The time and place of European admixture in Ashkenazi Jewish history

Open access The time and place of European admixture in Ashkenazi Jewish history, by Xue, Lencz, Darvasi, Pe’er, & Carmi, PLOS Genetics (2018).

Abstract (emphasis mine):

The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago.

ashkenazi-pca
Principal Component Analysis (PCA) of the European and Middle-Eastern samples used as reference panels in our study. The analysis was performed using SmartPCA [25] with default parameters (except no outlier removal). The populations included within each region are listed in Table 1 of the main text. The PCA plot supports the partitioning of the European and Middle-Eastern populations into the broad regional groups used in the analysis. https://doi.org/10.1371/journal.pgen.1006644.s001

Interesting excerpts:

(…) AJ genetics defies simple demographic theories. Hypotheses such as a wholly Khazar, Turkish, or Middle-Eastern origin have been disqualified [4–7, 17, 55], but even a model of a single Middle-Eastern and European admixture event cannot account for all of our observations. The actual admixture history might have been highly complex, including multiple geographic sources and admixture events. Moreover, due to the genetic similarity and complex history of the European populations involved (particularly in Southern Europe [51]), the multiple paths of AJ migration across Europe [10], and the strong genetic drift experienced by AJ in the late Middle Ages [9, 16], there seems to be a limit on the resolution to which the AJ admixture history can be reconstructed.

ashkenazi
A proposed model for the recent AJ history. The proposed intervals for the dates and admixture proportions are based on multiple methods, as described in the main text. https://doi.org/10.1371/journal.pgen.1006644.g007

Historical model and interpretation

Under our model, admixture in Europe first happened in Southern Europe, and was followed by a founder event and a minor admixture event (likely) in Eastern Europe. Admixture in Southern Europe possibly occurred in Italy, given the continued presence of Jews there and the proposed Italian source of the early Rhineland Ashkenazi communities [3]. What is perhaps surprising is the timing of the Southern European admixture to ≈24–49 generations ago, since Jews are known to have resided in Italy already since antiquity. This result would imply no gene flow between Jews and local Italian populations almost until the turn of the millennium, either due to endogamy, or because the group that eventually gave rise to contemporary Ashkenazi Jews did not reside in Southern Europe until that time. More detailed and/or alternative interpretations are left for future studies.

Recent admixture in Northern Europe (Western or Eastern) is consistent with the presence of Ashkenazi Jews in the Rhineland since the 10th century and in Poland since the 13th century. Evidence from the IBD analysis suggests that Eastern European admixture is more likely; however, the results are not decisive. An open question in AJ history is the source of migration to Poland in late Medieval times; various speculations have been proposed, including Western and Central Europe [2, 10]. The uncertainty on whether gene flow from Western Europeans did or did not occur leaves this question open.

ashkenazi-f4-statistics
The effect of gene flow from the Middle-East into Southern EU on f4 statistics. Panels (A) and (B) demonstrate f4(West-EU,YRI;AJ,ME) and f4(South-EU,YRI;AJ,ME), respectively (cf S4A Fig). Paths from the Middle-East into AJ are indicated with red arrows; paths from YRI to Western or Southern Europe with green arrows. The f4 statistic is proportional to the total overlap between these paths (black bars). Whereas panel (B) (f4(South-EU,YRI;AJ,ME)) has more overlapping branches than in (A), migration from the Middle-East into Southern EU introduces a branch where the arrows run in opposite directions (patterned bar). Hence, the observed f4 statistic in (B) may be lower (depending on branch lengths) than in (A), even if Southern EU is the true source of gene flow into AJ. https://doi.org/10.1371/journal.pgen.1006644.s005

Featured image: Expulsions of Jews, from Wikipedia.

Optimal Migration Routes of Initial Upper Palaeolithic Populations to Eurasia

Ecological_Niche_and_Least-Cost_Path_Anatolia

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

Abstract:

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

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

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

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

See also:

The Russian school and the Yamna cultural-historical community, with emphasis on the north-west Pontic region

eneolithic-forest-zone

I have already talked about the Russian school of thought and their position regarding a Mesolithic origin of Proto-Indo-European in Northern Europe (see below related posts).

Since their archaeologists (Ukrainian, Russian, and Kazakh) are the nearest to potential Indo-Uralic origins, I have also recommended to follow some renown researchers closely.

Recently Leo S. Klejn referred to the position of Svetlana Ivanova. I found a recent summary of her model for genetic finds in an article appeared in Генофонд.рф: Степное население в Центральной Европе эпохи ранней бронзы, или путешествие туда и обратно

Aspects I agree with

– There is a Yamna cultural-historical community (i.e. with a potential ethnolinguistic unity). Although many different inner groups can be distinguished (based on cultural, social, anthropological differences), one cannot divide the culture in distinct cultures.

EDIT (28 JAN 2018): You can read a more detailed report about the Yamna cultural-historical community, by Svetlana Ivanova (in Russian).

– There is an older Neolithic cultural-historical community of the Pontic-Caspian steppe (i.e. with a potential ethnolinguistic unity), marked in genetics by CHG ancestry in the region. It is impressive that they supported that before the Mathieson et al. third revision (september 2017) with their finding of “Yamnaya” component in Ukraine Eneolithic. Chapeau for archaeology, again.

ivanova-neolithic-ukraine
Late Eneolithic North-West Pontic zone (after Brujako and Samojlova (eds.), 2013)

Aspects I am neutral about, but are potentially quite relevant for the future

Repin is a culture different from Yamna.

– The Budzhak culture is likely the heir of Repin, which is compatible with its expansion westward. According to Klejn and Anthony (Usatovo), this region was connected to (and might have influenced) the Corded Ware culture. Therefore – that is my contribution, not theirs – a hidden community of R1a-M417 subclades (that a lot of people are eager to find) might have stemmed from there.

EDIT (28 JAN 2018): Read papers about the Budzhak jars and asks, by Svetlana Ivanova (in Russian).

NOTE: In my opinion, as I have said before, the Budzhak/Usatovo-Corded Ware connection is too late to be meaningful for Genomic finds (taking into account the earliest Corded Ware samples, their steppe ancestry, and the TMRCA for R1a-M417 subclades) – it is after all a late group appeared during or after the Yamna expansion along the Danube ca. 3000 BC or later, as supported by most archaeologists today, see e.g. Rassamakin. The most likely model is that R1a-M417 subclades with steppe ancestry expanded from groups near Eneolithic Ukraine, whether from steppe, forest-steppe, or forest zone. Also, in my opinion (supporting Anthony’s original interpretation of Repin, as closely connected to Yamna) it is more likely that the (until now) ‘hidden’ western Yamna community hosting R1b-L51 subclades that later evolved into East Bell Beaker is in fact represented by Repin…

Globular Amphorae and Corded Ware cultures are related, because GAC is actually not a uniform culture, but a ‘complex’ (i.e., in the same sense that Bell Beaker was not a culture, but a complex, as genetics has shown), and CWC is also a complex of cultures, as supported by Furholt. If that is true, the sampling of certain peoples classified as from Globular Amphorae – which some have rushed to cite as the end of the GAC-CWC connection might not be the last word, and Kristiansen’s model of long-lasting GAC-CWC connection may still be open.

ivanova2-chalcolithic-ukraine
Yamna culture and its surroundings (after Brujako and Samojlova (eds.), 2013)

Aspects I disagree with

– There is no migration, but long-lasting contacts that show up in genetics, since the Mesolithic-Neolithic transition. In my opinion, the expansion of admixture + haplogroup reduction and expansion depict clear migratory movements (although, obviously, without cultural identification no speculative ethnolinguistic grouping can be proposed). That much is obvious from Genomics, and if we are not going to accept the most basic findings as proof in favour of certain anthropological models, then Archaeology will not benefit at all from genetic studies.

– Because this is the Russian school of thought, when they talk about Proto-Indo-European they refer to a homeland dating to the Mesolithic-Neolithic transition, and therefore cultural-historical communities after that (and long-lasting contacts) refer to potential continuations of Proto-Indo-European. Following common language guesstimates, though, there is no reason to date the split of Anatolian from a common Indo-Hittite before ca- 4500 BC, since there is no reason to date a Late Proto-Indo-European beyond 4000-3000 BC, apart from controversial glottochronological studies…

A call for collaboration

Again, please, geneticists, archaeologists, and linguists: do collaborate. Merely by talking, the so-called ‘Yamnaya ancestral component’ would have never been given that dreadful name, and maybe we could end this quest to find a Mesolithic homeland for a reconstructed language guesstimated to have been spoken millennia after that time (and maybe turn it into a quest for an older macro-language)…

Related:

Massive Migrations? The Impact of Recent aDNA Studies on our View of Third Millennium Europe

Thanks to Joshua Jonathan, I have discovered the paper Massive Migrations? The Impact of Recent aDNA Studies on our View of Third Millennium Europe, by Martin Furholt, European Journal of Archaeology (28 SEP 2017).

Abstract:

New human aDNA studies have once again brought to the forefront the role of mobility and migration in shaping social phenomena in European prehistory, processes that recent theoretical frameworks in archaeology have downplayed as an outdated explanatory notion linked to traditional culture history. While these new genetic data have provided new insights into the population history of prehistoric Europe, they are frequently interpreted and presented in a manner that recalls aspects of traditional culture-historical archaeology that were rightly criticized through the 1970s to the 1990s. They include the idea that shared material culture indicates shared participation in the same social group, or culture, and that these cultures constitute one-dimensional, homogeneous, and clearly bounded social entities. Since the new aDNA data are used to create vivid narratives describing ‘massive migrations’, the so-called cultural groups are once again likened to human populations and in turn revitalized as external drivers for socio-cultural change. Here, I argue for a more nuanced consideration of molecular data that more explicitly incorporates anthropologically informed mobility and migration models.

I was copying and pasting whole excerpts to post them here, but I think it is best to read the full paper.

yamna-corded-ware-bell-beaker
From the paper: “Simplified map showing the extent of the most important archaeological units of classification in the third millennium cal BC in Europe discussed in this text.”

It is a great summary of potential flaws of the current reasoning in genetic papers.

It should be a must-read for any serious geneticist involved in discussions on migrations, especially regarding archaeology in Indo-European studies.

As for the answers to the paper, well, unsurprisingly quite disappointing that of Haak, neither addressing the main flaw of their proposed “Yamna -> Corded Ware migration” model, nor taking the opportunity to evaluate other potential models fitting their findings of steppe ancestry in Corded Ware peoples, not even those directly suggested to them (like the expansion of Suvorovo-Novodanilovka chiefs).

NOTE: A funny thing about the paper is that, although published at the end of September, it does not take into account certain recent developments supporting Furholt’s doubts, such as the Esperstedt’s family, the new sample of Sredni Stog (and consequently the change in interpretations of outliers in Eneolithic Ukraine populations), or even the elevated steppe ancestry found in East Bell Beaker peoples. I guess Haak’s answer to all that would still be the same thorough argument: “meh, massive Indo-European migration Yamnaya -> Corded Ware is right”…

#EDIT (30 DEC 2017): Check out the interesting article by Bruce G. Trigger, referenced by John Hawks, about the question of descriptive vs. theoretical archaeologist vs. ethnologist/anthropologist from the 1950s to the 1980s. Interesting to see how today the new playboys in Academia, geneticists, are playing the archaeologist playing the ethnologist playing the linguist in Indo-European questions, and how we are living a historical debate on essential questions for the future of all these disciplines.

Related:

Genetic landscapes showing human genetic diversity aligning with geography

world-effective-migration

New preprint at BioRxiv, Genetic landscapes reveal how human genetic diversity aligns with geography, by Peter, Petkova, and Novembre (2017).

Abstract:

Summarizing spatial patterns in human genetic diversity to understand population history has been a persistent goal for human geneticists. Here, we use a recently developed spatially explicit method to estimate “effective migration” surfaces to visualize how human genetic diversity is geographically structured (the EEMS method). The resulting surfaces are “rugged”, which indicates the relationship between genetic and geographic distance is heterogenous and distorted as a rule. Most prominently, topographic and marine features regularly align with increased genetic differentiation (e.g. the Sahara desert, Mediterranean Sea or Himalaya at large scales; the Adriatic, inter-island straits in near Oceania at smaller scales). We also see traces of historical migrations and boundaries of language families. These results provide visualizations of human genetic diversity that reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, there have regularly been factors that subtly distort the underlying relationship across space observed today. The fine-scale population structure depicted here is relevant to understanding complex processes of human population history and may provide insights for geographic patterning in rare variants and heritable disease risk.

world-migration-effective
Regional patterns of genetic diversity. a: scale bar for relative effective migration rate. Posterior effective migration surfaces for b: Western Eurasia (WEA) e: Central/Eastern Eurasia (CEA) g: Africa (AFR) h Southern African hunter-gatherers (SAHG) k: and Southeast Asian (SEA) analysis panels. ‘X’ marks locations of samples noted as displaced or recently admixed, ‘H’ denotes Hunter-Gatherer populations (both ‘X’ and ‘H’ samples are omitted from the EEMS model fit); in panel g, red circles indicate Nilo-Saharan speakers and in panel h, ‘B’ denotes Bantu-speaking populations. Approximate location of troughs are shown with dashed lines (see Extended Data Figure 4). PCA plots: c: WEA d:Europeans in WEA f: CEA i: SAHG j: AFR l: SEA. Individuals are displayed as grey dots. Large dots reflect median PC position for a sample; with colors reflecting geography matched to the corresponding EEMS figure. In the EEMS plots, approximate sample locations are annotated. For exact locations, see annotated Extended Data Figure 4 and Table S1. Features discussed in the main text and supplement are labeled. FST values per panelemphasize the low absolute levels of differentiation.”

Among ‘effective migration surfaces‘ (or potential past migration routes), the Pontic-Caspian steppe and its most direct connection with the Carpathian basin, the Danubian plains, appear maybe paradoxically as a constant ‘trough’ (below average migration rate) in all maps.

After all, we could have agreed that this region should be a priori thought as the route of many migrations from the steppe and Asia into Central Europe (and thus of ‘effective migration’) in prehistoric, proto-historic and historic times, such as Suvorovo-Novodanilovka (Pre-Anatolian), Yamna (Late Indo-European), probably Srubna, Scythian-Cimmerian, Sarmatian, Huns, Goths, Avars, Slavs, Mongols

It most likely (at least partially) represents a rather recent historical barrier to admixture, involving successive Byzantine, South Slavic, and Ottoman spheres of influence positioned against Balto-Slavic societies of Eastern Europe.

europe-migration-routes
Location of troughs in West Eurasia (below average migration rate in more than 95% of MCMC iterations) are given in brown. Sample locations and EEMS grid are displayed for the West Eurasian analysis panel. FST values are provided per panel to emphasize the low absolute levels of differentiation.

Featured image, from the article: “Large-scale patterns of population structure. a: EEMS posterior mean effective migration surface for Afro-Eurasia (AEA) panel. ‘X’ marks locations of samples excluded as displaced or recently admixed. ‘H marks locations of excluded hunter-gatherer populations. Regions and features discussed in the main text are labeled. Approximate locations of troughs are annotated with dashed lines (see Extended Data Figure 4). b: PCA plot of AEA panel: Individuals are displayed as grey dots, colored dots reflect median of sample locations; with colors reflecting geography and matching with the EEMS plot. Locations displayed in the EEMS plot reflect the position of populations after alignment to grid vertices used in the model (see methods).”

Images and text available under a CC-BY-NC-ND 4.0 International License.

Discovered via Razib Khan’s blog.

Related:

Asian ancestry of the Roma people in Europe

New article, Tau haplotypes support the Asian ancestry of the Roma population settled in the Basque Country, by Alfonso-Sánchez et al., Nature (2017).

Abstract:

We examined tau haplotype frequencies in two different ethnical groups from the Basque Country (BC): Roma people and residents of European ancestry (general population). In addition, we analyzed the spatial distribution of tau haplotypes in Eurasian populations to explore the genetic affinities of the Romani groups living in Europe in a broader scope. The 17q21.31 genomic region was characterized through the genotyping of two diagnostic single nucleotide polymorphisms, SNPs (rs10514879 and rs199451), which allow the identification of H1 and H2 haplotypes. A significant heterozygous deficit was detected in the Romani for rs10514879. The H2 haplotype frequency proved to be more than twice in the BC general population (0.283) than in the Roma people (0.127). In contrast, H2 frequency proved to be very similar between Basque and Hungarian Romani, and similar to the H2 frequencies found in northwestern India and Pakistan as well. Several statistical analyses unveiled genetic structuring for the MAPT diversity, mirrored in a significant association between geography and genetic distances, with an upward trend of H2 haplotype frequencies from Asia to Europe. Yet, Roma samples did not fit into this general spatial patterning because of their discrepancy between geographical position and H2 frequency. Despite the long spatial coexistence in the Basque region between the residents of European ancestry and the Roma, the latter have preserved their Asian genetic ancestry. Bearing in mind the lack of geographical barriers between both ethnical groups, these findings support the notion that sociocultural mores might promote assortative matings in human populations.

roma-tau-asian-genetic
“Regression line and 95% confidence intervals (dashed lines) in a regression analysis of tau H2 haplotype frequencies on the rotated geographical coordinates (H2 freq = 0.4256 − coord × 0.000083) of 35 European and Asian populations (coefficient of determination, r2 = 0.515). Populations examined in this study are highlighted with a frame. Solid circles are European populations, solid squares are Middle Eastern populations, and solid triangles represent South Asian populations. Romani populations are designated by stars. Population labels: BCRoma (Basque Country Roma), BC-resid (Basque Country general population), BC-Spain (Iberian Basques), BC-French (French Basques), UK (British), IT-Sardn (Sardinia, Italy), ITBergm (Bergamo, Italy), ITBresc (Brescia, Italy), IT-Tuscn (Tuscany, Italy), HU-Roma (Hungarian Roma), Palestn(Palestinians), and Samartn (Samaritans)”

I just realized I forgot to include the migration of Indo-Aryan Roma people in the map of medieval migrations… I shall correct that in future versions.

Migration_des_Roms
Map showing the migrations of Romani people through Europe and Asia minor. From Wikipedia.

Featured image: Map of Romani dialects. From Wikipedia, by ArnoldPlaton.

Migration vs. Acculturation models for Aegean Neolithic in Genetics — still depending strongly on Archaeology

aegean-neolithic-anatolia

Recent paper in Proceedings of the Royal Society B: Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean, by Kılınç et al. (2017).

Abstract:

The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.

The analysis of the paper highlights two points regarding the process of Neolithisation in the Aegean, which is essential to ascertain the impact of later Indo-European migrations of Proto-Anatolian and Proto-Greek and other Palaeo-Balkan speakers(texts partially taken verbatim from the paper):

  • The observation that the two central Anatolian populations cluster together to the exclusion of Neolithic populations of south Levant or of Iran restates the conclusion that farming in central Anatolia in the PPN was established by local groups instead of immigrants, which is consistent with the described cultural continuity between central Anatolian Epipalaeolithic and Aceramic communities. This reiterates the earlier conclusion that the early Neolithisation in the primary zone was largely a process of cultural interaction instead of gene flow.
aegean-neolithic-pca
Principal component analysis (PCA) with modern and ancient genomes. The eigenvectors were calculated using 50 modern west Eurasian populations, onto which genome data from ancient individuals were projected. The gray circles highlight the four ancient gene pools of west Eurasia. Modern-day individuals are shown as gray points. In the Near East, Pre-Neolithic (Epipaleolithic/Mesolithic) and Neolithic individuals genetically cluster by geography rather than by cultural context. For instance, Neolithic individuals of Anatolia cluster to the exclusion of individuals from the Levant or Iran). In Europe, genetic clustering reflects cultural context but not geography: European early Neolithic individuals are genetically distinct from European pre-Neolithic individuals but tightly cluster with Anatolians. PPN: Pre-Pottery/Aceramic Neolithic, PN: Pottery Neolithic, Tepecik: Tepecik-Çiftlik (electronic supplementary material, table S1 lists the number of SNPs per ancient individual).
  • The realisation that there are still two possibilities regarding the question of whether Aegean Neolithisation (post-7000 cal BC) involved similar acculturation processes, or was driven by migration similar to Neolithisation in mainland Europe — a long-standing debate in Archaeology:
    1. Migration from Anatolia to the Aegean: the Aegean Neolithisation must have involved replacement of a local, WHG-related Mesolithic population by incoming easterners. Central Anatolia or south Anatolia / north Levant (of which there is no data) are potential origins of the components observed. Notably, the north Aegeans – Revenia (ca. 6438-6264 BC) and Barcın (ca. 6500-6200 BC) – show higher diversity than the central Anatolians, and the population size of Aegeans was larger than that of central Anatolians. The lack of WHG in later samples indicates that they must have been fully replaced by the eastern migrant farmers.
    2. Adoption of Neolithic elements by local foragers: Alternatively, the Aegean coast Mesolithic populations may have been part of the Anatolian-related gene pool that occupied the Aegean seaboard during the Early Holocene, in an “out-of-the-Aegean hypothesis. Following the LGM, Aegean emigrants would have dispersed into central Anatolia and established populations that eventually gave rise to the local Epipalaeolithic and later Neolithic communities, in line with the earliest direct evidence for human presence in central Anatolia ca 14 000 cal BCE
  • On the archaeological evidence (excerpt):

    Instead of a single-sourced colonization process, the Aegean Neolithization may thus have flourished upon already existing coastal and interior interaction networks connecting Aegean foragers with the Levantine and central Anatolian PPN populations, and involved multiple cultural interaction events from its early steps onward [16,20,64,74]. This wide diversity of cultural sources and the potential role of local populations in Neolithic development may set apart Aegean Neolithization from that in mainland Europe. While Mesolithic Aegean genetic data are awaited to fully resolve this issue, researchers should be aware of the possibility that the initial emergence of the Neolithic elements in the Aegean, at least in the north Aegean, involved cultural and demographic dynamics different than those in European Neolithization.

    Featured image, from the article: “Summary of the data analyzed in this study. (a) Map of west Eurasia showing the geographical locations and (b) timeline showing the time period (years BCE) of ancient individuals investigated in the study. Blue circles: individuals from pre-Neolithic context; red triangles: individuals from Neolithic contexts”.

    Related:

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

neolithic-mesolithic-europe

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.

Abstract:

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:

mesolithic-neolithic-PCA
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-south-east-europe
PCA of South-East European and other European samples from Mathieson et al. (2017)
pca-ancient-modern-europe
Ancient and modern samples on Lazaridis et al. (2014)

Related:

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

estimating-mobility

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.

Significance

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.

Abstract

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.

Something is very wrong with models based on the so-called ‘steppe admixture’ – and archaeologists are catching up

steppe-admixture

Russian archaeologist Leo Klejn has published an article Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?, which includes the criticism received from Wolfgang Haak, Iosif Lazaridis, Nick Patterson, and David Reich (mainly on the genetic aspect), and from Kristian Kristiansen, Karl-Göran Sjögren, Morten Allentoft, Martin Sikora, and Eske Willerslev (mainly on the archaeological aspect).

I will not post details of Klejn’s model of North-South Proto-Indo-European expansion – which is explained in the article, and relies on the north-south cline of ‘steppe admixture’ in the modern European population -, since it is based on marginal anthropological methods and theories, including glottochronological dates, and archaeological theories from the Russian school (mainly Zalyzniak), which are obviously not mainstream in the field of Indo-European Studies, and (paradoxically) on the modern distribution of ‘steppe admixture’…

The most interesting aspects of the article are the reactions to the criticism, some of which can be used from the point of view of the Indo-European demic diffusion model, too. It is sad, however, that they didn’t choose to answer earlier to Heyd’s criticism (or to Heyd’s model, which is essentially also that of Mallory and Anthony), instead of just waiting for proponents of the least interesting models to react…

The answer by Haak et al.:

Klejn mischaracterizes our paper as claiming that practitioners of the Corded Ware culture spoke a language ancestral to all European Indo-European languages, including Greek and Celtic. This is incorrect: we never claim that the ancestor of Greek is the language spoken by people of the Corded Ware culture. In fact, we explicitly state that the expansion of steppe ancestry might account for only a subset of Indo-European languages in Europe. Klejn asserts that ‘a source in the north’ is a better candidate for the new ancestry manifested in the Corded Ware than the Yamnaya. While it is indeed the case that the present-day people with the greatest affinity to the Corded Ware are distributed in north-eastern Europe, a major part of the new ancestry of the Corded Ware derives from a population most closely related to Armenians (Haak et al., 2015) and hunter-gatherers from the Caucasus (Jones et al., 2015). This ancestry has not been detected in any European huntergatherers analysed to date (Lazaridis et al., 2014; Skoglund et al., 2014; Haak et al., 2015; Fu et al., 2016), but made up some fifty per cent of the ancestry of the Yamnaya. The fact that the Corded Ware traced some of its ancestry to the southern Caucasus makes a source in the north less parsimonious.

In our study, we did not speculate about the date of Proto-Indo-European and the locations of its speakers, as these questions are unresolved by our data, although we do think the genetic data impose constraints on what occurred. We are enthusiastic about the potential of genetics to contribute to a resolution of this longstanding issue, but this is likely to require DNA from multiple, as yet unsampled, ancient populations.

Klejn response to that:

Allegedly, I had accused the authors of tracing all Indo-European languages back to Yamnaya, whereas they did not trace all of them but only a portion! Well, I shall not reproach the authors for their ambiguous language: it remains the case that (beginning with the title of the first article) their qualifications are lost and their readers have understood them as presenting the solution to the whole question of the origins of Indo-European languages.

(…) they had in view not the Proto-Indo-European before the separation of the Hittites, but the language that was left after the separation. Yet, this was still the language ancestral to all the remaining Indo-European languages, and the followers of Sturtevan and Kluckhorst call only this language Proto-Indo-European (while they call the initial one Indo-Hittite). The majority of linguists (specialists in Indo-European languages) is now inclined to this view. True, the breakup of this younger language is several hundred years more recent (nearly a thousand years later according to some glottochronologies) than the separation of Anatolian languages, but it is still around a thousand years earlier than the birth of cultures derived from Yamnaya.
More than that, I analysed in my criticism both possibilities — the case for all Indo-European languages spreading from Yamnaya and the case for only some of them spreading from Yamnaya. In the latter case, it is argued that only the languages of the steppes, the Aryan (Indo- Iranian) are descended from Yamnaya, not the languages of northern Europe. Together with many scholars, I am in agreement with the last possibility. But, then, what sense can the proposed migration of the Yamnaya culture to the Baltic region have? It would bring the Indo-Iranian proto-language to that region! Yet, there are no traces of this language on the coasts of the Baltic!

My main concern is that, to my mind, one should not directly apply conclusions from genetics to events in the development of language because there is no direct and inevitable dependence between events in the life of languages, culture, and physical structure (both anthropological and genetic). They can coincide, but often they all follow divergent paths. In each case the supposed coincidence should be proved separately.

The authors’ third objection concerns the increase of the genetic similarity of European population with that of the Yamnaya culture. This increases in the north of Europe and is weak in the south, in the places adjacent to the Yamnaya area, i.e. in Hungary. This gradient is clearly expressed in the modern population, but was present already in the Bronze Age, and hence cannot be explained by shifts that occurred in the Early Iron Age and in medieval times. However, the supposed migration of the Yamnaya culture to the west and north should imply a gradient in just the opposite direction!

Regarding the arguments of Kristiansen and colleagues:

[They argue that] in two early burials of the Corded Ware culture (one in Germany, the other in Poland) some single attributes of Yamnaya origin have been found.

(…) if this is the full extent of Yamnaya infiltration into central Europe—two burials (one for each country) from several thousands (and from several hundreds of early burials)—then it hardly amounts to large-scale migration.

Quite recently we have witnessed the success of a group of geneticists from Stanford University and elsewhere (Poznik et al., 2016). They succeeded in revealing varieties of Y-chromosome connected with demographic expansions in the Bronze Age. Such expansion can give rise to migration. Among the variants connected with this expansion is R1b, and this haplogroup is typical for the Yamnaya culture. But what bad luck! This haplogroup connected with expansion is indicated by the clade L11, while the Yamnaya burials are associated with a different clade, Z2103, that is not marked by expansion. It is now time to think about how else the remarkable results reached by both teams of experienced and bright geneticists may be interpreted.

Regarding the work of Heyd,

(…) with regard to the barrow burials of the third millennium BC in the basin of the Danube, although they have been assigned to the Yamnaya culture, I would consider them as also belonging to
another, separate culture, perhaps a mixed culture: its burial custom is typical of the Yamnaya, but its pottery is absolutely not Yamnaya, but local Balkan with imports of distinctive corded beakers (Schnurbecher). I would not be surprised if
Y-chromosome haplogroups of this population were somewhat similar to those of the Yamnaya, while mitochondrial groups were indigenous. As yet, geneticists deal with great blocks of populations and prefer to match them to very large and generalized cultural blocks, while archaeology now analyses more concrete and smaller cultures, each of which had its own fate.

Iosif Lazaridis shares more thoughts on the discussion in his Twitter account:

As we mentioned in Haak, Lazaridis et al. (2015), the Yamnaya are the best proximate source for the new ancestry that first appears with the Corded Ware in central Europe, as it has the right mix of both ANE (related to Native Americans, MA1, and EHG), but also Armenian/Caucasus/Iran-like southern component of ancestry. The Yamnaya is a westward expansive culture that bears exactly the two new ancestral components (EHG + Caucasus/Iran/Armenian-like).
As for the Y-chromosome, it was already noted in Haak, Lazaridis et al. (2015) that the Yamnaya from Samara had Y-chromosomes which belonged to R-M269 but did not belong to the clade common in Western Europe (p. 46 of supplement). Also, not a single R1a in Yamnaya unlike Corded Ware (R1a-dominated). But Yamnaya samples = elite burials from eastern part of the Yamnaya range. Both R1a/R1b found in Eneolithic Samara and EHG, so in conclusion Yamnaya expansion still the best proximate source for the post-3,000 BCE population change in central Europe. And since 2015 steppe expansion detected elsewhere (Cassidy et al. 16, Martiniano et al. 17, Mittnik et al. 17, Mathieson et al. 17, Lazaridis et al. 2016 (South Asia) and …?…

I love the smell of new wording in the morning… viz. Yamnaya best proximate source for Corded Ware, Corded Ware might account for only a subset of Indo-European languages, Corded Ware representing Aryan languages (probably Klejn misinterprets what the authors mean, i.e. some kind of Indo-Slavonic or Germano-Balto-Slavic group)…

We shall expect more and more ambiguous rewording and more adjustments of previous conclusions as new papers and new criticisms appear.

Related:

Featured image from the article: Distribution of the ‘Yamnaya’ genetic component in the populations of Europe (data taken from Haak et al., 2015). The intensity of the colour corresponds to the contribution of this component in various modern populations