Modern Sardinians show elevated Neolithic farmer ancestry shared with Basques

sardinia-europe-relation

New paper (behind paywall), Genomic history of the Sardinian population, by Chiang et al. Nature Genetics (2018), previously published as a preprint at bioRxiv (2016).

#EDIT (18 Sep 2018): Link to read paper for free shared by the main author.

Interesting excerpts (emphasis mine):

Our analysis of divergence times suggests the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations ~140–250 generations ago, corresponding to ~4,300–7,000 years ago assuming a generation time of 30 years and a mutation rate of 1.25 × 10−8 per basepair per generation. (…) in terms of relative values, the divergence time between Northern and Southern Europeans is much more recent than either is to Sardinia, signaling the relative isolation of Sardinia from mainland Europe.

We documented fine-scale variation in the ancient population ancestry proportions across the island. The most remote and interior areas of Sardinia—the Gennargentu massif covering the central and eastern regions, including the present-day province of Ogliastra— are thought to have been the least exposed to contact with outside populations. We found that pre-Neolithic hunter-gatherer and Neolithic farmer ancestries are enriched in this region of isolation. Under the premise that Ogliastra has been more buffered from recent immigration to the island, one interpretation of the result is that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. Such admixture could have occurred principally on the island or on the mainland before the hypothesized Neolithic era influx to the island. Under the alternative premise that Ogliastra is simply a highly isolated region that has differentiated within Sardinia due to genetic drift, the result would be interpreted as genetic drift leading to a structured pattern of pre-Neolithic ancestry across the island, in an overall background of high Neolithic ancestry.

sardinia-pca
PCA results of merged Sardinian whole-genome sequences and the HGDP Sardinians. See below for a map of the corresponding regions.

We found Sardinians show a signal of shared ancestry with the Basque in terms of the outgroup f3 shared-drift statistics. This is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like, non-Indo-European words among Sardinian placenames. More recently, the Basque have been shown to be enriched for Neolithic farmer ancestry and Indo-European languages have been associated with steppe population expansions in the post-Neolithic Bronze Age. These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European Neolithic ancestry. To be cautious, while it seems unlikely, we cannot exclude that the genetic similarity between the Basque and Sardinians is due to an unsampled pre-Neolithic population that has affinities with the Neolithic representatives analyzed here.

density-nuraghi-sardinia-genetics
Left: Geographical map of Sardinia. The provincial boundaries are given as black lines. The provinces are abbreviated as Cag (Cagliari), Cmp (Campidano), Car (Carbonia), Ori (Oristano), Sas (Sassari), Olb (Olbia-tempio), Nuo (Nuoro), and Ogl (Ogliastra). For sampled villages within Ogliastra, the names and abbreviations are indicated in the colored boxes. The color corresponds to the color used in the PCA plot (Fig. 2a). The Gennargentu region referred to in the main text is the mountainous area shown in brown that is centered in western Ogliastra and southeastern Nuoro.
Right: Density of Nuraghi in Sardinia, from Wikipedia.

While we can confirm that Sardinians principally have Neolithic ancestry on the autosomes, the high frequency of two Y-chromosome haplogroups (I2a1a1 at ~39% and R1b1a2 at ~18%) that are not typically affiliated with Neolithic ancestry is one challenge to this model. Whether these haplogroups rose in frequency due to extensive genetic drift and/or reflect sex-biased demographic processes has been an open question. Our analysis of X chromosome versus autosome diversity suggests a smaller effective size for males, which can arise due to multiple processes, including polygyny, patrilineal inheritance rules, or transmission of reproductive success. We also find that the genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, suggesting that male lineages may more rapidly trace back to the mainland. Considering that the R1b1a2 haplogroup may be associated with post-Neolithic steppe ancestry expansions in Europe, and the recent timeframe when the R1b1a2 lineages expanded in Sardinia, the patterns raise the possibility of recent male-biased steppe ancestry migration to Sardinia, as has been reported among mainland Europeans at large (though see Lazaridis and Reich and Goldberg et al.). Such a recent influx is difficult to square with the overall divergence of Sardinian populations observed here.

sardinian-admixture
Mixture proportions of the three-component ancestries among Sardinian populations. Using a method first presented in Haak et al. (Nature 522, 207–211, 2015), we computed unbiased estimates of mixture proportions without a parameterized model of relationships between the test populations and the outgroup populations based on f4 statistics. The three-component ancestries were represented by early Neolithic individuals from the LBK culture (LBK_EN), pre-Neolithic huntergatherers (Loschbour), and Bronze Age steppe pastoralists (Yamnaya). See Supplementary Table 5 for standard error estimates computed using a block jackknife.

Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.

Interestingly, haplogroup I2a1a1 is actually found among northern Iberians during the Neolithic and Chalcolithic, and is therefore associated with Neolithic ancestry in Iberia, too, and consequently – unless there is a big surprise hidden somewhere – with the ancestry found today among Basques.

NOTE. In fact, the increase in Neolithic ancestry found in south-west Ireland with expanding Bell Beakers (likely Proto-Beakers), coupled with the finding of I2a subclades in Megalithic cultures of western Europe, would support this replacement after the Cardial and Epi-Cardial expansions, which were initially associated with G2a lineages.

I am not convinced about a survival of Palaeo-Sardo after the Bell Beaker expansion, though, since there is no clear-cut cultural divide (and posterior continuity) of pre-Beaker archaeological cultures after the arrival of Bell Beakers in the island that could be identified with the survival of Neolithic languages.

We may have to wait for ancient DNA to show a potential expansion of Neolithic ancestry from the west, maybe associated with the emergence of the Nuragic civilization (potentially linked with contemporaneous Megalithic cultures in Corsica and in the Balearic Islands, and thus with an Iberian rather than a Basque stock), although this is quite speculative at this moment in linguistic, archaeological, and genetic terms.

Nevertheless, it seems that the association of a Basque-Iberian language with the Neolithic expansion from Anatolia (see Villar’s latest book on the subject) is somehow strengthened by this paper. However, it is unclear when, how, and where expanding G2a subclades were replaced by native I2 lineages.

Related

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

halaf-ubaid-migrations

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):

Introduction

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) (…)

Discussion

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.

levant-chalcolithic-bronze-age
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.

levant-chalcolithic-pca
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

Comments

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.

semitic-languages
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.

haplogroup-t-levant
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…

Related

Yamna female shows decoration of bones after body decomposition

Interesting press release from the Institute of Archaeology at Adam Mickiewicz University in Poznań:

In an open access report last year, Anthropological Description of Skeletal Material from the Dniester Barrow-cemetery Complex, Yampil Region, Vinnitsa Oblast (Ukraine), the team lead by Liudmyla Litvinova – of the Ukrainian Academy of Science – published their findings from the skeletons in different burial mounds along the border with Moldavia, ranging from Eneolithic to Iron Age burials.

yampil-barrows-ukraine
Map of Yampil barrows, showing administrative borders: 1 – Klembivka barrow 1; 2 – Porohy, barrow 3A; 3 – Pidlisivka, barrow 1; 4 – Prydnistryanske, barrows 1-4; 5 – barrows; 6 – excavated barrows; 7 – Ukrainian-Moldovan frontier; 8 – Yampil Region border

In one Yamnaya burial rested a young woman aged 25-30. It was so described in the original paper:

Barrow 3A, feature 10. A very poorly-preserved skeleton with a badly damaged skull. The preserved bones include small fragments of the cranial vault and mandible and larger ones of the upper and lower limbs, pelvis fragments and vertebrae. The skeleton belonged to a female aged 25-30 years (adultus). Due to the poor state of preservation of long bones, it was not possible to reconstruct her stature. Palaeopathological lesions: LEH on both lower canines (age of the individual at the time of both defects: 4.5-5.0 years); caries on the upper left third molar.

reconstruction-yamna-female
Burial and reconstruction. Foto by Michał Podsiadło.

This is what the team has discovered since then:

While drawing and photographing the burial, our attention was drawn to regular patterns, such as parallel lines visible on both elbow bones. At first, we approached the discovery with caution – maybe the traces were left by animals, we wondered

– Says Danuta Żurkiewicz from the Institute of Archaeology, Adam Mickiewicz University in Poznań, who prepared an article on the decorations.

It is surprising that the procedure of decorating the bones had to be done after death and the process of body decomposition. This is clearly indicated by the location of the decoration on the bone surface and the way dye was applied.

yamna-female-marks-forearm
Detail of the forearm, from Żurkiewicz. Modified by me, I added rectangles around the marks on the distal end and middle third of the cubitus. You can see the marks on the cubitus with more detail in the original article.

Some time after the woman’s death the grave was reopened, bone decoration was performed and the bones were re-arranged in anatomical order.

According to Żurkiewicz, this discovery is unique – so far, no comparable custom among other prehistoric communities in Europe has been recorded.

Until now, the few similar discoveries have been interpreted as remnants of tattoos, but none of them have been analysed using so many modern methods, which is why they can not be confirmed with full confidence

Żurkiewicz believes that:

However, women were rarely buried in them. The deceased, whose bones were covered with patterns, had to be an important member of the community.

These findings will be detailed in volume 22 of Baltic-Pontic Studies, which will be available online on the De Gruyter Open platform in August.

My opinion – without knowing anything about the case, site, or archaeology of kurgans in general, just from my knowledge in Orthopaedic Surgery – is that it would be quite easy to make those marks on the cubitus post-mortem, because the cubitus has a very easy surgical access (just under the skin, mostly). On the other hand, opening the grave after decomposition to take the bone, make those marks, and put it back, seems too much work to achieve the same result…

If the marks had been on another anatomical site (say, the anterior aspect of the sacrum, or the inner aspect of the cranium, etc.) maybe the butchery needed to mark the bones would not be worth it (especially for a relative of the deceased), but in this case I hope they have a good reason to support why it must have been made after decomposition.

EDIT (4 AUG 2018): The published paper on this specific burial and the marks: Ritual position and “tattooing” techniques in the funeral practices of the “Barrow cultures” of the Pontic-Caspian steppe/forest-steppe area Porohy 3A, Yampil region, Vinnytsia Oblast: Specialist analysis research perspectives, by Żurkiewicz et al. (2018).

See also on the same region Eneolithic, Yamnaya and Noua culture cemeteries from the first half of the 3rd and the middle of the 2nd millennium BC, Porogy, site 3A, Yampil region, Vinnitsa oblast: Archaeometric and Chronometric Description, Ritual and Tazonomic-Topogenetic identification, by Viktor Klochko et al. (2015), B-P S, vol. 20, P. 78-141.

Related

Cereal cultivation and processing in Trypillian mega-sites

eneolithic-trypillia-cucuteni-steppe

New paper (behind paywall) Where are the cereals? Contribution of phytolith analysis to the study of subsistence economy at the Trypillia site Maidanetske (ca. 3900-3650 BCE), central Ukraine, by Dal Corso et al. Journal of Arid Environments (2018).

Interesting excerpts (only introduction and conclusions, emphasis mine):

Archaeological setting at the site of Maidanetske, Ukraine

From ca. 4800 to 3350 BCE, Trypillia settlements were widespread over parts of eastern Romania, Moldova and Ukraine (Menotti and Korvin-Piotrovskiy, 2012; Müller et al., 2016; Videiko, 2004). Maidanetske (Fig. 1B) is one of the so-called “mega-sites” which developed during ca. 3900–3400 BCE in central Ukraine, in the Uman region (Cherkasy district) (Müller and Videiko, 2016; Müller et al., 2017). In this region, nine of these “mega-sites” have been found. Mega-sites are characterized by a regular plan with concentric rings of houses around a large empty central space, additional quartiers, with radial and peripheral track ways (Fig. 1B). The three mega-sites Maidanetske, Taljanky and Dobrovody, lay ca. 15 km apart from each other (Fig. 1A); other mega-sites are located within a 50 km radius around Maidanetske. Archaeologically, these mega-sites consist of the remains of buildings most of them burnt, although a minority of unburnt buildings is known of as well (Burdo and Videiko, 2016; Müller and Videiko, 2016; Ohlrau, 2015). Most of these buildings have a standardized regular size (average 6×12 m) and architecture including domestic installations and a standardized assemblage of artifacts. At Maidanetske beside normal sized houses there are few larger rectangular buildings that are located regularly along the main pathways. Further archaeological contexts include pits, pottery kilns, and peripheral ditches. A huge variety of mostly painted pottery (including many with figurative animal and plant motives), some flint artifacts, rare copper objects, querns, adzes and a broad range of anthropomorphic and zoomorphic figurines are attested within houses and mega-structures. In terms of organic remains, animal bones are fairly common, while botanical macro-remains appear to be scarce and poorly preserved (Kirleis and Dal Corso, 2016; Pashkevich and Videjko, 2006).

trypillia-maidanetske-north-pontic-steppe-forest
The location of the Chalcolithic site of Maidanetske and of other sites mentioned in the text within the map of the natural vegetation (modified after Kirleis
and Dreibrodt, 2016, graphic K. Winter, Kiel University).

Environmental setting at Maidanetske

The Trypillia sites in central Ukraine, including Maidanetske, are located in a semi-arid forest-steppe ecozone, a mosaic-like ecosystem stretched between the dry steppe grasslands in the south and temperate woodland biomes in the north (Fig. 1A). In this transitional zone the natural vegetation is supposed to be patchy and sensitive to climate and topography (Feurdean et al., 2015; Molnàr et al., 2012; Walter, 1974). Since most of the accessible plateaus are converted to agricultural land and the scarce broadleaf woodlands are managed, the natural landscape heterogeneity is difficult to trace within the current landscape (Kuzemko et al., 2014). Besides agricultural fields and villages, narrow river valleys incised into the loess plateaus are present, with riparian vegetation and artificial lakes. This western Pontic area has a humid continental climate with wet winters and warm summers (Köppen and Geiger, 1939), which corresponds to a semi-arid 0.2–0.5 aridity index value according to UNEP (1997). Nevertheless, the reconstruction of past climatic as well as environmental conditions is not straightforward, since undisturbed archives for pollen analysis are lacking in the region and published climatic reconstructions combine evidences from peripheral areas (Gerasimenko, 1997; Harper, 2017; Kirleis and Dreibrodt, 2016). In the Transylvanian forest-steppe region, palynological investigations suggest that dry grasslands have expanded since the end of the 4th millennium BCE, fostered by Bronze Age forest clearance, while before this the area was largely forested (Feurdean et al., 2015). In the Hungarian forest-steppe, the mixed oak forest on Loess almost disappeared by the end of the 18th century AD, hampered by factors such as fragmentation, slow regeneration, spread of invasive species and lowering of the water table due to increased aridity (Molnàr et al., 2012). It is clear that forest-steppe environments are very sensitive to aridity and land use practices. To understand whether similar landscape change can have occurred in central Ukraine already at the time of Chalcolithic mega-sites, an understanding of the extent of crop growing and deforestation is crucial.

The site of Maidanetske is situated on a plateau covered by Loess deposited during the Last Glaciation. This plateau is dissected by valleys of different sizes with perennial rivers present within the large valleys. One of these rivers passes the site in a distance of less than 500 m. The soils that are present nowadays are Chernozems. They show dark greyish-brown A-horizons of thicknesses between 30 and 50 cm and a texture dominated by silt. Numerous filled crotowinas indicate an intensive bioturbation during the formation of these soils. The Chernozems cover the archaeological record. The variations in thickness of the A-horizon are probably reflecting post-depositional soil erosion processes. Buried soils discovered at lower slope positions below colluvial layers show properties of Cambisols, thus pointing towards a forested past of the surrounding landscape (Kirleis and Dreibrodt, 2016).

trypillia-maidanetske-mega-city-settlement-old-europe
The reconstruction of Maidanetske based on geomagnetic survey (modern and from the 1970s by
Dudkin), with the position of the trenches mentioned in this study.

Conclusion

At the site of Maidanetske, the phytolith record from different contexts including multiple houses, was studied, which confirmed cereal cultivation as part of the subsistence economy of the site. Furthermore, phytoliths gave information about wild grasses, whereas dicotyledonous material was scarce. For the house structures cereal byproducts, chaff and straw were identified as material selected for tempering daub for the wall construction. Ash layers in a pit filled with house remains show similar pattern. Daub fragments and pit filling are the most promising archives for further phytolith work on cereals at Trypillia sites. The sediment inside four burnt houses and the areas outside two houses, where also grinding stones were sampled, showed little presence of the remains of final cereal processing, suggesting that either the surfaces were cleaned and the chaff was collected after dehusking, or the cereal processing activity took place somewhere else. Specific archaeological contexts, such as vessels and grinding stones, did not differ much from the control samples from archaeological sediment nearby, suggesting disturbance of the record.(…)

Related

Expansion of domesticated goat echoes expansion of early farmers

goat-neolithic

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.

goat-middle-east
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.

Related

The end of the Kura-Araxes settlements: large-scale phenomenon but with varied causes

kura-araxes-indo-european-uralic-migrations

Open access The End of the Kura-Araxes Culture as Seen from Nadir Tepesi in Iranian Azerbaijan, by Alizadeh, Maziar & Mohammadi, American Journal of Archaeology (2018) 122(3):463-477.

Interesting excerpts (emphasis mine):

The test trenches at Nadir Tepesi suggest that the Kura-Araxes occupation ended abruptly in the mid third millennium B.C.E. and that the site was then occupied or visited by a new group of people with new cultural traditions. Evidence for a significant destruction followed by the sharp discontinuity in the material culture could represent a violent termination of the Kura-Araxes occupation at Nadir Tepesi. This possibility provides one hypothesis for the end of the Kura-Araxes culture elsewhere as well in the Mughan Steppe.

It appears that there is no subsequent substantial built settlement until possibly the Late Iron Age in the region. Our intensive and extensive surveys on the Mughan Steppe did not provide evidence for settlements until long after the Kura-Araxes time. For whatever reason, settlements on the Mughan Steppe seem to have reappeared only in the Iron Age and remained sparse until the Sassanian period in late antiquity.45 Although some ceramics with parallels in the Middle and Late Bronze Age and the Iron Age were found at a few sites, they do not seem to represent settlements.

kura-araxes-sites-caucasus
Major Kura-Araxes sites in the Caucasus region and location of Nadir Tepesi (modified from Bourrichon/Wikimedia Commons/CC BY-SA 3.0/GFDL).

Indeed, except for the sites that may possibly contain burials, we do not know much about the Middle and Late Bronze Ages through the Iron Age in the Mughan Steppe. Similarly, archaeological investigations in the southern Caucasus do not provide information on settlements in the Middle Bronze Age.46 From a broad perspective, the abrupt and possibly violent end to the Kura-Araxes occupation at Nadir Tepesi, together with the sudden disappearance of the Kura-Araxes settlements and the scarcity of post–Kura-Araxes sites in the Mughan Steppe,47 may indicate that these changes were part of a larger phenomenon. This evidence could suggest a major sociocultural and demographic transformation at a regional level, at least in the western Caspian littoral plain, in the middle of the third millennium B.C.E. Other archaeological investigations in the southern Caucasus portray a similar picture, that of newcomers with a significantly different lifestyle and means of subsistence possibly associated with a mobile economy. Except in some elements of the ceramic traditions, evidence of continuity of Kura-Araxes traditions and their coexistence with newcomers is scarce and uncertain.48

On one hand, Puturidze argues that there is no evidence supporting the notion of a migration of people into the southern Caucasus.50 Rather, she associates all the changes in the post–Kura-Araxes period with influences from Near Eastern societies as a result of developing interactions by the end of the third millennium B.C.E. On the other hand, Kohl hypothesizes the possibility of a “push-pull process”51 in which new groups of people with wheeled carts and oxen-pulled wagons gradually moved from the steppes of the north into the southern Caucasus, and the Kura-Araxes communities subsequently moved farther south.52.

kura-araxes-late-iindo-european-uralic-migrations
Early Chalcolithic migrations (3100-2600 BC)

Kohl also reminds us of the evidence of increased militarism from the Early to the Late Bronze Age that is reflected in more fortified sites, new weaponry, and an iconography of war as seen on the Karashamb Cup.53 The appearance of defensive mechanisms such as fortification walls, which can be seen at Köhne Shahar, a Kura-Araxes settlement near Chaldran in Iranian Azerbaijan, further emphasizes the increase of intergroup conflicts and militarism during the Early Bronze Age, before the Kura-Araxes culture came to an end.54 Kohl argues that, while the number of Kura-Araxes settlements decreased in the southern Caucasus, archaeological research indicates that the Kura-Araxes culture spread to western Iran in the Zagros region and to the Levant.55 In Kohl’s view, as new groups of people moved in, the Kura-Araxes communities abandoned the southern Caucasus and moved farther south, where some of them already resided. Although some scholars suggest the possible movement of new groups of people from the northern steppes to the southern Caucasus,56 others associate the cultures of the post–Kura-Araxes period, especially the Trialeti.

We believe that the evidence supports a less uniform scenario. The Kura-Araxes culture may have disappeared in various ways; the transition to the post–Kura-Araxes time may not be explained by a single model. Different Kura-Araxes settlements may have ended differently. The evidence from Nadir Tepesi could support a violent end at that site, and it is possible that similar evidence will be found at other sites in the Mughan Steppe. At some sites, such as Köhne Tepesi in the Khoda Afarin Plain,58 the Kura-Araxes occupation also ended abruptly but without any sign of destruction. In other regions, there may be evidence supporting the coexistence of newcomers with Kura-Araxes communities for some period.59 The results from Gegharot60 in Armenia and recent excavations by one of the authors of this report at Köhne Shahar, do not support any of these models. At Köhne Shahar, the Kura-Araxes culture ended around the middle of the third millennium B.C.E.61 In the last phase of Kura-Araxes occupation at the site, six storage jars in one of the workshop units stood intact, five of them still carefully covered by stone slabs. The evidence from Köhne Shahar may point to a nonviolent end or a planned abandonment of the site.62

late-kura-araxes-indo-european-uralic-migrations
Late Chalcolithic migrations (2600-2250 BC)

The picture continues to be somehow blurred for what happened in the Caucasus and North Iran after the Late Indo-European expansions, due to contradictory information.

With the analysis of the dataset from Narasimhan et al. (2018), it seemed that steppe peoples might have migrated into North Iran after the first Khvalynsk/Repin or Early Yamna expansions, because some samples from North Iran were reported to have steppe-related admixture.

NOTE. As I already said, the Hajji Firuz sample of R1b-Z2103 subclade (of uncertain date) clusters closer to the Iron Age sample F38 from Iran (Broushaki et al. 2016), of the same subclade, which is quite likely related to Proto-Armenian speakers, so it is possible that both belong to the same, Late Bronze Age / Iron Age group of migrants.

The other possibility, since it also clusters at a certain distance from the Hajji Firuz I4243 ‘outlier’, dated ca. 2326 BC (from the same archaeological site as other Chalcolithic samples, but being an intrusive Bronze Age burial), is that the Hajji Firuz sample is related to these hypothetical early migrations described here; or, that its date of I4243 is also not reliable…

These initial reports, coupled with archaeological descriptions of potential migrants from the steppe ending the Kura-Araxes culture, may suggest that peoples of steppe origin (or peoples with steppe admixture from the Caucasus) occupied territories further to the south (see here for potential early migration waves).

However, studies of samples from the Caucasus in Wang et al. (2018) have shown that no migrations related to EHG ancestry happened to the south, and that the minimal EHG/WHG contribution in Kura-Araxes individuals is probably part of the Anatolian farmer-related ancestry, and not from the steppe.

In fact, further contribution from Iran Chalcolithic-related ancestry was found intruding to the north during the Early Bronze Age, into Kura-Araxes and Maykop-Novosvobodnaya samples. In the Middle Bronze Age, some peoples from the North Caucasus show steppe ancestry (further to the south than the first steppe ancestry incursions of the North Caucasus piedmont), but most late Caucasus groups studied retain the ‘southern’ Armenian/Iran Chalcolithic profile.

trialeti-indo-european-uralic-migrations
Early Bronze Age migrations (2600-2250 BC)

All this casts doubts on the whole idea of intrusive steppe ancestry found in Iran Chalcolithic and Early Bronze Age (or, alternatively, on the proper dates of the Hajji Firuz ‘outliers’).

Also, the archaeological discontinuity in the region until the Iron Age, and the close relationship of Armenian to Greek (relative to other Palaeo-Balkan languages, which seem to have expanded to the south-west with Yamna settlers), does not support these hypothetical early steppe migrants as the Proto-Armenian community; earlier migrations of LPIE speakers without known modern descendants are obviously possible, but no clear archaeological or linguistic link has been offered to date to support this.

Until we have more samples with a clear archaeological and chronological context from Anatolia, Iran, and the Armenian Highlands during the Bronze and Iron Ages, and until they show clear steppe ancestry assessed in peer-reviewed papers (or at least thoroughly contrasted with other potential sources of such ancestry, and with solid statistical results), the question of intrusive steppe ancestry, and thus maybe LPIE-speakers (which may or may not be associated with Proto-Armenians) remains open.

NOTE. The Armenian question remains open, not because genetics has precedence over linguistics, but because the linguistic classification and date of separation, in this case, is not clear, and may be quite old. The fact that Palaeo-Balkan and Pre-Indo-Iranian might have separated quite early within the Khvalynsk – Volga-Ural (Early Yamna) community adds to the difficulty in assessing migration routes, although I do believe that the close similarity of Armenian with Greek among Palaeo-Balkan languages do not warrant such an early separation, and the Middle to Late Bronze Age period in the Balkans and Anatolia offers a better route for this expansion.

See also

On the Maykop – Upper Mesopotamia cultural province, distinct from the steppe

caucasus-europe

New paper (behind paywall) The Production of Thin‐Walled Jointless Gold Beads from the Maykop Culture Megalithic Tomb of the Early Bronze Age at Tsarskaya in the North Caucasus: Results of Analytical and Experimental Research, by Trifonov et al. Archaeometry (2018)

Interesting excerpts (emphasis mine):

In 1898, two megalithic tombs containing graves of a local social elite dated to the Early Bronze Age were discovered by N. I. Veselovsky near the village of Tsarskaya (modern Novosvobodnaya, Republic of Adygeya) (Fig. 1 (a)) (Baye 1900, 43–59; IAC 1901, 33–8; Sagona 2018, 281–97).

Radiocarbon dates place both tombs within the Novosvobodnaya phase of the Maykop culture, between c. 3200 and 2900 BC (Trifonov et al. 2017). Along with the human remains (one adult individual was interred in each dolmen), the tombs yielded rich funerary offerings, including artefacts made of gold, silver and semi-precious stones. (…) This paper presents results of a technical analysis of just one type of artefact, from kurgan 2 at Tsarskaya: thin-walled jointless beads made from gold.

caucasus-beads-mesopotamia-sumeria
(a) A map of the Caucasus and part of Western Asia, showing the locations of sites mentioned in the text: 1, Tsarskaya (modern Novosvobodnaya); 2, Maykop; 3, Staromyshastovskaya; 4, Andryukovskaya; 5, Psebaiskaya; 6, Inozemtsevo; 7, Kudakhurt; 8, Soyuq Bulaq; 9, Sé Girdan; 10, Tepe Gawra. (b) The string of thin-walled jointless gold beads, silver and carnelian beads from the dolmen in kurgan 2 at Tsarskaya, Western Caucasus (1898).

Ever since M. I. Rostovtzeff noted a stylistic similarity between Maykop art and Sumerian art (Rostovtzeff 1920) and M. V. Andreeva described this phenomenon within a broad cultural and chronological context (Andreeva 1977), new archaeological studies have only extended this picture of a vast cultural province that appeared between the Caucasus and the northern fringe of Western Asia (Trifonov 1987). The discovery of the Leyla-Tepe culture (Narimanov 1987) and Maykop-type kurgans in Azerbaijan (Lyonnet et al. 2008) and adjacent Iran (Muscarella 1969, 1971, 2003; Trifonov 2000) has confirmed the spatial and temporal unity of this phenomenon as a precondition for free circulation of cultural patterns and technical innovations across vast areas of the Caucasus and Western Asia. Jewellery made of gemstones and precious metals, primarily gold, was probably one such innovation.

Attempts to demarcate the historical region where the Maykop culture emerged and developed have emphasized the role of Upper Mesopotamia in the development of the Sumerian civilization and the definition of a northern centre of urbanization, independent from the centres of the south (Rothman 2002; Oats et al. 2007). The turn of the fourth millennium BC saw the development of various cultural traditions in south-east Anatolia, north-east Syria and north-west Iran; on the northern fringe, these traditions manifested themselves through the Maykop culture. Perhaps it is no coincidence that the first high-status burials containing gold and gemstone jewellery (including carnelian, turquoise and lapis lazuli) appear in these northern, rather than southern, centres in the first quarter of 4000 BC (e.g., Tepe Gawra, graves 109, 110) (Piasnall 2002). With regard to funeral rites and stylistic characteristics of jewellery pieces, these graves have many parallels with early Maykop burials (Munchaev 1975, 329; Trifonov 1987, 20).

It still remains unclear if the goldsmiths of Upper Mesopotamia mastered the technique of making thin-walled jointless beads. The gold beads from Tepe Gawra are described as spherical or ball-shaped, but their maximum diameter (5–8mm) always exceeds the length of the bore (3–4mm) (Tobler 1950, 89, 199, pl. LV, a). On the whole, these measurements are consistent with the proportions and sizes of some Maykop beads.(…)

It is quite possible that a distinctive technique of making thin-walled jointless beads from gold was a regional technological development of Maykop culture goldsmiths, within a wider tradition of Near East metalwork, as a type of production regulated by ritual beliefs (Gell 1992; Benzel 2013).

These deep-rooted Near East traditions of ritualization of the production and use of jewellery pieces made of gold, silver and gemstones in the Maykop culture, on the one hand, maintained familiar canons of ritual behaviour and, on the other, made perception of sophisticated symbolism of gemstones more difficult for neighbouring cultures with different living standards, levels of social development and value systems to understand. The jewellery traditions of the Maykop culture had no successors in the Caucasus or the adjacent steppes. In the third millennium BC, the goldsmiths of Europe and Asia had to reinvent the technique of making thin-walled jointless gold beads from scratch (Born et al. 2009).


Also interesting is Holocene environmental history and populating of mountainous Dagestan (Eastern Caucasus, Russia), by Ryabogina et al., Quaternary International (2018).

caucasus-dagestan-climate-population
The combination of Holocene environment changes and the settlement of the territory of Dagestan.

Related excerpts, about the climate of an adjacent region of the Caucasus before, during, and after the Maykop culture:

The 7th millennium BC featured a warm and arid climate, so that time corresponds to the steppe landscapes in the final stage of the Mesolithic. It is likely that the formation of a producing economy in the mountainous zone of Dagestan gradually emerged against this background. In the Neolithic period, the area remained almost treeless, as it was still warm and quite dry. However, archaeological data indicates that long-term settlements with well-developed farming spread in the mountainous zone around 6200-5500 BC.

The beginning of increasing humidity and the appearance of deciduous forests corresponds to the early Chalcolithic period of the Eastern Caucasus. It is the most poorly studied period in the history of this region. Covering a time span of 2000 years, this period was the least saturated by archaeological sites. At the start of this period, only the stands of herdsman in the mountain zone are known, dating to the second half of the 6th millennium BC (Gadgiev, 1991). It is still not clear whether the mountains were not settled in such a favorable climatic stage. The uncertainty may be due to the fact that people have chosen other ecological niches, or it could be we simply do not have data due to the insufficient archaeological survey of the territory. It is surprising that the turn to drier climate and the reduction of deciduous forests in the inner mountainous part of Dagestan, the large, long-term settlements like Ginchi emerge with pronounced specialization in agriculture (Fig. 7 panel (2)) (Gadgiev, 1991).

After the dry climate, simultaneously with cooling, the subsequent spread of pine forests coincides with the beginning of expansion of Kura-Araxes culture from the territory of Georgia through Chechnya to the mountainous Dagestan. Debates on the impact of past climate on Kura-Araxes societies in Transcaucasus have a long history (for the comprehensive review see, for example, Connor and Kvavadze, 2014 and references therein). In general, it is clear that after 3000 BC, forest cover in most areas of the Kura-Araxes region in the Transcaucasia reached its maximum extent in the Holocene (Connor and Kvavadze, 2014). However, at the same time lakes in Central Anatolia began to dry out and Caspian Sea levels fell (Roberts et al. 2011; Leroy et al. 2013), and arid conditions were identified in mountainous Dagestan in the 4th millennium. Clearly the regional moisture balance shifted in the Eastern Caucasus only in the late 4th to early 3rd millennium BC (this study). The only available radiocarbon dating of Dagestan confirms that the agricultural settlements of the Early Bronze Age appear not in the middle of the 4th millennium BC, but in the early 3rd millennium BC; that is not earlier than the stage of increasing moistening and the appearance of pine forests.

See also:

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.

north-africa-genomes-pca
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.

north-africa-iberia-admixture
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: