Agricultural origins on the Anatolian plateau


New paper (behind paywall) Agricultural origins on the Anatolian plateau, by Baird et al. PNAS (2018), published ahead of print (March 19).

Abstract (emphasis mine):

This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the mid ninth millennium cal BC, but also demonstrate that uptake was not uniform, and that some communities chose to actively disregard cultivation. Adoption of cultivation was accompanied by experimentation with sheep/goat herding in a system of low-level food production that was integrated into foraging practices rather than used to replace them. Furthermore, rather than being a short-lived transitional state, low-level food production formed part of a subsistence strategy that lasted for several centuries, although its adoption had significant long-term social consequences for the adopting community at Boncuklu. Material continuities suggest that Boncuklu’s community was ancestral to that seen at the much larger settlement of Çatalhöyük East from 7100 cal BC, by which time a modest involvement with food production had been transformed into a major commitment to mixed farming, allowing the sustenance of a very large sedentary community. This evidence from Central Anatolia illustrates that polarized positions explaining the early spread of farming, opposing indigenous adoption to farmer colonization, are unsuited to understanding local sequences of subsistence and related social change. We go beyond identifying the mechanisms for the spread of farming by investigating the shorter- and longer-term implications of rejecting or adopting farming practices.

Map of central Anatolia showing the principal sites mentioned in the text.

Interesting excerpts:

The persistence of foraging and rejection of farming at Pınarbaşı is also worthy of further consideration. Pınarbaşı’s longevity as a settlement locale in the early Holocene appears to have been based on hunting of wild mammals, wetland exploitation, and significant focus on nut exploitation, all afforded by its ecotonal setting between the hills, plain, and wetland. Perhaps this existing diversity, including nutritious storable plant resources, was a key factor in a lack of interest in adopting cultivation. Another factor may have been a conscious desire to maintain traditional identities and long-standing distinctions with other communities, in part reflected in its particular way of life and its specific connections with particular elements in landscape, for example the almond and terebinth woodlands whose harvests underwrote the continuity of the Pınarbaşı settlement.

The variability in response to the possibilities of early food production in a relatively small geographical area demonstrated here is notable and provides an example useful in evaluating the spread of farming in other regions. It shows the possible role of indigenous foragers, the potential patchwork and diffuse nature of the spread of farming, the lack of homogeneity likely in the communities caught up in the process, the probability of significant continuities in local cultural traditions within the process, and the potentially long-term stable adaptation offered by lowlevel food production. The strength of identities linked to exploitation of particular foods and particular parts of the landscape may have been a major factor contributing to rejection or adoption of food production by indigenous foragers.

The results are also relevant for understanding the processes that underpinned the initial development of farming within the Fertile Crescent itself: that is, the region in which the wild progenitors of the Old World founder crops and stock animals are found. Recent research has rejected the notion of a core area for farming’s first appearance in southwest Asia and demonstrated that farming developed in diverse ways over the Fertile Crescent zone from the southern Levant to the Zagros, very analogous to the situation just described for Central Anatolia (2). Cultivation, herding, and domestication developed in that region, and it seems inescapable that exchange of crops and herded animals occurred between communities (2), involving a spread of farming within the Fertile Crescent, leading eventually to the Neolithic farming package that was so similar across the region and which spread into Europe (5). Central Anatolia was clearly linked to the Fertile Crescent, with significant evidence of exchange and some shared cultural traditions from at least the Epipaleolithic (22). The evidence presented here demonstrates very clearly the movement of crops between settlements and regions in early phases of the Neolithic through exchange, and thus allows us to identify episodes of crop exchange that were probably taking place within the Fertile Crescent itself, but are difficult, if not impossible, to distinguish due to the presence of crop progenitors across much of the region.

A very interesting read in combination with 14C-radiometric data and climatic conditions showing potential triggers of dispersal of Neolithic lifeways from Turkey to Southeast Europe, e.g. Dispersal of Neolithic Lifeways: Absolute Chronology and Rapid Climate Change in Central and West Anatolia, by Lee Clare & Bernhard Weninger, in The Neolithic in Turkey, Vol.6 (2014), Edited by Mehmet Özdogan, Nezih Basgelen, Peter Kuniholm.

The Late Neolithic (6600-6000 cal. BC) witnesses the rapid westward dispersal of Neolithic communities, apparently reaching the Aegean in the space of a very short time (ca. 6600 cal. BC). This process is linked to the demand of individuals, groups, and communities for less vulnerable conditions in the face of climate fluctuation associated with RCC. Coastal areas not only offered respite from more frequently occurring physical impacts (extreme winters and high drought risk) in inner Anatolia, they may also have provided refuge for weaker (more vulnerable) social groups (…).

Featured image, from the latter: “In the Early Pottery Neolithic (7000-6600 cal. BC) there occurs a clear break with precedeing (PPN) traditions, attested by abandonment and decreasing size of settlements, albeit that evidence for migration of groups westwards towards the Aegean is still ambiguous (black arrows: human migrations; white arrows: Anatolian obsidian)”

See also:

The demographic history and mutational load of African hunter-gatherers and farmers


Interesting new article (behind paywall), The demographic history and mutational load of African hunter-gatherers and farmers, Nat Ecol Evol (2018)

Abstract (emphasis mine):

Understanding how deleterious genetic variation is distributed across human populations is of key importance in evolutionary biology and medical genetics. However, the impact of population size changes and gene flow on the corresponding mutational load remains a controversial topic. Here, we report high-coverage exomes from 300 rainforest hunter-gatherers and farmers of central Africa, whose distinct subsistence strategies are expected to have impacted their demographic pasts. Detailed demographic inference indicates that hunter-gatherers and farmers recently experienced population collapses and expansions, respectively, accompanied by increased gene flow. We show that the distribution of deleterious alleles across these populations is compatible with a similar efficacy of selection to remove deleterious variants with additive effects, and predict with simulations that their present-day additive mutation load is almost identical. For recessive mutations, although an increased load is predicted for hunter-gatherers, this increase has probably been partially counteracted by strong gene flow from expanding farmers. Collectively, our predicted and empirical observations suggest that the impact of the recent population decline of African hunter-gatherers on their mutation load has been modest and more restrained than would be expected under a fully recessive model of dominance.

“Inferred demographic models of the studied populations. a, EUR-first branching model, in which ancestors of EUR (aEUR) diverged from African populations before the divergence of the ancestors of RHG (aRHG) and AGR (aAGR). b, RHG-first branching model, in which aRHG were the first to diverge from the other groups. c, AGR-first branching model, in which aAGR were the first to diverge from the other groups. We assumed an ancient change in the size of the ancestral population of all humans (ANC). We assumed that each subsequent divergence of populations was followed by an instantaneous change in the effective population size (Ne). We also assumed that there were two epochs of migration between the following population pairs: wAGR/aAGR and wRHG/aRHG, eAGR/aAGR and eRHG/aRHG, and EUR and eAGR/aAGR. The figure labels correspond to the parameters of the model estimated by maximum likelihood and the 95% confidence intervals assessed by bootstrapping by site 100 times (Supplementary Table 4). Vertical arrow corresponds to the direction of time, from past to present, with divergence times given on the left and expressed in thousand years ago(ka). Effective population sizes (N) are given within the diagram and expressed in thousands of individuals. Bold horizontal arrows indicate an estimated parameter for the effective strength of migration 2Nm > 1, while thin horizontal arrows indicate 2Nm ≤ 1.”

See also:

Before steppe ancestry: Europe’s genetic diversity shaped mainly by local processes, with varied sources and proportions of hunter-gatherer ancestry


The definitive publication of a BioRxiv preprint article, in Nature: Parallel palaeogenomic transects reveal complex genetic history of early European farmers, by Lipson et al. (2017).

The dataset with all new samples is available at the Reich Lab’s website. You can try my drafts on how to do your own PCA and ADMIXTURE analysis with some of their new datasets.


Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 BC, n = 100), Germany (5500–3000 BC, n = 42) and Spain (5500–2200 BC, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

There were some interesting finds on a regional level, with some late survival of hunter-gatherer ancestry (and Y-DNA haplogroups) in certain specific sites, but nothing especially surprising. This survival of HG ancestry and lineages in Iberia and other regions may be used to revive (yet again) the controversy over the origin of non-Indo-European languages of Europe attested in historical times, such as the only (non-Uralic) one surviving to this day, the Basque language.

This study kept confirming the absence of Y-DNA R1b-M269 subclades in Central Europe before the arrival of Yamna migrants, though, which offers strong reasons to reject the Indo-European from the west hypothesis.

Here are first the PCA of samples included in this paper, and then the PCA of ancient Eurasians (Mathieson et al. 2017) and modern populations (Lazaridis et al. 2014) for comparison of similar clusters:

First two principal components from the PCA. We computed the principal components (PCs) for a set of 782 present-day western Eurasian individuals genotyped on the Affymetrix Human Origins array (background grey points) and then projected ancient individuals onto these axes. A close-up omitting the present-day Bedouin population is shown. From Lipton et al. (2017(
PCA of South-East European and other European samples from Mathieson et al. (2017)
Ancient and modern samples on Lazaridis et al. (2014)


Holocene rise in mobility in at least three stages: Strong link between technological change and human mobility in Western Eurasia


New interesting article at PNAS: Estimating mobility using sparse data: Application to human genetic variation, by Loog et al (2017).

Download links and supplemental information.


Migratory activity is a critical factor in shaping processes of biological and cultural change through time. We introduce a method to estimate changes in underlying migratory activity that can be applied to genetic, morphological, or cultural data and is well-suited to samples that are sparsely distributed in space and through time. By applying this method to ancient genome data, we infer a number of changes in human mobility in Western Eurasia, including higher mobility in pre- than post-Last Glacial Maximum hunter–gatherers, and oscillations in Holocene mobility with peaks centering on the Neolithic transition and the beginnings of the Bronze Age and the Late Iron Age.


Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to spatially and temporally sparsely sampled data, and permit only limited systematic comparison between different time periods or geographic regions. Here we present an estimator of past mobility that addresses these issues by explicitly linking trait differentiation in space and time. We demonstrate the efficacy of this estimator using spatiotemporally explicit simulations and apply it to a large set of ancient genomic data from Western Eurasia. We identify a sequence of changes in human mobility from the Late Pleistocene to the Iron Age. We find that mobility among European Holocene farmers was significantly higher than among European hunter–gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.

Featured image, from the article: Estimation of mobility through time from empirical data. (A) Relative mobility rate estimates in Western Eurasia over the last 14,000 y, using a 4,000-y sliding window (121 windows). The solid black line represents the mean α value from 10,000 date resampled iterations; the colored area represents the 95% confidence intervals of the jackknife distribution.

Iberian Peninsula: Discontinuity in mtDNA between hunter-gatherers and farmers, not so much during the Chalcolithic and EBA


A new preprint paper at BioRxiv, The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age, by Szécsényi-Nagy et al. (2017).


Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.

Iberian mtDNA samples

Detailed conclusions of their work,

The present study, based on 213 new and 125 published mtDNA data of prehistoric Iberian individuals suggests a more complex mode of interaction between local hunter-gatherers and incoming early farmers during the Early and Middle Neolithic of the Iberian Peninsula, as compared to Central Europe. A characteristic of Iberian population dynamics is the proportion of autochthonous hunter-gatherer haplogroups, which increased in relation to the distance to the Mediterranean coast. In contrast, the early farmers in Central Europe showed comparatively little admixture of contemporaneous hunter-gatherer groups. Already during the first centuries of Neolithic transition in Iberia, we observe a mix of female DNA lineages of different origins. Earlier hunter-gatherer haplogroups were found together with a variety of new lineages, which ultimately derive from Near Eastern farming groups. On the other hand, some early Neolithic sites in northeast Iberia, especially the early group from the cave site of Els Trocs in the central Pyrenees, seem to exhibit affinities to Central European LBK communities. The diversity of female lineages in the Iberian communities continued even during the Chalcolithic, when populations became more homogeneous, indicating higher mobility and admixture across different geographic regions. Even though the sample size available for Early Bronze Age populations is still limited, especially with regards to El Argar groups, we observe no significant changes to the mitochondrial DNA pool until the end of our time transect (1500 BCE). The expansion of groups from the eastern steppe, which profoundly impacted Late Neolithic and EBA groups of Central and North Europe, cannot (yet) be seen in the contemporaneous population substrate of the Iberian Peninsula at the present level of genetic resolution. This highlights the distinct character of the Neolithic transition both in the Iberian Peninsula and elsewhere and emphasizes the need for further in depth archaeogenetic studies for reconstructing the close reciprocal relationship of genetic and cultural processes on the population level.

So it seems more and more likely that the North-West Indo-European invasion during the Copper Age (signaled by changes in Y-DNA lineages) was not, as in central Europe, accompanied by much mtDNA turnover. What that means – either a male-dominated invasion, or a longer internal evolution of invasive Y-DNA subclades – remains to bee seen, but I am still more inclined to see the former as the most likely interpretation, in spite of admixture results.


Featured images: from the article, licensed BY-NC-ND.

Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains


PhD Thesis Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains, by Zuzana Hofmanova (2017) at the University of Mainz.

Palaeogenomic data have illuminated several important periods of human past with surprising im- plications for our understanding of human evolution. One of the major changes in human prehistory was Neolithisation, the introduction of the farming lifestyle to human societies. Farming originated in the Fertile Crescent approximately 10,000 years BC and in Europe it was associated with a major population turnover. Ancient DNA from Anatolia, the presumed source area of the demic spread to Europe, and the Balkans, one of the first known contact zones between local hunter-gatherers and incoming farmers, was obtained from roughly contemporaneous human remains dated to ∼6 th millennium BC. This new unprecedented dataset comprised of 86 full mitogenomes, five whole genomes (7.1–3.7x coverage) and 20 high coverage (7.6–93.8x) genomic samples. The Aegean Neolithic pop- ulation, relatively homogeneous on both sides of the Aegean Sea, was positively proven to be a core zone for demic spread of farmers to Europe. The farmers were shown to migrate through the central Balkans and while the local sedentary hunter-gathers of Vlasac in the Danube Gorges seemed to be isolated from the farmers coming from the south, the individuals of the Aegean origin infiltrated the nearby hunter-gatherer community of Lepenski Vir. The intensity of infiltration increased over time and even though there was an impact of the Danubian hunter-gatherers on genetic variation of Neolithic central Europe, the Aegean ancestry dominated during the introduction of farming to the continent.

Taking only admixture analyses using Yamna samples:

This increased genetic affinity of Neolithic farmers to Danubians was observed for Neolithic Hungarians, LBK from central Europe and LBK Stuttgart sample. Some post-Neolithic samples also proved to share more drift with Danubians, again samples from Hungary (Bronze Age and Copper Age samples and also Yamnaya and samples with elevated Yamnaya ancestry (Early Bronze Age samples from Únětice, Bell Beaker samples, Late Neolithic Karlsdorf sample and Corded Ware samples).


The results of our ADMIXTURE analysis for the dataset including also Yamnaya samples are shown in Figure S1c. The cross-validation error was the lowest for K=2. Supervised and unsupervised analyses for K=3 are again highly concordant. Early Neolithic farmers again demonstrate almost no evidence of hunter-gatherer admixture, while it is observable in the Middle Neolithic farmers. However, much of the Late Neolithic hunter-gatherer ancestry from the previous analysis is replaced by Yamnaya ancestry. These results are consistent with the results of Haak et al. who demonstrated a resurgence of hunter-gatherer ancestry followed by the establishment of Eastern hunter-gatherer ancestry.

Again, admixture results show that something in the simplistic Yamna -> Corded Ware model is off. It is still interesting to review admixture results of European Mesolithic and Late Neolithic genomic data in relation to the so-called steppe or yamna ancestry or component (most likely an eastern steppe / forest zone ancestry probably also present in the earlier Corded Ware horizons) and its interpretation…

Image composed by me, from two different images of the PhD Thesis. To the left: Supervised run of ADMIXTURE. The clusters to be supervised were chosen to best fit the presumed ancestral populations (for HG Motala and for farmers Bar8 and Bar31 and for later Eastern migration Yamnaya). To the Right: Unsupervised run of ADMIXTURE for the Anatolian genomic dataset with Yamnaya samples for K=8.

Discovered via Généalogie génétique

My European Family: The First 54,000 years, by Karin Bojs


I have recently read the book My European Family: The First 54,000 years (2015), by Karin Bojs, a known Swedish scientific journalist, former science editor of the Dagens Nyheter.

My European Family: The First 54,000 Years
It is written in a fresh, dynamic style, and contains general introductory knowledge to Genetics, Archaeology, and their relation to language, and is written in a time of great change (2015) for the disciplines involved.

The book is informed, it shows a balanced exercise between responsible science journalism and entertaining content, and it is at times nuanced, going beyond the limits of popular science books. It is not written for scholars, although you might learn – as I did – interesting details about researchers and institutions of the anthropological disciplines involved. It contains, for example, interviews with known academics, which she uses to share details about their personalities and careers, which give – in my opinion – a much needed context to some of their publications.

Since I am clearly biased against some of the findings and research papers which are nevertheless considered mainstream in the field (like the identification of haplogroup R1a with the Proto-Indo-European expansion, or the concept of steppe admixture), I asked my wife (who knew almost nothing about genetics, or Indo-European studies) to read it and write a summary, if she liked it. She did. So much, that I have convinced her to read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World (2007), by David Anthony.

Here is her summary of the book, translated from Spanish:

The book is divided in three main parts: The Hunters, The Farmers, and The Indo-Europeans, and each has in turn chapters which introduce and break down information in an entertaining way, mixing them with recounts of her interactions and personal genealogical quest.

Part one, The Hunters, offers intriguing accounts about the direct role music had in the development of the first civilizations, the first mtDNA analyses of dogs (Savolainen), and the discovery of the author’s Saami roots. Explanations about the first DNA studies and their value for archaeological studies are clear and comprehensible for any non-specialized reader. Interviews help give a close view of investigations, like that of Frederic Plassard’s in Les Combarelles cave.

Part two, The Farmers, begins with her travel to Cyprus, and arouses the interest of the reader with her description of the circular houses, her notes on the Basque language, the new papers and theories related to DNA analyses, the theory of the decision of cats to live with humans, the first beers, and the houses built over graves. Karin Bojs analyses the subgroup H1g1 of her grandmother Hilda, and how it belonged to the first migratory wave into Central Europe. This interest in her grandmother’s origins lead her to a conference in Pilsen about the first farmers in Europe, where she knows firsthand of the results of studies by János Jakucs, and studies of nuclear DNA. Later on she interviews Guido Brandt and Joachim Burguer, with whom she talks about haplogroups U, H, and J.

The chapter on Ötzi and the South Tyrol Museum of Archaeology (Bolzano) introduces the reader to the first prehistoric individual whose DNA was analysed, belonging to haplogroup G2a4, but also revealing other information on the Iceman, such as his lactose intolerance.

Part three, dealing with the origin of Indo-Europeans, begins with the difficulties that researchers have in locating the origin of horse domestication (which probably happened in western Kazakhstan, in the Russian steppe between the rivers Volga and Don). She mentions studies by David Anthony and on the Yamna culture, and its likely role in the diffusion of Proto-Indo-European. In an interview with Mallory in Belfast, she recalls the potential interest of far-right extremists in genetic studies (and early links of the Journal of Indo-European Studies to certain ideology), as well as controversial statements of Gimbutas, and her potentially biased vision as a refugee from communist Europe. During the interview, Mallory had a copy of the latest genetic paper sent to Nature Magazine by Haak et al., not yet published, for review, but he didn’t share it.

Then haplogroups R1a and R1b are introduced as the most common in Europe. She visits the Halle State Museum of Prehistory (where the Nebra sky disk is exhibited), and later Krakow, where she interviews Slawomir Kadrow, dealing with the potential creation of the Corded Ware culture from a mix of Funnelbeaker and Globular Amphorae cultures. New studies of ancient DNA samples, published in the meantime, are showing that admixture analyses between Yamna and Corded Ware correlate in about 75%.

In the following chapters there is a broad review of all studies published to date, as well as individuals studied in different parts of Europe, stressing the importance of ships for the expansion of R1b lineages (Hjortspring boat).

The concluding chapter is dedicated to vikings, and is used to demystify them as aggressive warmongers, sketching their relevance as founders of the Russian state.

To sum up, it is a highly documented book, written in a clear style, and is capable of awakening the reader’s interest in genetic and anthropological research. The author enthusiastically looks for new publications and information from researchers, but is at the same time critic with them, showing often her own personal reactions to new discoveries, all of which offers a complex personal dynamic often shared by the reader, engaged with her first-person account the full length of the book.

Mayte Batalla (July 2017)

DISCLAIMER: The author sent me a copy of the book (a translation into Spanish), so there is a potential conflict of interest in this review. She didn’t ask for a review, though, and it was my wife who did it.