Bayesian estimation of partial population continuity by using ancient DNA and spatially explicit simulations

europe-palaeolithic-neolithic

Open access Bayesian estimation of partial population continuity by using ancient DNA and spatially explicit simulations, by Silva et al., Evolutionary Applications (2018).

Abstract (emphasis mine):

The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here we extended this approach to estimate the proportion of genetic continuity between two populations, by using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter‐gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter‐gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre‐Neolithic hunter‐gatherers. It provides a useful tool for the analysis of the numerous aDNA datasets that are currently being produced for many different species.

central-european-neolithic
A) Different zones defined for computing proportions of ancestry in Central Europeans 4,500 BP. B) Schematic representation of various population contributions. C) Mean proportions of ancestry from the various PHG zones (A+B+C+D) in Central European populations from zone A at the end of the Neolithic transition 4,500 BP, computed for autosomal and mitochondrial markers.

Relevant excerpts:

Our results are in general accordance with two distinct ancestry components that have previously been detected at the continental scale by Lazaridis, Patterson et al. (2014): the “early European farmer” (EEF), which corresponds here to the NFA from Anatolia (zone C in Figure 3), and the “West European hunter-gatherer” (WHG), which corresponds here to the PHG from zones A and B in Figure 3. Notably, the contribution of an Ancient North Eurasians (ANE) component is not included in our model as we did not consider potential post-Neolithic immigration waves, which could have contributed to the modern European genetic pool, such as the wave that came from the Pontic steppes and was associated with the Yamnaya culture (Haak, Lazaridis et al. 2015). Without considering the ANE ancestry component, our estimate of the autosomal genetic contribution of Early farmers to the gene pool of Central European populations (25%) tends to be lower than the EEF ancestry estimated in most modern Western European populations, but is of the same order than the estimations in modern Estonians and in the ancient Late Neolithic genome “Karsdorf” from Germany (Lazaridis, Patterson et al. 2014, Haak, Lazaridis et al. 2015). Note that the contribution of hunter-gatherers to Neolithic communities appears to be variable in different regions of Europe (Skoglund, Malmstrom et al. 2012, Brandt, Haak et al. 2013, Lazaridis, Patterson et al. 2014), while we computed an average value for Central Europe. Moreover, we computed the ancestry of the two groups at the end of the Neolithic period while previous studies estimated it in modern times. Finally, previous studies used molecular information to directly estimate admixture proportions, while we use molecular information to estimate the model parameters and, then, we computed the expected genetic contributions of both groups using the best parameters, without using molecular information during this second step. Model assumptions may thus influence the inferences on the relative genetic contribution of both groups. In particular, we made the assumption of a uniform expansion of NFA with constant and similar assimilation of PHG over the whole continent but spatio-temporally heterogeneous environment, variable assimilation rate and long distance dispersal may have played an important role. The effects of those factors should be investigated in future studies.

Indo-Europeans and Finno-Ugric peoples might have shared the love for weed

paleobotany-cultures

Funny and interesting read to help relax the trolling wave caused by the first early Hittite samples:

Cannabis is indigenous to Europe and cultivation began during the Copper or Bronze age: a probabilistic synthesis of fossil pollen studies, by McPartland, Guy, & Hegman, Vegetation History and Archaeobotany (2018).

Abstract (emphasis mine):

Conventional wisdom states Cannabis sativa originated in Asia and its dispersal to Europe depended upon human transport. Various Neolithic or Bronze age groups have been named as pioneer cultivators. These theses were tested by examining fossil pollen studies (FPSs), obtained from the European Pollen Database. Many FPSs report Cannabis or Humulus (C/H) with collective names (e.g. Cannabis/Humulus or Cannabaceae). To dissect these aggregate data, we used ecological proxies to differentiate C/H pollen, as follows: unknown C/H pollen that appeared in a pollen assemblage suggestive of steppe (Poaceae, Artemisia, Chenopodiaceae) we interpreted as wild-type Cannabis. C/H pollen in a mesophytic forest assemblage (Alnus, Salix, Populus) we interpreted as Humulus. C/H pollen curves that upsurged and appeared de novo alongside crop pollen grains we interpreted as cultivated hemp. FPSs were mapped and compared to the territories of archaeological cultures. We analysed 479 FPSs from the Holocene/Late Glacial, plus 36 FPSs from older strata. The results showed C/H pollen consistent with wild-type C. sativa in steppe and dry tundra landscapes throughout Europe during the early Holocene, Late Glacial, and previous glaciations. During the warm and wet Holocene Climactic Optimum, forests replaced steppe, and Humulus dominated. Cannabis retreated to steppe refugia. C/H pollen consistent with cultivated hemp first appeared in the Pontic-Caspian steppe refugium. GIS mapping linked cultivation with the Copper age Varna/Gumelniţa culture, and the Bronze age Yamnaya and Terramara cultures. An Iron age steppe culture, the Scythians, likely introduced hemp cultivation to Celtic and Proto-Slavic cultures.

Interesting excerpts (modified to make them more readable):

C. sativa during the Copper age

We compared the territories of Copper age cultures with locations of C–H pollen consistent with Cannabis in Fig. 5. This suggests that two Copper age cultures had the potential to domesticate wild-type C. sativa: the Greek Chalcolithic, and the Cucuteni-Tripolye culture. C–H pollen consistent with cultivated Cannabis occurred at one site in Bulgaria. This site may correspond to the Varna culture or Gumelniţa culture. However, pollen at five other Varna and Gumelniţa sites was interpreted as Humulus, or undetermined C/H. Archaeological studies of Gumelniţa and Cucuteni-Tripolye sites have found C. sativa seeds and less-robust evidence—pottery seed impressions (Clarke and Merlin 2013; Long et al. 2017; McPartland and Hegman 2017).

paleobotany-cannabis-europe
Cannabis distribution ca. 4,500–2,300 cal BP.

C. sativa during the Bronze age

Eight Bronze age cultures had potential: C–H pollen consistent with wild-type Cannabis in Fig. 6 appeared within the boundaries of several Bronze age cultures. These include the Netted Ware culture, Ezero culture, Yamnaya culture, Corded Ware culture, Bell-Beaker culture, Terramara culture, Aegean Bronze age, and Mycenaean Greece. C–H pollen interpreted as cultivated C. sativa appeared in four studies: One study in Yamnaya territory agrees with archaeological studies, which have recovered C. sativa seeds or pottery seed impressions (Clarke and Merlin 2013; Long et al. 2017; McPartland and Hegman 2017). Two study sites are associated with the Terramara culture. However, pollen in 11 other studies at Terramara sites suggested Humulus or indeterminate C/H pollen. One FPS in France was likely contaminated by taphonomic processes, as admitted by its authors.

Scythian contacts with Celts and Balto-Slavs

The Scythians impacted deeply on the Celts, in the realms of art, animal husbandry, military strategy, language, and even clothing. The oldest evidence of Scythian–Celtic interactions that we could find was a 7th century bce burial in Bulgaria, which combined elements of Scythian culture along with a Hallstatt vessel (Braund 2015). Scythian artifacts in Hallstatt-occupied Hungary first appear around 550 bce (Bartosiewicz and Gál 2010). A Hallstatt burial at Vix in France from 525 bce contains items and motifs inspired by Scythian culture (Megaw 1966). These data collectively suggest a conservative date of 550 bce as the terminus post quem for Scythian contact with the Celts. Only three sites in Celtic territory showed pollen signals consistent with hemp cultivation prior to 550 bce. To wit, the oldest ones had problems with dating. In contrast, 28 FPSs in Celtic territory showed pollen signals of hemp cultivation arising post-550 bce, after their contact with the Scythians.

The Scythians also impacted Proto-Slavic cultures. The Scythians left a trail of burned-out settlements built by the Proto-Slavic Lusatian culture around 600 bce (Bukowski 1977). A horde of Scythian artifacts found at Witaszkowo in Lusatia dates to 550 bce (Furtwängler 1883). Only two pre-550 bce sites in Slavic/Baltic territory showed signals consistent with hemp cultivation, and they occurred in the southeast, towards the Scythian homeland. Ralska-Jasiewiczowa and van Geel (1998) linked the appearance of Cannabis pollen in Poland with Scythian incursions. The Scythians appear to be responsible for the spread of Cannabis amongst several Iron age European cultures.

There you have it, the long-sought Yamna – Corded Ware cultural connection. Finno-Ugric peoples liked it wild, though 😉

Brexit forces relocation of one of today’s main Yamna research projects to Finland

yamnaya_distribution

Archaeologist Volker Heyd is bringing his ERC Advanced Grant to Helsinki. So has proudly reported the University of Helskinki.

Some interesting excerpts (emphasis mine):

With his research group, Heyd wants to map out how the Yamnaya culture, also known as the Pit Grave culture, migrated from the Eurasian steppes to prehistoric south-eastern Europe approximately 3,000 years BCE. Most of the burial mounds typical of the Yamnaya culture have already been destroyed, but new techniques enable their identification and study.

The project is using multidisciplinary methods to solve the mystery. Archaeologists are collaborating with scholars of biological and environmental sciences, using the methods of funerary archaeology, landscape archaeology and remote sensing that are at the group’s disposal. From the field of biological sciences, the group is making use of genetics/DNA analysis, biological anthropology and biogeochemistry. As for environmental sciences, their contribution is in the form of palaeoclimatology, which studies climate before modern meteorological observations, and soil formation processes.

The project, coordinated by the discipline of archaeology at the University of Helsinki, will also welcome researchers from Mainz, London, Bristol and Budapest, in addition to which the group will collaborate with Czech, Slovak and Polish colleagues. Field studies and sample collection for the project will be conducted in Romania, Bulgaria, Hungary and Serbia.

In Helsinki, Volker Heyd’s main collaborator is Professor Heikki Seppä from the Department of Geosciences and Geography on the Kumpula Campus, while the team will also be hiring three postdoctoral researchers.

yamna-bell-beaker
Yamna – East Bell Beaker migration 3000-2300 BC, after Heyd (2007, 2012)

Yam­naya from the east changed Europe forever

The researchers wish to understand how the Yamnaya migrated to Europe and how the arrival of a new culture changed an entire continent.

How many people actually arrived? Taking the scale of the changes, some estimates range in the millions, but according to Volker Heyd, the number of people representing the Yamnaya culture in southeast Europe was around several ten thousands. It is indeed remarkable how such a relatively small group of people has had such a significant and far-reaching impact on Europe.

The Yamnaya also brought with them new cultural and social norms that have had far-reaching consequences. For instance, patriarchy and monogamy seems to be part of the Yamnaya legacy. Another established theory speculates that marriages made women migrate and travel even across great distances.

In accordance with primogeniture, the first-born son of the family inherited his parents’ possessions, while the younger siblings had to make their own way through other means. Among other things, this practice guaranteed ample human resources for the legions of the Roman Empire, which enabled its establishment and expansion, and later filled the ranks of medieval monasteries across Europe.

Another interesting question is what made representatives of the Yamnaya culture migrate from the eastern European steppes to the west. Heyd believes that the underlying reason may have been climate change. The Yamnaya were almost exclusively dependent on animal husbandry. As the climate changed – when rainfalls decreased in the east – they may have been forced to migrate west to secure the welfare of their cattle.

North-East Europe and Corded Ware

Heyd has already been here as a visiting professor in the Helsinki University Humanities programme since the beginning of the year, working on another project. Together with Postdoctoral Researcher Kerkko Nordqvist, he is investigating the prehistoric settlement of north-eastern Europe 3,000 – 6,000 years ago with research methods similar to the new Yamnaya project. One of their central research questions is what made people migrate to this region, and which innovations they brought with them. In this case also, the reasons behind the migration may be related to changes in the environment and climate.

This is probably bad news for research in the UK (I say probably because I guess many Brexiteers will be happy to have less foreign researchers in their country), but it is great news to see both researchers, Heyd and Nordqvist (whose Ph.D. thesis includes research on the Corded Ware culture that I have recently mentioned) – , be able to collaborate together to assess Indo-European and Uralic migrations.

Heyd’s website at the University of Bristol states that he is currently working on:

  1. The Milking Revolution in Temperate Neolithic Europe (NeoMilk)‘. Funded by an ERC Advanced Grant, European Union, to R. Evershed. See, for further information: www.neomilk-erc.eu
  2. The Yamnaya Impact‘: Archaeology and scientific research of/into the Yamnaya populations of Southeastern Europe and their impact on contemporary local and neighboring 3rd millennium BC societies as well as their role in the emergence of the Corded Ware and Bell Beaker complexes in Europe.
  3. The Prehistoric Peopling of Northeastern Europe‘: Inter-/crossdisciplinary studies on the archaeology, anthropology, linguistics, and bio- and environmental sciences of early Uralic speakers and their first horizon of interactions with Indo-European speakers. This wider project is in cooperation with colleagues from Helsinki and Turku Universities in Finland, as well as from Russia, Estonia and Poland.
  4. Czech Republic‘: I am closely cooperating with the Institute of Archaeology, Czech Academy of Sciences, in Prague for two research projects funded by the Czech Grant Agency in which we measure various isotopes from human remains in Bristol to understand past mobility and diet. The Humboldt-Kolleg -conference ‘Reinecke’s Heritage’ (with P. Pavúk, M. Ernée and J. Peska) held in June 2017 at Chateau Křtiny/Moravia is also part of this cooperation. See, for further information: http://ukar.ff.cuni.cz/reinecke.
yamna-late-proto-indo-european
Image modified from Narasimhan et al. (2018), including the most likely proto-language identification of different groups. Original description “Modeling results including Admixture events, with clines or 2-way mixtures shown in rectangles, and clouds or 3-way mixtures shown in ellipses”. See the original full image here.

On the genetic aspect, we have gross Yamna migrations today as clearly depicted as they will ever be: late Khvalynsk/Yamna expanded Late Proto-Indo-European languages, and Bell Beakers brought North-West Indo-European to almost all of Europe, as predicted in Harrison and Heyd (2007). Full stop.

There is still fine-grained population structure, though, as Lazaridis puts it, to be detected in migratory movements contemporary or subsequent to the Yamna settlements in South-East Europe and the East Bell Beaker expansion.

We will probably lack a comprehensive description of local archaeological cultural exchanges – to fit the potential dialectal developments and expansions – to be coupled with small-scale migratory movements in genetics, as more samples are made available.

This work from the University of Helsinki will hopefully provide the necessary detailed anthropological foundations to be used with future genetic studies to obtain a more precise picture of the formation and expansion of North-West Indo-Europeans.

Related:

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.

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