David Reich on social inequality and Yamna expansion with few Y-DNA subclades

Interesting article from David Reich that I had missed, at Nautilus, Social Inequality Leaves a Genetic Mark.

It explores one of the main issues we are observing with ancient DNA, the greater reduction in Y-DNA lineages relative to mtDNA lineages, and its most likely explanation (which I discussed recently).

Excerpts interesting for the Indo-European question (emphasis mine):

Gimbutas’s reconstruction has been criticized as fantastical by her critics, and any attempt to paint a vivid picture of what a human culture was like before the period of written texts needs to be viewed with caution. Nevertheless, ancient DNA data has provided evidence that the Yamnaya were indeed a society in which power was concentrated among a small number of elite males. The Y chromosomes that the Yamnaya carried were nearly all of a few types, which shows that a limited number of males must have been extraordinarily successful in spreading their genes. In contrast, in their mitochondrial DNA, the Yamnaya had more diverse sequences.9 The descendants of the Yamnaya or their close relatives spread their Y chromosomes into Europe and India, and the demographic impact of this expansion was profound, as the Y-chromosome types they carried were absent in Europe and India before the Bronze Age but are predominant in both places today.13

This Yamnaya expansion also cannot have been entirely friendly, as is clear from the fact that the proportion of Y chromosomes of steppe origin in both western Europe14 and in India15 today is much larger than the proportion of the rest of the genome. This preponderance of male ancestry coming from the steppe implies that male descendants of the Yamnaya with political or social power were more successful at competing for local mates than men from the local groups. The most striking example I know is from Iberia in far southwestern Europe, where Yamnaya-derived ancestry arrived suddenly at the onset of the Bronze Age between 4,500 and 4,000 years ago. Daniel Bradley’s laboratory and my laboratory independently produced ancient DNA from individuals of this period.14 We find that in the first Iberians with Yamnaya-derived ancestry, the proportion of Yamnaya ancestry across the whole genome is almost never more than around 15 percent. However, around 90 percent of males who carry Yamnaya ancestry have a Y-chromosome type of steppe origin that was absent in Iberia prior to that time. It is clear that there were extraordinary hierarchies and imbalances in power at work in the Yamnaya expansions.

David Reich clearly doesn’t give a damn about how other people might react to his commentaries. That’s nice.

In any case, if anyone was still in denial, R1b-M269 expanded with Yamna (through the Bell Beaker expansion) into Iberia, hence yes, 90% of modern Basque male lineages have an origin in the steppe, like the R1b-DF27 sample recently found, and their common ancestor spoke Late Proto-Indo-European.

Findings like these, which should be taken as normal developments of research, are apparently still a trauma for many – like R1a-fans from India realizing most of their paternal ancestors came from the steppe, or its fans from Northern Europe understanding that their paternal ancestors probably spoke Uralic or a related language; or N1c-fans seeing how their paternal ancestors probably didn’t speak Uralic. It seems life isn’t fair to stupid simplistic ethnolinguistic ideas

Let’s see which Y-DNA haplogroups we find in West Yamna, to verify the latest migration model of Late PIE speakers of the Reich Lab (featured image).

Check out also the BBC News coverage of David Reich and Nick Patterson, the two most influential researchers of the moment in Human Ancestry: How ancient DNA is transforming our view of the past.

Related:

Distribution of Southern Iberian haplogroup H indicates exchanges in the western Mediterranean

Recent open access paper The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean, by Hernández, Dugoujon, Novelletto, Rodríguez, Cuesta and Calderón, BMC Genetics (2017).

Abstract (emphasis mine):

Background
The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature.

Results
Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean.

Conclusions
Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.

mtdna-h1-h3-europe-frequency
a, b, c. Interpolated frequency surfaces of clade H and its main sub-clades (H1 and H3). Frequencies (%) are showed in a colour scale. See information about the populations used in Additional files 4 and 5. Map templates were taken from Natural Earth free map repository (http://www.naturalearthdata.com/)

I usually find mtDNA data, especially studies like this one based on modern populations, very difficult to interpret for anthropological purposes. It is well-known that there are important differences in the pattern of Y-DNA and mtDNA expansion and distribution.

A paragraph in this respect caught my attention:

The patterns of variation in the Y-chromosome between western and eastern Andalusians, based on 416 males, have also been investigated for a set of Y-Short Tandem Repeats (Y-STRs) and Y-SNPs [53, 54, 55], Calderón et al., unpublished data] in combination to mtDNA analyses ([18, 19] and present study). In general, for both uniparental makers, Andalusians exhibit a typical western European genetic background, with peak frequencies of mtDNA Hg H and Y-chromosome Hg R1b1b2-M269 (45% and 60%, respectively). Interestingly, our results have further revealed that the influence of African female input is far more significant when compared to male influence in contemporary Andalusians. The lack of correspondence between the maternal and paternal genetic profiles of human populations reflects intrinsic differences in migratory behavior related to sex-biased processes and admixture, as well as differences in male and female effective population sizes related to the variance in reproductive success affected, for example, by polygyny [56, 57].

I think that the greater reduction in patrilineal lineages compared to maternal lineages we usually see during and after prehistoric or historic migrations have more to do with the renown Uí Néill family case and with war-related casualties (since combatants were usually men) than with other more popular explanations, such as enslavement of women or polygyny.

The most successful paternal lines (anywhere in the world) were probably those who remained in power for a long time (be it a patriarchal society based on families, clans, or more complex organizational units), who were richer and thus more capable of having healthy offspring, who in turn were able to survive longer and have more children who inherited power, etc.

In case of recent migrations or population movements that disrupt the previously established organization, after a certain number of generations, successful patrilocal families (usually from incoming lineages) might slowly dominate over a whole region, with poorer families (usually of ‘indigenous’ lineages) suffering a greater – especially perinatal and child – mortality, without any obvious (pre)historic event associated to these gradual changes.

This gradual replacement of paternal lineages is compatible with the adoption of the native language by newcomers. If the number of migrants is greater that the native population, and especially if their technology is more advanced, then a more radical change including ethnolinguistic identification is more likely.

I don’t deny the (pre)historic existence of radical replacement of male populations with continuity of female lineages due to massacres of men, female slavery, or polygyny, but they are probably not the main explanation for most regional differences seen in paternal lineages, and should thus be used with caution.

Gradual replacement and founder effects are also the most logical explanation for why autochthonous continuity myths (that the modern regional prevalence of few successful lineages tended to create in the 2000s) haven’t been corroborated by ancient DNA; e.g. R1b-DF27 in Basques, N1c-M178 in Finnic populations, R1a-Z283 in Slavs, etc. There is nothing different in those areas from other recent founder effects and internal migratory flows seen everywhere in Europe in the past millennia.

Paper discovered via a link by Alberto Gonzalez on Facebook group Iberia ADN

Related:

Iberia in the Copper and Early Bronze Age: Cultural, demographic, and environmental analysis

bell-beaker-ritual

New paper (behind paywall), Cultural, Demographic and Environmental Dynamics of the Copper and Early Bronze Age in Iberia (3300–1500 BC): Towards an Interregional Multiproxy Comparison at the Time of the 4.2 ky BP Event, Blanco-González, Lillios, López-Sáez, et al. J World Prehist (2018).

Abstract (emphasis mine):

This paper presents the first comprehensive pan-Iberian overview of one of the major episodes of cultural change in later prehistoric Iberia, the Copper to Bronze Age transition (c. 2400–1900 BC), and assesses its relationship to the 4.2 ky BP climatic event. It synthesizes available cultural, demographic and palaeoenvironmental evidence by region between 3300 and 1500 BC. Important variation can be discerned through this comparison. The demographic signatures of some regions, such as the Meseta and the southwest, diminished in the Early Bronze Age, while other regions, such as the southeast, display clear growth in human activities; the Atlantic areas in northern Iberia barely experienced any changes. This paper opens the door to climatic fluctuations and inter-regional demic movements within the Peninsula as plausible contributing drivers of particular historical dynamics.

iberia-culture-history-areas
Division of Iberia into 5 study areas according to their culture history (3300–1550 BC)

Interesting excerpts summarizing key trends in the different regions:

  • Between 2200 and 1900 BC, the northernmost regions (i.e. Galicia, the Cantabrian strip and the northeastern sector to the north of the Ebro valley) underwent relatively minor changes in the realms of settlement and burial practices. (…) In addition, some Atlantic areas show a marked and statistically significant fall in human activity c. 2200 BC, with a subsequent recovery c. 1600 BC, and such observations are matched by paleoenvironmental proxies and a lack of known EBA sites
  • The overall impression from the Meseta is one of sharp disruption in cultural practices; these include both settlement and burial patterns, abrupt shifts in local climate conditions, and striking differences in human pressure on vegetation. However, there was also clear intra-regional variability, with remarkable internal particularities and differential tempos between the western and eastern sectors. In terms of material culture, discontinuity with the Copper Age is the main trend in the western Duero and the Tagus valleys, yet EBA communities to the north of the Central System adopted far more distinctive and therefore traceable site types (hilltops) and material repertoire. This shift was even stronger in the case of the Motillas culture at La Mancha, whose pathway seems closely tied to the Argaric area.
  • Intra-regional variability is also apparent within the northeast (…) In the second millennium BC, material culture changed, long-distance exchange intensified and anthropogenic pressure increased, despite continuity in diverse realms of social practice.
  • The pattern in the southwest was one of marked discontinuity with two key features: a) it follows the general decreasing trends manifest across Atlantic Iberia; and b) its temporality was clearly different from the rest of the Peninsula and apparently unrelated to the 4.2 ky BP event. Thus, a highly conspicuous and rich variety of cultural expressions in the Chalcolithic, with an early and marked peak in human activity during the Beaker phase c. 2500 BC, gave way to a sudden cultural collapse prior to the onset of the EBA
  • The southeast exhibits one of the most remarkable cultural shifts in Western Europe. (…) The radical transformation in Chalcolithic materiality and ways of life could be regarded as a kind of societal collapse. The Argaric, a highly hierarchical and integrated regional polity, is the clearest example of a new scenario that emerged after the 4.2 ky BP event, yet the contributing role of environmental change and immigration from other regions remains to be fully explored.

Since R1b-DF27 lineages are widely distributed in modern western Europe, it is only logical that the recent find of its first ancient sample in Iberia has sparked the interest for Chalcolithic and Early Bronze Age Iberian cultures.

There is not much literature in English about Iberian prehistory, especially on the evolution of Bell Beaker culture. Also, most papers in Spanish on this cultural phenomenon – in my humble opinion, as a non-archaeologist – seem to be written from a merely descriptive archaeological point of view, many of them still sharing the radiocarbon-based assessment of origin and distribution of materials, instead of more complex anthropological models of cultural change and potential migrations.

Nevertheless, changes and influences in Iberian cultures are obvious regardless of the view taken on population movements (which are becoming quite clear now), and this paper seems to me a thorough review, very interesting for international researchers when interpreting ancient DNA from Iberia.

Featured image, modified from the paper: “The Bell Beaker culture in the northern Meseta: an artistic recreation of funerary ritual at Fuente Olmedo (Valladolid). Source: Garrido-Pena et al. 2011, Fig. 7.7”.

EDIT (21 MAR 2018): Interesting C14 date repository project Cronología de la Prehistoria de la Península Ibérica (read a brief description, in Spanish).

Related:

Iberian prehistoric migrations in Genomics from Neolithic, Chalcolithic, and Bronze Age

iberia-neolithic-bronze-age

New open access paper Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia, by Valdiosera, Günther, Vera-Rodríguez, et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine)

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

iberia-admixture
(A) f4 statistics testing affinities of prehistoric European farmers to either early Neolithic Iberians or central Europeans, restricting these reference populations to SNP-captured individuals to avoid technical artifacts driving the affinities. The boxplots in A show the distributions of all individual f4 statistics belonging to the respective groups. The signal is not sensitive to the choice of reference populations and is not driven by hunter-gatherer–related admixture (Datasets S4 and S5). (B) Estimates of ancestry proportions in different prehistoric Europeans as well as modern southwestern Europeans. Individuals from regions of Iberia were grouped together for the analysis in A and B to increase sample sizes per group and reduce noise

Conclusion:

We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.

Related:

Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

Open access preprint (which I announced already) at bioRxiv Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula, by Bycroft et al. (2018).

Abstract (emphasis mine):

Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian Peninsula is linguistically diverse, has a complex demographic history, and is unique among European regions in having a centuries-long period of Muslim rule. Previous genetic studies of Spain have examined either a small fraction of the genome or only a few Spanish regions. Thus, the overall pattern of fine-scale population structure within Spain remains uncharacterised. Here we analyse genome-wide genotyping array data for 1,413 Spanish individuals sampled from all regions of Spain. We identify extensive fine-scale structure, down to unprecedented scales, smaller than 10 Km in some places. We observe a major axis of genetic differentiation that runs from east to west of the peninsula. In contrast, we observe remarkable genetic similarity in the north-south direction, and evidence of historical north-south population movement. Finally, without making particular prior assumptions about source populations, we show that modern Spanish people have regionally varying fractions of ancestry from a group most similar to modern north Moroccans. The north African ancestry results from an admixture event, which we date to 860 – 1120 CE, corresponding to the early half of Muslim rule. Our results indicate that it is possible to discern clear genetic impacts of the Muslim conquest and population movements associated with the subsequent Reconquista.

iberia-reconquista-dna
“(a) Binary tree showing the inferred hierarchical relationships between clusters. The colours and points correspond to each cluster as shown on the map, and the length of the coloured rectangles is proportional to the number of individuals assigned to that cluster. We combined some small clusters (Methods) and the thick black branches indicate the clades of the tree that we visualise in the map. We have labeled clusters according to the approximate location of most of their members, but geographic data was not used in the inference. (b) Each individual is represented by a point placed at (or close to) the centroid of their grandparents’ birthplaces. On this map we only show the individuals for whom all four grandparents were born within 80km of their average birthplace, although the data for all individuals were used in the fineSTRUCTURE inference. The background is coloured according to the spatial densities of each cluster at the level of the tree where there are 14 clusters (see Methods). The colour and symbol of each point corresponds to the cluster the individual was assigned to at a lower level of the tree, as shown in (a). The labels and boundaries of Spain’s Autonomous Communities are also shown.”

Some interesting excerpts:

Our results further imply that north west African-like DNA predominated in the migration. Moreover, admixture mainly, and perhaps almost exclusively, occurred within the earlier half of the period of Muslim rule. Within Spain, north African ancestry occurs in all groups, although levels are low in the Basque region and in a region corresponding closely to the 14th-century ‘Crown of Aragon’. Therefore, although genetically distinct this implies that the Basques have not been completely isolated from the rest of Spain over the past 1300 years.

NOTE. I must add here that the Expulsion of Moriscos is known to have been quite successful in the old Crown of Aragon – deeply affecting its economy – , in contrast with other territories of the Crown of Castille, where they either formed less sizeable communities, or were dispersed and eventually Christened and integrated with local communities. For example, thousands of Moriscos from Granada were dispersed following the War of Alpujarras (1567–1571) into different regions of the Crown of Castille, and many could not be later expelled due to the locals’ resistance to follow the expulsion edict.

Perhaps surprisingly, north African ancestry does not reflect proximity to north Africa, or even regions under more extended Muslim control. The highest amounts of north African ancestry found within Iberia are in the west (11%) including in Galicia, despite the fact that the region of Galicia as it is defined today (north of the Miño river), was never under Muslim rule and Berber settlements north of the Douro river were abandoned by. This observation is consistent with previous work using Y-chromosome data. We speculate that the pattern we see is driven by later internal migratory flows, such as between Portugal and Galicia, and this would also explain why Galicia and Portugal show indistinguishable ancestry sharing with non-Spanish groups more generally. Alternatively, it might be that these patterns reflect regional differences in patterns of settlement and integration with local peoples of north African immigrants themselves, or varying extents of the large-scale expulsion of Muslim people, which occurred post-Reconquista and especially in towns and cities.

iberia-north-african-morocco
We estimated ancestry profiles for each point on a fine spatial grid across Spain (Methods). Gray crosses show
the locations of sampled individuals used in the estimation. Map shows the fraction contributed from the donor group ‘NorthMorocco’.

Overall, the pattern of genetic differentiation we observe in Spain reflects the linguistic and geopolitical boundaries present around the end of the time of Muslim rule in Spain, suggesting this period has had a significant and long-term impact on the genetic structure observed in modern Spain, over 500 years later. In the case of the UK, similar geopolitical correspondence was seen, but to a different period in the past (around 600 CE). Noticeably, in these two cases, country-specific historical events rather than geographic barriers seem to drive overall patterns of population structure. The observation that fine-scale structure evolves at different rates in different places could be explained if observed patterns tend to reflect those at the ends of periods of significant past upheaval, such as the end of Muslim rule in Spain, and the end of the Anglo-Saxon and Danish Viking invasions in the UK.

Certain people want to believe (well into the 21st century) into ideal ancestral populations and ancient ethnolinguistic identifications linked to one’s own – or the own country’s dominant – ancestral components and Y-DNA haplogroup.

We are nevertheless seeing how mainly the most recent relevant geopolitical events and late internal migratory flows have shaped the genetic structure (including Y-DNA haplogroup composition) of modern regions and countries regardless of its population’s actual language or ethnic identification, whether (pre)historical or modern.

Another surprise for many, I guess.

Related:

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:

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

iberia-mtdna

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).

Abstract:

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
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.

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

Analysis of R1b-DF27 haplogroups in modern populations adds new information that contrasts with ‘steppe admixture’ results

R1b-DF27-iberia

New open access article published in Scientific Reports, Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ, by Solé-Morata et al. (2017).

Abstract

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.

Some people like to say that Y-DNA haplogroup analysis, or phylogeography in general, is of no use anymore (especially modern phylogeography), and they are content to see how ‘steppe admixture’ was (or even is) distributed in Europe to draw conclusions about ancient languages and their expansion. With each new paper, we are seeing the advantages of analysing ancient and modern haplogroups in ascertaining population movements.

Quite recently there was a suggestion based on steppe admixture that Basque-speaking Iberians resisted the invasion from the steppe. Observing the results of this article (dates of expansion and demographic data) we see a clear expansion of Y-DNA haplogroups precisely by the time of Bell Beaker expansion from the east. Y-DNA haplogroups of ancient samples from Portugal point exactly to the same conclusion.

The situation of R1b-DF27 in Basques, as I have pointed out elsewhere, is probably then similar to the genetic drift of Finns, mainly of N1c lineages, speaking today a Uralic language that expaned with Corded Ware and R1a subclades.

The recent article on Mycenaean and Minoan genetics also showed that, when it comes to Europe, most of the demographic patterns we see in admixture are reminiscent of the previous situation, only rarely can we see a clear change in admixture (which would mean an important, sudden replacement of the previous population).

Equating the so-called steppe admixture with Indo-European languages is wrong. Period.

The following are excerpts from the article (emphasis is mine):

Dates and expansions

The average STR variance of DF27 and each subhaplogroup is presented in Suppl. Table 2. As expected, internal diversity was higher in the deeper, older branches of the phylogeny. If the same diversity was divided by population, the most salient finding is that native Basques (Table 2) have a lower diversity than other populations, which contrasts with the fact that DF27 is notably more frequent in Basques than elsewhere in Iberia (Suppl. Table 1). Diversity can also be measured as pairwise differences distributions (Fig. 5). The distribution of mean pairwise differences within Z195 sits practically on top of that of DF27; L176.2 and Z220 have similar distributions, as M167 and Z278 have as well; finally, M153 shows the lowest pairwise distribution values. This pattern is likely to reflect the respective ages of the haplogroups, which we have estimated by a modified, weighted version of the ρ statistic (see Methods).

Z195 seems to have appeared almost simultaneously within DF27, since its estimated age is actually older (4570 ± 140 ya). Of the two branches stemming from Z195, L176.2 seems to be slightly younger than Z220 (2960 ± 230 ya vs. 3320 ± 200 ya), although the confidence intervals slightly overlap. M167 is clearly younger, at 2600 ± 250 ya, a similar age to that of Z278 (2740 ± 270 ya). Finally, M153 is estimated to have appeared just 1930 ± 470 ya.

Haplogroup ages can also be estimated within each population, although they should be interpreted with caution (see Discussion). For the whole of DF27, (Table 3), the highest estimate was in Aragon (4530 ± 700 ya), and the lowest in France (3430 ± 520 ya); it was 3930 ± 310 ya in Basques. Z195 was apparently oldest in Catalonia (4580 ± 240 ya), and with France (3450 ± 269 ya) and the Basques (3260 ± 198 ya) having lower estimates. On the contrary, in the Z220 branch, the oldest estimates appear in North-Central Spain (3720 ± 313 ya for Z220, 3420 ± 349 ya for Z278). The Basques always produce lower estimates, even for M153, which is almost absent elsewhere.

R1b-DF27-tree
Simplified phylogenetic tree of the R1b-M269 haplogroup. SNPs in italics were not analyzed in this manuscript.

Demography

The median value for Tstart has been estimated at 103 generations (Table 4), with a 95% highest probability density (HPD) range of 50–287 generations; effective population size increased from 131 (95% HPD: 100–370) to 72,811 (95% HPD: 52,522–95,334). Considering patrilineal generation times of 30–35 years, our results indicate that R1b-DF27 started its expansion ~3,000–3,500 ya, shortly after its TMRCA.

As a reference, we applied the same analysis to the whole of R1b-S116, as well as to other common haplogroups such as G2a, I2, and J2a. Interestingly, all four haplogroups showed clear evidence of an expansion (p > 0.99 in all cases), all of them starting at the same time, ~50 generations ago (Table 4), and with similar estimated initial and final populations. Thus, these four haplogroups point to a common population expansion, even though I2 (TMRCA, weighted ρ, 7,800 ya) and J2a (TMRCA, 5,500 ya) are older than R1b-DF27. It is worth noting that the expansion of these haplogroups happened after the TMRCA of R1b-DF27.

R1b-DF27-PCA
Principal component analysis of STR haplotypes. (a) Colored by subhaplogroup, (b) colored by population. Larger squares represent subhaplogroup or population centroids.

Sum up and discussion

We have characterized the geographical distribution and phylogenetic structure of haplogroup R1b-DF27 in W. Europe, particularly in Iberia, where it reaches its highest frequencies (40–70%). The age of this haplogroup appears clear: with independent samples (our samples vs. the 1000 genome project dataset) and independent methods (variation in 15 STRs vs. whole Y-chromosome sequences), the age of R1b-DF27 is firmly grounded around 4000–4500 ya, which coincides with the population upheaval in W. Europe at the transition between the Neolithic and the Bronze Age. Before this period, R1b-M269 was rare in the ancient DNA record, and during it the current frequencies were rapidly reached. It is also one of the haplogroups (along with its daughter clades, R1b-U106 and R1b-S116) with a sequence structure that shows signs of a population explosion or burst. STR diversity in our dataset is much more compatible with population growth than with stationarity, as shown by the ABC results, but, contrary to other haplogroups such as the whole of R1b-S116, G2a, I2 or J2a, the start of this growth is closer to the TMRCA of the haplogroup. Although the median time for the start of the expansion is older in R1b-DF27 than in other haplogroups, and could suggest the action of a different demographic process, all HPD intervals broadly overlap, and thus, a common demographic history may have affected the whole of the Y chromosome diversity in Iberia. The HPD intervals encompass a broad timeframe, and could reflect the post-Neolithic population expansions from the Bronze Age to the Roman Empire.

While when R1b-DF27 appeared seems clear, where it originated may be more difficult to pinpoint. If we extrapolated directly from haplogroup frequencies, then R1b-DF27 would have originated in the Basque Country; however, for R1b-DF27 and most of its subhaplogroups, internal diversity measures and age estimates are lower in Basques than in any other population. Then, the high frequencies of R1b-DF27 among Basques could be better explained by drift rather than by a local origin (except for the case of M153; see below), which could also have decreased the internal diversity of R1b-DF27 among Basques. An origin of R1b-DF27 outside the Iberian Peninsula could also be contemplated, and could mirror the external origin of R1b-M269, even if it reaches there its highest frequencies. However, the search for an external origin would be limited to France and Great Britain; R1b-DF27 seems to be rare or absent elsewhere: Y-STR data are available only for France, and point to a lower diversity and more recent ages than in Iberia (Table 3). Unlike in Basques, drift in a traditionally closed population seems an unlikely explanation for this pattern, and therefore, it does not seem probable that R1b-DF27 originated in France. Then, a local origin in Iberia seems the most plausible hypothesis. Within Iberia, Aragon shows the highest diversity and age estimates for R1b-DF27, Z195, and the L176.2 branch, although, given the small sample size, any conclusion should be taken cautiously. On the contrary, Z220 and Z278 are estimated to be older in North Central Spain (N Castile, Cantabria and Asturias). Finally, M153 is almost restricted to the Basque Country: it is rarely present at frequencies >1% elsewhere in Spain (although see the cases of Alacant, Andalusia and Madrid, Suppl. Table 1), and it was found at higher frequencies (10–17%) in several Basque regions; a local origin seems plausible, but, given the scarcity of M153 chromosomes outside of the Basque Country, the diversity and age values cannot be compared.

Within its range, R1b-DF27 shows same geographical differentiation: Western Iberia (particularly, Asturias and Portugal), with low frequencies of R1b-Z195 derived chromosomes and relatively high values of R1b-DF27* (xZ195); North Central Spain is characterized by relatively high frequencies of the Z220 branch compared to the L176.2 branch; the latter is more abundant in Eastern Iberia. Taken together, these observations seem to match the East-West patterning that has occurred at least twice in the history of Iberia: i) in pre-Roman times, with Celtic-speaking peoples occupying the center and west of the Iberian Peninsula, while the non-Indoeuropean eponymous Iberians settled the Mediterranean coast and hinterland; and ii) in the Middle Ages, when Christian kingdoms in the North expanded gradually southwards and occupied territories held by Muslim fiefs.

DF27-iberia-france
Contour maps of the derived allele frequencies of the SNPs analyzed in this manuscript. Population abbreviations as in Table 1. Maps were drawn with SURFER v. 12 (Golden Software, Golden CO, USA).

I wouldn’t trust the absence of R1b-DF27 outside France as a proof that its origin must be in Western Europe – especially since we have ancient DNA, and that assertion might prove quite wrong – but aside from that the article seems solid in its analysis of modern populations.

Related:

Text and figures from the article, licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Indo-European Demic Diffusion – The expansion of Proto-Indo-Europeans potentially explained as the expansion of R1b subclades

I published an essay (or “dissertation”) some weeks ago, about what seems to me one of the most likely models of expansion of Indo-European-speaking peoples, based on Y-DNA haplogroups. Recently J.P. Mallory had proposed* (although he was not the first) that North-West Indo-European (the ancestor of Italo-Celtic and Germanic, and Balto-Slavic**) expanded with the Bell Beaker culture, a hypothesis that is supported by the most recent radiocarbon data (and subsequent proposal of an eastern origin of the pre-Bell Beaker culture, linked to the Yamna expansion, by Volker and Heyd). As I outline in the paper, ancient DNA samples and genetic data from modern populations seem to support this new model.

The still most prevalent model followed by archaeologists, based on Gimbutas’ theory, links the Corded Ware culture expansion to an expansion of the Yamna culture. Gimbutas linked the expansion of Bell Beaker to the expansion of certain Indo-European dialects through Vucedol, and Corded Ware was associated with the expansion of Germano-Balto-Slavic. Even though linguistics has changed its mainstream view of the dialectalization of Late Indo-European in the past half century, the archaeological community (those who supported the steppe expansion, at least) has remained strongly linked to Gimbutas, and more recently David Anthony has supported a similar model (with a phylogenetic model of Proto-Indo-European dialects by Don Ringe), by explaining a dual expansion into Corded Ware by Pre-Germanic (through a mixed Old European / IE Usatovo culture) and Pre-Balto-Slavic (through the Middle Dnieper culture), while eastern Bell Beakers expanded with Italo-Celtic dialects. While a strong cultural connection between Yamna and Corded Ware is currently undeniable, and admixture analyses show a connection between steppe and both Bell Beaker and Corded Ware samples, the actual relationship is today far less clear than it was 10 years ago (when we would simply connect Yamna with a R1a-dominated Corded Ware), and far more ancient samples from the steppe, steppe-forest, and forest zone are needed to extract any strong conclusions.

During this time I have received some comments on the paper, and have discovered some interesting sources for more information, like BioRxiv (for the newest pre-print papers on Genetics), and Academia.edu (for papers on Archaeology), both of which I can’t hardly recommend enough for anyone interested in these topics. From what I have experienced, Linguistics – which seemed to me a quite closed, strongly conservative community, due to my proposal of speaking a reconstructed Proto-Indo-European dialect as a common language today – has been more open with my model than some archaeological/genetic tandems, and linguists have shown a clearer grasp of all anthropological disciplines involved in Indo-European studies than others… My model remains a theory that I expect to develop further with more details and more genetic data, as they are published.

There are some interesting upcoming samples (mainly from Bell Beaker) by the Reich Lab – and today its publication seems nearer. While the interpretation seems to be in line with what has been said in previous similar publications, the most interesting data will most likely be the actual samples, apparently already showing a lack of steppe ancestry in Iberian Bell Beaker, and a clear invasion of Bell Beaker peoples (hence R1b?) in Great Britain. Hopefully some new samples of Yamna and Corded Ware might give us interesting information.

It is always to be remembered that, when talking about Indo-European peoples, what matters is linguistics: after, all, the peoples whose place and time we want to find are defined by their language, Indo-European. Archaeology might be able to date some cultural developments potentially linked with Indo-European-speaking peoples, and genetics might give support to the expansion of peoples (and thus maybe languages) accompanying such cultural expansions. Recent genetic developments are quite interesting, in that we might be able to place Late Indo-European and North-West Indo-European speakers in place and time, but it seems to me that some people are trying to answer the Urheimat problem the other way around.

* J.P. Mallory, ‘The Indo-Europeanization of Atlantic Europe’, in Celtic From the West 2: Rethinking the Bronze Age and the Arrival of Indo-European in Atlantic Europe, eds J. T. Koch and B. Cunliffe (Oxford, 2013), p.17-40

** It has been proposed that Balto-Slavic derived partially from North-West Indo-European, and partially from a different Late Indo-European language, although there are different models to explain the pidginization of this dialect