Palaeolithic Caucasus samples reveal the most important component of West Eurasians

dzudzuana-ancestry-europe

Preprint Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, by Lazaridis et al. bioRxiv (2018).

Interesting excerpts:

We analyzed teeth from two individuals 63 recovered from Dzudzuana Cave, Southern Caucasus, from an archaeological layer previously dated to ~27-24kya (…). Both individuals had mitochondrial DNA sequences (U6 and N) that are consistent with deriving from lineages that are rare in the Caucasus or Europe today. The two individuals were genetically similar to each other, consistent with belonging to the same population and we thus analyze them jointly.

(…) our results prove that the European affinity of Neolithic Anatolians does not necessarily reflect any admixture into the Near East from Europe, as an Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya. Furthermore, Dzudzuana shares more alleles with Villabruna-cluster groups than with other ESHG (Extended Data Fig. 5b), suggesting that this European affinity was specifically related to the Villabruna cluster, and indicating that the Villabruna affinity of PGNE populations from Anatolia and the Levant is not the result of a migration into the Near East from Europe. Rather, ancestry deeply related to the Villabruna cluster was present not only in Gravettian and Magdalenian-era Europeans but also in the populations of the Caucasus, by ~26kya. Neolithic Anatolians, while forming a clade with Dzudzuana with respect to ESHG, share more alleles with all other PGNE (Extended Data Fig. 5d), suggesting that PGNE share at least partially common descent to the exclusion of the much older samples from Dzudzuana.

dzudzuana-anatolia-pca
Ancient West Eurasian population structure. PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).

Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed, but instead of specifying gene flow from the ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt is also consistent with being descended from the source of this gene flow, and appears to have no admixture from the Levantine Neolithic (Supplementary Information 166 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features and artifacts from North Africa into the Near East. Such a scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians 170 and Levantine farmers, a common link between the Levant and Africa.

(…) we cannot reject the hypothesis that Dzudzuana and the much later Neolithic Anatolians form a clade with respect to ESHG (P=0.286), consistent with the latter being a population largely descended from Dzudzuana-like pre-Neolithic populations whose geographical extent spanned both Anatolia and the Caucasus. Dzudzuana itself can be modeled as a 2-way mixture of Villabruna-related ancestry and a Basal Eurasian lineage.

In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.7±11.3% and Magdalenian ElMiron: 60.6±11.3%) and to populations of the Caucasus (Dzudzuana: 199 72.5±3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe, descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3 from Russia for the Gravettians and GoyetQ116-1 from Belgium for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe, while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE cline of ancestry [See PCA above]. In the Near East, the Dzudzuana-related population admixed with North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiated populations at the dawn of the Neolithic were primarily descended from Villabruna Cluster and Dzudzuana-related ancestors, with varying degrees of additional input related to both North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by future sampling of geographically and temporally intermediate populations.

qpgraph-dzudzuana
An admixture graph model of Paleolithic West Eurasians. An automatically generated admixture graph models fits populations (worst Z-score of the difference between estimated and fitted f-statistics is 2.7) or populations (also including South_Africa_HG, worst Z-score is 3.5). This is a simplified model assuming binary admixture events and is not a unique solution (Supplementary Information section 2). Sampled populations are shown with ovals and select labeled internal nodes with rectangles.

Interesting excerpts from the supplementary materials:

From our analysis of Supplementary Information section 3, we showed that these sources are indeed complex, and only one of these (WHG, represented by Villabruna) appears to be a contributor to all the remaining sources. This should not be understood as showing that hunter-gatherers from mainland Europe migrated to the rest of West Eurasia, but rather that the fairly homogeneous post-15kya population of mainland Europe labeled WHG appear to represent a deep strain of ancestry that seems to have contributed to West Eurasians from the Gravettian era down to the Neolithic period.

Villabruna is representative of the WHG group. We also include ElMiron, the best sample from the Magdalenian era as we noticed that within the WHG group there were individuals that could not be modeled as a simple clade with Villabruna but also had some ElMiron-related ancestry. Ddudzuana is representative of the Ice Age Caucasus population, differentiated from Villabruna by Basal Eurasian ancestry. AG3 represents ANE/Upper Paleolithic Siberian ancestry, sampled from the vicinity of Lake Baikal, while Russia_Baikal_EN related to eastern Eurasians and represents a later layer of ancestry from the same region of Siberia as AG3 Finally, Mbuti are a deeply diverged African population that is used here to represent deep strains of ancestry (including Basal Eurasian) prior to the differentiation between West Eurasians and eastern non-Africans that are otherwise not accounted for by the remaining five sources. Collectively, we refer to this as ‘Basal’ or ‘Deep’ ancestry, which should be understood as referring potentially to both Basal Eurasian and African ancestry.

It has been suggested that there is an Anatolia Neolithic-related affinity in hunter-gatherers from the Iron Gates. Our analysis confirms this by showing that this population has Dzudzuana-related ancestry as do many hunter-gatherer populations from southeastern Europe, eastern Europe and Scandinavia. These populations cannot be modeled as a simple mixture of Villabruna and AG3 but require extra Dzudzuana-related ancestry even in the conservative estimates, with a positive admixture proportion inferred for several more in the speculative ones. Thus, the distinction between European hunter-gatherers and Near Eastern populations may have been gradual in pre-Neolithic times; samples from the Aegean (intermediate between those from the Balkans and Anatolia) may reveal how gradual the transition between Dzudzuana-like Neolithic Anatolians and mostly Villabruna-like hunter-gatherers was in southeastern Europe.

ancient-modern-european-admixture
Modified image (cut, with important samples marked). Modeling present-day and ancient West-Eurasians. Mixture proportions computed with qpAdm (Supplementary Information section 4). The proportion of ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the 365 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (a) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown.

Villabruna: This type of ancestry differentiates between present-day Europeans and non-Europeans within West Eurasia, attaining a maximum of ~20% in the Baltic in accordance with previous observations and with the finding of a later persistence of significant hunter-gatherer ancestry in the region. Its proportion drops to ~0% throughout the Near East. Interestingly, a hint of such ancestry is also inferred in all North African populations west of Libya in the speculative proportions, consistent with an archaeogenetic inference of gene flow from Iberia to North Africa during the Late Neolithic.

ElMiron: This type of ancestry is absent in present-day West Eurasians. This may be because most of the Villabruna-related ancestry in Europeans traces to WHG populations that lacked it (since ElMiron-related ancestry is quite variable within European hunter-gatherers). However, ElMiron ancestry makes up only a minority component of all WHG populations sampled to date and WHG-related ancestry is a minority component of present-day Europeans. Thus, our failure to detect it in present day people may be simply be too little of it to detect with our methods.

Dzudzuana: Our analysis identifies Dzudzuana-related ancestry as the most important component of West Eurasians and the one that is found across West Eurasian-North African populations at ~46-88% levels. Thus, Dzudzuana-related ancestry can be viewed as the common core of the ancestry of West Eurasian-North African populations. Its distribution reaches its minima in northern Europe and appears to be complementary to that of Villabruna, being most strongly represented in North Africa, the Near East (including the Caucasus) and Mediterranean Europe. Our results here are expected from those of Supplementary Information section 3 in which we modeled ancient Near Eastern/North African populations (the principal ancestors of present-day people from the same regions) as deriving much of their ancestry from a Dzudzuana-related source. Migrations from the Near East/Caucasus associated with the spread of the Neolithic, but also the formation of steppe population introduced most of the Dzudzuana-related ancestry present in Europe, although (as we have seen above) some such ancestry was already present in some pre-agricultural hunter-gatherers in Europe.

AG3: Ancestry related to the AG3 sample from Siberia has a northern distribution, being strongly represented in both central-northern Europe and the north Caucasus.

Russia_Baikal_EN: Ancestry related to hunter-gatherers from Lake Baikal in Siberia (postdating AG3) appears to have affected primarily northeastern European populations which have been previously identified as having East Eurasian ancestry; some such ancestry is also identified for a Turkish population from Balıkesir, likely reflecting the Central Asian ancestry of Turkic speakers which has been recently confirmed directly in an Ottoman sample from Anatolia.

So, here we have the explanation for the “bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East” inferred from Anatolian hunter-gatherers.

Related

Modern Sardinians show elevated Neolithic farmer ancestry shared with Basques

sardinia-europe-relation

New paper (behind paywall), Genomic history of the Sardinian population, by Chiang et al. Nature Genetics (2018), previously published as a preprint at bioRxiv (2016).

#EDIT (18 Sep 2018): Link to read paper for free shared by the main author.

Interesting excerpts (emphasis mine):

Our analysis of divergence times suggests the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations ~140–250 generations ago, corresponding to ~4,300–7,000 years ago assuming a generation time of 30 years and a mutation rate of 1.25 × 10−8 per basepair per generation. (…) in terms of relative values, the divergence time between Northern and Southern Europeans is much more recent than either is to Sardinia, signaling the relative isolation of Sardinia from mainland Europe.

We documented fine-scale variation in the ancient population ancestry proportions across the island. The most remote and interior areas of Sardinia—the Gennargentu massif covering the central and eastern regions, including the present-day province of Ogliastra— are thought to have been the least exposed to contact with outside populations. We found that pre-Neolithic hunter-gatherer and Neolithic farmer ancestries are enriched in this region of isolation. Under the premise that Ogliastra has been more buffered from recent immigration to the island, one interpretation of the result is that the early populations of Sardinia were an admixture of the two ancestries, rather than the pre-Neolithic ancestry arriving via later migrations from the mainland. Such admixture could have occurred principally on the island or on the mainland before the hypothesized Neolithic era influx to the island. Under the alternative premise that Ogliastra is simply a highly isolated region that has differentiated within Sardinia due to genetic drift, the result would be interpreted as genetic drift leading to a structured pattern of pre-Neolithic ancestry across the island, in an overall background of high Neolithic ancestry.

sardinia-pca
PCA results of merged Sardinian whole-genome sequences and the HGDP Sardinians. See below for a map of the corresponding regions.

We found Sardinians show a signal of shared ancestry with the Basque in terms of the outgroup f3 shared-drift statistics. This is consistent with long-held arguments of a connection between the two populations, including claims of Basque-like, non-Indo-European words among Sardinian placenames. More recently, the Basque have been shown to be enriched for Neolithic farmer ancestry and Indo-European languages have been associated with steppe population expansions in the post-Neolithic Bronze Age. These results support a model in which Sardinians and the Basque may both retain a legacy of pre-Indo-European Neolithic ancestry. To be cautious, while it seems unlikely, we cannot exclude that the genetic similarity between the Basque and Sardinians is due to an unsampled pre-Neolithic population that has affinities with the Neolithic representatives analyzed here.

density-nuraghi-sardinia-genetics
Left: Geographical map of Sardinia. The provincial boundaries are given as black lines. The provinces are abbreviated as Cag (Cagliari), Cmp (Campidano), Car (Carbonia), Ori (Oristano), Sas (Sassari), Olb (Olbia-tempio), Nuo (Nuoro), and Ogl (Ogliastra). For sampled villages within Ogliastra, the names and abbreviations are indicated in the colored boxes. The color corresponds to the color used in the PCA plot (Fig. 2a). The Gennargentu region referred to in the main text is the mountainous area shown in brown that is centered in western Ogliastra and southeastern Nuoro.
Right: Density of Nuraghi in Sardinia, from Wikipedia.

While we can confirm that Sardinians principally have Neolithic ancestry on the autosomes, the high frequency of two Y-chromosome haplogroups (I2a1a1 at ~39% and R1b1a2 at ~18%) that are not typically affiliated with Neolithic ancestry is one challenge to this model. Whether these haplogroups rose in frequency due to extensive genetic drift and/or reflect sex-biased demographic processes has been an open question. Our analysis of X chromosome versus autosome diversity suggests a smaller effective size for males, which can arise due to multiple processes, including polygyny, patrilineal inheritance rules, or transmission of reproductive success. We also find that the genetic ancestry enriched in Sardinia is more prevalent on the X chromosome than the autosome, suggesting that male lineages may more rapidly trace back to the mainland. Considering that the R1b1a2 haplogroup may be associated with post-Neolithic steppe ancestry expansions in Europe, and the recent timeframe when the R1b1a2 lineages expanded in Sardinia, the patterns raise the possibility of recent male-biased steppe ancestry migration to Sardinia, as has been reported among mainland Europeans at large (though see Lazaridis and Reich and Goldberg et al.). Such a recent influx is difficult to square with the overall divergence of Sardinian populations observed here.

sardinian-admixture
Mixture proportions of the three-component ancestries among Sardinian populations. Using a method first presented in Haak et al. (Nature 522, 207–211, 2015), we computed unbiased estimates of mixture proportions without a parameterized model of relationships between the test populations and the outgroup populations based on f4 statistics. The three-component ancestries were represented by early Neolithic individuals from the LBK culture (LBK_EN), pre-Neolithic huntergatherers (Loschbour), and Bronze Age steppe pastoralists (Yamnaya). See Supplementary Table 5 for standard error estimates computed using a block jackknife.

Once again, haplogroup R1b1a2 (M269), and only R1b1a2, related to male-biased, steppe-related Indo-European migrations…just sayin’.

Interestingly, haplogroup I2a1a1 is actually found among northern Iberians during the Neolithic and Chalcolithic, and is therefore associated with Neolithic ancestry in Iberia, too, and consequently – unless there is a big surprise hidden somewhere – with the ancestry found today among Basques.

NOTE. In fact, the increase in Neolithic ancestry found in south-west Ireland with expanding Bell Beakers (likely Proto-Beakers), coupled with the finding of I2a subclades in Megalithic cultures of western Europe, would support this replacement after the Cardial and Epi-Cardial expansions, which were initially associated with G2a lineages.

I am not convinced about a survival of Palaeo-Sardo after the Bell Beaker expansion, though, since there is no clear-cut cultural divide (and posterior continuity) of pre-Beaker archaeological cultures after the arrival of Bell Beakers in the island that could be identified with the survival of Neolithic languages.

We may have to wait for ancient DNA to show a potential expansion of Neolithic ancestry from the west, maybe associated with the emergence of the Nuragic civilization (potentially linked with contemporaneous Megalithic cultures in Corsica and in the Balearic Islands, and thus with an Iberian rather than a Basque stock), although this is quite speculative at this moment in linguistic, archaeological, and genetic terms.

Nevertheless, it seems that the association of a Basque-Iberian language with the Neolithic expansion from Anatolia (see Villar’s latest book on the subject) is somehow strengthened by this paper. However, it is unclear when, how, and where expanding G2a subclades were replaced by native I2 lineages.

Related

A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP

indo-european-indo-iranian-migrations

New open access paper (in Chinese) A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP, by liu et al. Acta Anthropologica Sinitica (2018)

Abstract:

The Keriyan, Lopnur and Dolan peoples are isolated populations with sparse numbers living in the western border desert of our country. By sequencing and typing the complete Y-chromosome of 179 individuals in these three isolated populations, all mutations and SNPs in the Y-chromosome and their corresponding haplotypes were obtained. Types and frequencies of each haplotype were analyzed to investigate genetic diversity and genetic structure in the three isolated populations. The results showed that 12 haplogroups were detected in the Keriyan with high frequencies of the J2a1b1 (25.64%), R1a1a1b2a (20.51%), R2a (17.95%) and R1a1a1b2a2 (15.38%) groups. Sixteen haplogroups were noted in the Lopnur with the following frequencies: J2a1 (43.75%), J2a2 (14.06%), R2 (9.38%) and L1c (7.81%). Forty haplogroups were found in the Dolan, noting the following frequencies: R1b1a1a1 (9.21%), R1a1a1b2a1a (7.89%), R1a1a1b2a2b (6.58%) and C3c1 (6.58%). These data show that these three isolated populations have a closer genetic relationship with the Uygur, Mongolian and Sala peoples. In particular, there are no significant differences in haplotype and frequency between the three isolated populations and Uygur (f=0.833, p=0.367). In addition, the genetic haplotypes and frequencies in the three isolated populations showed marked Eurasian mixing illustrating typical characteristics of Central Asian populations.

population-distribution-map
Figure 1. The populations distribution map. Left: Uluru. Center: Dali Yabuyi. Right: Kaerqu.

My knowledge of written Chinese is almost zero, so here are some excerpts with the help of Google Translate:

The source of 179 blood samples used in the study is shown in Figure 1. The Keriyan blood samples were collected from Dali Yabuyi Township, Yutian County (39 samples). The blood samples of the Lopnur people were collected from Kaerqu Township, Yuli County (64 cases); the blood samples of the Dolan people were collected from the town of Uluru, Awati County (76).

haplotype-frequency-uighur
Columns one and two are the Keriyan haplotypes and frequencies, respectively; the third and fourth columns are the Lopnur haplotypes and frequencies; the last four columns are the Daolang haplotypes and frequencies.

The composition and frequency of the Keriyan people’s haplogroup are closest to those of the Uighurs, and both Principal Component Analysis and Phylogenetic Tree Analysis show that their kinship is recent. We initially infer that the Keriyan are local desert indigenous people. They have a connection with the source of the Uighurs. Chen et al. [42] studied the patriarchal and maternal genetic analysis of the Keriyan people and found that they are not descendants of the Tibetan ethnic group in the West. The Keriyan people are a mixed group of Eastern and Western Europeans, which may originate from the local Vil group. Duan Ranhui [43] and other studies have shown that the nucleotide variability and average nucleotide differences in the Keriyan population are between the reported Eastern and Western populations. The phylogenetic tree also shows that the populations in Central Asia are between the continental lineage of the eastern population and the European lineage of the western population, and the genetic distance between the Keriyan and the Uighurs is the closest, indicating that they have a close relationship.

y-chromosome-pca

Regarding the origin of the Lopnur people, Purzhevski judged that it was a mixture of Mongolians and Aryans according to the physical characteristics of the Lopnur people. In 1934, the Sino-Swiss delegation discovered the famous burials of the ancient tombs in the Peacock River. After research, they were the indigenous people before the Loulan period; the researcher Yang Lan, a researcher at the Institute of Cultural Relics of the Chinese Academy of Social Sciences, said that the Lopnur people were descendants of the ancient “Landan survivors”. However, the Loulan people speaking an Indo-European language, and the Lopnur people speaking Uyghur languages contradict this; the historical materials of the Western Regions, “The Geography of the Western Regions” and “The Western Regions of the Ming Dynasty” record the Uighurs who lived in Cao Cao in the late 17th and early 18th centuries. Because of the occupation of the land by the Junggar nobles and their oppression, they fled. Some of them were forced to move to the Lop Nur area. There are many similar archaeological discoveries and historical records. We have no way to determine their accuracy, but they are at different times, and there is a great difference in what is heard in the same region. (…) The genetic characteristics of modern Lopnur people are the result of the long-term ethnic integration of Uyghurs, Mongols, and Europeans. This is also consistent with the similarity of the genetic structure of the Y chromosome of Lopnur in this study with the Uighurs and Mongolians. For example, the frequency of J haplogroup is as high as 59.37%, while J and its downstream sub-haplogroup are mainly distributed in western Europe, West Asia and Central Asia; the frequency of O, R haplogroup is close to that of Mongolians.

y-chromosome-frequency
1) KA: Keriya, LB: Rob, DL: Daolang, HTW: Hetian Uygur, HTWZ: and Uygur, TLFW: Turpan Uighur, HZ: Hui, HSKZ: Kazakh, WZBKZ: Wuhuan Others, TJKZ: Tajik, KEKZZ: Kirgiz, TTEZ: Tatar, ELSZ: Russian XBZ: Xibo, MGZ: Mongolian, SLZ: Salar, XJH: Xinjiang Han, GSH: Gansu Han, GDH: Guangdong Han SCH: Sichuan Han. 2) Reference population data source literature 19-22. After the population names in the table have been marked, all the shorthands in the text are referred to in this table. 3) Because the degree of haplotypes of each reference population is different to each sub-group branch, the sub-group branches under the same haplogroup are merged when the population haplogroup data is aggregated, for example: for haplogroup G Some people are divided into G1a and G2a levels, others are assigned to G1, G2, and G3, while some people can only determine G this time. Therefore, each subgroup is merged into a single group G.

According to Ming History·Western Biography, the Mongolians originated from the Mobei Plateau and later ruled Asia and Eastern Europe. Mongolia was established, and large areas of southern Xinjiang and Central Asia were included. Later, due to the Mongolian king’s struggle for power, it fell into a long-term conflict. People of the land fled to avoid the war, and the uninhabited plain of the lower reaches of the Yarkant River naturally became a good place to live. People from all over the world gathered together and called themselves “Dura” and changed to “Dang Lang”. The long-term local Uyghur exchanges that entered the southern Mongolian monks and “Dura” were gradually assimilated [44]. According to the report, locals wore Mongolian clothes, especially women who still maintained a Mongolian face [45]. In 1976, the robes and waistbands found in the ancient time of the Daolang people in Awati County were very similar to those of the ancients. Dalang Muqam is an important part of Daolang culture. It is also a part of the Uyghur Twelve Muqam, and it retains the ancient Western culture, but it also contains a larger Mongolian culture and relics. The above historical records show that the Daolang people should appear in the Chagatai Khanate and be formed by the integration of Mongolian and Uighur ethnic groups. Through our research, we also found that the paternal haplotype of the Daolang people is contained in both Uygur and Mongolian, and the main haplogroups are the same, whereas the frequencies are different (see Table 3). The principal component analysis and the NJ analysis are also the same. It is very close to the Uyghur and the Mongolian people, which establishes new evidence for the “mixed theory” in molecular genetics.

main-haplogroup-uighur
Genetic relationship between the three isolated populations: the Uygur and the Mongolian is the closest, and the main haplogroup can more intuitively compare the source composition of the genetic structure of each population. Haplogroups C, D, and O are mainly distributed in Asia as the East Asian characteristic haplogroup; haplogroups G, J, and R are mainly distributed in continental Europe, and the high frequency distribution is in Europe and Central Asia.

If the nomenclature follows a recent ISOGG standard, it appears that:

The presence of exclusively R1a-Z93 subclades and the lack of R1b-M269 samples is compatible with the expansion of R1a-Z93 into the area with Proto-Tocharians, at the turn of the 3rd-2nd millennium BC, as suggested by the Xiaohe samples, supposedly R1a(xZ93).

Now that it is obvious from ancient DNA (as it was clear from linguistics) that Pre-Tocharians separated earlier than other Late PIE peoples, with the expansion of late Khvalynsk/Repin into the Altai, at the end of the 4th millennium, these prevalent R1a (probably Z93) samples may be showing a replacement of Pre-Tocharian Y-DNA with the Andronovo expansion already by 2000 BC.

Lacking proper assessment of ancient DNA from Proto-Tocharians, this potential early Y-DNA replacement is still speculative*. However, if that is the case, I wonder what the Copenhagen group will say when supporting this, but rejecting at the same time the more obvious Y-DNA replacement in East Yamna / Poltavka in the mid-3rd millennium with incoming Corded Ware-related peoples. I guess the invention of an Indo-Tocharian group may be near…

*NOTE. The presence of R1b-M269 among Proto-Tocharians, as well as the presence of R1b-M269 among Tarim Basin peoples in modern and ancient times is not yet fully discarded. The prevalence of R1a-Z93 may also be the sign of a more recent replacement by Iranian peoples, before the Mongolian and Turkic expansions that probably brought R1b(xM269).

Also, the presence of R1b (xM269) samples in east Asia strengthens the hypothesis of a back-migration of R1b-P297 subclades, from Northern Europe to the east, into the Lake Baikal area, during the Early Mesolithic, as found in the Botai samples and later also in Turkic populations – which are the most likely source of these subclades (and probably also of Q1a2 and N1c) in the region.

Related

Long-term matrilineal continuity in a nonisolated region of Tuscany

iron_age_europe_mediterranean

New paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, by Leonardi et al. Am J Phys Anthr (2018).

EDIT (10 SEP 2018): The main author has shared an open access link to read the PDF.

Interesting excerpts:

Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

In all cases, a simple model of a long-term genealogical continuity proved to fit the data better, and sometimes much better, than the alternative hypothesis of discontinuity.

The low number of samples analyzed requires some caution in the interpretation. Because we did not test for gene flow, it is at this stage impossible to reject it, but our results suggest at least significant levels of genealogical continuity. Moreover, as it has not been possible to obtain more precise information on the age of the Eneolithic samples, they were grouped together considering the average archaeological period of interest, which may cause a bias in the analyses. (…)

tuscany
Geographic location of the samples considered in this work

(…) clearly, our samples show high levels of continuity when considering the whole Tuscan region as a genetic reservoir during the Iron Age.

The posterior distributions of the parameters confirm a high degree of genetic isolation in the sampled population, with very small values for the female effective population sizes across time. Such values, in particular the Neolithic ones, are in accord with the estimates obtained in similar studies, both in Tuscany (Ghirotto et al., 2013) and in France (Rivollat et al., 2017).

tuscany-genetic-diversity

Taken at their face value, our results do not show any major shift in the composition of the maternal ancestry of the population, across 50 centuries. This does not mean that no demographic process of relevance has affected the population, and indeed the higher diversity accumulating in time is the likely consequence of immigrating people, enriching the mitochondrial gene pool.

(…) the population of the current Lucca province appears to have retained very ancient mitochondrial features, despite occupying a geographical corridor between the Ligurian and the Tyrrhenian coast, and despite not showing the persistence of unique cultural traits through the centuries.

tuscany-genetic-diversity-hap

Another possibility is that that the different populations passing through the area (Etruscans, Romans, and Lombards) had a consistent social and/or sex bias. An example of similar patterns has been observed several times. Between the Late Neolithic and the Early Bronze Age, female exogamy in patrilocal society has been observed in Southern Germany (Knipper et al., 2017); during the Bronze Age the migrations toward Europe from the steppes appears to have consisted prevalently of males (Goldberg, Günther, Rosenberg, & Jakobsson, 2017); and in more recent periods in the Canary Islands, the female ancestry maintains a significant amount of autochthonous lineages, while the male ancestry was strongly influenced by the European colonization (Fregel et al., 2009, b).

It is well known that military invasions may not have a significant genetic impact upon the invaded population (Schiffels et al., 2016; Sokal, Oden, Walker, Di Giovanni, & Thomson, 1996;Weale,Weiss, Jager, Bradman, & Thomas, 2002), especially at the mitochondrial level, because of the limited size of a sustainable army, and of the fact that armies are generally composed mostly or only of males. Even if a substantial share of invaders decided to remain and settle the region, this form of gene flow would affect mostly or only the paternal lineages, rather than the maternal ones. We can also hypothesize the immigration of a number of people (e.g., Romans, Lombards) that may have acted as ruler of the region, remaining socially (and so genetically) separated by the local population, and leaving few (if any) traces in the gene pools of the local population.

tuscany-mtdna-haplogroups
Supporting Information, Table S1 New ancient samples genotyped

We expect to see that certain migrations since the Iron Age – like the Celtic and Roman ones – were somehow different from previous ones, where, at least since the Neolithic, male-dominated expansions were the rule.

If, however, male-biased expansions are also seen during the Iron Age – probably driven by particular subclades then – , this would certainly justify the continuity of admixture in certain regions in spite of these population expansions, and thus the importance of Y-DNA to track more recent language changes.

One of the most interesting details of the upcoming paper of Italic peoples will be the Y-DNA (and admixture) of Etruscans compared to other neighbouring peoples, given the known conflicting theories regarding their recent vs. older origin in the East before the historical record.

Related

The father tongue and mother tongue hypotheses in Indo-European populations

New paper (behind paywall) Reconciling the father tongue and mother tongue hypotheses in Indo-European populations, by Zhang et al. National Science Review (2018) nwy083.

Interesting excerpts:

Here, we reassessed the correlation between genetic and linguistic characteristics in 34 modern IE populations (Fig. 1a), for which all four types of datasets (lexicon, phonemes, Y-chromosomal composition, and mitochondrial DNA (mtDNA) composition) are available. We assembled compositions of the Y-chromosomal and mtDNA haplogroups or paragroups from the corresponding IE populations, which reflect paternal and maternal lines, respectively (…)

Neighbour-Nets were constructed to delineate the differences between 34 IE population groups clustering at the genetic and linguistic levels (Fig. 2). The reticulations within each net reflect conflicting signals against tree-like structures and support incompatible groupings [21]. These structures are likely produced by potential horizontal transmissions between populations or languages such as admixture, and potential parallel evolution in linguistics as well [22]. The Neighbour-Net for Y-chromosomes with substantial reticulations shows complicated relationships among IE populations (Fig. 2a), indicating a substantial historical population contact and admixture among the males. In contrast, the Neighbour-Net for mtDNA in Fig. 2b clearly illustrates an East-West geographic polarization, indicating two major IE populations in matrilineages: Indo-Iranian and European. (…)

y-dna-mtdna-phoneme-lexicon
Neighbour-Nets of 34 Indo-European populations calculated from the Euclidean distance matrices using (a) Y-chromosomal haplogroups and (b) mtDNA haplogroups; Neighbour-Nets of IE languages calculated from the Hamming distance matrices using (c) lexicon and (d) phonemes. The colours in the legend correspond to the language groups.

The language learning by local women could constitute the reason for unbalanced correlation of mtDNA to lexicon and phonemes. Due to the social prestige of male immigrants, their local spouses have to adopt the language of their husbands and pass it to future generations [6, 10, 15]. This process is second language acquisition and easily develops language fossilization [31]. The language fossilization is a linguistic mechanism that a learner of a second language tends to preserve some linguistic features of the first language, and develops a form of inter-language [31]. Under this circumstance, women can easily replace the lexicon from another [21], but attempt to retain local accents influenced by their native language [32]. In other words, women change to adopt the same word usage as their husbands in daily life but still speak using their own pronunciation. In mixed-language marriages with these male immigrants, women prefer to pass down their inter-languages to offspring [10, 33]. As a result, it yields the correlation between mtDNA and phonemes we observed. Hence, we courageously proposed a hypothetical scenario in Indo-European populations that lexical system of language dominated by their father, while the phonemic system of language determined by their mother.

I am not a fan of this kind of statistical studies for Comparative Grammar, and there are many pitfalls just by looking at this paper superficially: use of modern languages and modern haplogroup distributions, improper classification of phonemes – as is usual in glottochronological studies – , etc… Which render their results ipso facto unacceptable.

But just yesterday I was discussing where the Copenhagen group and their fans were going to end up when Yamna samples turn out not to be the origin of haplogroup R1a-Z645 expansion, and Anthony’s proposal of a patron-client relationship came up. Since the Danish workgroup is always one step behind, such a reactionary view seems like a reasonable assumption for the future.

This mother tongue vs. father tongue theory is another good possibility for what we are going to see, then, when they use e.g. the exogamy of eastern Corded Ware groups with Yamna to explain the adoption of the language. Maybe that’s what Kristiansen’s invented Yamna → Corded Ware arrows mean… Anything to prove that Corded Ware peoples were Indo-European speakers.

Related

Migrations in the Levant region during the Chalcolithic, also marked by distinct Y-DNA

halaf-ubaid-migrations

Open access Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation, by Harney et al. Nature Communications (2018).

Interesting excerpts (emphasis mine, reference numbers deleted for clarity):

Introduction

The material culture of the Late Chalcolithic period in the southern Levant contrasts qualitatively with that of earlier and later periods in the same region. The Late Chalcolithic in the Levant is characterized by increases in the density of settlements, introduction of sanctuaries, utilization of ossuaries in secondary burials, and expansion of public ritual practices as well as an efflorescence of symbolic motifs sculpted and painted on artifacts made of pottery, basalt, copper, and ivory. The period’s impressive metal artifacts, which reflect the first known use of the “lost wax” technique for casting of copper, attest to the extraordinary technical skill of the people of this period.

The distinctive cultural characteristics of the Late Chalcolithic period in the Levant (often related to the Ghassulian culture, although this term is not in practice applied to the Galilee region where this study is based) have few stylistic links to the earlier or later material cultures of the region, which has led to extensive debate about the origins of the people who made this material culture. One hypothesis is that the Chalcolithic culture in the region was spread in part by immigrants from the north (i.e., northern Mesopotamia), based on similarities in artistic designs. Others have suggested that the local populations of the Levant were entirely responsible for developing this culture, and that any similarities to material cultures to the north are due to borrowing of ideas and not to movements of people.

Previous genome-wide ancient DNA studies from the Near East have revealed that at the time when agriculture developed, populations from Anatolia, Iran, and the Levant were approximately as genetically differentiated from each other as present-day Europeans and East Asians are today. By the Bronze Age, however, expansion of different Near Eastern agriculturalist populations — Anatolian, Iranian, and Levantine — in all directions and admixture with each other substantially homogenized populations across the region, thereby contributing to the relatively low genetic differentiation that prevails today. Showed that the Levant Bronze Age population from the site of ‘Ain Ghazal, Jordan (2490–2300 BCE) could be fit statistically as a mixture of around 56% ancestry from a group related to Levantine Pre-Pottery Neolithic agriculturalists (represented by ancient DNA from Motza, Israel and ‘Ain Ghazal, Jordan; 8300–6700 BCE) and 44% related to populations of the Iranian Chalcolithic (Seh Gabi, Iran; 4680–3662 calBCE). Suggested that the Canaanite Levant Bronze Age population from the site of Sidon, Lebanon (~1700 BCE) could be modeled as a mixture of the same two groups albeit in different proportions (48% Levant Neolithic-related and 52% Iran Chalcolithic-related). However, the Neolithic and Bronze Age sites analyzed so far in the Levant are separated in time by more than three thousand years, making the study of samples that fill in this gap, such as those from Peqi’in, of critical importance.

This procedure produced genome-wide data from 22 ancient individuals from Peqi’in Cave (4500–3900 calBCE) (…)

Discussion

We find that the individuals buried in Peqi’in Cave represent a relatively genetically homogenous population. This homogeneity is evident not only in the genome-wide analyses but also in the fact that most of the male individuals (nine out of ten) belong to the Y-chromosome haplogroup T, a lineage thought to have diversified in the Near East. This finding contrasts with both earlier (Neolithic and Epipaleolithic) Levantine populations, which were dominated by haplogroup E, and later Bronze Age individuals, all of whom belonged to haplogroup J.

levant-chalcolithic-bronze-age
Detailed sample background data for each of the 22 samples from which we successfully obtained ancient DNA. Additionally, background information for all samples from Peqi’in that were screened is included in Supplementary Data 1. *Indicates that Y-chromosome haplogroup call should be interpreted with caution, due to low coverage data.

Our finding that the Levant_ChL population can be well-modeled as a three-way admixture between Levant_N (57%), Anatolia_N (26%), and Iran_ChL (17%), while the Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry, can only be explained by multiple episodes of population movement. The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region. We additionally find that the Levant_ChL population does not serve as a likely source of the Levantine-related ancestry in present-day East African populations.

These genetic results have striking correlates to material culture changes in the archaeological record. The archaeological finds at Peqi’in Cave share distinctive characteristics with other Chalcolithic sites, both to the north and south, including secondary burial in ossuaries with iconographic and geometric designs. It has been suggested that some Late Chalcolithic burial customs, artifacts and motifs may have had their origin in earlier Neolithic traditions in Anatolia and northern Mesopotamia. Some of the artistic expressions have been related to finds and ideas and to later religious concepts such as the gods Inanna and Dumuzi from these more northern regions. The knowledge and resources required to produce metallurgical artifacts in the Levant have also been hypothesized to come from the north.

Our finding of genetic discontinuity between the Chalcolithic and Early Bronze Age periods also resonates with aspects of the archeological record marked by dramatic changes in settlement patterns, large-scale abandonment of sites, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries. This supports the view that profound cultural upheaval, leading to the extinction of populations, was associated with the collapse of the Chalcolithic culture in this region.

levant-chalcolithic-pca
Genetic structure of analyzed individuals. a Principal component analysis of 984 present-day West Eurasians (shown in gray) with 306 ancient samples projected onto the first two principal component axes and labeled by culture. b ADMIXTURE analysis of 984 and 306 ancient samples with K = 11
ancestral components. Only ancient samples are shown

Comments

I think the most interesting aspect of this paper is – as usual – the expansion of peoples associated with a single Y-DNA haplogroup. Given that the expansion of Semitic languages in the Middle East – like that of Anatolian languages from the north – must have happened after ca. 3100 BC, coinciding with the collapse of the Uruk period, these Chalcolithic north Levant peoples are probably not related to the posterior Semitic expansion in the region. This can be said to be supported by their lack of relationship with posterior Levantine migrations into Africa. The replacement of haplogroup E before the arrival of haplogroup J suggests still more clearly that Natufians and their main haplogroup were not related to the Afroasiatic expansions.

semitic-languages
Distribution of Semitic languages. From Wikipedia.

On the other hand, while their ancestry points to neighbouring regional origins, their haplogroup T1a1a (probably T1a1a1b2) may be closely related to that of other Semitic peoples to the south, as found in east Africa and Arabia. This may be due either to a northern migration of these Chalcolithic Levantine peoples from southern regions in the 5th millennium BC, or maybe to a posterior migration of Semitic peoples from the Levant to the south, coupled with the expansion of this haplogroup, but associated with a distinct population. As we know, ancestry can change within certain generations of intense admixture, while Y-DNA haplogroups are not commonly admixed in prehistoric population expansions.

Without more data from ancient DNA, it is difficult to say. Haplogroup T1a1 is found in Morocco (ca. 3780-3650 calBC), which could point to a recent expansion of a Berbero-Semitic branch; but also in a sample from Balkans Neolithic ca. 5800-5400 calBCE, which could suggest an Anatolian origin of the specific subclades encountered here. In any case, a potential origin of Proto-Semitic anywhere near this wide Near Eastern region ca. 4500-3500 BC cannot be discarded, knowing that their ancestors came probably from Africa.

haplogroup-t-levant
Distribution of haplogroup T of Y-chromosome. From Wikipedia.

Interesting from this paper is also that we are yet to find a single prehistoric population expansion not associated with a reduction of variability and expansion of Y-DNA haplogroups. It seems that the supposedly mixed Yamna community remains the only (hypothetical) example in history where expanding patrilineal clans will not share Y-DNA haplogroup…

Related

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model are likely to hold and to validate specific features of the results. Each also comes with its own pitfalls and difficulties of interpretation. It is not obvious that any single approach represents a direct replacement as a data summary tool. Here we build more directly on the results of STRUCTURE/ADMIXTURE by developing a new approach, badMIXTURE, to examine which features of the data are poorly fit by the model. Rather than intending to replace more specific or sophisticated analyses, we hope to encourage their use by making the limitations of the initial analysis clearer.

The default interpretation protocol

Most researchers are cautious but literal in their interpretation of STRUCTURE and ADMIXTURE results, as caricatured in Fig. 1, as it is difficult to interpret the results at all without making several of these assumptions. Here we use simulated and real data to illustrate how following this protocol can lead to inference of false histories, and how badMIXTURE can be used to examine model fit and avoid common pitfalls.

admixture-protocol
A protocol for interpreting admixture estimates, based on the assumption that the model underlying the inference is correct. If these assumptions are not validated, there is substantial danger of over-interpretation. The “Core protocol” describes the assumptions that are made by the admixture model itself (Protocol 1, 3, 4), and inference for estimating K (Protocol 2). The “Algorithm input” protocol describes choices that can further bias results, while the “Interpretation” protocol describes assumptions that can be made in interpreting the output that are not directly supported by model inference

Discussion

STRUCTURE and ADMIXTURE are popular because they give the user a broad-brush view of variation in genetic data, while allowing the possibility of zooming down on details about specific individuals or labelled groups. Unfortunately it is rarely the case that sampled data follows a simple history comprising a differentiation phase followed by a mixture phase, as assumed in an ADMIXTURE model and highlighted by case study 1. Naïve inferences based on this model (the Protocol of Fig. 1) can be misleading if sampling strategy or the inferred value of the number of populations K is inappropriate, or if recent bottlenecks or unobserved ancient structure appear in the data. It is therefore useful when interpreting the results obtained from real data to think of STRUCTURE and ADMIXTURE as algorithms that parsimoniously explain variation between individuals rather than as parametric models of divergence and admixture.

For example, if admixture events or genetic drift affect all members of the sample equally, then there is no variation between individuals for the model to explain. Non-African humans have a few percent Neanderthal ancestry, but this is invisible to STRUCTURE or ADMIXTURE since it does not result in differences in ancestry profiles between individuals. The same reasoning helps to explain why for most data sets—even in species such as humans where mixing is commonplace—each of the K populations is inferred by STRUCTURE/ADMIXTURE to have non-admixed representatives in the sample. If every individual in a group is in fact admixed, then (with some exceptions) the model simply shifts the allele frequencies of the inferred ancestral population to reflect the fraction of admixture that is shared by all individuals.

Several methods have been developed to estimate K, but for real data, the assumption that there is a true value is always incorrect; the question rather being whether the model is a good enough approximation to be practically useful. First, there may be close relatives in the sample which violates model assumptions. Second, there might be “isolation by distance”, meaning that there are no discrete populations at all. Third, population structure may be hierarchical, with subtle subdivisions nested within diverged groups. This kind of structure can be hard for the algorithms to detect and can lead to underestimation of K. Fourth, population structure may be fluid between historical epochs, with multiple events and structures leaving signals in the data. Many users examine the results of multiple K simultaneously but this makes interpretation more complex, especially because it makes it easier for users to find support for preconceptions about the data somewhere in the results.

In practice, the best that can be expected is that the algorithms choose the smallest number of ancestral populations that can explain the most salient variation in the data. Unless the demographic history of the sample is particularly simple, the value of K inferred according to any statistically sensible criterion is likely to be smaller than the number of distinct drift events that have practically impacted the sample. The algorithm uses variation in admixture proportions between individuals to approximately mimic the effect of more than K distinct drift events without estimating ancestral populations corresponding to each one. In other words, an admixture model is almost always “wrong” (Assumption 2 of the Core protocol, Fig. 1) and should not be interpreted without examining whether this lack of fit matters for a given question.

admixture-pitfalls
Three scenarios that give indistinguishable ADMIXTURE results. a Simplified schematic of each simulation scenario. b Inferred ADMIXTURE plots at K= 11. c CHROMOPAINTER inferred painting palettes.

Because STRUCTURE/ADMIXTURE accounts for the most salient variation, results are greatly affected by sample size in common with other methods. Specifically, groups that contain fewer samples or have undergone little population-specific drift of their own are likely to be fit as mixes of multiple drifted groups, rather than assigned to their own ancestral population. Indeed, if an ancient sample is put into a data set of modern individuals, the ancient sample is typically represented as an admixture of the modern populations (e.g., ref. 28,29), which can happen even if the individual sample is older than the split date of the modern populations and thus cannot be admixed.

This paper was already available as a preprint in bioRxiv (first published in 2016) and it is incredible that it needed to wait all this time to be published. I found it weird how reviewers focused on the “tone” of the paper. I think it is great to see files from the peer review process published, but we need to know who these reviewers were, to understand their whiny remarks… A lot of geneticists out there need to develop a thick skin, or else we are going to see more and more delays based on a perceived incorrect tone towards the field, which seems a rather subjective reason to force researchers to correct a paper.

PCA of SNP data

Open access Effective principal components analysis of SNP data, by Gauch, Qian, Piepho, Zhou, & Chen, bioRxiv (2018).

Interesting excerpts:

A potential hindrance to our advice to upgrade from PCA graphs to PCA biplots is that the SNPs are often so numerous that they would obscure the Items if both were graphed together. One way to reduce clutter, which is used in several figures in this article, is to present a biplot in two side-by-side panels, one for Items and one for SNPs. Another stratagem is to focus on a manageable subset of SNPs of particular interest and show only them in a biplot in order to avoid obscuring the Items. A later section on causal exploration by current methods mentions several procedures for identifying particularly relevant SNPs.

One of several data transformations is ordinarily applied to SNP data prior to PCA computations, such as centering by SNPs. These transformations make a huge difference in the appearance of PCA graphs or biplots. A SNPs-by-Items data matrix constitutes a two-way factorial design, so analysis of variance (ANOVA) recognizes three sources of variation: SNP main effects, Item main effects, and SNP-by-Item (S×I) interaction effects. Double-Centered PCA (DC-PCA) removes both main effects in order to focus on the remaining S×I interaction effects. The resulting PCs are called interaction principal components (IPCs), and are denoted by IPC1, IPC2, and so on. By way of preview, a later section on PCA variants argues that DC-PCA is best for SNP data. Surprisingly, our literature survey did not encounter even a single analysis identified as DC-PCA.

The axes in PCA graphs or biplots are often scaled to obtain a convenient shape, but actually the axes should have the same scale for many reasons emphasized recently by Malik and Piepho [3]. However, our literature survey found a correct ratio of 1 in only 10% of the articles, a slightly faulty ratio of the larger scale over the shorter scale within 1.1 in 12%, and a substantially faulty ratio above 2 in 16% with the worst cases being ratios of 31 and 44. Especially when the scale along one PCA axis is stretched by a factor of 2 or more relative to the other axis, the relationships among various points or clusters of points are distorted and easily misinterpreted. Also, 7% of the articles failed to show the scale on one or both PCA axes, which leaves readers with an impressionistic graph that cannot be reproduced without effort. The contemporary literature on PCA of SNP data mostly violates the prohibition against stretching axes.

pca-how-to
DC-PCA biplot for oat data. The gradient in the CA-arranged matrix in Fig 13 is shown here for both lines and SNPs by the color scheme red, pink, black, light green, dark green.

The percentage of variation captured by each PC is often included in the axis labels of PCA graphs or biplots. In general this information is worth including, but there are two qualifications. First, these percentages need to be interpreted relative to the size of the data matrix because large datasets can capture a small percentage and yet still be effective. For example, for a large dataset with over 107,000 SNPs for over 6,000 persons, the first two components capture only 0.3693% and 0.117% of the variation, and yet the PCA graph shows clear structure (Fig 1A in [4]). Contrariwise, a PCA graph could capture a large percentage of the total variation, even 50% or more, but that would not guarantee that it will show evident structure in the data. Second, the interpretation of these percentages depends on exactly how the PCA analysis was conducted, as explained in a later section on PCA variants. Readers cannot meaningfully interpret the percentages of variation captured by PCA axes when authors fail to communicate which variant of PCA was used.

Conclusion

Five simple recommendations for effective PCA analysis of SNP data emerge from this investigation.

  1. Use the SNP coding 1 for the rare or minor allele and 0 for the common or major allele.
  2. Use DC-PCA; for any other PCA variant, examine its augmented ANOVA table.
  3. Report which SNP coding and PCA variant were selected, as required by contemporary standards in science for transparency and reproducibility, so that readers can interpret PCA results properly and reproduce PCA analyses reliably.
  4. Produce PCA biplots of both Items and SNPs, rather than merely PCA graphs of only Items, in order to display the joint structure of Items and SNPs and thereby to facilitate causal explanations. Be aware of the arch distortion when interpreting PCA graphs or biplots.
  5. Produce PCA biplots and graphs that have the same scale on every axis.

I read the referenced paper Biplots: Do Not Stretch Them!, by Malik and Piepho (2018), and even though it is not directly applicable to the most commonly available PCA graphs out there, it is a good reminder of the distorting effects of stretching. So for example quite recently in Krause-Kyora et al. (2018), where you can see Corded Ware and BBC samples from Central Europe clustering with samples from Yamna:

NOTE. This is related to a vertical distorsion (i.e. horizontal stretching), but possibly also to the addition of some distant outlier sample/s.

pca-cwc-yamna-bbc
Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015). https://doi.org/10.7554/eLife.36666.006

The so-called ‘Yamnaya’ ancestry

Every time I read papers like these, I remember commenters who kept swearing that genetics was the ultimate science that would solve anthropological problems, where unscientific archaeology and linguistics could not. Well, it seems that, like radiocarbon analysis, these promising developing methods need still a lot of refinement to achieve something meaningful, and that they mean nothing without traditional linguistics and archaeology… But we already knew that.

Also, if this is happening in most peer-reviewed publications, made by professional geneticists, in journals of high impact factor, you can only wonder how many more errors and misinterpretations can be found in the obscure market of so many amateur geneticists out there. Because amateur geneticist is a commonly used misnomer for people who are not geneticists (since they don’t have the most basic education in genetics), and some of them are not even ‘amateurs’ (because they are selling the outputs of bioinformatic tools)… It’s like calling healers ‘amateur doctors’.

NOTE. While everyone involved in population genetics is interested in knowing the truth, and we all have our confirmation (and other kinds of) biases, for those who get paid to tell people what they want to hear, and who have sold lots of wrong interpretations already, the incentives of ‘being right’ – and thus getting involved in crooked and paranoid behaviour regarding different interpretations – are as strong as the money they can win or loose by promoting themselves and selling more ‘product’.

As a reminder of how badly these wrong interpretations of genetic results – and the influence of the so-called ‘amateurs’ – can reflect on research groups, yet another turn of the screw by the Copenhagen group, in the oral presentations at Languages and migrations in pre-historic Europe (7-12 Aug 2018), organized by the Copenhagen University. The common theme seems to be that Bell Beaker and thus R1b-L23 subclades do represent a direct expansion from Yamna now, as opposed to being derived from Corded Ware migrants, as they supported before.

NOTE. Yes, the “Yamna → Corded Ware → Únětice / Bell Beaker” migration model is still commonplace in the Copenhagen workgroup. Yes, in 2018. Guus Kroonen had already admitted they were wrong, and it was already changed in the graphic representation accompanying a recent interview to Willerslev. However, since there is still no official retraction by anyone, it seems that each member has to reject the previous model in their own way, and at their own pace. I don’t think we can expect anyone at this point to accept responsibility for their wrong statements.

So their lead archaeologist, Kristian Kristiansen, in The Indo-Europeanization of Europé (sic):

kristiansen-migrations
Kristiansen’s (2018) map of Indo-European migrations

I love the newly invented arrows of migration from Yamna to the north to distinguish among dialects attributed by them to CWC groups, and the intensive use of materials from Heyd’s publications in the presentation, which means they understand he was right – except for the fact that they are used to support a completely different theory, radically opposed to those defended in Heyd’s model

Now added to the Copenhagen’s unending proposals of language expansions, some pearls from the oral presentation:

  • Corded Ware north of the Carpathians of R1a lineages developed Germanic;
  • R1b borugh [?] Italo-Celtic;
  • the increase in steppe ancestry on north European Bell Beakers mean that they “were a continuation of the Yamnaya/Corded Ware expansion”;
  • Corded Ware groups [] stopped their expansion and took over the Bell Beaker package before migrating to England” [yep, it literally says that];
  • Italo-Celtic expanded to the UK and Iberia with Bell Beakers [I guess that included Lusitanian in Iberia, but not Messapian in Italy; or the opposite; or nothing like that, who knows];
  • 2nd millennium BC Bronze Age Atlantic trade systems expanded Proto-Celtic [yep, trade systems expanded the language]
  • 1st millennium BC expanded Gaulish with La Tène, including a “Gaulish version of Celtic to Ireland/UK” [hmmm, dat British Gaulish indeed].

You know, because, why the hell not? A logical, stable, consequential, no-nonsense approach to Indo-European migrations, as always.

Also, compare still more invented arrows of migrations, from Mikkel Nørtoft’s Introducing the Homeland Timeline Map, going against Kristiansen’s multiple arrows, and even against the own recent fantasy map series in showing Bell Beakers stem from Yamna instead of CWC (or not, you never truly know what arrows actually mean):

corded-ware-migrations
Nørtoft’s (2018) maps of Indo-European migrations.

I really, really loved that perennial arrow of migration from Volosovo, ca. 4000-800 BC (3000+ years, no less!), representing Uralic?, like that, without specifics – which is like saying, “somebody from the eastern forest zone, somehow, at some time, expanded something that was not Indo-European to Finland, and we couldn’t care less, except for the fact that they were certainly not R1a“.

This and Kristiansen’s arrows are the most comical invented migration routes of 2018; and that is saying something, given the dozens of similar maps that people publish in forums and blogs each week.

NOTE. You can read a more reasonable account of how haplogroup R1b-L51 and how R1-Z645 subclades expanded, and which dialects most likely expanded with them.

We don’t know where these scholars of the Danish workgroup stand at this moment, or if they ever had (or intended to have) a common position – beyond their persistent ideas of Yamnaya™ ancestral component = Indo-European and R1a must be Indo-European – , because each new publication changes some essential aspects without expressly stating so, and makes thus everything still messier.

It’s hard to accept that this is a series of presentations made by professional linguists, archaeologists, and geneticists, as stated by the official website, and still harder to imagine that they collaborate within the same professional workgroup, which includes experienced geneticists and academics.

I propose the following video to close future presentations introducing innovative ideas like those above, to help the audience find the appropriate mood:

Related

“Steppe people seem not to have penetrated South Asia”

indo-iranian-sintashta-uralic-migrations

Open access structured abstract for The first horse herders and the impact of early Bronze Age steppe expansions into Asia from Damgaard et al. Science (2018) 360(6396):eaar7711.

Abstract (emphasis mine):

The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples.

INTRODUCTION
According to the commonly accepted “steppe hypothesis,” the initial spread of Indo-European (IE) languages into both Europe and Asia took place with migrations of Early Bronze Age Yamnaya pastoralists from the Pontic-Caspian steppe. This is believed to have been enabled by horse domestication, which revolutionized transport and warfare. Although in Europe there is much support for the steppe hypothesis, the impact of Early Bronze Age Western steppe pastoralists in Asia, including Anatolia and South Asia, remains less well understood, with limited archaeological evidence for their presence. Furthermore, the earliest secure evidence of horse husbandry comes from the Botai culture of Central Asia, whereas direct evidence for Yamnaya equestrianism remains elusive.

RATIONALE
We investigated the genetic impact of Early Bronze Age migrations into Asia and interpret our findings in relation to the steppe hypothesis and early spread of IE languages. We generated whole-genome shotgun sequence data (~1 to 25 X average coverage) for 74 ancient individuals from Inner Asia and Anatolia, as well as 41 high-coverage present-day genomes from 17 Central Asian ethnicities.

damgaard-south-asia
Model-based admixture proportions for selected ancient and present-day individuals, assuming K = 6, shown with their corresponding geographical locations. Ancient groups are represented by larger admixture plots, with those sequenced in the present work surrounded by black borders and others used for providing context with blue borders. Present-day South Asian groups are represented by smaller admixture plots with dark red borders.

RESULTS
We show that the population at Botai associated with the earliest evidence for horse husbandry derived from an ancient hunter-gatherer ancestry previously seen in the Upper Paleolithic Mal’ta (MA1) and was deeply diverged from the Western steppe pastoralists. They form part of a previously undescribed west-to-east cline of Holocene prehistoric steppe genetic ancestry in which Botai, Central Asians, and Baikal groups can be modeled with different amounts of Eastern hunter-gatherer (EHG) and Ancient East Asian genetic ancestry represented by Baikal_EN.

In Anatolia, Bronze Age samples, including from Hittite speaking settlements associated with the first written evidence of IE languages, show genetic continuity with preceding Anatolian Copper Age (CA) samples and have substantial Caucasian hunter-gatherer (CHG)–related ancestry but no evidence of direct steppe admixture.

In South Asia, we identified at least two distinct waves of admixture from the west, the first occurring from a source related to the Copper Age Namazga farming culture from the southern edge of the steppe, who exhibit both the Iranian and the EHG components found in many contemporary Pakistani and Indian groups from across the subcontinent. The second came from Late Bronze Age steppe sources, with a genetic impact that is more localized in the north and west.

CONCLUSION
Our findings reveal that the early spread of Yamnaya Bronze Age pastoralists had limited genetic impact in Anatolia as well as Central and South Asia. As such, the Asian story of Early Bronze Age expansions differs from that of Europe. Intriguingly, we find that direct descendants of Upper Paleolithic hunter-gatherers of Central Asia, now extinct as a separate lineage, survived well into the Bronze Age. These groups likely engaged in early horse domestication as a prey-route transition from hunting to herding, as otherwise seen for reindeer. Our findings further suggest that West Eurasian ancestry entered South Asia before and after, rather than during, the initial expansion of western steppe pastoralists, with the later event consistent with a Late Bronze Age entry of IE languages into South Asia. Finally, the lack of steppe ancestry in samples from Anatolia indicates that the spread of the earliest branch of IE languages into that region was not associated with a major population migration from the steppe.

I think the wording of the abstract is weird, but consequent with their samples and results, so probably just clickbait / citebait for Indian journalists and social networks, or maybe a new attempt to ‘show respect for the sensibilities of Indians’ related to the artificially magnified “AIT vs. OIT” controversy, that is only present in India.

However, everything is possible, since it is brought to you by the same Danish group who proposed the Yamnaya ancestral component™, the CHG = Indo-European (and simultaneously EHG in Maykop = Anatolian??), and now also the CWC/R1a = Indo-European & Volosovo = Uralic

Here is the reaction of Narasimhan: Narasimhan has deleted the Tweet, it basically questioned the sentence that steppe people did not penetrate South Asia.

Related

On the origin of haplogroup R1b-L51 in late Repin / early Yamna settlers

steppe-eneolithic-migrations

A recent comment on the hypothetical Central European origin of PIE helped me remember that, when news appeared that R1b-L51 had been found in Khvalynsk ca. 4250-4000 BC, I began to think about alternative scenarios for the expansion of this haplogroup, with one of them including Central Europe.

Because, if YFull‘s (and Iain McDonald‘s) estimation of the split of R1b-L23 in L51 and Z2103 (ca. 4100 BC, TMRCA ca. 3700 BC) was wrong, by as much as the R1a-Z645 estimates proved wrong, and both subclades were older than expected, then maybe R1b-L51 was not part of the Yamna expansion, but rather part of an earlier expansion with Suvorovo-Novodanilovka into central Europe.

That is, R1b-L51 and R1b-Z2103 would have expanded wih Khvalynsk-Novodanilovka migrants, and they would have either disappeared among local populations, or settled and expanded with successful lineages in certain regions. I think this may give rise to two potential models.

A hidden group in the European east-central steppes?

Here is what Heyd (2011), for example, has to say about the effect of the Khvalynsk-Novodanilovka expansion in the 4th millennium BC, with the first Kurgan wave that shuttered the social, economic, and cultural foundations of south-eastern Europe (before the expansion of west Yamna migrants in the region):

indo-european-anatolian-uralic-migrations
Proto-Anatolian migrations with Khvalynsk-Novodanilovka expansion, including ADMIXTURE data from Wang et al. (2018).

As the Boleraz and Baden tumuli cases in Serbia and Hungary demonstrate, there are earlier, 4th millennium cal. B.C. round tumuli in the Carpathian basin. There are also earlier north-Pontic steppe populations who infiltrated similar environments west of the Black Sea prior to the rise of the Yamnaya culture. This situation can be traced back to the 2nd half of the 5th millennium cal. B.C. to a group of distinct burials, zoomorphic maceheads, long flint blades, triangular flint points, etc., summarized under the term Suvurovo-Novodanilovka (Govedarica 2004; Rassamakin 2004; Anthony 2007; Heyd forthcoming 2011). They also erected round personalized tumuli, though smaller in size and height, above inhumations of single individuals. Suvorovo and Casimcea are the key examples in the lower Danube region of Romania. In northeast Bulgaria, the primary grave of Polska Kosovo (ochre-stained supine extended body position: information communicated by S. Alexandrov) can also be seen as such, as should the Targovishte-“Gonova mogila” primary grave 1 in the Thracian plain with a burial arranged in a supine position with flexed legs, southeast-northwest orientated, and strewed with ochre (Kanchev 1991 , p. 56- 57; Ivanova Gaydarska 2007). In addition to the many copper and shell beads, the 17.4cm long obsidian blade is exceptional, which links this grave to the Csongrád-“Kettoshalom” grave in the south Hungarian plain (Ecsedy 1979). It also yielded an obsidian blade ( 13.2cm long) and copper, shell and limestone beads.

suvorovo-novodanilovka-expansion-europe
The Southeast European distribution of graves of the Suvorovo-Novodanilovka group and such unequipped ones mentioned in the text which can be attributed by burial custom and stratigraphic position in the barrow, plus zoomorphic and abstract animal head sceptres as well as specific maceheads with knobs as from Decea Maresului (mid-5th millennium until around 4000 BC). Heyd (2016).

However, no traces of a tumulus have been recorded above the Kettoshalom tomb. Conventionally, it is dated to the Bodrogkeresztur-period in east Hungary, shortly after 4000 cal. B.C., which would correspond very well with the suggested Cernavodă I (or its less known cultural equivalent in the Thracian plain) attribution for the “Gonova mogila” grave, a cultural background to which the Csongrád grave should have also belonged. Bodrogkeresztur and Cernavodă I periods are not the only examples of 4th millennium cal. B.C. tumuli and burials displaying this steppe connection. Indeed we can find this early steppe impact throughout the 4th millennium cal. B.C. These include adscriptions to the Horodiștea II (Corlateni-Dealul Stadole, grave I: Burtanescu l 998, p. 37; Holbocai, grave 34: Coma 1998, p. 16); to Gordinești-Cernavodă 11 (Liești-Movila Arbănașu, grave 22: Brudiu 2000); to Gorodsk-Usatovo (Corlăteni Dealul Cetăţii, grave I: Comșa 1998, p. 17- 18, in Romania; Durankulak, grave 982: Vajsov 2002, in Bulgaria); and to Cernavodă III(Golyama Detelina, tum. 4: Leshtakov, Borisov 1995), and early (end of 4th millennium cal. B.C.) Ezero in Ovchartsi, primary grave (Kalchev 1994, p. 134-138) and Golyama Detelina, tum. 2 (Kanchev 1991) in Bulgaria. Also the Boleráz and Baden tumuli of Banjevac-Tolisavac and Mokrin in the south Carpathian basin account for this, since one should perhaps take into account primary grave 12 of the Sárrédtudavari-Orhalom tumulus in the Hungarian Alfold: a left-sided crouched juvenile ( 15- 17 y) individual in an oval, NW-SE orientated grave pit 14C dated to 3350-3100 cal. B.C. at 2 sigma (Dani, Ncpper 2006). Neither the burial custom (no ochre strewing or depositing a lump of ochre has been recorded), nor date account for its ascription to the Yamnaya!

All of these tumuli and burials demonstrate, though, that there is already a constant but perhaps low-level 4th millennium cal. B.C. steppe interaction, linking the regions of the north of the Black Sea with those of the west, and reaching deep into the Carpathian basin. This has to be acknowledged. even if these populations remain small, bounded to their steppe habitat with an economy adapted to this special environment, and are not always visible in the record. Indirect hints may help in seeing them, such as the frequent occurrence of horse bones, regarded as deriving from domesticated horses, in Hungarian Baden settlements (Bokonyi 1978; Benecke 1998), and in those of the south German Cham Culture (Matuschik 1999, p. 80-82) and the east German Bernburg Culture (Becker 1999; Benecke 1999). These occur, however, always in low numbers, perhaps not enough to maintain and regenerate a herd. Does this point us towards otherwise archaeologically hidden horsebreeders in the Carpathian basin, before the Yamnaya? In any case, I hope to make one case clear: these are by no means Yamnaya burials in the strict definition! Attribution to the Yamnaya in its strict definition applies.

pit-graves-central-europe
Distribution of Pit-Grave burials west of the Black Sea likely dating to the 2nd half of the 4th millennium BC (triangles: side-crouched burials; filled circles: supine extended burials; open circles: suspected). In Alin Frînculeasa, Bianca Preda, Volker Heyd, Pit-Graves, Yamnaya and Kurgans along the Lower Danube.

Also, about the expansion of Yamna settlers along the steppes:

However, it should have been made clear by the distribution map of the Western Yamnaya that they were confining themselves solely to their own, well-known, steppe habitat and therefore not occupying, or pushing away and expelling, the locally settled farming societies. Also, living solely in the steppes requires another lifestyle, and quite different economic and social bases, most likely very different to the established farming societies. Although surely regarded as incoming strangers, they may therefore not have been seen as direct competitors. This argument can be further enforced when remembering that the lowlands and the steppes in the southeast of Europe had already been populated throughout the 4th millennium cal. B.C., as demonstrated above, by societies with a similar north-Pontic steppe origin and tradition, albeit in lower numbers. It is only for these groups that the Yamnaya may have become a threat, but their common origin and perhaps a similar economic/ social background with comparable lifestyles would surely have assisted to allow rapid assimilation. More important, though, is that farming societies in this region may therefore have been accustomed to dealing and interacting with different people and ethnic strangers for a long time. (…)

When assessing farming and steppe societies’ interaction from a general point of view, attitudes can diverge in three main directions:

  1. the violent one; with raids, fights, struggles, warfare, suppression and finally the superiority and exploitation of the one over the other;
  2. the peaceful one; with a continuous exchange of gifts, goods, work, information and genes in a balanced reciprocal system, leading eventually to the merging of the two societies and creation of a new identity;
  3. the neutral one; with the two societies ignoring each other for a long time.

What we see from trying to understand the record of the Yamnaya, based on their tumuli and burials, and the local and neighbouring contemporary societies, based on their settlements, hoards, and graves, is likely a mixture of all three scenarios, with the balance perhaps more towards exchange in a highly dynamic system with alterations over time. However, violence and raids cannot be ruled out; they would be difficult to see in the archaeological record; or only indirectly, such as the building of hill forts, particularly the defence-like chain of Vucedol hillforts along the south shore of the Danube on the Serbian/Croatian border zone (Tasic 1995a), and the retreat of people into them (Falkenstein 1998, p. 261-262), with other interpretations also possible. And finally, we are dealing here with very different local and neighbouring societies, as well as with more distant contemporary ones, looking, in reality, rather like a chequer board of societies and archaeological cultures (see Parzinger 1993 for the overview). These display different regional backgrounds and traditions leading to different social and settlement organizations, different economic bases and material cultures in the wide areas between Prut and Maritza rivers, and Black Sea and Tisza river. They surely found their individual way of responding to the incoming and settling Yamnaya people.

yamna-tumuli-west-carpathians
Yamnaya tumuli signalling the expansion of West Yamna from ca. 3100 BC (especially after ca. 2950 BC). Heyd (2011).

The best data we have about this potential non-Yamna origin of R1b-L51 – and thus in favour of its admixture in the Carpathian basin – lies in:

  1. The majority of R1a-Z2103 subclades found to date among Yamna samples.
  2. The presence of R1b-Z2103 in the Catacomb culture – in the Northern Caucasus and in Ukraine.
  3. The limited presence of (ancient and modern) R1b-L51 in eastern Europe and India, whose isolated finds are commonly (and simplistically) attributed to ‘late migrations’.
  4. The presence of R1b-L51 (xZ2103) in cultures related to the ‘Yamna package’, but supposedly not to Yamna settlers. So for example I7043, of haplogroup R1b-L151(xU106,xP312), ca. 2500-2200 BC from Szigetszentmiklós-Üdülősor, probably from the Bell Beaker (Csepel group), but maybe from the early Nagýrev culture.
  5. The expansion of its subclades apparently only from a single region, around the Carpathian basin, in contrast to R1b-Z2103.
  6. The already ‘diluted’ steppe admixture found in the earliest samples with respect to Yamna, which points to the appearance after the Yamna admixture with the local population.
  7. Ukrainian archaeologists (in contrast to their Russian colleagues) point to the relevance of North Pontic cultures like Kvitjana and Lower Mikhailovka in the development of Early Yamna in the west, and some eastern European researchers also believe in this similarity.
  8. If R1b-Z2103 and R1b-L51 had expanded with Suvorovo-Novodanilovka migrants to the west, and had admixed later as Hungary_LCA-LBA-like peoples with Yamna migrants during the long-term contacts with other ‘kurganized cultures’ ca. 2900-2500 BC in the Great Hungarian Plains, it could explain some peculiar linguistic traits of North-West Indo-European, and also why R1b-Z2103 appears in cultures associated with this earlier ‘steppe influence’ (i.e. not directly related to Yamna) such as Vučedol (with a R1b-Z2103 sample, see below). That could also explain the presence of R1b-L151(xP312, xU106) in similar Balkan cultures, possibly not directly related to Yamna.
PCA-r1b-l51
Image modified from Wang et al. (2018). PCA of ancient and modern samples. Red circle in dashed line around Varna, Greece Neolithic, and (approximate position of) Smyadovo outliers, part of Khvalynsk-Novodanilovka settlers.

A hidden group among north or west Pontic Eneolithic steppe cultures?

The expansion of Khvalynsk as Novodanilovka into the North Pontic area happened through the south across the steppe, near the coast, with the forest-steppe region working as a clear natural border for this culture of likely horse-riding chieftains, whose economy was probably based on some rudimentary form of mobile pastoralism.

Although archaeologists are divided as to the origin of each individual Middle Eneolithic group near the Black Sea after the end of the Khvalynsk-Novodanilovka period, it seems more or less clear that steppe cultures like Cernavodă, Lower Mikhailovka, or Kvitjana are closer (or “more archaic”) in their steppe features, which connects them to Volga–Ural and Northern Caucasus cultures, like Northern Caucasus, Repin or Khvalynsk.

On the other hand, forest-steppe cultures like Dereivka (including Alexandria) show innovative traits and contacts with para- or sub-Neolithic cultures to the north, like Comb-Pit Ware groups, apart from corded decoration influenced by Trypillian groups to the west, especially in their later (‘Proto-Corded Ware‘) stage after ca. 3500 BC.

If Ukrainian researchers like Rassamakin are right, Early Yamna expanded not only from Repin settlers, but also from local steppe cultures adopting Repin traits to develop an Early Yamna culture, similar to how eastern (Volga–Ural groups) seem to have synchronously adopted Early Yamna without massive affluence of Repin settlements.

Furthermore, local traits develop in southern groups, like anthropomorphic stelae (shared with Kemi-Oba, direct heir of Lower Mikhailovka), and rich burials featuring wagons. These traits are seen in west Yamna settlers.

north-pontic-kvityana-dereivka-repin
Modified from Rassamakin (1999), adding red color to Repin expansion. The system of the latest Eneolithic Pointic cultures and the sites of the Zhivotilovo-Volchanskoe type: 1) Volchanskoe; 2) Zhivotilovka; 3) Vishnevatoe; 4) Koisug.

Problems of this model include:

  1. On the North Pontic area – in contrast to the Volga–Ural region – , there was a clear “colonization” wave of Repin settlers, also supported by Ukrainian researchers, based on the number of new settlements and burials, and on the progressive retreat of Dereivka, Kvitjana, as well as (more recent) Maykop- and Trypillia-related groups from the North Pontic area ca. 3350/3300 BC. It seems unlikely that these expansionist, semi-nomadic, cattle-breeding, patrilineally-related steppe clans that were driving all native populations out of their territories suddenly decided, at some point during their spread into the North Pontic area ca. 3300-3100 BC, to join forces with some foreign male lineages from the area, and then continue their expansion to the west…
  2. Similar to the fate of R1b-P297 subclades in the Baltic after the expansion of Corded Ware migrants, previous haplogropus of the North Pontic region – such as R1a, R1b-V88, and I2 subclades basically disappeared from the ancient DNA record after the expansion of Khvalynsk-Novodanilovka, and then after the expansion of Yamna, as is clear from Yamna, Afanasevo, and Bell Beaker samples obtained to date. This, in combination with what we know about Y-chromosome bottlenecks in post-Neolithic expansions, leaves little space to think that a big enough territorial group with a majority of “native” haplogroups could survive later expansions (be it R1b-L51 or R1a-Z645).
  3. Supporting an expansion of the same male (and partly female) population, the Yamna admixture from east to west is quite homogeneous, with the only difference found in (non-significant) EEF-like proportion which becomes elevated in distant areas [apart from significant ‘southern’ contribution to certain outlier samples]. Based on the also homogeneous Y-DNA picture, the heterogeneity must come, in general, from the female exogamy practiced by expanding groups.
  4. There is a short period, spanning some centuries (approximately 3300-2700 BC), in which the North Pontic area – especially the forest-steppe territories to the west of the Dnieper, i.e. the Upper Dniester, Boh, and Prut-Siret areas – are a chaos of incoming and emigrating, expanding and shrinking groups of different cultures, such as late Trypillian groups, Maykop-related traits, TRB, GAC, (Proto-)Corded Ware, and Early Yamna settlements. No natural geographic frontier can be delimited between these groups, which probably interacted in different ways. Nevertheless, based on their cultural traits, admixture, and especially on their Y-DNA, it seems that they never incorporated foreign male lineages, beyond those they probably had during their initial expansion trends.
  5. The further expansionist waves of Early Yamna seen ca. 3100 BC, from the Danube Delta to the west, give an overall image of continuously expanding patrilineal clans of R1b-M269 subclades since the Khvalynsk-Novodanilovka migration, in different periodic steps, mostly from eastern Pontic-Caspian nuclei, usually overriding all encountered cultures and (especially male) populations, rather than showing long-term collaboration and interaction. Such interaction is seen only in exceptional cases, e.g. the long-term admixture between Abashevo and Poltavka, as seen in Proto-Indo-Iranian peoples and their language.
PCA-Ukraine-r1b-l51
Image modified from Wang et al. (2018). PCA of ancient and modern samples. Arrows depicting Khvalynsk -> Yamna drift (blue), and hypothetic approximate Ukraine Eneolithic -> Yamna drift accompanying R1b-L51 (red).

Consequences

We are living right now an exemplary ego-, (ethno-)nationalism-, and/or supremacy-deflating moment, for some individuals of eastern and northern European descent who believed that R1a or ‘steppe ancestry proportions’ meant something special. The same can be said about those who had interiorized some social or ethnolinguistic meaning for the origin of R1b in western Europe, N1c in north-eastern Europe, as well as Greeks, Iranians, Armenians, or Mediterranean peoples in general of ‘Near Eastern’ ancestry or haplogroups, or peoples of Near Eastern origin and/or language.

These people had linked their haplogroups or ancestry with some fantasy continuity of ‘their’ ancestral populations to ‘their’ territories or languages (or both), and all are being proven wrong.

Apart from teaching such people a lesson about what simplistic views are useful for – whether it is based on ABO or RH group, white skin, blond hair, blue eyes, lactase persistence, or on the own ancestry or Y-DNA haplogroup -, it teaches the rest of us what can happen in the near future among western Europeans. Because, until recently, most western Europeans were comfortably settled thinking that our ancestors were some remnant population from an older, Palaeolithic or Mesolithic population, who acquired Indo-European languages by way of cultural diffusion in different periods, including only minor migrations.

Judging by what we can see now among some individuals of Northern and Eastern European descent, the only thing that can worsen the air of superiority among western Europeans is when they realize (within a few years, when all these stupid battles to control the narrative fade) that not only are they the cultural ‘heirs’ of the Graeco-Roman tradition that began with the Roman Empire, but that most of them are the direct patrilineal descendants of Khvalynsk, Yamna, Bell Beaker, and European Bronze Age peoples, and thus direct descendants of Middle PIE, Late PIE, and NWIE speakers.

steppe-chalcolithic-migrations
Steppe-related migrations ca. 3100-2600 BC with tentative linguistic identification.

The finding of R1b-L51 and R1b-Z2103 among expanding Suvorovo-Novodanilovka chieftains, with pockets of R1b-L51 remaining in steppe-like societies of the Balkans and the Carpathian Basin, would have beautifully complemented what we know about the East Yamna admixture with R1a-Z93 subclades (Uralic speakers) ca. 2600-2100 BC to form Proto-Indo-Iranian, and about the regional admixtures seen in the Balkans, e.g. in Proto-Greeks, with the prevalent J subclades of the region.

It would have meant an end to any modern culture or nation identifying themselves with the ‘true’ Late PIE and Yamna heirs, because these would be exclusively associated with the expansion of R1b-Z2103 subclades with late Repin, and later as the full-fledged Late PIE with Yamna settlers to south-east and central Europe, and to the southern Urals. The language would have had then obviously undergone different language changes in all these territories through long-lasting admixture with other populations. In that sense, it would have ended with the ideas of supremacy in western Europe before they even begin.

The most likely future

However limited the evidence, it seems that R1b-L51 expanded with Yamna, though, based on the estimates for the haplogroups involved, and on marginal hints at the variability of L23 subclades within Yamna and neighbouring populations. If R1b-L51 expanded with West Repin / Early Yamna settlers, this is why they have not yet been found among Yamna samples:

steppe-eneolithic-migrations
Simplified map of Repin expansions from ca. 3500/3400 BC.
  • The subclade division of Yamna settlers needs not be 50:50 for L51:Z2103, either in time or in space. I think this is the simplistic view underlying many thoughts on this matter. Many different expanding patrilineal clans of L23 subclades may have been more or less successful in different areas, and non-Z2103 may have been on the minority, or more isolated relative to Z2103-clans among expanding peoples on the steppe, especially on the east. In fact, we usually talk in terms of “Z2103 vs. L51” as if
    1. these two were the only L23 subclades; and
    2. both had split and succeeded (expanding) synchronously;

    that is, as if there had not been multiple subclades of both haplogroups, and as if there had not been different expansion waves for hundreds of years stemming from different evolving nuclei, involving each time only limited (successful) clans. Many different subclades of haplogroups L23 (xZ2103, xL51), Z2103, and L51 must have been unsuccessful during the ca. 1,500 years of late Khvalynsk and late Repin-Early Yamna expansions in which they must have participated (for approximately 60-75 generations, based on a mean 20-25 years).

  • If we want to imagine a pocket of ‘hidden’ L51 for some region of the North Pontic or Carpathian region, the same can be imagined – and much more likely – for any unsampled territory of expanding late Repin/Early Yamna settlers from the Lower Don – Lower Volga region (probably already a mixed society of L51 and Z2103 subclades since their beginning, as the early Repin culture, ca. 3800 BC), with L51 clans being probably successful to the west.
  • The Repin culture expanded only in small, mobile settlements from the Lower Don – Lower Volga to the north, east, and south, starting ca. 3500/3400 BC, in the waves that eventually gave a rather early distant offshoot in the Altai region, i.e. Afanasevo. Starting ca. 3300 BC in the archaeological record, the majority of R1b-Z2103 subclades found to date in Afanasevo also supports either
    • a mixed Repin society, with Z2103-clans predominating among eastern settlers; or
    • a Repin society marked by haplogroup L51, and thus a cultural diffusion of late Repin/Early Yamna traits among neighbouring (Khvalynsk, Samara, etc.) groups of essentially the same (early Khvalynsk-Novodanilovka) genetic stock in the Volga–Ural region.

    Both options could justify a majority of Z2103 in the Lower Volga–Ural region, with the latter being supported by the scattered archaeological remains of late Repin in the region before the synchronous emergence of Early Yamna findings in the whole Pontic-Caspian steppe.

  • Most Z2103 from Yamna samples to date are from around 3100 BC (in average) onward, and from the right bank of the Lower Don to the east, particularly from the Lower Volga–Ural area (especially the Samara region), which – based on the center of expansion of late Repin settlers – may be depicting an artificially high Z2103-distribution of the whole Yamna community.
repin-expansion-khvalynsk-cultures
Repin expansion into the Volga–Ural region from ca. 3500/3400 BC. Map made by me based on maps and data from Morgunova (2014, 2016). Lopatino is marked with number 64.
  • Yamna sample I0443, R1b-L23 (Y410+, L51-), ca. 3300-2700 BCE from Lopatino II, points to an intermediate subclade between L23 and L51, near one of the supposed late Repin sites (based on kurgan burials with late Repin cultural traits) in the Samara region.
  • Other Balkan cultures potentially unrelated to the Yamna expansion also show Z2103 (and not only L51) subclades, like I3499 (ca. 2884-2666 calBC), of the Vučedol culture, from Beli Manastir-Popova zemlja, which points to the infiltration of Yamna peoples in other cultures. In any case, the appearance of R1b-L23 subclades in the region happens only after the Yamna expansion ca. 3100 BC, probably through intrusions into different neighbouring regions, if these Balkan cultures are not directly derived from Yamna settlements (which is probably the case of the Csepel Bell Beaker or early Nagýrev sample, see above).
  • The diversity of haplogroups found in or around the Carpathian Basin in Late Chalcolithic / Early Bronze Age samples, including L151(xP312, xU106), P312, U106, Z2103, makes it the most likely sink of Yamna settlers, who spread thus with expanding family clans of different R1b-L23 subclades.
  • Even though some Yamna vanguard groups are known to have expanded up to Saxony-Anhalt before ca. 2700 BC, haplogroup Z2103 seems to be restricted to more eastern regions, which suggests that R1b-L51 was already successful among expanding West Yamna clans in Hungary, which gave rise only later to expanding East Bell Beakers (overwhelmingly of L151 subclades). The source of R1b-L51 and L151 expansion over Z2103 must lie therefore in the West Yamna period, and not in the Bell Beaker expansion.
indo-european-uralic-migrations-yamna-gac
Yamna migrants ca. 3300-2600. Most likely site of admixture with GAC circled in red.
  • The R1b-Z2103 found in Poltavka, Catacomb, and to the south point to a late migration displacing the western R1b-L51, only after the late Repin expansion. This is also seen in the steppe ancestry and R1b-Z2103 south of the Caucasus, in Hajji Firuz, which points to this route as a potential source of the supposed “Earliest Proto-Indo-Iranian” (the mariannu term) of the Near East. A similar replacement event happened some centuries later with expanding R1a-Z93 subclades from the east wiping out haplogroup R1b-Z2103 from the Pontic-Caspian steppe.
  • Many ancient samples from Khvalynsk, Northern Caucasus, Yamna, or later ones are reported simply as R1b-M269 or L23, without a clear subclade, so the simplistic ‘Yamna–Z2103’ picture is not real: if one takes into account that Z2103 might have been successful quite early in the eastern region, it is more likely to obtain a successful Y-SNP call of a Z2103 subclade in the Volga–Ural region than a xZ2103 one.
  • There are some modern samples of R1b-L51 in eastern Europe and Asia, whose common simplistic attribution to “late expansions” is usually not substantiated; and also ancient R1b-L51 samples might be confirmed soon for Asia.
  • ‘Western’ features described by archaeologists for West Yamna settlers, associated with Kemi Oba and southern Yamna groups in the North Pontic area – like rich burials with anthropomorphic stelae and wagons – are actually absent in burials from settlers beyond Bulgaria, which does not support their affiliation with these local steppe groups of the Black Sea. Also, a mix with local traditions is seen accross all Early Yamna groups of the Pontic-Caspian steppe, and still genetics and common cultural traits point to their homogeneization under the same patrilineal clans expanding continuously for centuries. The maintenance of local traditions (as evidenced by East Bell Beakers in Iberia related to Iberian Proto-Beakers) is often not a useful argument in genetics, especially when the female population is not replaced.
yamna-settlers-hungary
Yamna settlers in the Great Pannonian Plain, showing only kurgans of Hungary ca. 2950-2500 BC. Yamna Hungary was one of the biggest West Yamna provinces. From Hórvath et al. (2013).

Conclusion

This is what we know, using linguistics, archaeology, and genetics:

  • Middle Proto-Indo-European expanded with Khvalynsk-Novodanilovka after ca. 4800 BC, with the first Suvorovo settlements dated ca. 4600 BC.
  • Archaic Late Proto-Indo-European expanded with late Repin (or Volga–Ural settlers related to Khvalynsk, influenced by the Repin expansion) into Afanasevo ca. 3500/3400 BC.
  • Late Proto-Indo-European expanded with Early Yamna settlers to the west into central Europe and the Balkans ca. 3100 BC; and also to the east (as Pre-Proto-Indo-Iranian) into the southern Urals ca. 2600 BC.
  • North-West Indo-European expanded with Yamna Hungary -> East Bell Beakers, from ca. 2500 BC.
  • Proto-Indo-Iranian expanded with Sintashta, Potapovka, and later Andronovo and Srubna from ca. 2100 BC.

It seems that the subclades from Khvalynsk ca. 4250-4000 BC were wrongly reported – like those of Narasimhan et al. (2018). However, even if they are real and YFull estimates have to be revised, and even if the split had happened before the expansion of Suvorovo-Novodanilovka, the most likely origin of R1b-L51 among Bell Beakers will still be the expansion of late Repin / Early Yamna settlers, and that is what ancient DNA samples will most likely show, whatever the social or political consequences.

The only relevance of the finding of R1b-L51 in one place or another – especially if it is found to be a remnant of a Middle PIE expansion coupled with centuries of admixture and interaction in the Carpathian Basin – is the potential influence of an archaic PIE (or non-IE) layer on the development of North-West Indo-European in Yamna Hungary -> East Bell Beaker. That is, more or less like the Uralic influence related to the appearance of R1a-Z93 among Proto-Indo-Iranians, of R1a-Z284 among Pre-Germanic peoples, and of R1a-Z282 among Balto-Slavic peoples.

I think there is little that ancient DNA samples from West Yamna could add to what we know in general terms of archaeology or linguistics at this point regarding Late PIE migrations, beyond many interesting details. I am sure that those who have not attributed some random 6,000-year-old paternal ancestor any magical (ethnic or nationalist) meaning are just having fun, enjoying more and more the precise data we have now on European prehistoric populations.

As for those who believe in magical consequences of genetic studies, I don’t think there is anything for them to this quest beyond the artificially created grand-daddy issues. And, funnily enough, those who played (and play) the ‘neutrality’ card to feel superior in front of others – the “I only care about the truth”-type of lie, while secretly longing for grandpa’s ethnolinguistic continuity – are suffering the hardest fall.

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When Bell Beakers mixed with Eneolithic Europeans: Pömmelte and the Europe-wide concept of sanctuary

pommelte-enclosure

Recent open access paper The ring sanctuary of Pömmelte, Germany: a monumental, multi-layered metaphor of the late third millennium BC, by Spatzier and Bertemes, Antiquity (2018) 92(363):655-673.

Interesting excerpts (emphasis mine):

In recent decades, evidence has accumulated for comparable enclosures of later dates, including the Early Bronze Age Únětice Culture between 2200 and 1600 BC, and thus into the chronological and cultural context of the Nebra sky disc. Based on the analysis of one of these enclosure sites, recently excavated at Pömmelte on the flood plain of the Elbe River near Magdeburg, Saxony-Anhalt, and dating to the late third millennium BC

The main occupation began at 2321–2211 cal BC, with the stratigraphically earliest features containing exclusively Bell Beaker finds. Bell Beaker ceramics continue after 2204–2154 cal BC (boundary occupation I/II), although they were probably undecorated, but are now complemented by Únětice Culture (and other Early Bronze Age) types. At this time, with features common to both cultures predominate. Only contexts dating to the late main occupation phase (late phase II) and thereafter contained exclusively Únětice Culture finds. Evidently, the bearers of the Bell Beaker Culture were the original builders of the enclosure. During a second phase of use, Final Neolithic and Early Bronze Age cultures coexisted and intermingled. The material remains, however, should not be taken as evidence for successive groups of differing archaeological cultures, but as witnesses to a cultural transition from the Bell Beaker Culture to the Únětice Culture (Spatzier 2015). The main occupation ended 2086–2021 cal BC with the deconstruction of the enclosure; Bell Beaker finds are now absent. Finally, a few features (among them one shaft) and radiocarbon dates attest the sporadic re-use of the site in a phase of abandonment/re-use that ended 1636– 1488 cal BC.

pommelte-enclosure-occupation-stratigraphy
Cultural sequence and chronological model of the Pömmelte enclosure’s occupation (dates in 1σ-precision) (designed by André Spatzier).

How the above-ground structures possibly influenced perception may reveal another layer of meaning that highlights social functions related to ritual. While zone I was disconnected from the surroundings by a ‘semi-translucent’ post-built border, zones II/III were separated from the outside world by a wooden wall (i.e. the palisade), and zone III probably separated individuals from the crowd gathered in zone II. Accessing the interior or centre therefore meant passing through transitional zones, to first be secluded and then segregated. Exiting the structure meant re-integration and re-connection. The experience possibly induced when entering and leaving the monument reflects the three stages of ‘rites of passage’ described by van Gennep (1909): separation, liminality and incorporation. The enclosure’s outer zone(s) represents the pre- and post-liminal phase; the central area, the liminal phase. Seclusion and liminality in the interior promoted a sense of togetherness, which can be linked to Turner’s “communitas” (1969: 132–33). We might therefore see monuments such as the Pömmelte enclosure as important communal structures for social regulation and the formation of identity.

ring-sanctuary-of-pommelte
Layers of meaning of the Pömmelte enclosure as deduced from the archaeological record (design by André Spatzier).

(…) The long-term stability of these connotations must be emphasised. As with the tradition of making depositions, these meanings were valid from the start of the occupation — c. 2300 BC — until at least the early period following the deconstruction event, c. 2050 BC. While the spatial organisation and the solar alignment of the main entrances were maintained throughout the main occupation, stone axes and ‘formal’ graves indicate the continuation of the spatial concepts described above until the twentieth to nineteenth centuries BC.

These layers of meaning mirror parallel concepts of space including, although not necessarily restricted to, the formation of group identities (see Hansen & Meyer 2013: 5). They can perhaps be better understood as a ‘cosmological geography’ manifested in the symbolism of superimposed levels of conceptual ideas related to space and to certain cardinal points (Figure 8). This idea is closely related to Eliade’s (1959: 29–36) understanding of “organized — hence comicized — territory”, that is territory consecrated to provide orientation within the homogeneity of the chaotic ‘outside world’, and the equivalence of spatial consecration and cosmogony. Put differently, the Pömmelte enclosure can be interpreted as a man-made metaphor and an icon of the cosmos, reflecting the Weltanschauung (a comprehensive conception of the world) of the people who built and used it. By bringing together Eliade and Rappaport’s ideas of meaningfulness in relation to religious experience (Rappaport 1999: 391–95), it may be argued that Pömmelte was a place intended to induce oneness with the cosmos. In combining multiple layers that symbolically represent different aspects of life (first-ordermeaning), the enclosure became an icon metaphorically representing the world (second-order-meaning). As this icon was the place to reaffirm life symbolism ritually, through their actions, people perhaps experienced a sense of rootedness in, or unity with, the cosmos (highest-order-meaning). Although we can only speculate about the perceptions of ancient people, such a theory aiming to describe general principles of religious experience can provide insight.

Conclusions

The circular enclosure of Pömmelte is the first Central European monumental complex of primarily sacred importance that has been excavated and studied in detail. It reveals aspects of society and belief during the transition from the Final Neolithic to the Early Bronze Age, in the second half of the third millennium BC. Furthermore, it offers details of ritual behaviour and the way that people organised their landscape. A sacred interior was separated from the profane environment, and served as a venue for rites that secured the continuity of the social, spiritual and cosmic order. Ancestor worship formed another integral part of this: a mound-covered burial hut and a square-shaped ditch sanctuary (located, respectively, within and near the enclosure’s south-eastern sector; cf. Figure 2)—dating to 2880–2580 cal BC and attributed to the Corded Ware Culture (Spatzier 2017a: 235–44)—suggest that this site was deliberately chosen. With construction of the ring sanctuary, this place gained an immense expansion in meaning—comparable to Stonehenge. Through architectural transformation, both of these sites developed into sanctuaries with increasingly complex religious functions, including in relation to the cult of the dead. The cosmological and social functions, and the powerful symbolism of the Nebra sky disc and hoard (Meller 2010: 59–70), are reflected in Pömmelte’s monumental architecture.

All of these features—along with Pömmelte’s dating, function and complex ring structure—are well documented for British henge monuments (Harding 2003; Gibson 2005). The continuous use of circular enclosures in Central Europe from around 3000– 1500 BC remains to be confirmed, but strong evidence indicates usage spanning from the fifth to the first millennia BC (Spatzier 2017a: 273–96). From 2500 BC onwards, examples in Central Europe, Iberia and Bulgaria (Bertemes 2002; Escudero Carrillo et al. 2017) suggest a Europe-wide concept of sanctuary. This indicates that in extensive communication networks at the beginning of bronze metallurgy (Bertemes 2016), intellectual and religious contents circulated alongside raw materials. The henge monuments of the British Isles are generally considered to represent a uniquely British phenomenon, unrelated to Continental Europe; this position should now be reconsidered. The uniqueness of Stonehenge lies, strictly speaking, with its monumental megalithic architecture.

pommelte-enclosure-space
Model of the spatial organisation of the Pömmelte enclosure (designed by André Spatzier).

The Classical Bell Beaker heritage

No serious scholar can argue at this point against the male-biased East Bell Beaker migrations that expanded the European languages related to Late Proto-Indo-European-speaking Yamna (see David Reich’s comments), and thus most likely North-West Indo-European – the ancestor of Italo-Celtic, Germanic, and Balto-Slavic, apart from Pre-Celtic IE in the British Isles, Lusitano-Galician in Iberia, or Messapic in Italy (see here a full account).

With language, these migrants (several ten thousands) brought their particular Weltanschauung to all of Western, Central, and Northern Europe. Their admixture precisely in Hungary shows that they had close interactions with non-Indo-European peoples (genetically related to the Globular Amphorae culture), something that we knew from the dozens of non-Indo-European words reconstructed exclusively for North-West Indo-European, apart from the few reconstructed non-Indo-European words that NWIE shares with Palaeo-Balkan languages, which point to earlier loans from their ancestors, Yamna settlers migrating along the lower Danube.

It is not difficult to imagine that the initial East Bell Beaker group shared a newly developed common cosmological point of view that clashed with other neighbouring Yamna-related worldviews (e.g. in Balkan EBA cultures) after the cultural ties with Yamna were broken. Interesting in this respect is for example their developed (in mythology as in the new North-West Indo-European concept) *Perkwūnos, the weather god – probably remade (in language as in concept) from a Yamna minor god also behind Old Indian parjányas, the rain god – as one of the main gods from the new Pantheon, distinct from *Dyēus patēr, the almighty father sky god. In support of this, the word *meldh-n- ‘lightning’, behind the name of the mythological hammer of the weather god (cf. Old Norse Mjǫllnir or Latvian Milna), was also a newly coined North-West Indo-European term, although the myth of the hero slaying the dragon with the magical object is older.

perkunos-perkunas
The Hand of Perkūnas by Mikalojus Konstantinas Čiurlionis, from Wikipedia

Circular enclosures are known in Europe since the Neolithic. Also, the site selected for the Pömmelte enclosure had been used to bury Corded Ware individuals some centuries before its construction, and Corded Ware symbolism (stone axe vs. quern) is seen in the use given by Bell Beakers and later Únětice at this place. All this and other regional similarities between Bell Beakers and different local cultures (see here an example of Iberian Bell Beakers) points to syncretism of the different Bell Beaker groups with preceding cultures in the occupied regions. After all, their genealogical ancestors included also those of their maternal side, and not all encountered males disappeared, as is clearly seen in the resurge of previous paternal lineages in Central-East Europe and in Scandinavia. The admixture of Bell Beakers with previous groups (especially those of similar steppe-related ancestry from Corded Ware) needs more complex analyses to clarify potential early dialectal expansions (read what Iosif Lazaridis has to say).

The popular “big and early” expansions

These syncretic trends gave rise to distinct regional cultures, and eventually different local groups rose to power in the new cultural regions and ousted the old structures. Social norms, hierarchy, and pantheons were remade. Events like this must have been repeated again and again in Bronze and Iron Age Europe, and in many cases it was marked by a difference in the prevailing archaeological culture attested, and probably accompanied by certain population replacements that will be seen with more samples and studies of fine-scale population structure.

Some of these cultural changes, marked by evident haplogroup or admixture replacement, are defined as a ‘resurge’ of ancestry linked to previous populations, although that is obviously not equivalent to a resurge of a previous cultural group, because they usually represent just a successful local group of the same supraregional culture with a distinct admixture and/or haplogroup (see e.g. resurge of R1a-Z645 in Central-East European Bronze Age). Social, religious, or ethnic concepts may have changed in each of these episodes, along with the new prestige dialect.

NOTE. A recent open access paper on two newly studied Middle Bronze Age inhumations from Stonehenge give an interesting idea of potential differences in social identities, in ancestry and geographic origin (which characterize ethnicity) may have been marked by differences in burial ceremonies: Lives before and after Stonehenge: An osteobiographical study of four prehistoric burials recently excavated from the Stonehenge World Heritage Site, by Mays et al. Journal of Archaeological Science: Reports (2018) 20:692-710.

This must have happened then many times during the hundreds (or thousands in some cases) of years until the first attestation of a precise ancient language and culture (read e.g. about one of the latest branches to be attested, Balto-Slavic). Ancient language contacts, like substrates or toponymy, can only rarely be detected after so many changes, so their absence (or the lack of proper studies on them) is usually not relevant – and certainly not an argument – in scholarly discussions. Their presence, on the other hand, is a proof of such contacts.

chalcolithic_late_Europe_Bell_Beaker
Diachronic map of Late Copper Age migrations including Classical Bell Beaker (east group) expansion from central Europe ca. 2600-2250 BC

We have dozens of papers supporting Uralic dialectal substrate influence on Pre-Germanic, Proto-Balto-Slavic, and Pre- and Proto-Indo-Iranian (and even Proto-Celtic), as well as superstrate influence of Palaeo-Germanic (i.e. from Pre- to Proto-Germanic) and Proto-Balto-Slavic into Proto-Finno-Saamic, much stronger than the Indo-Iranian adstrate influence on Finno-Ugric (see the relative importance of each influence) which locates all these languages and their evolution to the north and west of the steppe (with Proto-Permic already separated, in North-East Europe, as is Proto-Ugric further east near the Urals), probably around the Baltic and Scandinavia after the expansion of Bell Beakers. These connections have been known in linguistics for decades.

Apart from some early 20th century scholars, only a minority of Indo-Europeanists support nowadays an Indo-European (i.e. centum) substrate for Balto-Slavic, to keep alive an Indo-Slavonic group based on a hypothetical 19th century Satem group; so e.g. Holzer with his Temematic, and Kortlandt supporting him, also with some supposed Indo-European substrate with heavy non-Indo-European influence for Germanic and Balto-Slavic, that now (thanks mainly to the views of the Copenhagen group) have been linked to the Corded Ware culture, as it has become clear even to them that Bell Beakers expanded North-West Indo-European.

NOTE. The Temematic etymologies have been (all of them) fully dismissed e.g. in Matasović (2013). I have already explained why an Indo-Slavonic group from Sredni Stog is not tenable, and genetics (showing Late PIE only from Yamna expansions) is proving that, too.

For their part, only a minority among Uralicists, such as Kuz’mina, Parpola or Häkkinen, believe in an ‘eastern’ origin of Uralic languages, around the Southern Urals. Genomic finds – like their peers – are clearly not supporting their views. But even if we accept this hypothesis, there is little space beyond Abashevo and related East Corded Ware cultures after the recent papers on Corded Ware and Fennoscandian samples. And yet here we are:

The Copenhagen “Homeland” interactive map

copenhagen-group-map
Brought to you by the Copenhagen fantasy map series, Indo-Europeans after (no, really, after) the expansion of Yamna settlers in Hungary ca. 2700 BC: Yamna settlers have magically disappeared. Yamna-related Balkan EBA cultures and the hundreds of Yamna kurgans around the Lower Danube and in Hungary up to Saxony-Anhalt do not exist. Dat huge mythical Middle Dnieper territory lasting (unchanged) for a thousand years, in sooo close contact with Yamna territory (so beautifully ‘linked’ together that they must have been BFFs and admixed!). Uralic Mesolithic hunter-gatherers resisting IE invasions in Volosovo for 1,500 years like Asterix’ Gaulish village against the Romans. Tiny pockets of Bell Beakers will eventually emerge from (surprise!) Corded Ware territories beautifully scattered over Central and Northern Europe (unlike those eastern CWC mega-regions). And, of course, you can almost see Kroonen & Iversen’s Kurgan Pre-Germanic mixing already with their agricultural substrate TRB precisely in full-IE Denmark (quite appropriate for the Danish school). And sheep symbols representing wool finds, for no reason. A great map to mock for years to come, with each new genetic paper.

The new propaganda tool GIS timeline map of the Copenhagen group:

  • consciously ignores Yamna settlers along the Danube, in the Balkans, and in Hungary, and initial East Bell Beakers, i.e. the obvious origin and expansion of North-West Indo-Europeans, but in contrast magnifies (and expands in time) regions for Sredni Stog / Corded Ware cultures (which suggests that this is yet another absurd attempt to revive the theories of the Danish school…);
  • substitutes arrows for Kron-like colors (where danger red = Indo-European) with the same end result of many other late 20th century whole-Europe Kurgan maps, linking Sredni Stog and Corded Ware with Yamna, but obviating the precise origin of Corded Ware peoples (is it Sredni Stog, or is it that immutable Middle Dnieper group? is it West Yamna, or Yamna Hungary? is it wool, or is it wheels?);
  • relegates Uralic speakers to a tiny corner, a ‘Volosovo’ cultural region, thus near Khvalynsk/Yamna (but not too much), that miraculously survives surrounded by all-early-splitting, all-Northern Eneolithic Indo-Europeans, thus considering Uralic languages irrelevant not only to locate the PIE Urheimat, but also to locate their own homeland; also, cultures identified in color with Uralic speakers expand until the Iron Age with enough care not to even touch in the map one of the known R1a samples published to date (because, for some people, apparently R1a must be Indo-European); and of course N1c or Siberian ancestry are irrelevant, too;
  • and adds findings of wheels and wool probably in support of some new ideas based on yet another correlation = causation argument (that I cannot then properly criticize without access to its reasoning beyond cute SmartArt-like symbols) similar to their model – already becoming a classic example of wrong use of statistical methods – based on the infamously named Yamnaya ancestral component, which is obviously still used here, too.

The end result is thus similar to any other simplistic 1990s Gimbutas (or rather the recently radicalized IE Sredni Stog -> Corded Ware -> BBC version by the Danish workgroup) + 2000s R1a-map + 2010s Yamnaya ancestry; but, hard to believe, it is published in mid-2018. A lot of hours of senseless effort, because after its publication it becomes ipso facto outdated.

For comparison of Yamna and Bell Beaker expansions, here is a recent simplistic, static (and yet more accurate) pair of maps, from the Reich Lab:

corded-ware-bell-beaker
Cultural maps from Eneolithic and Chalcolithic cultures in Wang et al. (2018).

If the Copenhagen group keeps on pushing Gimbutas’ long ago outdated IE Sredni Stog -> Corded Ware theory as modified by Kristiansen, with their recently invented Corded Ware -> Bell Beaker model in genetics, at some point they are bound to clash with the Reich-Jena team, which seems to have less attachment to the classic Kurgan model and the wrong interpretations of the 2015 papers, and that would be something to behold. Because, as Cersei would say: “When you play the game of thrones, you win or you die. There is no middle ground.” And when you play the game of credibility, after so many, so wrong publications, well…

NOTE. I have been working on a similar GIS tool for quite some time, using my own maps and compiled genetic data, which I currently only use for my 2018 revision of the Indo-European demic diffusion model. Maybe within some weeks or months I will be able to publish the maps properly, after the revised papers. It’s a pitty that so much work on GIS and analysis with genetic data and cultural regions has to be duplicated, but I intend to keep some decent neutrality in my revised cultural maps, and this seems impossible at this point with some workgroups who have put all their eggs in one broken basket…

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