of craft specialization at Köhne Shahar clearly shows that Kura-Araxes communities were not all homogenous and undifferentiated. Excavations and a geophysical survey at Köhne Shahar demonstrate that multi-craft production activities were practiced at a community-level inside the citadel at the site, and that a large portion of the population may have engaged in this specialized, extrahousehold craft economy. The possible involvement of a political apparatus with a specialized craft economy at Köhne Shahar may have necessitated control over various aspects of production such as labor, commodities, resource procurement, exchange, and grain storage. As Adam Smith (Smith, 2015: 106) argues, all of these point to complex labor coordination at Köhne Shahar.

Although excavations exposed a limited area, the scale of craft production at Köhne Shahar and the scarcity of finished products may suggest that consumers of finished goods were not necessarily residents of Köhne Shahar, but instead occupied other areas on the landscape. Communication between these nodes of production and consumption necessitated a network of exchange and interaction. The miniature sumptuary container at Köhne Shahar points to possible interaction with regions of Central Asia and the Persian Gulf, while the bitumen used to mend vessels points to interaction with northern Mesopotamia or the Zagros mountains in western Iran. It is possible that long-distance interaction brought Köhne Shahar chiefs into contact with other complex societies in the region, connecting them to a larger inter-regional exchange and trade network.

Archaeological and geophysical evidence for community-level production documents Köhne Shahar’s emergence as a regional economic center. The extent of Köhne Shahar’s regional engagements and ambitions, however, have yet to be fully understood. Köhne Shahar’s economic focus on production may have enabled its producers to contribute to regional transformations. When trade became a significant part of the economy of early complex societies in the Near East in the second half of the 4th millennium BC (Surenhagen, 1986; Algaze, 1989, 2004), Kura-Araxes communities like Köhne Shahar may have emerged as a primary center of specialized craft production in the late 4th/early 3rd millennium BC. Alternatively, Köhne Shahar’s economic success may have been due to its ability to satisfy regional demand (highlands of NW Iran, eastern Anatolia, or northern Mesopotamia) by filling a supply vacuum created following the collapse of Uruk colonies. Political and entrepreneurial ambitions of Köhne Shahar chiefs may have also provided the impetus for the selection of the site’s naturally defensible area and the construction of a large and defensive fortification wall; two barriers intended to safeguard the production machinery of the citadel from the onset of the site’s occupation in the late 4th millennium BC (Alizadeh et al., 2015).

I don’t have much to add to what I recently wrote about potential intrusive steppe admixture in the Caucasus.


Human sacrifice as means of social control and power display in Upper Mesopotamia (early 3rd mill. BC)


Radical ‘royals’? Burial practices at Başur Höyük and the emergence of early states in Mesopotamia, by Hasset and Sağlamtimur, Antiquity (2018) 92:640-654.

Interesting excerpts:

The discovery of sacrificial burials attending a ‘royal’ burial in a cist tomb at Early Bronze Age Arslantepe in Anatolia (Frangipane 2006; Erdal 2012) has dramatically broadened the known range of social responses to the political upheaval of the early third millennium BC. Following the longstanding interpretation of human sacrifice at the Royal Cemetery of Ur just a few hundred years later (Woolley 1934), this raises new questions about the role of human sacrifice in processes of early state formation (Sürenhagen 2002; Croucher 2012). Power over the physical bodies of a population to the point of death has been associated with the hierarchical social structures that accompanied early state-formation processes across the globe (Watts et al. 2016). There is, however, considerable variation in the practice. Sacrifice can be employed variously to achieve spiritual, ritual, political, martial or even economic ends (see Bremmer 2007; Turchin 2016), and the role of human sacrifice in ancient Near Eastern burial practices remains unclear (Porter & Schwartz 2012).

“The mound site of Ba¸sur Höyük, with the archaeological plan of the Early Bronze Age cemetery. Graves are outlined in red, Uruk-period architecture in black. Each grid square is 10 × 10m.”

Wengrow draws an interesting distinction between “sacrificial” and “archival” ritual economies, using metal finds from the much wider context of the Eurasian Bronze Age (Wengrow 2011: 137). For Wengrow, the ‘sacrificial’ deposit of metal work, particularly in burial contexts, indicates a system of metal exchange that is most frequently found on the edges of more complex, centrally administrated urban exchange systems. Metalwork serves here to consolidate and display personal wealth rather than as a standardised commodity for equitable exchange. Wilkinson has highlighted the role of shifting economic modes in marking social change, observing such a transition in ritual-economic systems in the Early Bronze Age Trans-Caucasian sphere of influence that stretched from Anatolia to Iran (Wilkinson 2014). The bronze objects buried at Başur Höyük fall into a pattern of ritual deposits that clearly mark Early Bronze Age funerary rituals as locations for the communication of wealth and status (Săglamtimur & Massimino 2015). The importance of that display is not diminished by the presence of administrative artefacts such as the cylinder seals and ceramics marked with seal impressions that were also found inside the cist tomb. The material culture of the Early Bronze Age cemetery at Başur Höyük demonstrates connections to the Anatolian world, with clear Trans-Caucasian links similar to those found along the Euphrates, and also to the southern, urban networks of the Mesopotamian core.

The utility of such sacrificial gestures waned as other means of social control and power display were brought to bear by an administrated, ‘archival’ economy that did not require the sacrifice of its human subjects.(…) In the vacuum of political centralisation that followed the withdrawal of Uruk material culture in the Mesopotamian sphere, we see precisely the instability among smaller polities that would be expected to underlie the introduction of human sacrifice. In the vast administrative state systems that rose up in southern Mesopotamia in the next millennium, it disappears again from the archaeological record and it is not unreasonable to see in this pattern an implication for the value and economy of human life during the formation of early states.

Ebla’ first kingdom at its height c. 2340 BC. Hipothetical location of Armi depicted. The first Eblaite kingdom extended from Urshu in the north,1 to Damascus area in the south.2 And from Phoenicia and the coastal mountains in the west,3 4 to Tuttul,5 and Haddu in the east.6 The eastern kingdom of Nagar controlled most of the Khabur basin from the river junction with the Euphrates to the northwestern part at Nabada.7 Page 101. From Wikipedia.

Given the potential Anatolian names in Armi inscriptions (ca. 2500-2300 BC), this crucial period of political upheaval after the fall of Uruk-period Mesopotamian interregional networks and before the rise of new state system, i.e. in the early third millennium BC, is probably to be identified with the arrival of Anatolian speakers from the west.

Similar to the Early Indo-Aryan elites ruling over Hurrian-speaking Mitanni, it is possible that some Anatolian-speaking groups imposed their rule as elites (and thus their language) after this period of instability – at least in certain regions, as is obvious from the multilingualism and multiethnic situation found in the Old Assyrian tablets of Kaneš.


Ancient genomes from North Africa evidence Neolithic migrations to the Maghreb

BioRxiv preprint now published (behind paywall) Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe, by Fregel et al., PNAS (2018).

NOTE. I think one of the important changes in this version compared to the preprint is the addition of the recent Iberomaurusian samples.

Abstract (emphasis mine):

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. PCA analysis using the Human Origins panel (European, Middle Eastern, and North African populations) and LASER projection of aDNA samples.

Relevant excerpts:

FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ∼15,000-y old and ∼7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa.

Genetic analyses have revealed that the population history of modern North Africans is quite complex (11). Based on our aDNA analysis, we identify an Early Neolithic Moroccan component that is (i) restricted to North Africa in present-day populations (11); (ii) the sole ancestry in IAM samples; and (iii) similar to the one observed in Later Stone Age samples from Morocco (17). We conclude that this component, distantly related to that of Epipaleolithic communities from the Levant, represents the autochthonous Maghrebi ancestry associated with Berber populations. Our data suggests that human populations were isolated in the Maghreb since Upper Paleolithic times. Our hypothesis is in agreement with archaeological research pointing to the first stage of the Neolithic expansion in Morocco as the result of a local population that adopted some technological innovations, such as pottery production or farming, from neighboring areas.

By 3,000 BCE, a continuity in the Neolithic spread brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Other archaeological remains, such as African elephant ivory and ostrich eggs found in Iberian sites, confirm the existence of contacts and exchange networks through both sides of the Gibraltar strait at this time. Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/ Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves. Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today.

Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. (B) ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, and North African populations) for modern and ancient samples (K = 8). (D) Detail of ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, North African, and sub-Saharan African populations) for modern and ancient samples, including Taforalt.

Also, from the main author’s Twitter account:

I just realized that the paragraph with information on data availability is missing! Sequence data in the European Nucleotide Archive (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology Information (Accession Numbers MF991431-MF991448).

I find it hard to believe that this genetic continuity from Upper Palaeolithic to Late Neolithic could be representative of an autochthonous development of Afroasiatic. An important population movement – likely more than one – must be found in ancient DNA influencing North-Central and North-East Africa, probably during the time of the Green Sahara corridor.

See here:

Steppe and Caucasus Eneolithic: the new keystones of the EHG-CHG-ANE ancestry in steppe groups


Some interesting excerpts from Wang et al. (2018):

An interesting observation is that steppe zone individuals directly north of the Caucasus (Eneolithic Samara and Eneolithic steppe) had initially not received any gene flow from Anatolian farmers. Instead, the ancestry profile in Eneolithic steppe individuals shows an even mixture of EHG and CHG ancestry, which argues for an effective cultural and genetic border between the contemporaneous Eneolithic populations in the North Caucasus, notably Steppe and Caucasus. Due to the temporal limitations of our dataset, we currently cannot determine whether this ancestry is stemming from an existing natural genetic gradient running from EHG far to the north to CHG/Iran in the south or whether this is the result of farmers with Iranian farmer/ CHG-related ancestry reaching the steppe zone independent of and prior to a stream of Anatolian farmer-like ancestry, where they mixed with local hunter-gatherers that carried only EHG ancestry.

Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. An Eastern European (blue) and a Caucasus (brown) ‘clouds’ have been drawn in dotted circles, leaving Pontic-Caspian steppe and derived groups between them.See the original file here.

Concerning the influences from the south, our oldest dates from the immediate Maykop predecessors Darkveti-Meshoko (Eneolithic Caucasus) indicate that the Caucasus genetic profile was present north of the range ~6500 BP, 4500 calBCE. This is in accordance with the Neolithization of the Caucasus, which had started in the flood plains of the great rivers in the South Caucasus in the 6th millennium BCE from where it spread to the West and Northwest Caucasus during the 5th millennium BCE9, 49. It remains unclear whether the local CHG ancestry profile (represented by Late Upper Palaeolithic/Mesolithic individuals from Kotias Klde and Satsurblia in today’s Georgia) was also present in the North Caucasus region before the Neolithic. However, if we take the Caucasus hunter-gatherer individuals from Georgia as a local baseline and the oldest Eneolithic Caucasus individuals from our transect as a proxy for the local Late Neolithic ancestry, we notice a substantial increase in Anatolian farmer-related ancestry. This in all likelihood is linked to the process of Neolithization, which also brought this type of ancestry to Europe. As a consequence, it is possible that Neolithic groups could have reached the northern flanks of the Caucasus earlier50 (Supplementary Information 1) and in contact with local hunter gatherers facilitated the exploration of the steppe environment for pastoralist economies. Hence, additional sampling from older individuals is needed to fill this temporal and spatial gap.

The newest paper of the Reich/Jena group has brought samples (probably) much nearer to the actual CHG and ANE contribution seen in Eneolithic steppe peoples than the previously available Kotias Klde, Satsurblia, Afontova Gora 3, or Mal’ta.

It is impossible to say without direct access to the samples, but it is very likely that we will soon be able to break down different gross contributions from groups similar to these Steppe/Caucasus Neolithic ancestral groups into the diverse Eneolithic cultures of the Pontic-Caspian steppe, and thus trace more precisely each of these cultures to their genetic (and thus ethnolinguistic) heirs.

Admixture Graph modelling of the population history of the Caucasus region. We started with a skeleton tree without admixture including Mbuti, Loschbour and MA1. We grafted onto this EHG, CHG, Globular_Amphora, Eneolithic_steppe, Maykop, and Yamnaya_Caucasus, adding them consecutively to all possible edges in the tree and retaining only graph solutions that provided no differences of |Z|>3 between fitted and estimated statistics. The worst match is |Z|=2.824 for this graph. We note that the maximum discrepancy is f4(MA1, Maykop; EHG, Eneolithic_steppe) = -3.369 if we do not add the 4% EHG ancestry to Maykop. Drifts along edges are multiplied by 1000 and dashed lines represent admixture.”

Some more representative samples from Eneolithic steppe, steppe-forest and forest zone cultures of Eastern Europe will probably help with the fine-scale structure of different Chalcolithic groups, especially the homeland of early Corded Ware groups.

These new samples seem another good reason (like the Botai and R1b-M73) to rethink the role of (what I assumed were) different westward Mesolithic Eurasian waves of expansion influencing the formation of an Indo-Uralic and Indo-European community in Eastern Europe, and return to the simpler idea of local contributions from North Caucasus and steppe peoples absorbed by expanding EHG-like groups.


Optimal Migration Routes of Initial Upper Palaeolithic Populations to Eurasia


Ecological Niche and Least-Cost Path Analyses to Estimate Optimal Migration Routes of Initial Upper Palaeolithic Populations to Eurasia, by Kondo et al. (2018), from The Middle and Upper Paleolithic Archeology of the Levant and Beyond, Replacement of Neanderthals by Modern Humans Series. Chapter downloadable at Academia.edu.


This paper presents a computer-based method to estimate optimal migration routes of early human population groups by a combination of ecological niche analysis and least-cost path analysis. In the proposed method, niche probability is predicted by MaxEnt, an ecological niche model based on the maximum entropy theory. Location of known archaeological sites and environmental factors derived from palaeoterrain and palaeoclimate models, are input to the model to calculate the niche probability at each spatial pixel and weights of the environmental factors. The inverse of probability score is then used as an index of relative dispersal rate to accumulate the travel cost from a given origin. Based on this cumulative cost surface, least-cost paths from the origin to given destinations are visualised. This method was applied to the Initial Upper Palaeolithic population group (probably of modern humans) in Eurasia. The model identified three migration routes from the Levant to (1) Central Europe via Anatolia and Eastern Europe, (2) the Russian steppe via Caucasus Mountains, and (3) the Altai region via the southern coastal Iran and Afghanistan.

Cumulative cost to the southernmost IUP site (Wadi Aghir) using the inverse of the niche probability of the recovery experiment (corresponding to a warm/humid phase) as friction value

Check out also the chapter The Middle to Upper Paleolithic Transition in the Zagros: The Appearance and Evolution of the Baradostian, by Sonia Shidrang, from the same book. Also downloadable at Academia.edu.

Featured image from the chapter: “Niche probability for the IUP lithic industry predicted by MaxEnt using the palaeoclimate model from the recovery experiment (corresponding to a warm/humid phase).”

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Ancient Phoenician mtDNA from Sardinia, Lebanon reflects settlement, genetic diversity, and female mobility


New article at PLOS One, Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility, by Matisoo-Smith et al. (2018).


The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700–400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.

Haplogroup assignments, dates, locations and Genbank accession details of all aDNA samples included in analyses.

Featured image, from the article: Map showing phoenician maritime expansions across the Mediterranean starting from around 800 BCE. Arrows indicate maritime movement. Blue dots indicate coastal sites and pink shaded areas indicate the extent of Phoenician settlements. https://doi.org/10.1371/journal.pone.0190169.g001

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