Scythians in Ukraine, Natufian and sub-Saharan ancestry in North Africa (ISBA 8, 21st Sep)

jena-isba8

Interesting information from ISBA 8 sesions today, as seen on Twitter (see programme in PDF, and sessions from the 19th and the 20th september).

Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

Scythian population genetics and settlement patterns

Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.

The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP1. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

However, the transition from the Scythian to the Chernyakhov culture between 2,100 and 1,700 cal BP does mark a shift in the Ponto-Caspian genetic landscape, with various analyses showing that Chernyakhov culture samples share more drift and derived alleles with Bronze/Iron Age and modern Europeans, while the Scythians position outside modern European variation. Our results agree well with the Ostrogothic origins of the Chernyakhov culture and support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

Detail of the slide with admixture of Scythian groups in Ukraine:

scythians-admixture

Interesting to read in combination with yesterday’s re-evaluation of Scythian mobility and settlement patterns in the west (showing adaptation to the different regional cultures), The Steppe was Sown – multi-isotopic research changes our understandings of Scythian diet and mobility, by Ventresca Miller et al.

Nomadic pastoralists conventionally known as the Scythians occupied the Pontic steppe during the Iron Age, c. 700-200 BC, a period of unprecedented pan-regional interaction. Popular science accounts of the Scythians promote narratives of roving bands of nomadic warriors traversing the steppe from the Altai Mountains to the Black Sea coastline. The quantity and scale of mobility in the region is usually emphasized based on the wide distribution of material culture and the characterization of Iron Age subsistence economies in the Pontic steppe and forest-steppe as mobile pastoralism. Yet, there remains a lack of systematic, direct analysis of the mobility of individuals and their animals. Here, we present a multi-isotopic analysis of humans from Iron Age Scythian sites in Ukraine. Mobility and dietary intake were documented through strontium, carbon and oxygen isotope analyses of tooth enamel. Our results provide direct evidence for mobility among populations in the steppe and forest-steppe zones, demonstrating a range of localized mobility strategies. However, we found that very few individuals came from outside of the broader vicinity of each site, often staying within a 90 km radius. Dietary intake varied at the intrasite level and was based in agro-pastoralism.

While terrestrial protein did form a portion of the diet for some individuals, there were also high levels of a 13C-enriched food source among many individuals, which has been interpreted as millet consumption. Individuals exhibiting 87Sr/86Sr ratios that fell outside the local range were more likely to have lower rates of millet consumption than those that fell within the local range. This suggests that individuals moving to the site later in life had different economic pursuits and consumed less millet. There is also strong evidence that children and infants moved at the pan-regional scale. Contrary to the popular narrative, the majority of Scythians engaged in localized mobility as part of agricultural lifeways while pan-regional movements included family groups.

North-Africans show ancestry from the ancient Near East and sub-Saharan Africa

Pleistocene North Africans show dual genetic ancestry from the ancient Near East and sub-Saharan Africa, by van de Loosdrecht et al.

North Africa, connecting sub-Saharan Africa and Eurasia, is important for understanding human history. However, the genetic history of modern humans in this region is largely unknown before the introduction of agriculture. After the Last Glacial Maximum modern humans, associated with the Iberomaurusian culture, inhabited a wide area spanning from Morocco to Libya. The Iberomaurusian is part of the early Later Stone Age and characterized by a distinct microlithic bladelet technology, complex hunter-gathering and tooth evulsion.

Here we present genomic data from seven individuals, directly dated to ~15,000-year-ago, from Grotte des Pigeons, Taforalt in Morocco. Uni-parental marker analyses show mitochondrial haplogroup U6a for six individuals and M1b for one individual, and Y-chromosome haplogroup E-M78 (E1b1b1a1) for males. We find a strong genetic affinity of the Taforalt individuals with ancient Near Easterners, best represented by ~12,000 year old Levantine Natufians, that made the transition from complex hunter-gathering to more sedentary food production. This suggests that genetic connections between Africa and the Near East predate the introduction of agriculture in North Africa by several millennia. Notably, we do not find evidence for gene flow from Paleolithic Europeans into the ~15,000 year old North Africans as previously suggested based on archaeological similarities. Finally, the Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West Africans (Yoruba, Mende) and Africans from Tanzania (Hadza). In contrast, modern North Africans have a much smaller sub-Saharan African component with no apparent link to Hadza. Our results provide the earliest direct evidence for genetic interactions between modern humans across Africa and Eurasia.

A detail of the cultures involved in these population movements:

north-africa-natufian-saharan

So, most likely, Natufian-related ancestry – as sub-Saharan ancestry – not related to the Afroasiatic expansion.

NOTE. This now probably outdated already by the new preprint on Dzudzuana samples, from the Caucasus.

Impact of colonization in north-eastern Siberia

Exploring the genomic impact of colonization in north-eastern Siberia by Seguin-Orlando et al.

Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

Also interesting to read Balanovsky’s session, and a previous paper on the expansion of Yakuts.

Expansion of haplogroup G2a in Anatolia possibly associated with the Mature Aceramic period

anatolian-hunter-gatherer-sampling

Preprint Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, by Feldman et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

Anatolian hunter-gatherers experienced climatic changes during the last glaciation and inhabited a region that connects Europe to the Near East. However, interactions between Anatolia and Southeastern Europe in the later Upper Palaeolithic/Epipalaeolithic are so far not well documented archaeologically. Interestingly, a previous genomic study showed that present-day Near-Easterners share more alleles with European hunter-gatherers younger than 14,000 BP (‘Later European HG’) than with earlier ones (‘Earlier European HG’). With ancient genomic data available, we could directly compare the Near-Eastern hunter-gatherers (AHG and Natufian) with the European ones. As is the case for present-day Near-Easterners, the Near-Eastern hunter-gatherers share more alleles with the Later European HG than with the Earlier European HG, shown by the significantly positive statistic D(Later European HG, Earlier European HG; AHG/Natufian, Mbuti). Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’), are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna and Ranchot respectively) as the next two European hunter-gatherers genetically closest to AHG. Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component.

anatolian-hunter-gatherer-pca
Ancient genomes (marked with color-filled symbols) projected onto the principal components 5 computed from present-day west Eurasians (grey circles) (fig. S4). The geographic location of each ancient group is marked in (A). Ancient individuals newly reported in this study are additionally marked with a black dot inside the symbol

We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry 5 component (α), which is prevalent in the Near East but undetectable in European hunter-gatherers. Following a published approach, we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians, consistent with previous estimates for the latter. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 %, suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

near-eastern-european-hg
Basal Eurasian ancestry proportions (α) as a marker for Near-Eastern gene flow. Mixture proportions inferred by qpAdm for AHG and the Iron Gates HG are schematically represented. The lower schematic shows the expected α in Iron Gates HG under 10 assumption of unidirectional gene flow, inferred from α in the AHG source population. The observed α for Iron Gates HG is considerably smaller than expected thus, the unidirectional gene flow from the Near East to Europe is not sufficient to explain the above affinity.

While ancestry is not always relevant to distinguish certain population movements (see here), especially – as in this case – when there are few samples (thus neither geographically nor chronologically representative) and no previous model to test, it seems that ancestry and Y-DNA show a great degree of continuity in Anatolia since the Palaeolithic until the Neolithic, at least in the sampled regions. C1a2 appears in Europe since ca. 40,000 years ago (viz. Kostenki, Goyet, Vestonice, etc., and later emerges again in the Balkans after the Anatolian Neolithic expansion, probably a resurge of European groups).

The potential transition of a G2a-dominated agricultural society – that is later prevalent in Anatolian and European farmers – may have therefore happened during the Aceramic III period (ca. 8000 BC), a process of haplogroup expansion probably continuing through the early part of the Pottery Neolithic, as the society based on kinship appeared (Rosenberg and Erim-Özdoğan 2011). There is still much to know about the spread of ceramic technology and southwestern Asia domesticate complex, though.

anatolian-palaeolithic-hg

Without a proper geographical sampling, representative of previous and posterior populations, it is impossible to say. But the expansion of R1b-L754 through Anatolia to form part of the Villabruna cluster (and also the Iron Gates HG) seems perfectly possible with this data, although this paper does not help clarify the when or how. We have seen significant changes in ancestry happen within centuries with expanding populations admixing with locals. Palaeolithic sampling – like this one – shows few individuals scattered geographically over thousands of km and chronologically over thousands of years…

Related

Evolution of Steppe, Neolithic, and Siberian ancestry in Eurasia (ISBA 8, 19th Sep)

jena-isba8

Some information is already available from ISBA 8 (see programme in PDF), thanks to the tweets from Alexander M. Kim.

Official abstracts are listed first (emphasis mine), then reports and images with link to Kim’s tweets. Here is the list for quick access:

Updates (17:00 CET):

Turkic and Hunnic expansions

Tracing the origin and expansion of the Turkic and Hunnic confederations, by Flegontov et al.

Turkic-speaking populations, now spread over a vast area in Asia, are highly heterogeneous genetically. The first confederation unequivocally attributed to them was established by the Göktürks in the 6th c. CE. Notwithstanding written resources from neighboring sedentary societies such as Chinese, Persian, Indian and Eastern Roman, earlier history of the Turkic speakers remains debatable, including their potential connections to the Xiongnu and Huns, which dominated the Eurasian steppe in the first half of the 1st millennium CE. To answer these questions, we co-analyzed newly generated human genome-wide data from Central Asia (the 1240K panel), spanning the period from ca. 3000 to 500 YBP, and the data published by de Barros Damgaard et al. (137 ancient human genomes from across the Eurasian steppes, Nature, 2018). Firstly, we generated a PCA projection to understand genetic affinities of ancient individuals with respect to present-day Tungusic, Mongolic, Turkic, Uralic, and Yeniseian-speaking groups. Secondly, we modeled hundreds of present-day and few ancient Turkic individuals using the qpAdm tool, testing various modern/ancient Siberian and ancient West Eurasian proxies for ancestry sources.

A majority of Turkic speakers in Central Asia, Siberia and further to the west share the same ancestry profile, being a mixture of Tungusic or Mongolic speakers and genetically West Eurasian populations of Central Asia in the early 1st millennium CE. The latter are themselves modelled as a mixture of Iron Age nomads (western Scythians or Sarmatians) and ancient Caucasians or Iranian farmers. For some Turkic groups in the Urals and the Altai regions and in the Volga basin, a different admixture model fits the data: the same West Eurasian source + Uralic- or Yeniseian-speaking Siberians. Thus, we have revealed an admixture cline between Scythians and the Iranian farmer genetic cluster, and two further clines connecting the former cline to distinct ancestry sources in Siberia. Interestingly, few Wusun-period individuals harbor substantial Uralic/Yeniseian-related Siberian ancestry, in contrast to preceding Scythians and later Turkic groups characterized by the Tungusic/Mongolic-related ancestry. It remains to be elucidated whether this genetic influx reflects contacts with the Xiongnu confederacy. We are currently assembling a collection of samples across the Eurasian steppe for a detailed genetic investigation of the Hunnic confederacies.

jeong-population-clines
Three distinct East/West Eurasian clines across the continent with some interesting linguistic correlates, as earlier reported by Jeong et al. (2018). Alexander M. Kim.
siberian-genetic-component-chronology
Very important observation with implication of population turnover is that pre-Turkic Inner Eurasian populations’ Siberian ancestry appears predominantly “Uralic-Yeniseian” in contrast to later dominance of “Tungusic-Mongolic” sort (which does sporadically occur earlier). Alexander M. Kim

New interesting information on the gradual arrival of the “Uralic-Yeniseian” (Siberian) ancestry in eastern Europe with Iranian and Turkic-speaking peoples. We already knew that Siberian ancestry shows no original relationship with Uralic-speaking peoples, so to keep finding groups who expanded this ancestry eastwards in North Eurasia should be no surprise for anyone at this point.

Central Asia and Indo-Iranian

The session The Genomic Formation of South and Central Asia, by David Reich, on the recent paper by Narasimhan et al. (2018).

bmac-reich
One important upside of dense genomic sampling at single localities – greater visibility of outliers and better constraints on particular incoming ancestries’ arrival times. Gonur Tepe as a great case study of this. Alexander M. Kim
ani-asi-steppe-cline
– Tale of three clines, with clear indication that “Indus Periphery” samples drawn from an already-cosmopolitan and heterogeneous world of variable ASI & Iranian ancestry. (I know how some people like to pore over these pictures – so note red dots = just dummy data for illustration.)
– Some more certainty about primary window of steppe ancestry injection into S. Asia: 2000-1500 BC
Alexander M. Kim

British Isles

Ancient DNA and the peopling of the British Isles – pattern and process of the Neolithic transition, by Brace et al.

Over recent years, DNA projects on ancient humans have flourished and large genomic-scale datasets have been generated from across the globe. Here, the focus will be on the British Isles and applying aDNA to address the relative roles of migration, admixture and acculturation, with a specific focus on the transition from a Mesolithic hunter-gatherer society to the Neolithic and farming. Neolithic cultures first appear in Britain ca. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, in Britain, at the margins of the expansion the pattern and process of the British Neolithic transition remains unclear. To examine this we present genome-wide data from British Mesolithic and Neolithic individuals spanning the Neolithic transition. These data indicate population continuity through the British Mesolithic but discontinuity after the Neolithic transition, c.6000 BP. These results provide overwhelming support for agriculture being introduced to Britain primarily by incoming continental farmers, with surprisingly little evidence for local admixture. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

british-isles
Millennium of lag between farming establishment in NW mainland Europe & British Isles. Only 25 Mesolithic human finds from Britain. Alexander M. Kim.
british-admixture
– Evidently no resurgence of hunter-gatherer ancestry across Neolithic
– Argument for at least two geographically distinct entries of Neolithic farmers
Alexander M. Kim.

MN Atlantic / Megalithic cultures

Genomics of Middle Neolithic farmers at the fringe of Europe, by Sánchez Quinto et al.

Agriculture emerged in the Fertile Crescent around 11,000 years before present (BP) and then spread, reaching central Europe some 7,500 years ago (ya.) and eventually Scandinavia by 6,000 ya. Recent paleogenomic studies have shown that the spread of agriculture from the Fertile Crescent into Europe was due mainly to a demic process. Such event reshaped the genetic makeup of European populations since incoming farmers displaced and admixed with local hunter-gatherers. The Middle Neolithic period in Europe is characterized by such interaction, and this is a time where a resurgence of hunter-gatherer ancestry has been documented. While most research has been focused on the genetic origin and admixture dynamics with hunter-gatherers of farmers from Central Europe, the Iberian Peninsula, and Anatolia, data from farmers at the North-Western edges of Europe remains scarce. Here, we investigate genetic data from the Middle Neolithic from Ireland, Scotland, and Scandinavia and compare it to genomic data from hunter-gatherers, Early and Middle Neolithic farmers across Europe. We note affinities between the British Isles and Iberia, confirming previous reports. However, we add on to this subject by suggesting a regional origin for the Iberian farmers that putatively migrated to the British Isles. Moreover, we note some indications of particular interactions between Middle Neolithic Farmers of the British Isles and Scandinavia. Finally, our data together with that of previous publications allow us to achieve a better understanding of the interactions between farmers and hunter-gatherers at the northwestern fringe of Europe.

megalithic-europe
-Novel genomic data from 21 individuals from 6 sites.
– “Megalithic” individuals not systematically diff. from geographically proximate “non-megalithic” burials
– Mild evidence for over-representation of males in some British Isles megalithic tombs
– Megalithic tombs in W & N Neolithic Europe may have link to kindred structures
Alexander M. Kim

Central European Bronze Age

Ancient genomes from the Lech Valley, Bavaria, suggest socially stratified households in the European Bronze Age, by Mittnik et al.

Archaeogenetic research has so far focused on supra-regional and long-term genetic developments in Central Europe, especially during the third millennium BC. However, detailed high-resolution studies of population dynamics in a microregional context can provide valuable insights into the social structure of prehistoric societies and the modes of cultural transition.

Here, we present the genomic analysis of 102 individuals from the Lech valley in southern Bavaria, Germany, which offers ideal conditions for such a study. Several burial sites containing rich archaeological material were directly dated to the second half of the 3rd and first half of the 2nd millennium BCE and were associated with the Final Neolithic Bell Beaker Complex and the Early and Middle Bronze Age. Strontium isotope data show that the inhabitants followed a strictly patrilocal residential system. We demonstrate the impact of the population movement that originated in the Pontic-Caspian steppe in the 3rd millennium BCE and subsequent local developments. Utilising relatedness inference methods developed for low-coverage modern DNA we reconstruct farmstead related pedigrees and find a strong association between relatedness and grave goods suggesting that social status is passed down within families. The co-presence of biologically related and unrelated individuals in every farmstead implies a socially stratified complex household in the Central European Bronze Age.

lech-bavaria
Diminishing steppe ancestry and resurgent Neolithic ancestry over time. Alexander M. Kim

Notice how the arrival of Bell Beakers, obviously derived from Yamna settlers in Hungary, and thus clearly identified as expanding North-West Indo-Europeans all over Europe, marks a decrease in steppe ancestry compared to Corded Ware groups, in a site quite close to the most likely East BBC homeland. Copenhagen’s steppe ancestry = Indo-European going down the toilet, step by step…

UPDATES

Russian Far East populations

Gene geography of the Russian Far East populations – faces, genome-wide profiles, and Y-chromosomes, by Balanovsky et al.

Russian Far East is not only a remote area of Eurasia but also a link of the chain of Pacific coast regions, spanning from East Asia to Americas, and many prehistoric migrations are known along this chain. The Russian Far East is populated by numerous indigenous groups, speaking Tungusic, Turkic, Chukotko-Kamchatka, Eskimo-Aleut, and isolated languages. This linguistic and geographic variation opens question about the patterns of genetic variation in the region, which was significantly undersampled and received minor attention in the genetic literature to date. To fill in this gap we sampled Aleuts, Evenks, Evens, Itelmens, Kamchadals, Koryaks, Nanais, Negidals, Nivkhs, Orochi, Udegeis, Ulchi, and Yakuts. We also collected the demographic information of local populations, took physical anthropological photos, and measured the skin color. The photos resulted in the “synthetic portraits” of many studied groups, visualizing the main features of their faces.

north-eurasia

far-east-pca
Impressive North Eurasian biobank including 30,500 individual samples with broad consent, some genealogical info, phenotypic data. Alexander M. Kim

Finland AD 5th-8th c.

Sadly, no information will be shared on the session A 1400-year transect of ancient DNA reveals recent genetic changes in the Finnish population, by Salmela et al. We will have to stick to the abstract:

Objectives: Our objective was to use aDNA to study the population history of Finland. For this aim, we sampled and sequenced 35 individuals from ten archaeological sites across southern Finland, representing a time transect from 5th to 18th century.

Methods: Following genomic DNA extraction and preparation of indexed libraries, the samples were enriched for 1,2 million genomewide SNPs using in-solution capture and sequenced on an Illumina HighSeq 4000 instrument. The sequence data were then compared to other ancient populations as well as modern Finns, their geographical neighbors and worldwide populations. Authenticity testing of the data as well as population history inference were based on standard computational methods for aDNA, such as principal component analysis and F statistics.

Results: Despite the relatively limited temporal depth of our sample set, we are able to see major genetic changes in the area, from the earliest sampled individuals – who closely resemble the present-day Saami population residing markedly further north – to the more recent ancient individuals who show increased affinity to the neighboring Circum-Baltic populations. Furthermore, the transition to the present-day population seems to involve yet another perturbation of the gene pool.

So, most likely then, in my opinion – although possibly Y-DNA will not be reported – Finns were in the Classical Antiquity period mostly R1a with secondary N1c in the Circum-Baltic region (similar to modern Estonians, as I wrote recently), while Saami were probably mostly a mix of R1a-Z282 and I1 in southern Finland. That’s what the first transition after the 5th c. probably reflects, the spread of Finns (with mainly N1c lineages) to the north, while the more recent transition shows probably the introduction of North Germanic ancestry (and thus also R1b-U106, R1a-Z284, and I1 lineages) in the west.

Dairying in ancient Mongolia

The History of Dairying in ancient Mongolia, by Wilkin et al.

The use of mass spectrometry based proteomics presents a novel method for investigating human dietary intake and subsistence strategies from archaeological materials. Studies of ancient proteins extracted from dental calculus, as well as other archaeological material, have robustly identified both animal and plant-based dietary components. Here we present a recent case study using shotgun proteomics to explore the range and diversity of dairying in the ancient eastern Eurasian steppe. Contemporary and prehistoric Mongolian populations are highly mobile and the ephemerality of temporarily occupied sites, combined with the severe wind deflation common across the steppes, means detecting evidence of subsistence can be challenging. To examine the time depth and geographic range of dairy use in Mongolia, proteins were extracted from ancient dental calculus from 32 individuals spanning burial sites across the country between the Neolithic and Mongol Empire. Our results provide direct evidence of early ruminant milk consumption across multiple time periods, as well as a dramatic increase in the consumption of horse milk in the late Bronze Age. These data provide evidence that dairy foods from multiple species were a key part of subsistence strategies in prehistoric Mongolia and add to our understanding of the importance of early pastoralism across the steppe.

The confirmation of the date 3000-2700 BC for dairying in the eastern steppe further supports what was already known thanks to archaeological remains, that the pastoralist subsistence economy was brought for the first time to the Altai region by expanding late Khvalynsk/Repin – Early Yamna pastoralists that gave rise to the Afanasevo culture.

Neolithic transition in Northeast Asia

Genomic insight into the Neolithic transition peopling of Northeast Asia, by C. Ning

East Asian representing a large geographic region where around one fifth of the world populations live, has been an interesting place for population genetic studies. In contrast to Western Eurasia, East Asia has so far received little attention despite agriculture here evolved differently from elsewhere around the globe. To date, only very limited genomic studies from East Asia had been published, the genetic history of East Asia is still largely unknown. In this study, we shotgun sequenced six hunter-gatherer individuals from Houtaomuga site in Jilin, Northeast China, dated from 12000 to 2300 BP and, 3 farming individuals from Banlashan site in Liaoning, Northeast China, dated around 5300 BP. We find a high level of genetic continuity within northeast Asia Amur River Basin as far back to 12000 BP, a region where populations are speaking Tungusic languages. We also find our Compared with Houtaomuga hunter-gatherers, the Neolithic farming population harbors a larger proportion of ancestry from Houtaomuga related hunter-gathers as well as genetic ancestry from central or perhaps southern China. Our finding further suggests that the introduction of farming technology into Northeast Asia was probably introduced through demic diffusion.

A detail of the reported haplogroups of the Houtaomuga site:

houtaomuga-site-y-dna-mtdna

Y-DNA in Northeast Asia shows thus haplogroup N1b1 ~5000 BC, probably representative of the Baikal region, with a change to C2b-448del lineages before the Xiongnu period, which were later expanded by Mongols.

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

Polygyny as a potential reason for Y-DNA bottlenecks among agropastoralists

polygyny-estimates

Open access Greater wealth inequality, less polygyny: rethinking the polygyny threshold model by Ross et al. Journal of the Royal Society Interface (2018).

Interesting excerpts, from the discussion (emphasis mine):

We use cross-cultural data and a new mutual mate choice model to propose a resolution to the polygyny paradox. Following Oh et al. [17], we extend the standard polygyny threshold model to a mutual mate choice model that accounts for both female supply to, and male demand for, polygynous matchings, in the light of the importance of, and inequality in, rival and non-rival forms of wealth. The empirical results presented in figures 5 and 6 demonstrate two phenomena that are jointly sufficient to generate a transition to more frequent monogamy among populations with a co-occurring transition to a more unequal, highly stratified, class-based social structure. In such populations, fewer men can cross the wealth threshold required to obtain a second wife, and those who do may be fabulously wealthy, but—because of diminishing marginal fitness returns to increasing number of marriages—do not acquire wives in full proportion to their capacity to support them with rival wealth. Together, these effects reduce the population-level fraction of wives in polygynous marriages.

Our model demonstrates that a low population-level frequency of polygyny will be an equilibrium outcome among fitness maximizing males and females in a society characterized by a large class of wealth-poor peasants and a small class of exceptionally wealthy elite. Our mutual mate choice model thus provides an empirically plausible resolution to the polygyny paradox and the transition to monogamy which co-occurred with the rise of highly unequal agricultural populations.

polygyny-pastoralists
(a) Mean frequency of married women who are married polygynously by production system (+2 s.e.) using the Standard Cross-Cultural Sample [30]. Rates of polygyny are measured with variable ]872, per cent of wives with co-wives. (b) Rates of monogamy and polygyny by production system are measured with variable ]861, the standard polygamy code. Data on subsistence come from variable ]858, categorized subsistence. In general, agricultural populations show reduced rates of polygyny and increased rates of monogamy relative to other subsistence systems. See electronic supplementary material for more information. (c) Gini of wealth by production system in our sample.

The reasons for this decrease in marginal fitness returns are explained as either a) a potential missing of important rival forms of wealth in the statistical model, or b) one or more of the following reasons:

  • [A] male’s time and attention are rival inputs to his own fitness (…) A single rich man will have to defend his 10 wives from nine unmarried men on average.”As the wealth ratio grows even more skewed, this situation could become increasingly difficult to manage (e.g. requiring the use of eunochs to defend harems [74]).
  • A related possibility is that a growing number of unmarried men could socially censure wealthy polygynous males, imposing costs on them that reduce male demand for and/or female supply to polygynous marriage [23,24]. (…)
  • A third possibility is that sexually transmitted infection (STI) burden [22,75] could diminish returns to polygyny, if polygyny enhances infection rates [76,77]. (…)
  • Finally, impediments to cooperation or even outright conflict among co-wives can be greater as the number of wives increases. Interference competition among co-wives could impose significant fitness costs in settings where effective child rearing benefits from cooperation [79,80].(…)
polygyny-agropastoralists
between the Gini coefficient on completed rival wealth and per cent completed female polygyny.

I have previously argued against some reasons traditionally given to explain the replacement of native male populations after migrations (i.e. polygyny, slavery, targeted male extermination, etc.), because I believe that a gradual successful expansion of patrilineal clans over some generations based on wealth alone is enough to explain the obvious Y-DNA bottlenecks that happened in many different prehistoric and historic cultures (especially among steppe pastoralists, including Indo-Europeans).

I realize that I haven’t really used any study to support my opinion, though, and data from modern and ancient pastoralists from different regions seem to contradict it, so maybe ancient DNA can show that Indo-Europeans had often children with more than one woman at the same time. I don’t remember seeing that kind of information in supplementary materials to date. From memory I can think of maybe two or three examples of agnate siblings published, but I doubt the archaeological age estimation (based on simple observation of skeletal remains) combined with radiocarbon age (usually given with broad CI) could be enough to prove a similar age of conception. Maybe a case of many siblings clearly of the same age and from many different mothers in the same burial could be a strong proof of this…

I recently read that theoretical models are actually trusted by no one except for the researchers who propose them, and experimental data are trusted by everyone except for the researchers who worked with them. I cannot agree more. However, we lack information about this question (as far as I know), so we may have to rely on indirect estimations, like the kind of models presented in the paper (or the one proposed for Post-Neolithic Y-chromosome bottlenecks).

The Late Proto-Indo-European word for bride comes from a root meaning ‘drive, lead’, hence literally ‘deportation’, so the bride was transferred from her father’s family to her husband’s house. Marriage was certainly an asymmetrical contract for its members, and the reconstructible word for ‘dowry’ further supports the weaker position of the wife in it. Also, ancient marriage could differ from a family agreement, because marriage by elopement, bride kidnapping or hostage was probably common (more or less socially regulated) for people belonging the same culture. Apart from this, I don’t know about reconstructed linguistic data pointing to polygyny, and I doubt archaeological data alone – without genetics – can help.

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

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:

Improving environmental conditions favoured higher local population density, which favoured domestication

agricultural-origins

New paper (behind paywall) Hindcasting global population densities reveals forces enabling the origin of agriculture, by Kavanagh et al., Nature Human Behaviour (2018)

Abstract (emphasis mine):

The development and spread of agriculture changed fundamental characteristics of human societies1,2,3. However, the degree to which environmental and social conditions enabled the origins of agriculture remains contested4,5,6. We test three hypothesized links between the environment, population density and the origins of plant and animal domestication, a prerequisite for agriculture: (1) domestication arose as environmental conditions improved and population densities increased7 (surplus hypothesis); (2) populations needed domestication to overcome deteriorating environmental conditions (necessity hypothesis)8,9; (3) factors promoting domestication were distinct in each location10 (regional uniqueness hypothesis). We overcome previous data limitations with a statistical model, in which environmental, geographic and cultural variables capture 77% of the variation in population density among 220 foraging societies worldwide. We use this model to hindcast potential population densities across the globe from 21,000 to 4,000 years before present. Despite the timing of domestication varying by thousands of years, we show that improving environmental conditions favoured higher local population densities during periods when domestication arose in every known agricultural origin centre. Our results uncover a common, global factor that facilitated one of humanity’s most significant innovations and demonstrate that modelling ancestral demographic changes can illuminate major events deep in human history.

cultural-variables-population-densities
Path diagram for piecewise-SEM exploring the effects of environmental and cultural variables on population densities of foraging societies. Measured variables are represented by the large boxes and R2 GLMM values (see Methods) are provided for response variables. n = 220. Red arrows depict negative relationships among variables, black arrows positive relationships, and dashed grey arrows depict non-significant paths (P ≥ 0.05). Standardized coefficients are presented for all paths (small boxes) and arrow widths are scaled to reflect the magnitude of path coefficients.

Interesting excerpts:

(…) our results are consistent with the surplus hypothesis, which suggests that improving environmental conditions and the potential for increased population density may have facilitated the domestication of plants and animals in agricultural origin centres4,7 (Fig. 3). Several factors may explain the links between environmental conditions, potential population density and the origin of domestication. For one, rates of innovation may scale positively with the number of potential innovators13,14. In turn, the likelihood of domestication innovations may have increased in environments that could support increasingly higher densities of foraging people.

In addition, foraging societies may have become more sedentary to take advantage of locally abundant resources, some of which were later domesticated35. Our results indicate that residential mobility scales negatively with population density in foraging societies (Fig. 1). Therefore, increasingly sedentary lifestyles may have contributed further to increases in population density and the potential for innovation. Increases in the productivity of wild progenitors of important domesticates may have also facilitated growing population densities and the viability of cultivation for food production15,16.

population-density-foragers
Predictions of potential population density for foragers. a–c, Predicted population densities at 4,000 (a), 10,000 (b) and 21,000 (c) YBP. Blue hues depict potential population densities below the median population density of observed foraging societies, and red hues depict potential population densities above the median. The second red hue and above are greater than the mean population density of observed foraging societies. Note the increase in area, through time, with potential population densities greater than the mean of observed foraging societies (number of 0.5° × 0.5° cells: 21,000 YBP = 3,027; 4,000 YBP = 4,673). For example, a notable increase in the number of red cells in the Sudanic savannah and Ganges of East India (Northeast India) between panels c and a.

It is also possible that improving environmental conditions may have resulted in a situation where necessity drove the origins of domestication. For example, population densities may have increased in foraging societies that occupied productive, coastal areas, causing an outflow of groups into regions with less ideal conditions where the cultivation of plants and animals was required to secure adequate food resources6,17,18. Our results cannot support, or refute, the possible influence the outflow of people from hospitable locations to less ideal environments may have played. A detailed understanding of the movements of ancient populations is required for more rigorous testing of the role that forced habitation of marginal environments may have played in the origins of domestication at particular sites.

See also: