Corded Ware and Bell Beaker related groups defined by patrilocality and female exogamy

tumulus-culture-eba-danube

Two new interesting papers concerning Corded Ware and Bell Beaker peoples appeared last week, supporting yet again what is already well-known since 2015 about West Uralic and North-West Indo-European speakers and their expansion.

Below are relevant excerpts (emphasis mine) and comments.

#UPDATE (27 OCT 2019): I have updated Y-DNA and mtDNA maps of Corded Ware, Bell Beaker, EBA, MBA, and LBA migrations. I have also updated PCA plots, which now include the newly reported samples and those from the Tollense valley, and I have tried some qpAdm models (see below).

I. Corded Ware and Battle Axe cultures

Open access The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon, by Malmström, Günther, et al. Philos. Trans. R. Soc. (2019).

I.1. Origins of Corded Ware peoples

The discovery of the Alexandria outlier represented a clear support for a long-lasting genomic difference between the two distinct cultural groups, Yamnaya and Corded Ware, already visible in an opposition Khvalynsk vs. late Sredni Stog ca. 4000 BC, i.e. well before the formation of both Late Eneolithic/Early Bronze Age groups.

However, the realization that it may not have been an Eneolithic individual, but rather a (Middle?) Bronze Age one, suggests that Sredni Stog was possibly not directly related to Corded Ware, and a potential direct connection with Yamnaya might have to be reevaluated, e.g. through the Carpathian Basin, as Anthony (2017) proposed.

pca-yamnaya-corded-ware-oblaczkowo
Principal component analysis of modern Europeans (grey) and projected ancient Europeans.

This new paper shows two early Corded Ware individuals from Obłaczkowo, Poland (ca. 2900-2600 BC) – hence close to the supposed original Proto-Corded Ware community – with an apparently (almost) full “Steppe-like” ancestry, clustering (almost) with Yamnaya individuals:

Similar to the BAC individuals, the newly sequenced individuals from the present-day Karlova in Estonia and Obłaczkowo in Poland appear to have strong genetic affinities to other individuals from BAC and CWC contexts across the Baltic Sea region. Some individuals from CWC contexts, including the two from Obłaczkowo, cluster closely with the potential source population of steppe-related ancestry, the Yamnaya herders. Notably, these individuals appear to be those with the earliest radiocarbon dates among all genetically investigated individuals from CWC contexts. Overall, for CWC-associated individuals, there is a clear trend of decreasing affinity to Yamnaya herders with time.

NOTE. Interestingly, this sample is almost certainly attributed to the skeleton E8-A, which had been supposedly already investigated by the Copenhagen group as the RISE1 sample:

We note that RISE1 is also described as the individual from Obłaczkowo feature E8-A. However, their genetic results differ from ours. They present this individual as a molecularly determined male that belongs to Y-chromosomal haplogroup (hg) R1b and to mtDNA hg K1b1a1 while our results show this individual to be female, carrying a mtDNA hg U3a’c profile

Since the typical Steppe_MLBA ancestry of Corded Ware groups does not show good fits for (Pre-)Yamnaya-derived ancestry, it is almost certain that these individuals will show no (or almost no) direct Yamnaya-related contribution, but rather a contribution of East European sub-Neolithic groups, more or less close to the steppe-forest region.

NOTE. They might show contributions from Pre-Yamnaya-influenced Sredni Stog, though, but if they show a contribution of Yamnaya, then they are probably outliers, related to Yamnaya vanguard groups (see image below). And for them to show it, then both sources, Yamnaya and Corded Ware, should be clearly distinguishable from each other and their relative contribution quantifiable in formal stats, something difficult (if not impossible) to ascertain today.

trypillian-yamnaya-influence-baltic
Trypillian routes of influence and Yamnaya culture influences in Central and Central-East Europe during the Late Eneolithic / Early Bronze Age. Images by Klochko (2009).

Their position in the published PCA – a plot apparently affected by projection bias – suggests a cluster in common with early Baltic samples, which are known to show contributions from East European sub-Neolithic populations (see qpAdm values for Baltic CWC samples).

NOTE. Results for previous samples labelled as Poland CWC are unreliable due to their low coverage.

The most interesting aspect about the ancestry shown by these early samples is their further support for an origin of the culture different than Sredni Stog, and for a rejection of the Alexandria outlier as ancestral to them, hence for a Volhynian-Podolian homeland of Proto-Corded Ware peoples, with an ancestry probably more closely related to the late Maykop Steppe- and Trypillian/GAC groups admixed with sub-Neolithic populations of the Eastern European Late Eneolithic.

NOTE. That is, unless there is a reason for the apparent increase in so-called “Steppe-ancestry” during the northward and westward migration of CWC peoples that represents another thing entirely…

#UPDATE (27 OCT 2019): Apparently, the PCA was actually not affected by projection bias:

Sample poz44 clusters ‘to the south’, with other early German ones, but also close to Yamnaya. Its poor coverage makes qpAdm results unreliable, but its common cluster close to central European and eastern CWC groups – despite belonging to the same Obłaczkowo site – supports that it is more representative of the Proto-CWC population than poz81.

Sample poz81 clusters with Yamnaya samples – or at least with the wider, Steppe-related cluster. Nevertheless, analyses with qpAdm – in combination with values obtained for other early Baltic samples – support that the ancestry of poz81 is more closely related to a core Corded Ware population admixed with sub-Neolithic peoples (similar to Samara LN).

NOTE. I have selected Czech CWC as a potential source closer to the Proto-CWC population, similar to models with Baltic samples. Since Czech CWC samples are later than these from Obłaczkowo, I have also checked the reverse model, with Poz81 and GAC Poland as a source for Czech CWC, and the fits are slightly worse. Anyway, ‘better’ or ‘worse’ p-values can’t determine the direction of migration

pca-corded-ware-poland-oblaczkowo-baltic-yamnaya
Detail of the PCA of Eurasian samples, including Corded Ware groups and related clusters, as well as outliers. Also marked is poz81.

I.2. CWC expansion under R1a bottlenecks

The two males in our dataset (ber1 and poz81) belonged to Y-chromosome R1a haplogroups, as do the majority of males (16/24) from the previously published CWC contexts, while a smaller fraction belonged to R1b [3/24] or I2a [3/24] lineages. The R1a haplogroup has not been found among Neolithic farmer populations nor in hunter–gatherer groups in central and western Europe, but it has been reported from eastern European hunter–gatherers and Eneolithic groups. Individuals from the Pontic–Caspian steppe, associated with the Yamnaya Culture, carry mostly R1b and not R1a haplotypes.

Sample poz81 is of basal hg. R1a-CTS4385*, an R1a-M417 subclade, supporting once again that most Corded Ware individuals from western and central European groups expanded under R1a-M417 (xZ645) lineages. The Battle Axe sample from Bergsgraven (ca. 2620-2470 BC) shows a basal hg. R1a-Y2395*, a R1a-Z283 subclade leading to the typically Fennoscandian R1a-Z284.

Both findings further support that typical lineages of West CWC groups, including R1a-M417 (xZ645) subclades, were fully replaced by incoming East Bell Beakers, and that the limited expansion of R1a-Z284 and I1 (the latter found in one newly reported Late Neolithic sample from Sweden) was the outcome of later regional bottlenecks within Scandinavia, after the creation of a maritime dominion by the Bell Beaker elites during the Dagger Period.

I.3. CWC and lactase persistence

(…) one of these individuals (kar1) carried at least one allele (-13910 C->T) associated with lactose tolerance, while the other two individuals (ber1 and poz81) carried at least one ancestral variant each, consistent with previous observations of low levels of lactose tolerance variants in the Neolithic and a slight increase among individuals from CWC contexts.

The fact that two early CWC individuals carry ancestral variants could be said to support the improbability of the individual from Alexandria representing a community ancestral to the Corded Ware community. On the other hand, the late CWC individual from Estonia carries one allele, but it still seems that only Bell Beakers and Steppe-related groups show the necessary two alleles during the Early Bronze Age, which is in line with a late Repin/early Yamnaya-related origin of the successful selection of the trait, consistent with the expansion of their specialized semi-nomadic cattle-breeding economy through the steppe biome during the Late Eneolithic.

rs4988235-lactase-persistence-history
Maps part of the public data used for the post by Iain Mathieson on Lactase Persistence. “By 2500 BP, the allele is present over a band stretching from Ireland to Central Asia at around 50 degrees latitude. This probably reflects the spread of Steppe ancestry populations in which the allele originated. However, the allele is still rare (say less than 1% frequency) over this entire range. It does not become common anywhere until some time in the past 2500 years – when it reaches its present-day high frequency in Britain and Central Europe”.

I.4. West Uralic spread from the East

The BAC groups fit as a sister group to the CWC-associated group from Estonia but not as a sister group to the CWC groups from Poland or Lithuania (|Z| > 3), indicating some differences in ancestry between these CWC groups and BAC. Supervised admixture modelling suggests that BAC may be the CWC-related group with the lowest YAM-related ancestry and with more ancestry from European Neolithic groups.

While the results of the paper are compatible with a migration from either the Eastern or the Western Baltic into Scandinavia, phylogeography and archaeology support that Battle Axe peoples emerged as a Baltic Corded Ware group close to the Vistula that expanded first to the north-east, and then to the west from Finland, continuing mostly unscathed during the whole Bronze Age mostly in eastern Fennoscandia with the development of Balto-Finnic- and Samic-speaking communities.

corded-ware-culture-ancestry-over-time
Correlation between f4(Chimp, LBK, YAM, X), where X is a CWC or BAC individual, and the date (BCE) of each individual. This statistic measures shared drift between CWC and Linear Pottery Culture (LBK) as opposed to YAM and should increase with the higher proportion of Neolithic farmer ancestry in CWC and BAC.

Radiocarbon dating showed that the three individuals from the Öllsjö megalithic tomb derived from later burials, where oll007 (2860–2500 cal BCE) overlaps with the time interval of the BAC, and oll009 and oll010 (1930–1650 cal BCE) fall within the Scandinavian Late Neolithic and Early Bronze Age

For more on how the Pitted Ware culture may have influenced Uralic-speaking Battle Axe peoples earlier than Indo-European-speaking Bell Beakers in Scandinavia, read more about Early Bronze Age Scandinavia and about the emergence of the Pre-Proto-Germanic community.

II. Bell Beakers through the Bronze Age

New paper (behind paywall) Kinship-based social inequality in Bronze Age Europe, by Mittnik et al. Science (2019).

II.1. Yamnaya vanguard settlers

In my last post, I showed how the ancestry of Corded Ware from Esperstedt is consistent with influence by incoming Yamnaya vanguard settlers or early Bell Beakers, stemming ultimately from the Carpathian Basin, something that could be inferred from the position of the Esperstedt outlier in the PCA, and by the knowledge of Yamnaya archaeological influences up to Saxony-Anhalt.

Yamnaya settlers are strongly suspected to have migrated in small so-called vanguard groups to the west and north of the Carpathians in the first half of the 3rd millennium BC, well before the eventual adoption of the Proto-Beaker package and their expansion ca. 2500 BC as East Bell Beakers.

Tauber Valley infiltration

As I mentioned in the books, one of the known – among the many more unknown – sites displaying Yamnaya-related traits and suggesting the expansion of Yamnaya settlers into Central Europe is Lauda-Königshofen, in the Tauber Valley.

From Diet and Mobility in the Corded Ware of Central Europe, by Sjögren, Price, & Kristiansen PLoS One (2017):

A series of CW cemeteries have been excavated in the Tauber valley. There are three large cemeteries known and some 30 smaller sites. The larger ones are Tauberbischofsheim-Dittingheim with 62 individuals, Tauberbischofsheim-Impfingen with 40 individuals, and Lauda-Königshofen with 91 individuals. The cemeteries are dispersed rather regularly along the Tauber valley, on both sides of the river, suggesting a quite densely settled landscape.

The Lauda-Königshofen graves consisted mostly of single inhumations in contracted position, usually oriented E-W or NE-SW. A total of 91 individuals were buried in 69 graves. At least 9 double graves and three graves with 3–4 individuals were present. In contrast to the common CW pattern, sexes were not distinguished by body position, only by grave goods. This trait is common in the Tauber valley and suggests a local burial tradition in this area. Stone axes were restricted to males, pottery to females, while other artifacts were common to both sexes. About a third of the graves were surrounded by ring ditches, suggesting palisade enclosures and possibly over-plowed barrows.

In particular, Frînculeasa, Preda, & Heyd (2015) used Lauda-Königshofen as representative of the mobility of horse-riding Yamnaya nomadic herders migrating into southern Germany, referring to the findings in Trautmann (2012) about the nomadic herders from the Tauber Valley, and their already known differences with other Corded Ware groups.

The likely influence of Yamnaya in the region has been reported at least since the 2000s, repeatedly mentioned by Jozef Bátora (2002, 2003, 2006), who compiled Yamnaya influences in a map that has been copied ever since, with little improvement over time. Heyd believes that there are potentially many Yamnaya remains along the Middle and Lower Danube and tributaries not yet found, though.

NOTE. Looking for this specific site, I realized that Bátora (and possibly many after him who, like me, copied his map) located Lauda-Königshofen in a more south-western position within Baden-Württemberg than its actual location. I have now corrected it in the maps of Chalcolithic migrations.

yamnaya-corded-ware-europe
Yamnaya influences in Central Europe suggestive of vanguard settlements, contemporary with Corded Ware groups. See full map.

Althäuser Hockergrab…Bell Beakers

Unfortunately, though, it is very difficult to attribute the reported R1b-L51 sample from the Tauber valley to a population preceding the arrival of East Bell Beakers in the region, so there is no uncontroversial smoking gun of Yamnaya vanguard settlers – yet. Reasons to doubt a Pre-Beaker origin are as follows:

1. This family of the Tauber valley shows a late radiocarbon date (ca. 2500 BC), i.e. from a time where East Bell Beakers are known to have been already expanding in all directions from the Middle and Upper Danube and its tributaries.

tauber-valley-althauser-hockergrab
Crouched burial from Althausen (Althäuser Hockergrab), dated ca. 2500 BC.

2. Archaeological information is scarce. Remains of these four individuals were discovered in 1939 and officially reported together with other findings in 1950, without any meaningful data that could distinguish between Bell Beakers and Corded Ware individuals.

This site is located in the Tauber valley, ca. 100 km to the northwest of the Lech valley. The site was discovered during the construction of a sports field in 1939 and was subsequently excavated by G. Müller and O. Paret. Four individuals in crouched position were found in the burial pit of a flat grave. The burial did not contain any grave goods, but due to the type of grave and positioning of the bodies (with heads pointing towards southwest) the site was attributed to the Corded Ware complex.

The classification of this burial as of CWC and not BBC seems to have been based entirely on the numerous CWC findings in the Tauber valley, rather than on its particular burial orientation following a regional custom (foreign to the described standard of both cultures), and on its grave type that was also found among Bell Beaker groups. Like many human remains recovered in dubious circumstances in the 20th century, these samples should have probably been labelled (at least in the genetic paper) more properly as Tauber_LN or Tauber_EBA.

yamnaya-bias-tauber-lech-valley
Changes in ancestry over time. (A) Median ages of individuals plotted against z scores of f4 (Mbuti, Test; Yamnaya_Samara, Anatolia_Neolithic) show increase of Anatolian farmer-related ancestry (indicated by more positive z-scores) and decrease of variation in ancestry over time. Grey shading indicates significant z scores, red line shonw near correlation (r = -0.35971; P = 0.003) and dotted lines the 95% confidence interval. (B) ancestry proportions on autosomes calculated with qpAdm. (C) Sex-bias z scores between autosomes and X chromosomes show significant male bias for steppe-related ancestry in the Tauber samples. Image modified from the paper: Surrounded with a blue circle in (A) are females with more Steppe-related ancestry, and in (C) surrounded by squares are the distinct sex biases found in the earliest BBC from the Tauber valley vs. later groups from the Lech valley.

3. In terms of ancestry, there seem to be no gross differences between the Lech Valley BBC individuals and previously reported South German Beakers, originally Yamnaya-like settlers admixing through exogamy with locals, including Corded Ware peoples, as the sex bias of the Lech Valley Beakers proves (see PCA plot below). In other words, northern and eastern Beakers admixed with regional (Epi-)Corded Ware females during their respective expansions, similar to how southern and western Beakers admixed with regional EEF-related females.

The two available Tauber Valley samples (“Tauber_CWC”) show the same pattern: a quite recent Steppe-related male bias and Anatolia_Neolithic-related female bias. Nevertheless, the male sample clusters ‘to the south’ in the PCA relative to all sampled Corded Ware individuals (see PCA plot below), and shows less Yamnaya-like ancestry than what is reported (or can be inferred) for Yamnaya from Hungary or early Bell Beakers of elevated Steppe-related ancestry.

yamnaya-ancestry-tauber-cwc-bbc-lech-eba-mba
Table S9. Three-way qpAdm admixture model for European MN/Chalcolithic group+Yamnaya_Samara. P-values greater than 0.05 (model is not rejected) marked in green.

The ancestry and position of the Althäuser male in the PCA is thus fully compatible with recently incoming East Bell Beakers admixing with local peoples (including Corded Ware) through exogamy, but not so much with a sample that would be expected from Yamanaya vanguard + Corded Ware-related ancestry (more like the Esperstedt outlier or the early France Beaker). Compared to the more ‘northern’ (fully Corded Ware-like) position ancestry of his female counterpart, there is little to support that both are part of the same native Tauber valley community after generations of ancestry levelling…

#UPDATE (27 OCT 2019): The PCA shows that the Althäuser male clusters, in fact, ‘to the north’ of the female one, almost on the same spot as a Bell Beaker sample from the Lech Valley.

Despite their reported damage and poor coverage, there seems to be a trend for qpAdm values to prefer a source population for the male (Alt_4) close to Germany Beakers, whereas the female sample (Alt_3) shows ‘better’ fits when a Corded Ware source is selected.

Also relevant is the Corded Ware ancestry of the male – closer to a Czech rather than German CWC source – compatible with an eastern origin, hence supporting a recent arrival via the Danube, in contrast to the local source of the CWC admixture of the female. The poorer coverage of the female sample makes these results questionable, though.

pca-bell-beaker-tauber-lech-valley-yamnaya-cwc
Detail of the PCA of Eurasian samples, including Bell Beaker groups and related clusters, as well as outliers. Also marked are the Tauber Valley male (M) and female (F).

4. The haplogroup inference is also unrevealing: whereas the paper reports that it is R1b-P310* (xU106, xP312), there is no data to support a xP312 call, so it may well be even within the P312 branch, like most sampled Bell Beaker males. Similarly, the paper also reports that HUGO_180Sk1 (ca. 2340 BC) shows a positive SNP for the U106 trunk, which would make it the earliest known U106 sample and originally from Central Europe, but there is no clear support for this SNP call, either. At least not in their downloadable BAM files, as far as I can tell. Even if both were true, they would merely confirm the path of expansion of Yamnaya / East Bell Beakers through the Danube, already visible in confirmed genomic data:

r1b-l51-archaic-yamnaya-bell-beakers
Distribution of ‘archaic’ R1b-L51 subclades in ancient samples, overlaid over a map of Yamnaya and Bell Beaker migrations. In blue, Yamnaya Pre-L51 from Lopatino (not shown) and R1b-L52* from BBC Augsburg. In violet, R1b-L51 (xP312,xU106) from BBC Prague and Poland. In maroon, hg. R1b-L151* from BBC Hungary, BA Bohemia, and (not shown) a potential sample from the Tauber Valley and one from BBC at Mondelange, which is certainly xU106, maybe xP312. Interestingly, the earliest sample of hg. R1b-U106 (a lineage more proper of northern Europe) has been found in a Bell Beaker from Radovesice (ca. 2350 BC), between two of these ‘archaic’ R1b-L51 samples; and a sample possibly of hg. R1b-ZZ11+ (ancestral to DF27 and U152) was found in a Bell Beaker from Quedlinburg, Germany (ca. 2290 BC), to the north-west of Bohemia. The oldest R1b-U152 are logically from Central Europe, too.

II.2. Proto-Celts and the Tumulus culture

The most interesting data from Mittnik et al. (2019) – overshadowed by the (at first sight) striking “CWC” label of the Althäuser male – is the finding that the most likely (Pre-)Proto-Celtic community of Southern Germany shows, as expected, major genetic continuity over time with Yamnaya/East Bell Beaker-derived patrilineal families, which suggests an almost full replacement of other Y-chromosome haplogroups in Southern German Bronze Age communities, too.

Sampled families form part of an evolving Bell Beaker-derived European BA cluster in common with other Indo-European-speaking cultures from Western, Southern, and Northern Europe, also including early Balto-Slavs, clearly distinct from the Corded Ware-related clusters surviving in the Eastern Baltic and the forest zone.

This Central European Bronze Age continuity is particularly visible in many generations of different patrilocal families practising female exogamy, showing patrilineal inheritance mainly under R1b-P312 (mostly U152+) lineages proper of Central European bottlenecks, all of them apparently following a similar sociopolitical system spanning roughly a thousand years, since the arrival of East Bell Beakers in the region (ca. 2500 BC) until – at least – the end of the Middle Bronze Age (ca. 1300 BC):

Here, we show a different kind of social inequality in prehistory, i.e., complex households that consisted of i) a higher-status core family, passing on wealth and status to descendants, ii) unrelated, wealthy and high-status non-local women and iii) local, low-status individuals. Based on comparisons of grave goods, several of the high-status non-local females could have come from areas inhabited by the Unetice culture, i.e., from a distance of at least 350 km. As the EBA evidence from most of Southern Germany is very similar to the Lech valley, we suggest that social structures comparable to our microregion existed in a much broader area. The EBA households in the Lech valley, however, seem similar to the later historically known oikos, the household sphere of classic Greece, as well as the Roman familia, both comprising the kin-related family and their slaves.

pca-lech-valley-bell-beaker-eba
Genetic structure of Late Neolithic and Bronze Age individuals from southern Germany. (A) Ancient individuals (covered at 20,000 or more SNPs) projected onto principal components defined by 1129 present day west Eurasians (shown in fig. S6); individuals in this study shown with outlines corresponding to their 87Sr/86Sr isotope value (black: consistent with local values, orange: uncertain/intermediate, red: inconsistent with local values). Selected published ancient European individuals are shown without outlines. Image modified from the paper. Surrounded by triangles in cyan, Corded Ware-like females; with a blue triangle, Yamnaya/Early BBC-like sample from the Tauber valley.

NOTE. For those unfamiliar with the usual clusters formed by the different populations in the PCA, you can check similar graphics: PCA with Bell Beaker communities, PCA with Yamnaya settlers from the Carpathians, a similar one from Wang et al. (2019) showing the Yamnaya-Hungary cline, or the chronological PCAs prepared by me for the books.

The gradual increase in local EEF-like ancestry among South Germany EBA and MBA communities over the previous BBC period offers a reasonable explanation as to how Italic and Celtic communities remained in loose contact (enough to share certain innovations) despite their physical separation by the Alps during the Early Bronze Age, and probably why sampled Bell Beakers from France were found to be the closest source of Celts arriving in Iberia during the Urnfield period.

Furthermore, continued contacts with Únětice-related peoples through exogamy also show how Celtic-speaking communities closer to the Danube might have influenced (and might have been influenced by) Germanic-speaking communities of the Nordic Late Neolithic and Bronze Age, helping explain their potentially long-lasting linguistic exchange.

Like other previous Neolithic or Chalcolithic groups that Yamnaya and Bell Beakers encountered in Europe, ancestry related to the Corded Ware culture became part of Bell Beaker groups during their expansion and later during the ancestry levelling in the European Early Bronze Age, which helps us distinguish the evolution of Indo-European-speaking communities in Europe, and suggests likely contacts between different cultural groups separated hundreds of km. from each other.

All in all, there is nothing to support that (epi-)Corded Ware groups might have survived in any way in Central or Western Europe: whether through their culture, their Y-chromosome haplogroups, or their ancestry, they followed the fate of other rapidly expanding groups before them, viz. Funnelbeaker, Baden, or Globular Amphorae cultural groups. This is very much unlike the West Uralic-speaking territory in the Eastern Baltic and the Russian forests, where Corded Ware-related cultures thrived during the Bronze Age.

lech-valley-yamnaya-ancestry-over-time
f4-statistics showing differences in ancestry in populations grouped by period. An increase in affinity to ancestry related to Anatolia Neolithic over time. Males and females grouped together shown as upward and downward pointing triangles, respectively.

Conclusion

It was about time that geneticists caught up with the relevance of Y-DNA bottlenecks when assessing migrations and cultural developments.

From Malmström et al. (2019):

The paternal lineages found in the BAC/CWC individuals remain enigmatic. The majority of individuals from CWC contexts that have been genetically investigated this far for the Y-chromosome belong to Y-haplogroup R1a, while the majority of sequenced individuals of the presumed source population of Yamnaya steppe herders belong to R1b. R1a has been found in Mesolithic and Neolithic Ukraine. This opens the possibility that the Yamnaya and CWC complexes may have been structured in terms of paternal lineages—possibly due to patrilineal inheritance systems in the societies — and that genetic studies have not yet targeted the direct sources of the expansions into central and northern Europe.

From Gibbons (2019), a commentary to Mittnik et al. (2019):

Some of the early farmers studied were part of the Neolithic Bell Beaker culture, named for the shape of their pots. Later generations of Bronze Age men who retained Bell Beaker DNA were high-ranking, buried with bronze and copper daggers, axes, and chisels. Those men carried a Y chromosome variant that is still common today in Europe. In contrast, low-ranking men without grave goods had different Y chromosomes, showing a different ancestry on their fathers’ side, and suggesting that men with Bell Beaker ancestry were richer and had more sons, whose genes persist to the present.

There was no sign of these women’s daughters in the burials, suggesting they, too, were sent away for marriage, in a pattern that persisted for 700 years. The only local women were girls from high-status families who died before ages 15 to 17, and poor, unrelated women without grave goods, probably servants, Mittnik says. Strontium levels from three men, in contrast, showed that although they had left the valley as teens, they returned as adults.

Also, from Scientific American:

(…) it has long been assumed that prior to the Athenian and Roman empires,—which arose nearly 2,500 and more than 2,000 years ago, respectively—human social structure was relatively straightforward: you had those who were in power and those who were not. A study published Thursday in Science suggests it was not that simple. As far back as 4,000 years ago, at the beginning of the Bronze Age and long before Julius Caesar presided over the Forum, human families of varying status levels had quite intimate relationships. Elites lived together with those of lower social classes and women who migrated in from outside communities. It appears early human societies operated in a complex, class-based system that propagated through generations.

It seems wrong (to me, at least) that the author and – as he believes – archaeologists and historians had “assumed” a different social system for the European Bronze Age, which means they hadn’t read about how Indo-European societies were structured. For example, long ago Benveniste (1969) already drew some coherent picture of these prehistoric peoples based on their reconstructed language alone: regarding their patrilocal and patrilineal family system; regarding their customs of female exogamy and marriage system; and regarding the status of foreigners and slaves as movable property in their society.

A long-lasting and pervasive social system of Bronze Age elites under Yamnaya lineages strikingly similar to this Southern German region can be easily assumed for the British Isles and Iberia, and it is likely to be also found in the Low Countries, Northern Germany, Denmark, Italy, France, Bohemia and Moravia, etc., but also (with some nuances) in Southern Scandinavia and Central-East Europe during the Bronze Age.

Therefore, only the modern genetic pool of some border North-West Indo-European-speaking communities of Europe need further information to describe a precise chain of events before their eventual expansion in more recent times:

  1. the relative geographical isolation causing the visible regional founder effects in Scandinavia, proper of the maritime dominion of the Nordic Late Neolithic (related thus to the Island Biogeography Theory); and
  2. the situation of the (Pre-)Proto-Balto-Slavic community close to the Western Baltic which, I imagine, will be shown to be related to a resurge of local lineages, possibly due to a shift of power structures similar to the case described for Babia Góra.

NOTE. Rumour has it that R1b-L23 lineages have already been found among Mycenaeans, while they haven’t been found among sampled early West European Corded Ware groups, so the westward expansion of Indo-European-speaking Yamnaya-derived peoples mainly with R1b-L23 lineages through the Danube Basin merely lacks official confirmation.

Related

Bell Beakers and Mycenaeans from Yamnaya; Corded Ware from the forest steppe

eba-yamnaya-ancestry-hungary

I have recently written about the spread of Pre-Yamnaya or Yamnaya ancestry and Corded Ware-related ancestry throughout Eurasia, using exclusively analyses published by professional geneticists, and filling in the gaps and contradictory data with the most reasonable interpretations. I did so consciously, to avoid any suspicion that I was interspersing my own data or cherry picking results.

Now I’m finished recapitulating the known public data, and the only way forward is the assessment of these populations using the available datasets and free tools.

Understanding the complexities of qpAdm is fairly difficult without a proper genetic and statistical background, which I won’t pretend to have, so its tweaking to get strictly correct results would require an unending game of trial and error. I have sadly little time for this, even taking my tendency to procrastination into account… so I have used a simple model akin to those published before – in particular, the outgroup selection by Ning, Wang et al. (2019), who seem to be part of the only group interested in distinguishing Yamnaya-related from Corded Ware-related ancestry, probably the most relevant question discussed today in population genomics regarding the Proto-Indo-European and Proto-Uralic homelands.

eneolithic-steppe-best-fits
Supplementary Table 13. P values of rank=2 and admixture proportions in modelling Steppe ancestry populations as a three-way admixture of Eneolithic steppe Anatolian_Neolithic and WHG using 14 outgroups.
Left populations: Test, Eneolithic_steppe, Anatolian_Neolithic, WHG.
Right populations: Mbuti.DG, Ust_Ishim.DG, Kostenki14, MA1, Han.DG, Papuan.DG, Onge.DG, Villabruna, Vestonice16, ElMiron, Ethiopia_4500BP.SG, Karitiana.DG, Natufian, Iran_Ganj_Dareh_Neolithic.

I have used for all analyses below a merged dataset including the curated one of the Reich Lab, the latest on Central and South Asia by Narasimhan, Patterson et al. (2019), on Iberia by Olalde et al. (2019), and on the East Baltic by Saag et al. (2019), as well as datasets including samples from Wang et al. (2019) and Lamnidis et al. (2018). I used (and intend to use) the same merged dataset in all cases, despite its huge size, to avoid adding one more uncontrolled variable to the analyses, so that all results obtained can be compared.

I try to prepare in advance a bunch of relevant files with left pops and right pops for each model:

  1. It seems a priori more reasonable to use geographically and chronologically closer proxy populations (say, Trypillia or GAC for Steppe-related peoples) than hypothetic combinations of ancestral ones (viz. Anatolian farmer, WHG, and EHG).
  2. This also means using subgroups closer to the most likely source population, such as (Don-Volga interfluve) Yamnaya_Kalmykia rather than (Middle Volga) Yamnaya_Samara for the western expansion of late Repin/early Yamnaya, or the early Germany_Corded_Ware.SG or Czech_Corded Ware for the group closest to the Proto-Corded Ware population (see below), likely neighbouring the Upper Vistula region.
  3. I usually test two source populations for different targets, which seems like a much more efficient way of using computer resources, whenever I know what I want to test, since I need my PC back for its normal use; whenever I don’t know exactly what to test, I use three-way admixture models and look for subsets to try and improve the results.

I have probably left out some more complex models by individualizing the most relevant groups, but for the time being this would have to do. Also, no other formal stats have been used in any case, which is an evident shortcoming, ruling out an interpretation drawn directly and only from the results below.

Full qpAdm results for each batch of samples are presented in a Google Spreadsheet, with each tab (bottom of the page) showing a different combination of sources, usually in order of formally ‘best’ (first to the left) to ‘worst’ (last to the right) fits, although the order is difficult to select in highly heterogeneous target groups, as will be readily visible.

maykop-trypillia-intrusion-steppes
Disintegration, migration, and imports of the Azov–Black Sea region. First migration event (solid arrows): Gordineşti–Maikop expansion (groups: I – Bursuchensk; II – Zhyvotylivka; III – Vovchans’k; IV – Crimean; V – Lower Don; VI – pre-Kuban). Second migration event (hollow arrows): Repin expansion. After Rassamakin (1999), Demchenko (2016).

Corded Ware origins

The latest publications on the Yampil barrow complex have not improved much our understanding of the complexity of Corded Ware origins from an archaeological point of view, involving multiple cultural (hence likely population) influences. This bit is from Ivanova et al., Baltic-Pontic Studies (2015) 20:1, and most hypotheses of the paper remain unanswered (except maybe for the relevance of the Złota group):

In the light of the above outline therefore one should argue that the ‘architecture of barrows’ associated in the ‘Yampil landscape’ of the Middle Dniester Area with the Eneolithic (specifically, mainly with the TC), precedes the development of a similar phenomenon that can be observed from 2900/2800 BC in the Upper Dniester Area and drainage basin of the Upper Vistula, associated with the CWC [Goslar et al. 2015; Włodarczak 2006; 2007; 2008; Jarosz, Włodarczak 2007]. The most consuming research question therefore is whether ritual customs making use of Eneolithic (Tripolye) ‘barrow architecture’ could have penetrated northwards along the Dniester route, where GAC communities functioned. One could also ask what role the rituals played among the autochthons [Kośko 2000; Włodarczak 2008; 2014: 335; Ivanova, Toshchev 2015b].

This issue has already been discussed with a resulting tentative systemic taxonomy in the studies of Włodarczak, arguing for the Złota culture (ZC) in the Vistula region as an illustration of one of the (Małopolska) reception centres of civilization inspirations from the oldest Pontic ‘barrow culture’ circle associated with the Eneolithic and Early Bronze Age [Włodarczak 2008]. Notably, it is in the ZC that one can notice a set of cultural traits (catacomb grave construction, burial details, forms and decoration of vessels) analogous to those shared by the north-western Black Sea Coast groups of the forest-steppe Eneolithic (chiefly Zhyvotilovka-Volchansk) and the Late Tripolye circle (chiefly Usatovo-Gordinești-Horodiștea-Kasperovtsy).

gac-trypillia-usatovo-corded-ware
Globular Amphorae culture „exodus” to the Danube Delta: a – Globular Amphorae culture; b – GAC (1), Gorodsk (2), Vykhvatintsy (3) and Usatovo (4) groups of Trypillia culture; c – Coţofeni culture; d – northern border of the late phase of Baden culture;red arrows – direction of Globular Amphora culture expansion; blue arrow – direction of „reflux” of Globular Amphora culture (apud Włodarczak, 2008, with changes).

Taking into account that I6561 might be wrongly dated, we cannot include the Corded Ware-like sample of the end-5th millennium BC in the analysis of Corded Ware origins. That uncertainty in the chronology of the appearance of “Steppe ancestry” in Proto-Corded Ware peoples complicates the selection of any potential source population from the CHG cline.

Nevertheless, the lack of hg. R1a-M417 and sizeable Pre-Yamnaya-related ancestry in the sampled Pontic forest-steppe Eneolithic populations (represented exclusively by two samples from Dereivka ca. 3600-3400 BC) would leave open the interesting possibility that a similar ancestry got to the forest-steppe region between modern Poland and Ukraine during the known complex population movements of the Late Eneolithic.

It is known that Corded Ware-derived groups and Steppe Maykop show bad fits for Pre-Yamnaya/Yamnaya ancestry, and also that Steppe Maykop is a potential source of “Steppe-related ancestry” within the Eneolithic CHG mating network of the Pontic-Caspian steppes and forest-steppes. Testing Corded Ware for recent Trypillia and Maykop influences, proper of Late Trypillia and Late Maykop groups in the North Pontic area (such as Zhyvotylivka–Vovchans’k and Gordineşti) side by side with potential Pre-Yamnaya and Yamnaya sources makes thus sense:

Now, the main obvious difference between Khvalynsk-Yamnaya and Corded Ware is the long-lasting, pervasive Y-chromosome bottlenecks under R1b lineages in the former, compared to the haplogroup variability and late bottleneck under R1a-M417 in the latter, which speaks in favour – on top of everything else – of a different community of sub-Neolithic hunter-gatherers including hg. R1a-M417 hijacking the expansion of Steppe_Maykop-related ancestry around the Volhynian-Podolian Upland.

Akin to how Yamnaya patrilineal descendants hijacked regional EEF (±CWC) ancestry components mainly through exogamy, dragging them into the different expanding Bell Beaker groups (see below), but kept their Indo-European languages, these hunter-gatherers that admixed with peoples of “Steppe ancestry” were the most likely vector of expansion of Uralic languages in Eastern Europe.

corded-ware-from-trypillia-maykop
PCA of ancient Eurasian samples. Marked likely Proto-Corded Ware samples and potential origin of its PCA cluster based on qpAdm results. See full PCA and more related files.

Baltic Corded Ware

One of the most interesting aspects of the results above is the surprising heterogeneity of the different regional groups, which is also reflected in the Y-DNA variability of early Corded Ware samples.

Seeing how Baltic CWC groups, especially the early Latvia_LN sample, show particularly bad fits with the models above, it seems necessary to test how this population might have come to be. My first impression in 2017 was that they could represent early Corded Ware groups admixed with Yamnaya settlers through their interactions along the Dnieper-Dniester corridor.

However, I recently predicted that the most likely admixture leading to their ancestry and PCA cluster would involve a Corded Ware-like group and a group related to sub-Neolithic cultures of eastern Europe, whose best proxy to date are EHG-like Khvalynsk samples (i.e. excluding the outlier with Pre-Yamnaya ancestry, I0434):

corded-ware-pca-sub-neolithic-europe
Detail of the PCA of the Corded Ware expansion. See full PCA and more related files.

Late Corded Ware + Yamnaya vanguard

Relevant are also the mixtures of Corded Ware from Esperstedt, and particularly those of the sample I0104, which I have repeated many times in this blog I suspected to be influenced by vanguard Yamnaya settlers:

The infeasible models of CWC + Yamnaya_Kalmykia ± Hungary_Baden (see below for Bell Beakers) and the potential cluster formed with other samples from the Baltic suggest that it could represent a more complex set of mixtures with sub-Neolithic populations. On the other hand, its location in Germany, late date (ca. 2500 BC or later), and position in the PCA, together with the good fits obtained for Germany_Beaker as a source, suggest that the increase in Steppe-related ancestry + EEF makes it impossible for the model (as I set it) to directly include Yamnaya_Kalmykia, despite this excess Steppe-related ancestry actually coming from Yamnaya vanguard groups.

I think it is very likely that the future publication of EEF-admixed Yamnaya_Hungary samples (or maybe even Yamnaya vanguard samples) will improve the fits of this model.

These results confirm at least the need to distrust the common interpretation of mixtures including late Corded Ware samples from Esperstedt (giving rise to the “up to 75% Yamnaya ancestry of CWC” in the 2015 papers) as representative of the Corded Ware culture as a whole, and to keep always in mind that an admixture of European BA groups including Corded Ware Esperstedt as a source also includes East BBC-like ancestry, unless proven otherwise.

yamnaya-vanguard-corded-ware-chalcolithic-early
Yamnaya vanguard groups in Corded Ware territory before the expansion of Bell Beakers (ca. 2500 BC). See full map.

Bell Beaker expansion

A hotly (re)debated topic in the past 6 months or so, and for all the wrong reasons, is the origin of the Bell Beaker folk. Archaeology, linguistics, and different Y-chromosome bottlenecks clearly indicate that Bell Beakers were at the origin of the North-West Indo-European expansion in Europe, while the survival of Corded Ware-related groups in north-eastern Europe is clearly related to the expansion of Uralic languages.

NOTE. For the interesting case of Proto-Indo-Iranians expanding with Corded Ware-like ancestry, see more on the formation of Sintashta-Potapovka-Filatovka from East Uralic-speaking Abashevo and Pre-Proto-Indo-Iranian-speaking Poltavka herders. See also more on R1a in Indo-Iranians and on the social complexity of Sintashta.

Nevertheless, every single discarded theory out there seems to keep coming back to life from time to time, and a new wave of interest in “Bell Beaker from the Single Grave culture” somehow got revived in the process, too, because this obsession – unlike the “Bell Beakers from Iberia Chalcolithic” – is apparently acceptable in certain circles, for some reason.

We know that Iberian Beakers, British Beakers, or Sicilian EBA – representing the most likely closest source population of speakers of Proto-Galaico-Lusitanian, Pre-Celtic Indo-European, and Proto-Elymian, respectively – have already been successfully tested for a direct origin among Western European Beakers in Olalde et al. (2018), Olalde et al. (2019), and Fernandes et al. (2019).

This success in ascertaining a closer Beaker source is probably due to the physical isolation of the specific groups (related to Germany_Beaker, Netherlands_Beaker, and NE_Mediterranean_Beaker samples, respectively) after their migration into regions dominated by peoples without Steppe-related ancestry. Furthermore, Celtic-speaking populations expanding with Urnfield south of the Pyrenees also show a good fit with a source close to France_Beaker.

So I decided to test sampled Bell Beaker populations, to see if it could shed light to the most likely source population of individual Beaker groups and the direction of migration within Central Europe, i.e. roughly eastwards or westwards. As it was to be expected for closely related populations (see the relevant discussion here), an attempt to offer a simplistic analysis of direction based on formal stats does not make any sense, because most of the alternative hypotheses cannot be rejected:

Not only because of the similar values obtained, but because it is absurd to take p-values as a measure of anything, especially when most of these conflicting groups with slightly ‘better’ or ‘worse’ p-values represent multiple different mixtures of the type (Yamnaya + EEF) + (Corded Ware + EEF ± Yamnaya), impossible to distinguish without selecting proper, direct ancestral populations…

A further example of how explosive the Bell Beaker expansion was into different territories, and of their extensive local admixture, is shown by the unsuccessful attempt by Olalde et al. (2018) to obtain an origin of the EEF source for all Beaker groups (excluding Iberian Beakers):

bell-beaker-local-population-iberia
Investigating the genetic makeup of Beaker-complex-associated individuals. Testing different populations as a source for the Neolithic ancestry component in Beaker-complex-associated individuals. The table shows P values (* indicates values > 0.05) for the fit of the model: ‘Steppe_EBA + Neolithic/Copper Age’ source population.
burials-yamnaya-hungary
Map of attested Yamnaya pit-grave burials in the Hungarian plains; superimposed in shades of blue are common areas covered by floods before the extensive controls imposed in the 19th century; in orange, cumulative thickness of sand, unfavourable loamy sand layer. Marked are settlements/findings of Boleráz (ca. 3500 BC on), Baden (until ca. 2800 BC), Kostolac (precise dates unknown), and Yamna kurgans (from ca. 3100/3000 BC on).

Now, there is a simpler way to understand what kind of Steppe-related ancestry is proper of Bell Beakers. I tested two simple models for some Beaker groups: Yamnaya + Hungary Baden vs. Corded Ware + GAC Poland. After all, the Bell Beaker folk should prefer a source more closely related to either Yamnaya Hungary or Central European Corded Ware:

Interestingly, models including Yamnaya + Baden show good fits for the most important groups related to North-West Indo-Europeans, including Bell Beakers from Germany, the Netherlands, Italy, and Poland, representing the most likely closest source populations of speakers of Pre-Proto-Celtic, Pre-Proto-Germanic, Proto-Italo-Venetic, and Pre-Proto-Balto-Slavic, respectively.

The admixed Yamnaya samples from Hungary that will hopefully be published soon by the Jena Lab will most likely further improve these fits, especially in combination with intermediate Chalcolithic populations of the Middle and Upper Danube and its tributaries, to a point where there will be an absolute chronological and geographical genomic trail from the fully Yamnaya-like Yamnaya settlers from Hungary to all North-West Indo-European-speaking groups of the Early Bronze Age.

The only difference between groups will be the gradual admixture events of their source Beaker group with local populations on their expansion paths, including peoples of mainly EEF, CWC+EEF, or CWC+EEF+Yamnaya related ancestry. There is ample evidence beyond ancestry models to support this, in particular continued Y-DNA bottlenecks under typical Yamnaya paternal lineages, mainly represented by R1b-L51 subclades.

east-bell-beaker-group-expansion
Distribution of the Bell Beaker East Group, with its regional provinces, as of c. 2400 cal BC (after Heyd et al. 2004, modified). See full maps.

European Early Bronze Age

European EBA groups that might show conflicting results due to multiple admixture events with Corded Ware-related populations are the Únětice culture and the Nordic Late Neolithic.

The results for Únětice groups seem to be in line with what is expected of a Central European EBA population derived from Bell Beakers admixed with surrounding poulations of East Bell Beaker and/or late (Epi-)Corded Ware descent.

Potential models of mixture for Nordic Late Neolithic samples – despite the bad fits due to the lack of direct ancestral CWC and BBC groups from Denmark – seem to be impossible to justify as derived exclusively from Single Grave or (even less) from Battle Axe peoples, supporting immigration waves of Bell Beakers from the south and further admixture events with local groups through maritime domination.

PCA of ancient European samples. Marked are Bronze Age clusters. See full PCAs.

Balkans Bronze Age

The potential origin of the typical Corded Ware Steppe-related ancestry in the social upheaval and population movements of the Dnieper-Dniester forest-steppe corridor during the 4th millennium BC raises the question: how much do Balkan Bronze Age groups owe their ancestry to a population different than the spread of Pre-Yamnaya-like Suvorovo-Novodanilovka chieftains? Furthermore, which Bronze Age groups seem to be more likely derived exclusively from Pre-Yamnaya groups, and which are more likely to be derived from a mixture of Yamnaya and Pre-Yamnaya? Do the formal stats obtained correspond to the expected results for each group?

Since the expansion of hg. I2a-L699 (TMRCA ca. 5500 BC) need not be associated with Yamnaya, some of these values – together with the assessment of each individual archaeological culture – may question their origin in a Yamnaya-related expansion rather than in a Khvalynsk-related one.

NOTE. These are the last ones I was able to test yesterday, and I have not thought these models through, so feel free to propose other source and target groups. In particular, complex movements through the North Pontic area during the Late Eneolithic would suggest that there might have been different Steppe-ancestry-related vs. EEF-related interactions in the north-west and west Pontic area before and during the expansion of Yamnaya.

Mycenaeans

One of the key Indo-European populations that should be derived from Yamnaya to confirm the Steppe hypothesis, together with North-West Indo-Europeans, are Proto-Greeks, who will in turn improve our understanding of the preceding Palaeo-Balkan community. Unfortunately, we only have Mycenaean samples from the Aegean, with slight contributions of Steppe-related ancestry.

Still, analyses with potential source populations for this Steppe ancestry show that the Yamnaya outlier from Bulgaria is a good fit:

The comparison of all results makes it quite evident the why of the good fits from (Srubnaya-related) Bulgaria_MLBA I2163 or of Sintashta_MLBA relative to the only a priori reasonable Yamnaya and Catacomb sources: it is not about some hypothetical shared ancestor in Graeco-Aryan-speaking East Yamnaya– or even Catacomb-Poltavka-related groups, because all available Yamnaya-related peoples are almost indistinguishable from each other (at least with the sampling available today). These results reflect a sizeable contribution of similar EEF-related populations from around the Carpathians in both Steppe-related groups: Corded Ware and Yamnaya settlers from the Balkans.

mycenaeans-minyan-ware-greece-minoan
Cultural groups in and around the Balkans during the Early Bronze Age. See full maps.

qpAdm magic

In hobby ancestry magic, as in magic in general, it is not about getting dubious results out of thin air: misdirection is the key. A magician needs to draw the audience attention to ‘remarkable’ ancestry percentages coupled with ‘great’ (?) p-values that purportedly “prove” what the audience expects to see, distracting everyone from the true interesting aspects, like statistical design, the data used (and its shortcomings), other opposing models, a comparison of values, a proper interpretation…you name it.

I reckon – based on the examples above – that the following problems lie at the core of bad uses of qpAdm:

  1. In the formal aspect, the poor understanding of what p-values and other formal stats obtained actually mean, and – more importantly – what they don’t mean. The simplistic trend to accept results of a few analyses at face value is necessarily wrong, in so far as there is often no proper reasoning of what is being assessed and how, and there is never a previous opinion about what could be expected if the alternative hypotheses were true.
  2. In the interpretation aspect, the poor judgement of accompanying any results with simplistic, superficial, irrelevant, and often plainly wrong archaeological or linguistic data selected a posteriori; the inclusion of some racial or sociopolitical overtones in the mixture to set a propitious mood in the target audience; and a sort of ritualistic theatrics with the main theme of ‘winning’, that is best completed with ad hominems.

If you get rid of all this, the most reasonable interpretation of the output of a model proposed and tested should be similar to Nick Patterson’s words in his explanation of qpWave and qpAdm use:

Here we see that, at least in this analysis there are reasonable models with CordedWareNeolithic is a mix of either WHG or LBKNeolithic and YamnayaEBA. (…) The point of this note is not to give a serious phylogenetic analysis but the results here certainly support a major Steppe contribution to the Corded Ware population, which is entirely concordant with the archaeology [?].

Very far, as you can see, from the childish “Eureka! I proved the source!”-kind of thinking common among hobbyists.

The Mycenaean case is an illustrative example: if the Yamnaya outlier from Bulgaria were not available, and if one were not careful when designing and assessing those mixture models, the interpretation would range from erroneous (viz. a Graeco-Aryan substrate, as I initially thought) to impossible (say, inventing migration waves of Sintashta or Srubnaya peoples into Crete). The models presented above show that a contribution of Yamnaya to Mycenaeans couldn’t be rejected, and this alone should have been enough to accept Yamnaya as the most likely source population of “Steppe ancestry” in Proto-Greeks, pending intermediate samples from the Balkans. In other words, one could actually find that ‘the best’ p-values for source populations of Mycenaeans is a combination of modern Poles + Turks, despite the impracticality of such a model…

I haven’t been able to reproduce results which supposedly showed that Corded Ware is more likely to be derived from (Pre-)Yamnaya than other source population, or that Corded Ware is better suited as the ancestral population of Bell Beakers. The analyses above show values in line with what has been published in recent scientific papers, and what should be expected based on linguistics and archaeology. So I’ll go out on a limb here and say that it’s only through a careful selection of outgroups and samples tested, and of as few compared models as possible, that you could eventually get this kind of results and interpretation, if at all.

Whether that kind of special care for outgroups and samples is about (a) an acceptable fine-tuning of the analyses, (b) a simplistic selection dragged from the first papers published and applied indiscriminately to all models, or (c) cherry picking analyses until results fit the expected outcome, is a question that will become mostly irrelevant when future publications continue to support an origin of the expansion of ancient Indo-European languages in Khvalynsk- and Yamnaya-related migrations.

Feel free to suggest (reasonable) modifications to correct some of these models in the comments. Also, be sure to check out other values such as proportions, SD or SNPs of the different results that I might have not taken into account when assessing ‘good’ or ‘bad’ fits.

Related

On the Ukraine Eneolithic outlier I6561 from Alexandria

sredni-stog-eneolithic-late

Over the past week or so, since the publication of new Corded Ware samples in Narasimhan, Patterson et al. (2019) and after finding out that the R1a-M417 star-like phylogeny may have started ca. 3000 BC, I have been ruminating the relevance of contradictory data about the Ukraine_Eneolithic_o sample from Alexandria, its potential wrong radiocarbon date, and its implications for the Indo-European question.

How many other similar ‘controversial’ samples are there which we haven’t even considered? And what mechanisms are in place to control that the case of Hajji_Firuz_CA I2327 is not repeated?

Ukraine Eneolithic outlier I6561

It was not the first time that I (or many others) have alternatively questioned its subclade or its date, but the contradictory data seem to keep piling up. We can still explain all these discrepancies by assuming that the radiocarbon date is correct – seeing how it is a direct and newly reported lab analysis – because it is an isolated individual from a poorly sampled region, so he may actually be the first one to show features proper of later Corded Ware-related samples.

ukraine-eneolithic-from-caucasus
PCA of ancient Eurasian samples. An interpretation of the evolution of the Pontic-Caspian steppe populations in the Eneolithic. See full PCA.

The individual seems to be especially relevant for the Indo-European and Uralic homeland question. The last one to mention this sample in a publication was Anthony (2019), who considered it in common with two other Eneolithic samples from Dereivka to show how Anatolian farmer-related ancestry first appeared in the recently opened CHG mating network of the Pontic-Caspian steppes and forest-steppes during the Middle Eneolithic, after the expansion of Khvalynsk:

The currently oldest sample with Anatolian Farmer ancestry in the steppes in an individual at Aleksandriya, a Sredni Stog cemetery on the Donets in eastern Ukraine. Sredni Stog has often been discussed as a possible Yamnaya ancestor in Ukraine (Anthony 2007: 239- 254). The single published grave is dated about 4000 BC (4045–3974 calBC/ 5215±20 BP/ PSUAMS-2832) and shows 20% Anatolian Farmer ancestry and 80% Khvalynsk-type steppe ancestry (CHG&EHG). His Y-chromosome haplogroup was R1a-Z93, similar to the later Sintashta culture and to South Asian Indo-Aryans, and he is the earliest known sample to show the genetic adaptation to lactase persistence (I3910-T). Another pre-Yamnaya grave with Anatolian Farmer ancestry was analyzed from the Dnieper valley at Dereivka, dated 3600-3400 BC (grave 73, 3634–3377 calBC/ 4725±25 BP/ UCIAMS-186349). She also had 20% Anatolian Farmer ancestry, but she showed less CHG than Aleksandriya and more Dereivka-1 ancestry, not surprising for a Dnieper valley sample, but also showing that the old fifth-millennium-type EHG/WHG Dnieper ancestry survived into the fourth millennium BC in the Dnieper valley (Mathieson et al. 2018).

The main problem is that this sample has more than one inconsistent, anachronistic data compared to its reported precise radiocarbon date ca. 4045–3974 calBCE (5215±20BP, PSUAMS-2832). I summarized them on Twitter:

  • First known R1a-M417 sample, with subclade R1a-Y26 (Y2-), with formation date and TMRCA ca. 2750 BC (CI 95% ca. 3750–1950 BC), and proper of much later Steppe_MLBA bottlenecks. The closest available sample would be the Poltavka outlier of hg. R1a-Z94 (ca. 2700 BC), from a mixed cemetery that could belong to a later (likely Abashevo) layer; the closest related subclade is probably found in sample I12450 of Butkara_IA (ca. 800 BC).
  • NOTE. The formation date of upper clade R1a-Z93 is estimated ca. 3000 BC, with a CI 95% ca. 3550–2550 BC, suggesting that the actual TMRCA range for the subclade has most likely a lower maximum formation date than estimated with the available samples under Y3.

  • Ancestry and PCA cluster like Steppe_MLBA (see PCA below), different from neighbouring Sredni Stog samples of the roughly coetaneous Dereivka site (ca. 3600-3400 BC), and from a later Yamnaya sample from Dereivka (ca. 2800 BC), even more shifted toward WHG-related ancestry.
  • Allele for lactase persistence (I3910-T), found only much later among Bell Beakers, and still later in Sintashta and Steppe_MLBA samples. This suggests a strong selection in northern Europe and South Asia stemming from steppe-related (and not forest-steppe-related) peoples, postdating the age of massive Indo-European migrations.
  • Hajji Firuz Chalcolithic outlier

    My impression is that the Hajji_Firuz Chalcolithic outlier, initially dated ca. 5900-5500 BC, had much less reason to be questioned than this sample, since Pre-Yamnaya ancestry was (and apparently is still) believed by members of the Reich Lab to have come from south of the Caucasus, and to have arrived around that time or earlier to the North Caspian steppe, i.e. before the 5th millennium BC.

    The formation date of its initially reported haplogroup, R1b-Z2103, is ca. 4100 BC (CI 95% 4800-3500 BC), which seems also roughly compatible with that date and site – at least as compatible as R1a-Y3(xY2) is for ca. 4000 BC -, so it could have been interpreted as a migrant from the South Caspian region, potentially related to Proto-Anatolians, especially before the description of the Caucasus genetic barrier in Wang et al (2018). For some reason, though, the Hajji_Firuz sample was questioned, but this one didn’t even merited an interrogation mark.

    There was already a similar situation with two samples (RISE568 and RISE569) initially reported as belonging to Czech Corded Ware groups, that turned out to be Early Slavs ca. 3,000 years younger, in turn more closely related to Bell Beaker-derived cultures of Central-East Europe. It seems little has changed since that case.

    All in all, my guess is that genomic data of I6561 would have been a priori more compatible with a later period, during the expansion of East Corded Ware groups: at least Middle Dnieper culture, potentially Multi-Cordoned Ware culture, but most likely a Srubnaya-related one, given the most likely SNP mutation and TMRCA date, and the haplogroup variability found in the few samples available from that culture.

    ukraine-eneolithic-from-srubna
    PCA of ancient Eurasian samples. Marked I6561 sample within the cluster formed by Srubnaya samples. See full PCA.

    Compatibility checks

    I tried to start a thread on the possibility that the radiocarbon date was wrong, and IF it were, how likely it would be that formal stats could actually show this, or how could we automatically prevent ancestry magic fiascos.

    In other words: if this guy were a Srubnaya-related individual actually dated e.g. ca. 1700 BC, and someone would try to ‘prove’ – based on the current open source tools alone – that he was the ancestor of expanding peoples of the 4th and 3rd millennium BC (i.e. Balkan outliers, Yamnaya, Corded Ware, you name it), could these results be formally challenged?

    I was hoping for some original brainstorming where people would propose crazy, essentially impossible to understand statistical models, say plotting dozens of well-studied mutations of different geographically related ancient samples with their reported dates, to visually highlight samples that don’t exactly fit with such a feature-based time series analysis; I mean, the kind of theoretical models I wouldn’t even be able to follow after the first two tweets or so. I didn’t receive an answer like that, but still:

    I have nothing to add to these answers, because I agree that all contradictory data are circumstancial.

    The current absolute lack of this kind of validity checks for ancestry models is disappointing, though, and leaves the so-called outliers in a dangerous limbo between “potentially very interesting samples” and “potentially wrongly dated samples”. Radiocarbon date is thus – together with compatibility of population source in terms of archaeological cultures and their potential relationship – a necessary variable to take into account in any statistical design: an error in one of these variables means a catastrophic error in the whole model.

    Formal stats

    For example, in these qpAdm models, I assumed Srubnaya, Ukraine_Eneolithic_outlier, and Bulgaria_MLBA samples were roughly coetaneous and potentially related to the Srubnaya-SabatinovkaNoua cultural horizon, hence stemming from a source close to:

    1. Abashevo-like individuals (whose best proxy to date should be Poltavka_outlier I0432) potentially admixed with Poltavka-like herders; or
    2. Potapovka-like individuals potentially admixed with Catacomb-like peoples (whose best proxy until recently were probably Yamnaya_Kalmykia*).

    *To avoid adding more potential errors by merging different datasets, I have used only proxy samples available in the Reich Lab’s curated dataset of published ancient DNA.

    srubnaya-noua-sabatinovka-mlba
    Srubnaya and Noua-Sabatinovka cultural horizon during the MLBA. See full maps.

    Apart from the lack of more models for comparison (I’m not going to dedicate more time to this), the results can’t be interpreted without a proper sampling and context, either, because (1) Poltavka_o may actually be from a much later group closely related to Srubnaya; (2) Bulgaria_MLBA is only one sample; and (3) there are only two samples from Potapovka; so the models here presented are basically useless, as many similar models that have been tested looking just for a formal “best fit”.

    So feel free to chime in and contribute with ideas as to how to detect in the future whether a sample is ancestral to or derived from others. I will post here informative answers from Twitter, too, if there are any. I don’t think a discussion about the potentially wrong date in this specific sample is very useful, because this seems impossible to prove or disprove at this point. Just what tools or data would you use to at least try and assess whether samples are compatible with its reported date or not – preferably in some kind of automated sieve that takes dozens or hundreds of samples into account.

    On the bright side, there is so much more than formal stats to arrive to relevant inferences about prehistoric populations, their movements and languages. That’s why I6561 didn’t matter for the conclusion by Anthony (2019) that it was the R1b-rich Eneolithic Don-Volga-Caucasus region the most likely Indo-Anatolian and Late Proto-Indo-European homeland, due to the creation of a wide Eneolithic mating network with extended exogamy practices, where Y-chromosome bottlenecks seem to be one of the main genomic data to take into account from the Neolithic to the Middle Bronze Age.

    And that is the same reason why it doesn’t matter that much for the Proto-Indo-European or Uralic question for me, either.

    Related

Yamnaya replaced Europeans, but admixed heavily as they spread to Asia

narasimhan-spread-yamnaya-ancestry

Recent papers The formation of human populations in South and Central Asia, by Narasimhan, Patterson et al. Science (2019) and An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers, by Shinde et al. Cell (2019).

NOTE. For direct access to Narasimhan, Patterson et al. (2019), visit this link courtesy of the first author and the Reich Lab.

I am currently not on holidays anymore, and the information in the paper is huge, with many complex issues raised by the new samples and analyses rather than solved, so I will stick to the Indo-European question, especially to some details that have changed since the publication of the preprint. For a summary of its previous findings, see the book series A Song of Sheep and Horses, in particular the sections from A Clash of Chiefs where I discuss languages and regions related to Central and South Asia.

I have updated the maps of the Preshistory Atlas, and included the most recently reported mtDNA and Y-DNA subclades. I will try to update the Eurasian PCA and related graphics, too.

NOTE. Many subclades from this paper have been reported by Kolgeh (download), Pribislav and Principe at Anthrogenica on this thread. I have checked some out for comparison, but even if it contradicted their analyses mine would be the wrong ones. I will upload my spreadsheets and link to them from this page whenever I find the time.

caucasus-cline-narasimhan
Ancestry clines (1) before and (2) after the advent of farming. Colour modified from the original to emphasize the CHG cline: notice the apparent relevance of forest-steppe groups in the formation of this CHG mating network from which Pre-Yamnaya peoples emerged.

Indo-Europeans

I think the Narasimhan, Patterson et al. (2019) paper is well-balanced, and unexpectedly centered – as it should – on the spread of Yamnaya-related ancestry (now Western_Steppe_EMBA) as the marker of Proto-Indo-European migrations, which stretched ca. 3000 BC “from Hungary in the west to the Altai mountains in the east”, spreading later Indo-European dialects after admixing with local groups, from the Atlantic to South Asia.

I. Afanasievo

I.1. East or West PIE?

I expected Afanasievo to show (1) R1b-L23(xZ2103, xL51) and (2) R1b-L51 lineages, apart from (3) the known R1b-Z2103 ones, pointing thus to an ancestral PIE community before the typical Yamnaya bottlenecks, and with R1b-L51 supporting a connection with North-West Indo-European. The presence of some samples of hg. Q pointed in this direction, too.

However, Afanasievo samples show overwhelmingly R1b-Z2103 subclades (all except for those with low coverage), all apparently under R1b-Z2108 (formed ca. 3500 BC, TMRCA ca. 3500 BC), like most samples from East Yamnaya.

This necessarily shifts the split and spread of R1b-L23 lineages to Khvalynsk/early Repin-related expansions, in line with what TMRCA suggested, and what advances by Anthony (2019) and Khokhlov (2018) on future samples from the Reich Lab suggest.

Given the almost indistinguishable ancestry between Afanasievo and Early Yamnaya, there seems to be as of yet little potential information to support in population genomics that Pre-Tocharians were more closely related to North-West Indo-Europeans than to Graeco-Aryans, as it is proposed in linguistics based on the few shared traits between them, and the lack of innovations proper of the Graeco-Aryan community.

NOTE. A new issue of Wekʷos contains an abstract from a relevant paper by Blažek on vocabulary for ‘word’, including the common NWIE *wrdʰo-/wordʰo-, but also a new (for me, at least) Northern Indo-European one: *rēki-/*rēkoi̯-, shared by Slavic and Tocharian.

The fact that bottlenecks happened around the time of the late Repin expansion suggests that we might be able to see different clans based on the predominant lineages developing around the Don-Volga area in the 4th millennium BC. The finding of Pre-R1b-L51 in Lopatino (see below), and of a Catacomb sample of hg. R1b-Z2103(Z2105-) in the North Caucasus steppe near Novoaleksandrovskij also support a star-like phylogeny of R1b-L23 stemming from the Don-Volga area.

NOTE. Interestingly, a dismissal of a common trunk between Tocharian and North-West Indo-European would mean that shared similarities between such disparate groups could be traced back to a Common Late PIE trunk, and not to a shared (western) Repin community. For an example of such a ‘pure’ East-West dialectal division, see the diagram of Adams & Mallory (2007) at the end of the post. It would thus mean a fatal blow to Kortlandt’s Indo-Slavonic group among other hypothetical groupings (remade versions of the ancient Centum-Satem division), as well as to certain assumptions about laryngeal survival or tritectalism that usually accompany them. Still, I don’t think this is the case, so the question will remain a linguistic one, and maybe some similarities will be found with enough number of samples that differentiate Northern Indo-Europeans from the East Yamna/Catacomb-Poltavka-Balkan_EBA group.

afanasievo-y-dna
Y-chromosome haplogroups of Afanasievo samples and neighbouring groups. See full maps.

I.2. Expansion or resurgence of hg. Q1b?

Haplogroup Q1b-Y6802(xY6798) seems to be the main lineage that expanded with Afanasievo, or resurged in their territory. It’s difficult to tell, because the three available samples are family, and belong to a later period.

NOTE. I have finally put some order to the chaos of Q1a vs. Q1b subclades in my spreadsheet and in the maps. The change of ISOGG 2016 to 2017 has caused that many samples reported as of Q1 subclades from papers prepared during the 2017-2018 period, and which did not provide specific SNP calls, were impossible to define with certainty. By checking some of them I could determine the specific standard used.

In favour of the presence of this haplogroup in the Pre-Yamnaya community are:

  • The statement by Anthony (2019) that Q1a [hence maybe Q1b in the new ISOGG nomenclature] represented a significant minority among an R1b-rich community.
  • The sample found in a Sintastha WSHG outlier (see below), of hg. Q1b-Y6798, and the sample from Lola, of hg. Q1b-L717, are thus from other lineage(s) separated thousands of years from the Afanasievo subclade, but might be related to the Khvalynsk expansion, like R1b-V1636 and R1b-M269 are.

These are the data that suggest multiple resurgence events in Afanasievo, rather than expanding Q1b lineages with late Repin:

  • Overwhelming presence of R1b in early Yamnaya and Afanasievo samples; one Q1(xQ1b) sample reported in Khvalynsk.
  • The three Q1b samples appear only later, although wide CI for radiocarbon dates, different sites, and indistinguishable ancestry may preclude a proper interpretation of the only available family.
    • Nevertheless, ancestry seems unimportant in the case of Afanasievo, since the same ancestry is found up to the Iron Age in a community of varied haplogroups.
  • Another sample of hg. Q1b-Y6802(xY6798) is found in Aigyrzhal_BA (ca. 2120 BC), with Central_Steppe_EMBA (WSHG-related) ancestry; however, this clade formed and expanded ca. 14000 BC.
  • The whole Altai – Baikal area seems to be a Q1b-L54 hotspot, although admittedly many subclades separated very early from each other, so they might be found throughout North Eurasia during the Neolithic.
  • One Afanasievo sample is reported as of hg. C in Shin (2017), and the same haplogroup is reported by Hollard (2014) for the only available sample of early Chemurchek to date, from Kulala ula, North Altai (ca. 2400 BC).
afanasievo-chemurchek-y-dna
Y-chromosome haplogroups of late Afanasievo – early Chemurchek samples and neighbouring groups. See full maps.

I.3. Agricultural substrate

Evidence of continuous contacts of Central_Steppe_MLBA populations with BMAC from ca. 2100 BC on – visible in the appearance of Steppe ancestry among BMAC samples and BMAC ancestry among Steppe pastoralists – supports the close interaction between Indo-Iranian pastoralists and BMAC agriculturalists as the origin of the Asian agricultural substrate found in Proto-Indo-Iranian, hence likely related to the language of the Oxus Civilization.

Similar to the European agricultural substrate adopted by West Yamnaya settlers (both NWIE and Palaeo-Balkan speakers), Tocharian shows a few substrate terms in common with Indo-Iranian, which can be explained by contacts in different dialectal stages through phonetic reconstruction alone.

The recent Hermes et al. (2019) supports the early integration of pastoralism and millet cultivation in Central Asia (ca. 2700 BC or earlier), with the spread of agriculture to the north – through the Inner Asian Mountain Corridor – being thus unrelated to the Indo-Iranian expansions, which might support independent loans.

However, compared to the huge number of parallel shared loans between NWIE and Palaeo-Balkan languages in the European substratum, Indo-Iranians seem to have been the first borrowers of vocabulary from Asian agriculturalists, while Proto-Tocharian shows just one certain related word, with phonetic similarities that warrant an adoption from late Indo-Iranian dialects.

chemurchek-sintashta-bmac
Y-chromosome haplogroups of Sintashta, Central Asia, and neighbouring groups in the Early Bronze Age. See full maps.

The finding of hg. (pre-)R1b-PH155 in a BMAC sample from Dzharkutan (to the west of Xinjiang) together with hg. R1b in a sample from Central Mongolia previously reported by Shin (2017) support the widespread presence of this lineage to the east and west of Xinjiang, which means it might have become incorporated to Indo-Iranian migrants into the Xiaohe horizon, to the Afanasievo-Chemurchek-derived groups, or the later from the former. In other words, the Island Biogeography Theory with its explanation of founder effects might be, after all, applicable to the whole Xinjiang area, not only during the Chemurchek – Tianshan-Beilu – Xiaohe interaction.

Of course, there is no need for too complicated models of haplogroup resurgence events in Central and South Asia, seeing how the total amount of hg. R1a-L657 (today prevalent among Indo-Aryan speakers from South Asia) among ancient Western/Central_Steppe_MLBA-related samples amounts to a total of 0, and that many different lineages survived in the region. Similar cases of haplogroup resurgence and Y-DNA bottleneck events are also found in the Central and Eastern Mediterranean, and in North-Eastern Europe. From the paper:

[It] could reflect stronger ecological or cultural barriers to the spread of people in South Asia than in Europe, allowing the previously established groups more time to adapt and mix with incoming groups. A second difference is the smaller proportion of Steppe pastoralist– related ancestry in South Asia compared with Europe, its later arrival by ~500 to 1000 years, and a lower (albeit still significant) male sex bias in the admixture (…).

Y-chromosome haplogroups of samples from the Srubna-Andronovo and Andronovo-related horizon, Xiaohe, late BMAC, and neighbouring groups. See full maps.

II. R1b-Beakers replaced R1a-CWC peoples

II.1. R1a-M417-rich Corded Ware

Newly reported Corded Ware samples from Radovesice show hg. R1a-M417, at least some of them xZ645, ‘archaic’ lineages shared with the early Bergrheinfeld sample (ca. 2650 BC) and with the coeval Esperstedt family, hence supporting that it eventually became the typical Western Corded Ware lineage(s), probably dominating over the so-called A-horizon and the Single Grave culture in particular. On the other hand, R1a-Z645 was typical of bottlenecks among expanding Eastern Corded Ware groups.

Interestingly, it is supported once again that known bottlenecks under hg. R1a-M417 happened during the Corded Ware expansion, evidenced also by the remarkable high variability of male lineages among early Corded Ware samples. Similarly, these Corded Ware samples from Bohemia form part of the typical ‘Central European’ cluster in the PCA, which excludes once again not only the ‘official’ Espersted outlier I1540, but also the known outlier with Yamnaya ancestry.

NOTE. The fact that Esperstedt is closely related geographically and in terms of ancestry to later Únětice samples further complicates the assumption that Únětice is a mixture of Bell Beakers and Corded Ware, being rather an admixture of incoming Bell Beakers with post-Yamnaya vanguard settlers who admixed with Corded Ware (see more on the expansion of Yamnaya ancestry). In other words, Únětice is rather an admixture of Yamnaya+EEF with Yamnaya+(CWC+EEF).

Y-chromosome haplogroups of samples from Catacomb, Poltavka, Balkan EBA, and Bell Beaker, as well as neighbouring groups. See full maps.

On Ukraine_Eneolithic I6561

If the bottlenecks are as straightforward as they appear, with a star-like phylogeny of R1a-M417 starting with the Pre-Corded Ware expansion, then what is happening with the Alexandria sample, so precisely radiocarbon dated to ca. 4045-3974 BC? The reported hg. R1a-M417 was fully compatible, while R1a-Z645 could be compatible with its date, but the few positive SNPs I got in my analysis point indeed to a potential subclade of R1a-Z94, and I trust more experienced hobbyists in this ‘art’ of ascertaining the SNPs of ancient samples, and they report hg. R1a-Z93 (Z95+, Y26+, Y2-).

Seeing how Y-DNA bottlenecks worked in Yamnaya-Afanasievo and in Corded Ware and related groups, and if this sample really is so deep within R1a-Z93 in a region that should be more strongly affected by the known Neolithic Y-chromosome bottlenecks and forest-steppe ecotone, someone from the lab responsible for this sample should check its date once again, before more people keep chasing their tails with an individual that (based on its derived SNPs’ TMRCA) might actually be dated to the Bronze Age, where it could make much more sense in terms of ancestry and position in the PCA.

EDIT (14 SEP 2019): … and with the fact that he is the first individual to show the genetic adaptation for lactase persistence (I3910-T), which is only found later among Bell Beakers, and much later in Sintashta and related Steppe_MLBA peoples (see comments below).

This is also evidenced by the other Ukraine_Eneolithic (likely a late Yamnaya) sample of hg. R1b-Z2103 from Dereivka (ca. 2800 BC) and who – despite being in a similar territory 1,000 years later – shows a wholly diluted Yamnaya ancestry under typically European HG ancestry, even more so than other late Sredni Stog samples from Dereivka of ca. 3600-3400 BC, suggesting a decrease in Steppe ancestry rather than an increase – which is supposedly what should be expected based on the ancestry from Alexandria…

Like the reported Chalcolithic individual of Hajji Firuz who showed an apparently incompatible subclade and Yamnaya ancestry at least some 1,000 years before it should, and turned out to be from the Iron Age (see below), this may be another case of wrong radiocarbon dating.

NOTE. It would be interesting, if this turns out to be another Hajji Firuz-like error, to check how well different ancestry models worked in whose hands exactly, and if anyone actually pointed out that this sample was derived, and not ancestral, to many different samples that were used in combination with it. It would also be a great control to check if those still supporting a Sredni Stog origin for PIE would shift their preference even more to the north or west, depending on where the first “true” R1a-M417 samples popped up. Such a finding now could be thus a great tool to discover whether haplogroup-based bias plays a role in ancestry magic as related to the Indo-European question, i.e. if it really is about “pure statistics”, or there is something else to it…

II.1. R1b-L51-rich Bell Beakers

The overwhelming majority of R1b-L51 lineages in Radovesice during the Bell Beaker period, just after the sampled Corded Ware individuals from the same site, further strengthen the hypothesis of an almost full replacement of R1a-M417 lineages from Central Europe up to southern Scandinavia after the arrival of Bell Beakers.

Yet another R1b-L151* sample has popped up in Central Europe, in the individual classified as Bilina_BA (ca. 2200-800 BC), which clusters with Bell Beakers from Bohemia, with the outlier from Turlojiškė, and with Early Slavs, suggesting once again that a group of central-east European Beakers represented the Pre-Proto-Balto-Slavic community before their spread and admixture events to the east.

The available ancient distribution of R1b-L51*, R1b-L52* or R1b-L151* is getting thus closer to the most likely origin of R1b-L51 in the expansion of East Bell Beakers, who trace their paternal ancestors to Yamnaya settlers from the Carpathian Basin:

NOTE. Some of these are from other sources, and some are samples I have checked in a hurry, so I may have missed some derived SNPs. If you send me a corrected SNP call to dismiss one of these, or more ‘archaic’ samples, I’ll correct the map accordingly. See also maps of modern distributionof R1b-M269 subclades.

r1b-l51-ancient-europe
Distribution of ‘archaic’ R1b-L51 subclades in ancient samples, overlaid over a map of Yamnaya and Bell Beaker migrations. In blue, Yamnaya Pre-L51 from Lopatino (not shown) and R1b-L52* from BBC Augsburg. In violet, R1b-L51 (xP312,xU106) from BBC Prague and Poland. In maroon, hg. R1b-L151* from BBC Hungary, BA Bohemia, and (not shown) a potential sample from BBC at Mondelange, which is certainly xU106, maybe xP312. Interestingly, the earliest sample of hg. R1b-U106 (a lineage more proper of northern Europe) has been found in a Bell Beaker from Radovesice (ca. 2350 BC), between two of these ‘archaic’ R1b-L51 samples; and a sample possibly of hg. R1b-ZZ11+ (ancestral to DF27 and U152) was found in a Bell Beaker from Quedlinburg, Germany (ca. 2290 BC), to the north-west of Bohemia. The oldest R1b-U152 are logically from Central Europe, too.

III. Proto-Indo-Iranian

Before the emergence of Proto-Indo-Iranian, it seems that Pre-Proto-Indo-Iranian-speaking Poltavka groups were subjected to pressure from Central_Steppe_EMBA-related peoples coming from the (south-?)east, such as those found sampled from Mereke_BA. Their ‘kurgan’ culture was dated correctly to approximately the same date as Poltavka materials, but their ancestry and hg. N2(pre-N2a) – also found in a previous sample from Botai – point to their intrusive nature, and thus to difficulties in the Pre-Proto-Indo-Iranian community to keep control over the previous East Yamnaya territory in the Don-Volga-Ural steppes.

We know that the region does not show genetic continuity with a previous period (or was not under this ‘eastern’ pressure) because of an Eastern Yamnaya sample from the same site (ca. 3100 BC) showing typical Yamnaya ancestry. Before Yamnaya, it is likely that Pre-Yamnaya ancestry formed through admixture of EHG-like Khvalynsk with a North Caspian steppe population similar to the Steppe_Eneolithic samples from the North Caucasus Piedmont (see Anthony 2019), so we can also rule out some intermittent presence of a Botai/Kelteminar-like population in the region during the Khvalynsk period.

It is very likely, then, that this competition for the same territory – coupled with the known harsher climate of the late 3rd millennium BC – led Poltavka herders to their known joint venture with Abashevo chiefs in the formation of the Sintashta-Potapovka-Filatovka community of fortified settlements. Supporting these intense contacts of Poltavka herders with Central Asian populations, late ‘outliers’ from the Volga-Ural region show admixture with typical Central_Steppe_MLBA populations: one in Potapovka (ca. 2220 BC), of hg. R1b-Z2103; and four in the Sintashta_MLBA_o1 cluster (ca. 2050-1650 BC), with two samples of hg. R1b-L23 (one R1b-Z2109), one Q1b-L56(xL53), one Q1b-Y6798.

central-steppe-pastoralists
Outlier analysis reveals ancient contacts between sites. We plot the average of principal component 1 (x axis) and principal component 2 (y axis) for the West Eurasian and All Eurasian PCA plots (…). In the Middle to Late Bronze Age Steppe, we observe, in addition to the Western_Steppe_MLBA and Central_Steppe_MLBA clusters (indistinguishable in this projection), outliers admixed with other ancestries. The BMAC-related admixture in Kazakhstan documents northward gene flow onto the Steppe and confirms the Inner Asian Mountain Corridor as a conduit for movement of people.

Similar to how the Sintashta_MLBA_o2 cluster shows an admixture with central steppe populations and hg. R1a-Z645, the WSHG ancestry in those outliers from the o1 cluster of typically (or potentially) Yamnaya lineages show that Poltavka-like herders survived well after centuries of Abashevo-Poltavka coexistence and admixture events, supporting the formation of a Proto-Indo-Iranian community from the local language as pronounced by the incomers, who dominated as elites over the fortified settlements.

The Proto-Indo-Iranian community likely formed thus in situ in the Don-Volga-Ural region, from the admixture of locals of Yamnaya ancestry with incomers of Corded Ware ancestry – represented by the ca. 67% Yamnaya-like ancestry and ca. 33% ancestry from the European cline. Their community formed thus ca. 1,000 years later than the expansion of Late PIE ca. 3500 BC, and expanded (some 500 years after that) a full-fledged Proto-Indo-Iranian language with the Srubna-Andronovo horizon, further admixing with ca. 9% of Central_Steppe_EMBA (WSHG-related) ancestry in their migration through Central Asia, as reported in the paper.

IV. Armenian

The sample from Hajji Firuz, of hg. R1b-Z2103 (xPF331), has been – as expected – re-dated to the Iron Age (ca. 1193-1019 BC), hence it may offer – together with the samples from the Levant and their Aegean-like ancestry rapidly diluted among local populations – yet another proof of how the Late Bronze Age upheaval in Europe was the cause of the Armenian migration to the Armenoid homeland, where they thrived under the strong influence from Hurro-Urartian.

middle-east-armenia-y-dna
Y-chromosome haplogroups of the Middle East and neighbouring groups during the Late Bronze Age / Iron Age. See full maps.

Indus Valley Civilization and Dravidian

A surprise came from the analysis reported by Shinde et al. (2019) of an Iran_N-related IVC ancestry which may have split earlier than 10000 BC from a source common to Iran hunter-gatherers of the Belt Cave.

For the controversial Elamo-Dravidian hypothesis of the Muscovite school, this difference in ancestry between both groups (IVC and Iran Neolithic) seems to be a death blow, if population genomics was even needed for that. Nevertheless, I guess that a full rejection of a recent connection will come down to more recent and subtle population movements in the area.

EDIT (12 SEP): Apparently, Iosif Lazaridis is not so sure about this deep splitting of ‘lineages’ as shown in the paper, so we may be talking about different contributions of AME+ANE/ENA, which means the Elamo-Dravidian game is afoot; at least in genomics:

I shared the idea that the Indus Valley Civilization was linked to the Proto-Dravidian community, so I’m inclined to support this statement by Narasimhan, Patterson, et al. (2019), even if based only on modern samples and a few ancient ones:

The strong correlation between ASI ancestry and present-day Dravidian languages suggests that the ASI, which we have shown formed as groups with ancestry typical of the Indus Periphery Cline moved south and east after the decline of the IVC to mix with groups with more AASI ancestry, most likely spoke an early Dravidian language.

india-steppe-indus-valley-andamanese-ancestry
Natural neighbour interpolation of qpAdm results – Maximum A Posteriori Estimate from the Hierarchical Model (estimates used in the Narasimhan, Patterson et al. 2019 figures) for Central_Steppe_MLBA-related (left), Indus_Periphery_West-related (center) and Andamanese_Hunter-Gatherer-related ancestry (right) among sampled modern Indian populations. In blue, peoples of IE language; in red, Dravidian; in pink, Tibeto-Burman; in black, unclassified. See full image.

I am wary of this sort of simplistic correlation with modern speakers, because we have seen what happened with the wrong assumptions about modern Balto-Slavic and Finno-Ugric speakers and their genetic profile (see e.g. here or here). In fact, I just can’t differentiate as well as those with deep knowledge in South Asian history the social stratification of the different tribal groups – with their endogamous rules under the varna and jati systems – in the ancestry maps of modern India. The pattern of ancestry and language distribution combined with the findings of ancient populations seem in principle straightforward, though.

Conclusion

The message to take home from Shinde et al. (2019) is that genomic data is fully at odds with the Anatolian homeland hypothesis – including the latest model by Heggarty (2014)* – whose relevance is still overvalued today, probably due in part to the shift of OIT proponents to more reasonable Out-of-Iran models, apparently more fashionable as a vector of Indo-Aryan languages than Eurasian steppe pastoralists?
*The authors listed this model erroneously as Heggarty (2019).

The paper seems to play with the occasional reference to Corded Ware as a vector of expansion of Indo-European languages, even after accepting the role of Yamnaya as the most evident population expanding Late PIE to western Europe – and the different ancestry that spread with Indo-Iranian to South Asia 1,000 years later. However, the most cringe-worthy aspect is the sole citation of the debunked, pseudoscientific glottochronological method used by Ringe, Warnow, and Taylor (2002) to support the so-called “steppe homeland”, a paper and dialectal scheme which keeps being referenced in papers of the Reich Lab, probably as a consequence of its use in Anthony (2007).

On the other hand, these are the equivalent simplistic comments in Narasimhan, Patterson et al. (2019):

The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique features shared between Indo-Iranian and Balto-Slavic languages. (…), which despite their vast geographic separation share the “satem” innovation and “ruki” sound laws.

mallory-adams-tree
Indo-European dialectal relationships, from Mallory and Adams (2006).

The only academic closely related to linguistics from the list of authors, as far as I know, is James P. Mallory, who has supported a North-West Indo-European dialect (including Balto-Slavic) for a long time – recently associating its expansion with Bell Beakers – opposed thus to a Graeco-Aryan group which shared certain innovations, “Satemization” not being one of them. Not that anyone needs to be a linguist to dismiss any similarities between Balto-Slavic and Indo-Iranian beyond this phonetic trend, mind you.

Even Anthony (2019) supports now R1b-rich Pre-Yamnaya and Yamnaya communities from the Don-Volga region expanding Middle and Late Proto-Indo-European dialects.

So how does the underlying Corded Ware ancestry of eastern Europe (where Pre-Balto-Slavs eventually spread to from Bell Beaker-derived groups) and of the highly admixed (“cosmopolitan”, according to the authors) Sintashta-Potapovka-Filatovka in the east relate to the similar-but-different phonetic trends of two unrelated IE dialects?

If only there was a language substrate that could (as Shinde et al. put it) “elegantly” explain this similar phonetic evolution, solving at the same time the question of the expansion of Uralic languages and their strong linguistic contacts with steppe peoples. Say, Eneolithic populations of mainly hunter-fisher-gatherers from the North Pontic forest-steppes with a stronger connection to metalworking

Related

Yamnaya ancestry: mapping the Proto-Indo-European expansions

steppe-ancestry-expansion-europe

The latest papers from Ning et al. Cell (2019) and Anthony JIES (2019) have offered some interesting new data, supporting once more what could be inferred since 2015, and what was evident in population genomics since 2017: that Proto-Indo-Europeans expanded under R1b bottlenecks, and that the so-called “Steppe ancestry” referred to two different components, one – Yamnaya or Steppe_EMBA ancestry – expanding with Proto-Indo-Europeans, and the other one – Corded Ware or Steppe_MLBA ancestry – expanding with Uralic speakers.

The following maps are based on formal stats published in the papers and supplementary materials from 2015 until today, mainly on Wang et al. (2018 & 2019), Mathieson et al. (2018) and Olalde et al. (2018), and others like Lazaridis et al. (2016), Lazaridis et al. (2017), Mittnik et al. (2018), Lamnidis et al. (2018), Fernandes et al. (2018), Jeong et al. (2019), Olalde et al. (2019), etc.

NOTE. As in the Corded Ware ancestry maps, the selected reports in this case are centered on the prototypical Yamnaya ancestry vs. other simplified components, so everything else refers to simplistic ancestral components widespread across populations that do not necessarily share any recent connection, much less a language. In fact, most of the time they clearly didn’t. They can be interpreted as “EHG that is not part of the Yamnaya component”, or “CHG that is not part of the Yamnaya component”. They can’t be read as “expanding EHG people/language” or “expanding CHG people/language”, at least no more than maps of “Steppe ancestry” can be read as “expanding Steppe people/language”. Also, remember that I have left the default behaviour for color classification, so that the highest value (i.e. 1, or white colour) could mean anything from 10% to 100% depending on the specific ancestry and period; that’s what the legend is for… But, fere libenter homines id quod volunt credunt.

Sections:

  1. Neolithic or the formation of Early Indo-European
  2. Eneolithic or the expansion of Middle Proto-Indo-European
  3. Chalcolithic / Early Bronze Age or the expansion of Late Proto-Indo-European
  4. European Early Bronze Age and MLBA or the expansion of Late PIE dialects

1. Neolithic

Anthony (2019) agrees with the most likely explanation of the CHG component found in Yamnaya, as derived from steppe hunter-fishers close to the lower Volga basin. The ultimate origin of this specific CHG-like component that eventually formed part of the Pre-Yamnaya ancestry is not clear, though:

The hunter-fisher camps that first appeared on the lower Volga around 6200 BC could represent the migration northward of un-admixed CHG hunter-fishers from the steppe parts of the southeastern Caucasus, a speculation that awaits confirmation from aDNA.

neolithic-chg-ancestry
Natural neighbor interpolation of CHG ancestry among Neolithic populations. See full map.

The typical EHG component that formed part eventually of Pre-Yamnaya ancestry came from the Middle Volga Basin, most likely close to the Samara region, as shown by the sampled Samara hunter-gatherer (ca. 5600-5500 BC):

After 5000 BC domesticated animals appeared in these same sites in the lower Volga, and in new ones, and in grave sacrifices at Khvalynsk and Ekaterinovka. CHG genes and domesticated animals flowed north up the Volga, and EHG genes flowed south into the North Caucasus steppes, and the two components became admixed.

neolithic-ehg-ancestry
Natural neighbor interpolation of EHG ancestry among Neolithic populations. See full map.

To the west, in the Dnieper-Dniester area, WHG became the dominant ancestry after the Mesolithic, at the expense of EHG, revealing a likely mating network reaching to the north into the Baltic:

Like the Mesolithic and Neolithic populations here, the Eneolithic populations of Dnieper-Donets II type seem to have limited their mating network to the rich, strategic region they occupied, centered on the Rapids. The absence of CHG shows that they did not mate frequently if at all with the people of the Volga steppes (…)

neolithic-whg-ancestry
Natural neighbor interpolation of WHG ancestry among Neolithic populations. See full map.

North-West Anatolia Neolithic ancestry, proper of expanding Early European farmers, is found up to border of the Dniester, as Anthony (2007) had predicted.

neolithic-anatolia-farmer-ancestry
Natural neighbor interpolation of Anatolia Neolithic ancestry among Neolithic populations. See full map.

2. Eneolithic

From Anthony (2019):

After approximately 4500 BC the Khvalynsk archaeological culture united the lower and middle Volga archaeological sites into one variable archaeological culture that kept domesticated sheep, goats, and cattle (and possibly horses). In my estimation, Khvalynsk might represent the oldest phase of PIE.

(…) this middle Volga mating network extended down to the North Caucasian steppes, where at cemeteries such as Progress-2 and Vonyuchka, dated 4300 BC, the same Khvalynsk-type ancestry appeared, an admixture of CHG and EHG with no Anatolian Farmer ancestry, with steppe-derived Y-chromosome haplogroup R1b. These three individuals in the North Caucasus steppes had higher proportions of CHG, overlapping Yamnaya. Without any doubt, a CHG population that was not admixed with Anatolian Farmers mated with EHG populations in the Volga steppes and in the North Caucasus steppes before 4500 BC. We can refer to this admixture as pre-Yamnaya, because it makes the best currently known genetic ancestor for EHG/CHG R1b Yamnaya genomes.

From Wang et al (2019):

Three individuals from the sites of Progress 2 and Vonyuchka 1 in the North Caucasus piedmont steppe (‘Eneolithic steppe’), which harbour EHG and CHG related ancestry, are genetically very similar to Eneolithic individuals from Khvalynsk II and the Samara region. This extends the cline of dilution of EHG ancestry via CHG-related ancestry to sites immediately north of the Caucasus foothills

eneolithic-pre-yamnaya-ancestry
Natural neighbor interpolation of Pre-Yamnaya ancestry among Neolithic populations. See full map. This map corresponds roughly to the map of Khvalynsk-Novodanilovka expansion, and in particular to the expansion of horse-head pommel-scepters (read more about Khvalynsk, and specifically about horse symbolism)

NOTE. Unpublished samples from Ekaterinovka have been previously reported as within the R1b-L23 tree. Interestingly, although the Varna outlier is a female, the Balkan outlier from Smyadovo shows two positive SNP calls for hg. R1b-M269. However, its poor coverage makes its most conservative haplogroup prediction R-M343.

The formation of this Pre-Yamnaya ancestry sets this Volga-Caucasus Khvalynsk community apart from the rest of the EHG-like population of eastern Europe.

eneolithic-ehg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya EHG ancestry among Eneolithic populations. See full map.

Anthony (2019) seems to rely on ADMIXTURE graphics when he writes that the late Sredni Stog sample from Alexandria shows “80% Khvalynsk-type steppe ancestry (CHG&EHG)”. While this seems the most logical conclusion of what might have happened after the Suvorovo-Novodanilovka expansion through the North Pontic steppes (see my post on “Steppe ancestry” step by step), formal stats have not confirmed that.

In fact, analyses published in Wang et al. (2019) rejected that Corded Ware groups are derived from this Pre-Yamnaya ancestry, a reality that had been already hinted in Narasimhan et al. (2018), when Steppe_EMBA showed a poor fit for expanding Srubna-Andronovo populations. Hence the need to consider the whole CHG component of the North Pontic area separately:

eneolithic-chg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya CHG ancestry among Eneolithic populations. See full map. You can read more about population movements in the late Sredni Stog and closer to the Proto-Corded Ware period.

NOTE. Fits for WHG + CHG + EHG in Neolithic and Eneolithic populations are taken in part from Mathieson et al. (2019) supplementary materials (download Excel here). Unfortunately, while data on the Ukraine_Eneolithic outlier from Alexandria abounds, I don’t have specific data on the so-called ‘outlier’ from Dereivka compared to the other two analyzed together, so these maps of CHG and EHG expansion are possibly showing a lesser distribution to the west than the real one ca. 4000-3500 BC.

eneolithic-whg-ancestry
Natural neighbor interpolation of WHG ancestry among Eneolithic populations. See full map.

Anatolia Neolithic ancestry clearly spread to the east into the north Pontic area through a Middle Eneolithic mating network, most likely opened after the Khvalynsk expansion:

eneolithic-anatolia-farmer-ancestry
Natural neighbor interpolation of Anatolia Neolithic ancestry among Eneolithic populations. See full map.
eneolithic-iran-chl-ancestry
Natural neighbor interpolation of Iran Chl. ancestry among Eneolithic populations. See full map.

Regarding Y-chromosome haplogroups, Anthony (2019) insists on the evident association of Khvalynsk, Yamnaya, and the spread of Pre-Yamnaya and Yamnaya ancestry with the expansion of elite R1b-L754 (and some I2a2) individuals:

eneolithic-early-y-dna
Y-DNA haplogroups in West Eurasia during the Early Eneolithic in the Pontic-Caspian steppes. See full map, and see culture, ADMIXTURE, Y-DNA, and mtDNA maps of the Early Eneolithic and Late Eneolithic.

3. Early Bronze Age

Data from Wang et al. (2019) show that Corded Ware-derived populations do not have good fits for Eneolithic_Steppe-like ancestry, no matter the model. In other words: Corded Ware populations show not only a higher contribution of Anatolia Neolithic ancestry (ca. 20-30% compared to the ca. 2-10% of Yamnaya); they show a different EHG + CHG combination compared to the Pre-Yamnaya one.

eneolithic-steppe-best-fits
Supplementary Table 13. P values of rank=2 and admixture proportions in modelling Steppe ancestry populations as a three-way admixture of Eneolithic steppe Anatolian_Neolithic and WHG using 14 outgroups.
Left populations: Test, Eneolithic_steppe, Anatolian_Neolithic, WHG.
Right populations: Mbuti.DG, Ust_Ishim.DG, Kostenki14, MA1, Han.DG, Papuan.DG, Onge.DG, Villabruna, Vestonice16, ElMiron, Ethiopia_4500BP.SG, Karitiana.DG, Natufian, Iran_Ganj_Dareh_Neolithic.

Yamnaya Kalmykia and Afanasievo show the closest fits to the Eneolithic population of the North Caucasian steppes, rejecting thus sizeable contributions from Anatolia Neolithic and/or WHG, as shown by the SD values. Both probably show then a Pre-Yamnaya ancestry closest to the late Repin population.

wang-eneolithic-steppe-caucasus-yamnaya
Modelling results for the Steppe and Caucasus cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional AF ancestry in Steppe groups and additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups. See tables above. Modified from Wang et al. (2019). Within a blue square, Yamnaya-related groups; within a cyan square, Corded Ware-related groups. Green background behind best p-values. In red circle, SD of AF/WHG ancestry contribution in Afanasevo and Yamnaya Kalmykia, with ranges that almost include 0%.

EBA maps include data from Wang et al. (2018) supplementary materials, specifically unpublished Yamnaya samples from Hungary that appeared in analysis of the preprint, but which were taken out of the definitive paper. Their location among Yamnaya settlers from Hungary is speculative, although most uncovered kurgans in Hungary are concentrated in the Tisza-Danube interfluve.

eba-yamnaya-ancestry
Natural neighbor interpolation of Pre-Yamnaya ancestry among Early Bronze Age populations. See full map. This map corresponds roughly with the known expansion of late Repin/Yamnaya settlers.

The Y-chromosome bottleneck of elite males from Proto-Indo-European clans under R1b-L754 and some I2a2 subclades, already visible in the Khvalynsk sampling, became even more noticeable in the subsequent expansion of late Repin/early Yamnaya elites under R1b-L23 and I2a-L699:

chalcolithic-early-y-dna
Y-DNA haplogroups in West Eurasia during the Yamnaya expansion. See full map and maps of cultures, ADMIXTURE, Y-DNA, and mtDNA of the Early Chalcolithic and Yamnaya Hungary.

Maps of CHG, EHG, Anatolia Neolithic, and probably WHG show the expansion of these components among Corded Ware-related groups in North Eurasia, apart from other cultures close to the Caucasus:

NOTE. For maps with actual formal stats of Corded Ware ancestry from the Early Bronze Age to the modern times, you can read the post Corded Ware ancestry in North Eurasia and the Uralic expansion.

eba-chg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya CHG ancestry among Early Bronze Age populations. See full map.
eba-ehg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya EHG ancestry among Early Bronze Age populations. See full map.
eba-whg-ancestry
Natural neighbor interpolation of WHG ancestry among Early Bronze Age populations. See full map.
eba-anatolia-farmer-ancestry
Natural neighbor interpolation of Anatolia Neolithic ancestry among Early Bronze Age populations. See full map.
eba-iran-chl-ancestry
Natural neighbor interpolation of Iran Chl. ancestry among Early Bronze Age populations. See full map.

4. Middle to Late Bronze Age

The following maps show the most likely distribution of Yamnaya ancestry during the Bell Beaker-, Balkan-, and Sintashta-Potapovka-related expansions.

4.1. Bell Beakers

The amount of Yamnaya ancestry is probably overestimated among populations where Bell Beakers replaced Corded Ware. A map of Yamnaya ancestry among Bell Beakers gets trickier for the following reasons:

  • Expanding Repin peoples of Pre-Yamnaya ancestry must have had admixture through exogamy with late Sredni Stog/Proto-Corded Ware peoples during their expansion into the North Pontic area, and Sredni Stog in turn had probably some Pre-Yamnaya admixture, too (although they don’t appear in the simplistic formal stats above). This is supported by the increase of Anatolia farmer ancestry in more western Yamna samples.
  • Later, Yamnaya admixed through exogamy with Corded Ware-like populations in Central Europe during their expansion. Even samples from the Middle to Upper Danube and around the Lower Rhine will probably show increasing contributions of Steppe_MLBA, at the same time as they show an increasing proportion of EEF-related ancestry.
  • To complicate things further, the late Corded Ware Espersted family (from ca. 2500 BC or later) shows, in turn, what seems like a recent admixture with Yamnaya vanguard groups, with the sample of highest Yamnaya ancestry being the paternal uncle of other individuals (all of hg. R1a-M417), suggesting that there might have been many similar Central European mating networks from the mid-3rd millennium BC on, of (mainly) Yamnaya-like R1b elites displaying a small proportion of CW-like ancestry admixing through exogamy with Corded Ware-like peoples who already had some Yamnaya ancestry.
mlba-yamnaya-ancestry
Natural neighbor interpolation of Yamnaya ancestry among Middle to Late Bronze Age populations (Esperstedt CWC site close to BK_DE, label is hidden by BK_DE_SAN). See full map. You can see how this map correlated with the map of Late Copper Age migrations and Yamanaya into Bell Beaker expansion.

NOTE. Terms like “exogamy”, “male-driven migration”, and “sex bias”, are not only based on the Y-chromosome bottlenecks visible in the different cultural expansions since the Palaeolithic. Despite the scarce sampling available in 2017 for analysis of “Steppe ancestry”-related populations, it appeared to show already a male sex bias in Goldberg et al. (2017), and it has been confirmed for Neolithic and Copper Age population movements in Mathieson et al. (2018) – see Supplementary Table 5. The analysis of male-biased expansion of “Steppe ancestry” in CWC Esperstedt and Bell Beaker Germany is, for the reasons stated above, not very useful to distinguish their mutual influence, though.

Based on data from Olalde et al. (2019), Bell Beakers from Germany are the closest sampled ones to expanding East Bell Beakers, and those close to the Rhine – i.e. French, Dutch, and British Beakers in particular – show a clear excess “Steppe ancestry” due to their exogamy with local Corded Ware groups:

Only one 2-way model fits the ancestry in Iberia_CA_Stp with P-value>0.05: Germany_Beaker + Iberia_CA. Finding a Bell Beaker-related group as a plausible source for the introduction of steppe ancestry into Iberia is consistent with the fact that some of the individuals in the Iberia_CA_Stp group were excavated in Bell Beaker associated contexts. Models with Iberia_CA and other Bell Beaker groups such as France_Beaker (P-value=7.31E-06), Netherlands_Beaker (P-value=1.03E-03) and England_Beaker (P-value=4.86E-02) failed, probably because they have slightly higher proportions of steppe ancestry than the true source population.

olalde-iberia-chalcolithic

The exogamy with Corded Ware-like groups in the Lower Rhine Basin seems at this point undeniable, as is the origin of Bell Beakers around the Middle-Upper Danube Basin from Yamnaya Hungary.

To avoid this excess “Steppe ancestry” showing up in the maps, since Bell Beakers from Germany pack the most Yamnaya ancestry among East Bell Beakers outside Hungary (ca. 51.1% “Steppe ancestry”), I equated this maximum with BK_Scotland_Ach (which shows ca. 61.1% “Steppe ancestry”, highest among western Beakers), and applied a simple rule of three for “Steppe ancestry” in Dutch and British Beakers.

NOTE. Formal stats for “Steppe ancestry” in Bell Beaker groups are available in Olalde et al. (2018) supplementary materials (PDF). I didn’t apply this adjustment to Bk_FR groups because of the R1b Bell Beaker sample from the Champagne/Alsace region reported by Samantha Brunel that will pack more Yamnaya ancestry than any other sampled Beaker to date, hence probably driving the Yamnaya ancestry up in French samples.

The most likely outcome in the following years, when Yamnaya and Corded Ware ancestry are investigated separately, is that Yamnaya ancestry will be much lower the farther away from the Middle and Lower Danube region, similar to the case in Iberia, so the map above probably overestimates this component in most Beakers to the north of the Danube. Even the late Hungarian Beaker samples, who pack the highest Yamnaya ancestry (up to 75%) among Beakers, represent likely a back-migration of Moravian Beakers, and will probably show a contribution of Corded Ware ancestry due to the exogamy with local Moravian groups.

Despite this decreasing admixture as Bell Beakers spread westward, the explosive expansion of Yamnaya R1b male lineages (in words of David Reich) and the radical replacement of local ones – whether derived from Corded Ware or Neolithic groups – shows the true extent of the North-West Indo-European expansion in Europe:

chalcolithic-late-y-dna
Y-DNA haplogroups in West Eurasia during the Bell Beaker expansion. See full map and see maps of cultures, ADMIXTURE, Y-DNA, and mtDNA of the Late Copper Age and of the Yamnaya-Bell Beaker transition.

4.2. Palaeo-Balkan

There is scarce data on Palaeo-Balkan movements yet, although it is known that:

  1. Yamnaya ancestry appears among Mycenaeans, with the Yamnaya Bulgaria sample being its best current ancestral fit;
  2. the emergence of steppe ancestry and R1b-M269 in the eastern Mediterranean was associated with Ancient Greeks;
  3. Thracians, Albanians, and Armenians also show R1b-M269 subclades and “Steppe ancestry”.

4.3. Sintashta-Potapovka-Filatovka

Interestingly, Potapovka is the only Corded Ware derived culture that shows good fits for Yamnaya ancestry, despite having replaced Poltavka in the region under the same Corded Ware-like (Abashevo) influence as Sintashta.

This proves that there was a period of admixture in the Pre-Proto-Indo-Iranian community between CWC-like Abashevo and Yamnaya-like Catacomb-Poltavka herders in the Sintashta-Potapovka-Filatovka community, probably more easily detectable in this group because of the specific temporal and geographic sampling available.

srubnaya-yamnaya-ehg-chg-ancestry
Supplementary Table 14. P values of rank=3 and admixture proportions in modelling Steppe ancestry populations as a four-way admixture of distal sources EHG, CHG, Anatolian_Neolithic and WHG using 14 outgroups.
Left populations: Steppe cluster, EHG, CHG, WHG, Anatolian_Neolithic
Right populations: Mbuti.DG, Ust_Ishim.DG, Kostenki14, MA1, Han.DG, Papuan.DG, Onge.DG, Villabruna, Vestonice16, ElMiron, Ethiopia_4500BP.SG, Karitiana.DG, Natufian, Iran_Ganj_Dareh_Neolithic.

Srubnaya ancestry shows a best fit with non-Pre-Yamnaya ancestry, i.e. with different CHG + EHG components – possibly because the more western Potapovka (ancestral to Proto-Srubnaya Pokrovka) also showed good fits for it. Srubnaya shows poor fits for Pre-Yamnaya ancestry probably because Corded Ware-like (Abashevo) genetic influence increased during its formation.

On the other hand, more eastern Corded Ware-derived groups like Sintashta and its more direct offshoot Andronovo show poor fits with this model, too, but their fits are still better than those including Pre-Yamnaya ancestry.

mlba-ehg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya EHG ancestry among Middle to Late Bronze Age populations. See full map.
mlba-chg-ancestry
Natural neighbor interpolation of non-Pre-Yamnaya CHG ancestry among Middle to Late Bronze Age populations. See full map.
mlba-anatolia-farmer-ancestry
Natural neighbor interpolation of Anatolia Neolithic ancestry among Middle to Late Bronze Age populations. See full map.
mlba-iran-chl-ancestry
Natural neighbor interpolation of Iran Chl. ancestry among Middle to Late Bronze Age populations. See full map.

NOTE For maps with actual formal stats of Corded Ware ancestry from the Early Bronze Age to the modern times, you should read the post Corded Ware ancestry in North Eurasia and the Uralic expansion instead.

The bottleneck of Proto-Indo-Iranians under R1a-Z93 was not yet complete by the time when the Sintashta-Potapovka-Filatovka community expanded with the Srubna-Andronovo horizon:

early-bronze-age-y-dna
Y-DNA haplogroups in West Eurasia during the European Early Bronze Age. See full map and see maps of cultures, ADMIXTURE, Y-DNA, and mtDNA of the Early Bronze Age.

4.4. Afanasevo

At the end of the Afanasevo culture, at least three samples show hg. Q1b (ca. 2900-2500 BC), which seemed to point to a resurgence of local lineages, despite continuity of the prototypical Pre-Yamnaya ancestry. On the other hand, Anthony (2019) makes this cryptic statement:

Yamnaya men were almost exclusively R1b, and pre-Yamnaya Eneolithic Volga-Caspian-Caucasus steppe men were principally R1b, with a significant Q1a minority.

Since the only available samples from the Khvalynsk community are R1b (x3), Q1a(x1), and R1a(x1), it seems strange that Anthony would talk about a “significant minority”, unless Q1a (potentially Q1b in the newer nomenclature) will pop up in some more individuals of those ca. 30 new to be published. Because he also mentions I2a2 as appearing in one elite burial, it seems Q1a (like R1a-M459) will not appear under elite kurgans, although it is still possible that hg. Q1a was involved in the expansion of Afanasevo to the east.

middle-bronze-age-y-dna
Y-DNA haplogroups in West Eurasia during the Middle Bronze Age. See full map and see maps of cultures, ADMIXTURE, Y-DNA, and mtDNA of the Middle Bronze Age and the Late Bronze Age.

Okunevo, which replaced Afanasevo in the Altai region, shows a majority of hg. Q1b, but also some R1b-M269 samples proper of Afanasevo, suggesting partial genetic continuity.

NOTE. Other sampled Siberian populations clearly show a variety of Q subclades that likely expanded during the Palaeolithic, such as Baikal EBA samples from Ust’Ida and Shamanka with a majority of Q1b, and hg. Q reported from Elunino, Sagsai, Khövsgöl, and also among peoples of the Srubna-Andronovo horizon (the Krasnoyarsk MLBA outlier), and in Karasuk.

From Damgaard et al. Science (2018):

(…) in contrast to the lack of identifiable admixture from Yamnaya and Afanasievo in the CentralSteppe_EMBA, there is an admixture signal of 10 to 20% Yamnaya and Afanasievo in the Okunevo_EMBA samples, consistent with evidence of western steppe influence. This signal is not seen on the X chromosome (qpAdm P value for admixture on X 0.33 compared to 0.02 for autosomes), suggesting a male-derived admixture, also consistent with the fact that 1 of 10 Okunevo_EMBA males carries a R1b1a2a2 Y chromosome related to those found in western pastoralists. In contrast, there is no evidence of western steppe admixture among the more eastern Baikal region region Bronze Age (~2200 to 1800 BCE) samples.

This Yamnaya ancestry has been also recently found to be the best fit for the Iron Age population of Shirenzigou in Xinjiang – where Tocharian languages were attested centuries later – despite the haplogroup diversity acquired during their evolution, likely through an intermediate Chemurchek culture (see a recent discussion on the elusive Proto-Tocharians).

Haplogroup diversity seems to be common in Iron Age populations all over Eurasia, most likely due to the spread of different types of sociopolitical structures where alliances played a more relevant role in the expansion of peoples. A well-known example of this is the spread of Akozino warrior-traders in the whole Baltic region under a partial N1a-VL29-bottleneck associated with the emerging chiefdom-based systems under the influence of expanding steppe nomads.

early-iron-age-y-dna
Y-DNA haplogroups in West Eurasia during the Early Iron Age. See full map and see maps of cultures, ADMIXTURE, Y-DNA, and mtDNA of the Early Iron Age and Late Iron Age.

Surprisingly, then, Proto-Tocharians from Shirenzigou pack up to 74% Yamnaya ancestry, in spite of the 2,000 years that separate them from the demise of the Afanasevo culture. They show more Yamnaya ancestry than any other population by that time, being thus a sort of Late PIE fossils not only in their archaic dialect, but also in their genetic profile:

shirenzigou-afanasievo-yamnaya-andronovo-srubna-ulchi-han

The recent intrusion of Corded Ware-like ancestry, as well as the variable admixture with Siberian and East Asian populations, both point to the known intense Old Iranian and Old/Middle Chinese contacts. The scarce Proto-Samoyedic and Proto-Turkic loans in Tocharian suggest a rather loose, probably more distant connection with East Uralic and Altaic peoples from the forest-steppe and steppe areas to the north (read more about external influences on Tocharian).

Interestingly, both R1b samples, MO12 and M15-2 – likely of Asian R1b-PH155 branch – show a best fit for Andronovo/Srubna + Hezhen/Ulchi ancestry, suggesting a likely connection with Iranians to the east of Xinjiang, who later expanded as the Wusun and Kangju. How they might have been related to Huns and Xiongnu individuals, who also show this haplogroup, is yet unknown, although Huns also show hg. R1a-Z93 (probably most R1a-Z2124) and Steppe_MLBA ancestry, earlier associated with expanding Iranian peoples of the Srubna-Andronovo horizon.

All in all, it seems that prehistoric movements explained through the lens of genetic research fit perfectly well the linguistic reconstruction of Proto-Indo-European and Proto-Uralic.

Related

Iron Age Tocharians of Yamnaya ancestry from Afanasevo show hg. R1b-M269 and Q1a1

New open access Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan, by Ning et al. Current Biology (2019).

Interesting excerpts (emphasis mine, changes for clarity):

Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.

Haplogroups

The dominant mtDNA lineages of the Shirenzigou people are commonly found in modern and ancient West Eurasian populations, such as U4, U5, and H, while they also have East Eurasian-specific haplogroups A, D4, and G3, preliminarily documenting admixed ancestry from eastern and western Eurasia.

The admixture profile is also shown on the paternal Y chromosome side that 4 out of 6 males in Shirenzigou (Figure S2) belong to the West Eurasian-specific haplogroup R1b (n = 2) and East Eurasian-specific haplogroup Q1a (n = 2), the former is predominant in ancient Yamnaya and nearly 100% in Afanasievo, different from the Middle and Late Bronze Age Steppe groups (Steppe_MLBA) such as Andronovo, [Potapovka], Srubnaya, and Sintashta whose Y chromosomal haplogroup is mainly R1a.

tocharians-y-dna-mtdna

Autosomal

We first carried out principal component analysis (PCA) to assess the genetic affinities of the ancient individuals qualitatively by projecting them onto present-day Eurasian variation (Figure 2). We observed a distinct separation between East and West Eurasians. Our ancient Shirenzigou samples and present-day populations from Central Asia and northwestern China form a genetic cline from East to West in the first PC. The distribution of Shirenzigou samples on the cline is relatively scattered with two major clusters, one being closer to modern-day Uygurs and Kazakhs and the other being closer to recently published ancient Saka and Huns from the Tianshan in Kazakhstan (…).

We applied a formal admixture test using f3 statistics in the form of f3 (Shirenzigou; X, Y) where X and Y are worldwide populations that might be the genetic sources for the Shirenzigou individuals. We observed the most significant signals of admixture in the Shirenzigou samples when using Yamnaya_Samara or Srubnaya as the West Eurasian source and some Northern Asians or Koreans as the East Eurasian source (Table S1). We also plotted the outgroup f3 statistics in the form of f3 (Mbuti; X, Anatolia_Neolithic) and f3 (Mbuti; X, Kostenki14) to visualize the allele sharing between population X and Anatolian farmers. As shown in Figure S3, the Steppe_MLBA populations including Srubnaya, Andronovo, and Sintashta were shifted toward farming populations compared with Yamnaya groups and the Shirenzigou samples. This observation is consistent with ADMIXTURE analysis that Steppe_MLBA populations have an Anatolian and European farmer-related component that Yamnaya groups and the Shirenzigou individuals do not seem to have. The analysis consistently suggested Yamnaya-related Steppe populations were the better source in modeling the West Eurasian ancestry in Shirenzigou.

tocharians-pca-admixture
PCA and ADMIXTURE for Shirenzigou Samples. Modified from the original to include in black squares samples related to Yamnaya.

Genetic Composition of Iron Age Shirenzigou Individuals

We continued to use qpAdm to estimate the admixture proportions in the Shirenzigou samples by using different pairs of source populations, such as Yamnaya_Samara, Afanasievo, Srubnaya, Andronovo, BMAC culture (Bustan_BA and Sappali_Tepe_BA) and Tianshan_Hun as the West Eurasian source and Han, Ulchi, Hezhen, Shamanka_EN as the East Eurasian source. In all cases, Yamnaya, Afanasievo, or Tianshan_Hun always provide the best model fit for the Shirenzigou individuals, while Srubnaya, Andronovo, Bustan_BA and Sappali_Tepe_BA only work in some cases. The Yamnaya_Samara or Afanasievo-related ancestry ranges from ∼20% to 80% in different Shirenzigou individuals, consistent with the scattered distribution on the East-West cline in the PCA

ancestry-tocharians

(…) we then modeled Shirenzigou as a three-way admixture of Yamnaya_Samara, Ulchi (or Hezhen) and Han to infer the source from the East Eurasia side that contributed to Shirenzigou. We found the Ulchi or Hezhen and Han-related ancestry had a complicated and unevenly distribution in the Shirenzigou samples. The most Shirenzigou individuals derived the majority of their East Eurasian ancestry from Ulchi or Hezhen-related populations, while the following two individuals M820 and M15-2 have more Han related than Ulchi/Hezhen-related ancestry.

One important question remains, though: how and when did these Proto-Tocharian speakers migrate from the Afanasevo culture in the Altai into the Tarim Basin? The traditional answer, now more likely than ever, is through the Chemurchek culture. See e.g. A re-analysis of the Qiemu’erqieke (Shamirshak) cemeteries, Xinjiang, China, by Jia and Betts JIES (2010) 38(4).

Also, given the apparent lack of (extra farmer ancestry that characterizes) Corded Ware ancestry, if the results were already suspicious before, how likely are now the published R1a(xZ93) and/or radiocarbon dates of the Xiaohe mummies from Li et al. (2010, 2015)? Because, after all, one should have expected in such a late date a generalized admixture with neighbouring Srubna/Andronovo-like populations.

Related

Złota a GAC-CWC transitional group…but not the origin of Corded Ware peoples

koszyce-gac-zlota-cwc

Open access Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave, by Schroeder et al. PNAS (2019).

Interesting excerpts of the paper and supplementary materials, about the Złota group variant of Globular Amphora (emphasis mine):

A special case is the so-called Złota group, which emerged around 2,900 BCE in the northern part of the Małopolska Upland and existed until 2,600-2,500 BCE. Originally defined as a separate archaeological “culture” (15), this group is mainly defined by the rather local introduction of a distinct form of burial in the area mentioned. Distinct Złota settlements have not yet been identified. Nonetheless, because of the character of its burial practices and material culture, which both retain many elements of the GAC and yet point forward to the Corded Ware tradition, and because of its geographical location, the Złota group has attracted significant archaeological attention (15, 16).

The Złota group buried their dead in a new, distinct type of funerary structure; so-called niche graves (also called catacomb graves). These structures featured an entrance shaft or pit and, below that, a more or less extensive niche, sometimes connected to the entrance area by a narrow corridor. Local limestone was used to seal off the entrance shaft and to pave the floor of the niche, on which the dead were usually placed along with grave goods. This specific and relatively sophisticated form of burial probably reflects contacts between the northern Małopolska Upland and the steppe and forest-steppe communities further to the east, who also buried their dead in a form of catacomb graves. Individual cases of the use of ochre and of deformation of skulls in Złota burials provide further indications of such a connection (15). At the same time, the Złota niche grave practice also retains central elements of the GAC funerary tradition, such as the frequent practice of multiple burials in one grave, often entailing redeposition and violation of the anatomical order of corpses, and thus differs from the catacomb grave customs found on the steppes which are strongly dominated by single graves. Nonetheless, at Złota group cemeteries single burial graves appear, and even in multiple burial graves the identity of each individual is increasingly emphasized, e.g. by careful deposition of the body and through the personal nature of grave goods (16).

globular-amphorae-corded-ware-zlota-amphorae
Correspondence analysis of amphorae from the Złota-graveyards reveals that there is no typological break between Globular Amphorae and Corded Ware Amphorae, including ‘Strichbündelamphorae’ (after Furholt 2008)

Just like its burial practices, the material culture and grave goods of the Złota group combine elements of the GAC, such as amber ornaments and central parts of the ceramic inventory, with elements also found in the Corded Ware tradition, such as copper ornaments, stone shaft-hole axes, bone and shell ornaments, and other stylistic features of the ceramic inventory. In particular, Złota group ceramic styles have been seen as a clear transitional phenomenon between classical GAC styles and the subsequent Corded Ware ceramics, probably playing a key role in the development of the typical cord decoration patterns that came to define the latter (17).

As briefly summarized above, the Złota group displays a distinct funerary tradition and combination of material culture traits, which give the clear impression of a cultural “transitional situation”. While the group also appears to have had long-distance contacts directed elsewhere (e.g. to Baden communities to the south), it is the combination of Globular Amphora traits, on the one hand, and traits found among late Yamnaya or Catacomb Grave groups to the east as well as the closely related Corded Ware groups that emerged around 2,800 BCE, on the other hand, that is such a striking feature of the Złota group and which makes it interesting when attempting to understand cultural and demographic dynamics in Central and Eastern Europe during the early 3rd millennium BCE.

catacomb-grave-ksiaznice
Catacomb grave no. 2a/06 from Książnice, Złota culture (acc. to Wilk 2013). Image from Włodarczak (2017)

Książnice (site 2, grave 3ZC), Świętokrzyskie province. This burial, a so-called niche grave of the Złota type (with a vertical entrance shaft and perpendicularly situated niche), was excavated in 2006 and contained the remains of 8 individuals, osteologically identified as three adult females and five children, positioned on limestone pavement in the niche part of the grave. Radiocarbon dating of the human remains indicates that the grave dates to 2900-2630 BCE, 95.4% probability (Dataset S1). The grave had an oval entrance shaft with a diameter of 60 cm and depth of 130 cm; the depth of the niche reached to 170 cm (both measured from the modern surface), and it also contained a few animal bones, a few flint artefacts and four ceramic vessels typical of the Złota group. Książnice is located in the western part of the Małopolska Upland, which only has a few Złota group sites but a stronger presence of other, contemporary groups (including variants of the Baden culture).

Wilczyce (site 90, grave 10), Świętokrzyskie province. A rescue excavation in 2001 uncovered a niche grave of the Złota type, which had a round entrance shaft measuring 90 cm in diameter. The grave was some 60-65 cm deep below the modern surface and the bottom of the niche was paved with thin limestone plates, on which remains of three individuals had been placed; two adults, one female and one male, and one child. Four ceramic vessels of Złota group type were deposited in the niche along with the bodies. Wilczyce is located in the Sandomierz Upland, an area with substantial presence of both the Globular Amphora culture and Złota group, as well as the Corded Ware culture from 2800 BCE.

zlota-gac-cwc
Genetic affinities of the Koszyce individuals and other GAC groups (here including Złota) analyzed in this study. (A) Principal component analysis of previously published and newly sequenced ancient individuals. Ancient genomes were projected onto modern reference populations, shown in gray. (B) Ancestry proportions based on supervised ADMIXTURE analysis (K = 3), specifying Western hunter-gatherers, Anatolian Neolithic farmers, and early Bronze Age steppe populations as ancestral source populations. LP, Late Paleolithic; M, Mesolithic; EN, Early Neolithic; MN, Middle Neolithic; LN, Late Neolithic; EBA, Early Bronze Age; PWC, Pitted Ware culture; TRB, Trichterbecherkultur/Funnelbeaker culture; LBK, Linearbandkeramik/Linear Pottery culture; GAC, Globular Amphora culture; Złota, Złota culture. Image modified to outline in red GAC and Złota groups.

To further investigate the ancestry of the Globular Amphora individuals, we performed a supervised ADMIXTURE (6) analysis, specifying typical western European hunter-gatherers (Loschbour), early Neolithic Anatolian farmers (Barcın), and early Bronze Age steppe populations (Yamnaya) as ancestral source populations (Fig. 2B). The results indicate that the Globular Amphora/Złota group individuals harbor ca. 30% western hunter-gatherer and 70% Neolithic farmer ancestry, but lack steppe ancestry. To formally test different admixture models and estimate mixture proportions, we then used qpAdm (7) and find that the Polish Globular Amphora/Złota group individuals can be modeled as a mix of western European hunter-gatherer (17%) and Anatolian Neolithic farmer (83%) ancestry (SI Appendix, Table S2), mirroring the results of previous studies.

zlota-steppe-ancestry-cwc
Table S2. qpADM results. The ancestry of most Globular Amphora/Złota group individuals
can be modelled as a two-way mixture of Mesolithic western hunter-gatherers (WHG), and early Anatolian Neolithic farmers (Barcın). The five individuals from Książnice (Złota group) show evidence for additional gene flow, most likely from an eastern source.

The lack of a direct genetic connection of Corded Ware peoples with the Złota group despite their common “steppe-like traits” – shared with Yamna – reveals, once more, how the few “Yamna-like” traits of Corded Ware do not support a direct connection with Indo-Europeans, and are the result of the expansion of the so-called steppe package all over Europe, and particularly among cultures closely related to the Khvalynsk expansion, and later under the influence of expanding Yamna peoples.

The results from Książnice may support that early Corded Ware peoples were in close contact with GAC peoples in Lesser Poland during the complex period of GAC-Trypillia-CWC interactions, and especially close to the Złota group at the beginning of the 3rd millennium BC. Nevertheless, patrilineal clans of Złota apparently correspond to Globular Amphorae populations, with the only male sample available yet being within haplogroup I2a-L801, prevalent in GAC.

NOTE. The ADMIXTURE of Złota samples in common with GAC samples (and in contrast with the shared Sredni Stog – Corded Ware “steppe ancestry”) makes the possibility of R1a-M417 popping up in the Złota group from now on highly unlikely. If it happened, that would complicate further the available picture of unusually diverse patrilineal clans found among Uralic speakers expanding with early Corded Ware groups, in contrast with the strict patrilineal and patrilocal culture of Indo-Europeans as found in Repin, Yamna and Bell Beakers.

Once again the traditional links between groups hypothesized by archaeologists – like Gimbutas and Kristiansen in this case – are wrong, as is the still fashionable trend in descriptive archaeology, of supporting 1) wide cultural relationships in spite of clear-cut inter-cultural differences (and intra-cultural uniformity kept over long distances by genetically-related groups), 2) peaceful interactions among groups based on few common traits, and 3) regional population continuities despite cultural change. These generalized ideas made some propose a steppe language shared between Pontic-Caspian groups, most of which have been proven to be radically different in culture and genetics.

gimbutas-kurgan-indo-european
The background shading indicates the tree migratory waves proposed by Marija Gimbutas, and personally checked by her in 1995. Image from Tassi et al. (2017).

Furthermore, paternal lines show once again marked bottlenecks in expanding Neolithic cultures, supporting their relevance to follow the ethnolinguistic identity of different cultural groups. The steppe- or EHG-related ancestry (if it is in fact from early Corded Ware peoples) in Książnice was thus probably, as in the case of Trypillia, in the form of exogamy with females of neighbouring groups:

The presence of unrelated females and related males in the grave is interesting because it suggests that the community at Koszyce was organized along patrilineal lines of descent, adding to the mounting evidence that this was the dominant form of social organization among Late Neolithic communities in Central Europe. Usually, patrilineal forms of social organization go hand in hand with female exogamy (i.e., the practice of women marrying outside their social group). Indeed, several studies (11, 12) have shown that patrilocal residence patterns and female exogamy prevailed in several parts of Central Europe during the Late Neolithic. (…) the high diversity of mtDNA lineages, combined with the presence of only a single Y chromosome lineage, is certainly consistent with a patrilocal residence system.

funnelbeaker-trypillia-corded-ware
Map of territorial ranges of Funnel Beaker Culture (and its settlement concentrations in Lesser Poland), local Tripolyan groups and Corded Ware Culture settlements (■) at the turn of the 4th/3rd millennia BC.

Since ancient and modern Uralians show predominantly Corded Ware ancestry, and Proto-Uralic must have been in close contact with Proto-Indo-European for a very long time – given the different layers of influence that can be distinguished between them -, it follows as logical consequence that the North Pontic forest-steppes (immediately to the west of the PIE homeland in the Don-Volga-Ural steppes) is the most likely candidate for the expansion of Proto-Uralic, accompanying the spread of Sredni Stog ancestry and a bottleneck under R1a-M417 lineages.

The early TMRCAs in the 4th millennium BC for R1a-M417 and R1a-Z645 support this interpretation, like the R1a-M417 sample found in Sredni Stog. On the other hand, the resurgence of typical GAC-like ancestry in late Corded Ware groups, with GAC lineages showing late TMRCAs in the 3rd millennium BC, proves the disintegration of Corded Ware all over Europe (except in Textile Ceramics- and Abashevo-related groups) as the culture lost its cohesion and different local patrilineal clans used the opportunity to seize power – similar to how eventually I2a-L621 infiltrated eastern (Finno-Ugrian) groups.

Related

Yamna the likely source of modern horse domesticates; the closest lineage, from East Bell Beakers

Open access Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series, by Fages et al. Cell (2019).

Interesting excerpts (emphasis mine):

The earliest archaeological evidence of horse milking, harnessing, and corralling is found in the ∼5,500-year-old Botai culture of Central Asian steppes (Gaunitz et al., 2018, Outram et al., 2009; see Kosintsev and Kuznetsov, 2013 for discussion). Botai-like horses are, however, not the direct ancestors of modern domesticates but of Przewalski’s horses (Gaunitz et al., 2018). The genetic origin of modern domesticates thus remains contentious, with suggested candidates in the Pontic-Caspian steppes (Anthony, 2007), Anatolia (Arbuckle, 2012, Benecke, 2006), and Iberia (Uerpmann, 1990, Warmuth et al., 2011). Irrespective of the origins of domestication, the horse genome is known to have been reshaped significantly within the last ∼2,300 years (Librado et al., 2017, Wallner et al., 2017, Wutke et al., 2018). However, when and in which context(s) such changes occurred remains largely unknown.

To clarify the origins of domestic horses and reveal their subsequent transformation by past equestrian civilizations, we generated DNA data from 278 equine subfossils with ages mostly spanning the last six millennia (n = 265, 95%) (Figures 1A and 1B; Table S1; STAR Methods). Endogenous DNA content was compatible with economical sequencing of 87 new horse genomes to an average depth-of-coverage of 1.0- to 9.3-fold (median = 3.3-fold; Table S2). This more than doubles the number of ancient horse genomes hitherto characterized. With a total of 129 ancient genomes, 30 modern genomes, and new genome-scale data from 132 ancient individuals (0.01- to 0.9-fold, median = 0.08-fold), our dataset represents the largest genome-scale time series published for a non-human organism (Tables S2, S3, and S4; STAR Methods).

genetic-affinities-horse-domesticates-pca
Genetic Affinities.
(A)
Principal Component Analysis (PCA) of 159 ancient and modern horse genomes showing at least 1-fold average depth-of-coverage. The overall genetic structure is shown for the first three principal components, which summarize 11.6%, 10.4% and 8.2% of the total genetic variation, respectively. The two specimens MerzlyYar_Rus45_23789 and Dunaujvaros_Duk2_4077 discussed in the main text are highlighted. See also Figure S7 and Table S5 for further information.
(B) Visualization of the genetic affinities among individuals, as revealed by the struct-f4 algorithm and 878,475 f4 permutations. The f4 calculation was conditioned on nucleotide transversions present in all groups, with samples were grouped as in TreeMix analyses (Figure 3). In contrast to PCA, f4 permutations measure genetic drift along internal branches. They are thus more likely to reveal ancient population substructure.

Discovering Two Divergent and Extinct Lineages of Horses

Domestic and Przewalski’s horses are the only two extant horse lineages (Der Sarkissian et al., 2015). Another lineage was genetically identified from three bones dated to ∼43,000–5,000 years ago (Librado et al., 2015, Schubert et al., 2014a). It showed morphological affinities to an extinct horse species described as Equus lenensis (Boeskorov et al., 2018). We now find that this extinct lineage also extended to Southern Siberia, following the principal component analysis (PCA), phylogenetic, and f3-outgroup clustering of an ∼24,000-year-old specimen from the Tuva Republic within this group (Figures 3, 5A and S7A). This new specimen (MerzlyYar_Rus45_23789) carries an extremely divergent mtDNA only found in the New Siberian Islands some ∼33,200 years ago (Orlando et al., 2013) (Figure 6A; STAR Methods) and absent from the three bones previously sequenced. This suggests that a divergent ghost lineage of horses contributed to the genetic ancestry of MerzlyYar_Rus45_23789. However, both the timing and location of the genetic contact between E. lenensis and this ghost lineage remain unknown.

modern-horse-domesticates-przewalski-hungary
Population modeling of the demographic changes and admixture events in extant and extinct horse lineages. The two models presented show best fitting to the observed multi-dimensional SFS in momi2. The width of each branch scales with effective size variation, while colored dashed lines indicate admixture proportions and their directionality. The robustness of each model was inferred from 100 bootstrap pseudo-replicates. Time is shown in a linear scale up to 120,000 years ago and in a logarithmic scale above.

Modeling Demography and Admixture of Extinct and Extant Horse Lineages

Phylogenetic reconstructions without gene flow indicated that IBE differentiated prior to the divergence between DOM2 and Przewalski’s horses (Figure 3; STAR Methods). However, allowing for one migration edge in TreeMix suggested closer affinities with one single Hungarian DOM2 specimen from the 3rd mill. BCE (Dunaujvaros_Duk2_4077), with extensive genetic contribution (38.6%) from the branch ancestral to all horses (Figure S7B).This, and the extremely divergent IBE Y chromosome (Figure 6B), suggest that a divergent but yet unidentified ghost population could have contributed to the IBE genetic makeup.

Rejecting Iberian Contribution to Modern Domesticates

The genome sequences of four ∼4,800- to 3,900-year-old IBE specimens characterized here allowed us to clarify ongoing debates about the possible contribution of Iberia to horse domestication (Benecke, 2006, Uerpmann, 1990, Warmuth et al., 2011). Calculating the so-called fG ratio (Martin et al., 2015) provided a minimal boundary for the IBE contribution to DOM2 members (Cahill et al., 2013) (Figure 7A). The maximum of such estimate was found in the Hungarian Dunaujvaros_Duk2_4077 specimen (∼11.7%–12.2%), consistent with its TreeMix clustering with IBE when allowing for one migration edge (Figure S7B). This specimen was previously suggested to share ancestry with a yet-unidentified population (Gaunitz et al., 2018). Calculation of f4-statistics indicates that this population is not related to E. lenensis but to IBE (Figure 7B; STAR Methods). Therefore, IBE or horses closely related to IBE, contributed ancestry to animals found at an Early Bronze Age trade center in Hungary from the late 3rd mill. BCE. This could indicate that there was long-distance exchange of horses during the Bell Beaker phenomenon (Olalde et al., 2018). The fG minimal boundary for the IBE contribution into an Iron Age Spanish horse (ElsVilars_UE4618_2672) was still important (~9.6%–10.1%), suggesting that an IBE genetic influence persisted in Iberia until at least the 7th century BCE in a domestic context. However, fG estimates were more limited for almost all ancient and modern horses investigated (median = ~4.9%–5.4%; Figure 7A).

horse-lineages-domesticates-przewalski-dom2-botai
TreeMix Phylogenetic Relationships. The tree topology was inferred using a total of ∼16.8 million transversion sites and disregarding migration. The name of each sample provides the archaeological site as a prefix, and the age of the specimen as a suffix (years ago). Name suffixes (E) and (A) denote European and Asian ancient horses, respectively. See Table S5 for dataset information. Image modified to include the likely ancestor of domesticates in a red circle, represented by Yamna, the most likely direct ancestor of the Dunaujvarus specimen.

Iron Age horses

Y chromosome nucleotide diversity (π) decreased steadily in both continents during the last ∼2,000 years but dropped to present-day levels only after 850–1,350 CE (Figures 2B and S2E; STAR Methods). This is consistent with the dominance of an ∼1,000- to 700-year-old oriental haplogroup in most modern studs (Felkel et al., 2018, Wallner et al., 2017). Our data also indicate that the growing influence of specific stallion lines post-Renaissance (Wallner et al., 2017) was responsible for as much as a 3.8- to 10.0-fold drop in Y chromosome diversity.

We then calculated Y chromosome π estimates within past cultures represented by a minimum of three males to clarify the historical contexts that most impacted Y chromosome diversity. This confirmed the temporal trajectory observed above as Byzantine horses (287–861 CE) and horses from the Great Mongolian Empire (1,206–1,368 CE) showed limited yet larger-than-modern diversity. Bronze Age Deer Stone horses from Mongolia, medieval Aukštaičiai horses from Lithuania (C9th–C10th [ninth through the tenth centuries of the Common Era]), and Iron Age Pazyryk Scythian horses showed similar diversity levels (0.000256–0.000267) (Figure 2A). However, diversity was larger in La Tène, Roman, and Gallo-Roman horses, where Y-to-autosomal π ratios were close to 0.25. This contrasts to modern horses, where marked selection of specific patrilines drives Y-to-autosomal π ratios substantially below 0.25 (0.0193–0.0396) (Figure 2A). The close-to-0.25 Y-to-autosomal π ratios found in La Tène, Roman, and Gallo-Roman horses suggest breeding strategies involving an even reproductive success among stallions or equally biased reproductive success in both sexes (Wilson Sayres et al., 2014).

Lineage is used in this paper, as in many others in genetics, as defined by a specific ancestry. I keep that nomenclature below. It should not be confused with the “lineages” or “lines” referring to Y-chromosome (or mtDNA) haplogroups.

Supporting the “archaic” nature of the Hungarian BBC horses expanding from the Pontic-Caspian steppes are:

  • Among Y-chromosome lines, the common group formed by Botai-Borly4 (closely related to DOM2), Scythian horses from Aldy Bel (Arzhani), Iron Age horses from Estonia (Ridala), horses from the Xiongnu culture (Uushgiin Uvur), and Roman horses from Autricum (Chartres).
  • Among mtDNA lines, the common group formed by Botai samples, LebyazhinkaIV NB35, and different Eurasian domesticates, including many ancient Western European ones, which reveals a likely expansion of certain subclades east and west with the Repin culture.
  • (…) DOM2 contributed 22% to the ancestor of Przewalski’s horses ca. 9.47 kya, suggesting the Holocene optimum, rather than the Eneolithic Botai culture (∼5.5 kya), as a period of population contact. This pre-Botai introgression could explain the Y chromosome topology, where Botai horses were reported to carry two different segregating haplogroups: one occupied a basal position in the phylogeny while the other was closely related to DOM2. Multiple admixture pulses, however, are known to have occurred along the divergence of DOM2 and the Botai-Borly4 lineage, including 2.3% post-Borly4 contribution to DOM2, and a more recent 6.8% DOM2 intogression into Przewalski’s horses (Gaunitz et al., 2018). Model C2 parameters accommodate all these as a single admixture pulse, likely averaging the contributions of all these multiple events.

    horse-domesticate-y-dna-mtdna
    Tip labels are respectively composed of individual sample names, their reference number as well as their age (years ago, from 2017). Red, orange, light green, green, dark green and blue refer to modern horses, ancient DOM2, Botai horses, Borly4 horses, Przewalski’s horses and E. lenensis, respectively. Black refers to wild horses not yet identified to belong to any particular cluster in absence of sufficient genome-scale data. Clades composed of only Przewalski’s horses or ancient DOM2 horses were collapsed to increase readability.

    (A) Best maximum likelihood tree retracing the phylogenetic relationships between 270 mitochondrial genomes.

    B) Best Y chromosome maximum likelihood tree (GTRGAMMA substitution model) excluding outgroup. Node supports are indicated as fractions of 100 bootstrap pseudoreplicates. Bootstrap supports inferior to 90% are not shown. The root was placed on the tree midpoint. See also Table S5 for dataset information.

    Image modified from the paper, including a red square in archaic groups that contain the Hungarian sample, and a red circle around the most likely common ancestral stallion and mare from the Pontic-Caspian steppes.

    The paper cannot offer a detailed picture of ancient horse domestication, but it is yet another step in showing how Repin/Yamna is the most likely source of expansion of horse domesticates in Eurasia. Even more interestingly, Yamna settlers in Hungary probably expanded an ancient lineage of that horse at the same time as they spread with the Classical Bell Beaker culture. Remarkable parallels are thus found between:

    The expansion of an ancient line of horse domesticates related to Yamna Hungary/East Bell Beakers seems to be confirmed by the pre-Iberian sample from Vilars I, Els Vilars4618 2672 (ca. 700-550 BC), likely of Iberian Beaker descent, showing a lineage older than the Indo-Iranian ones, which later replaced most European lines.

    NOTE. For known contacts between Yamna and Proto-Beakers just before the expansion of East Bell Beakers, see a recent post on Vanguard Yamna groups.

    The findings of the paper confirm the expansion of the horse firstly (and mainly) through the steppe biome, mimicking the expansion of Proto-Indo-Europeans first, and then replaced gradually (or not so gradually) by lines brought to Europe during westward expansions of Bronze Age, Iron Age, and later specialized horse-riding steppe cultures. The expansion also correlates well with the known spread of animal traction and pastoralism before 2000 BC:

    animal-traction-europe
    Top image: Map with evidence of animal traction before ca. 2000 BC. Bottom image: frequency of finds of evidence for animal traction (orange), cylinder seals (purple) and potter’s wheels (green) in the 4th and 3rd millennium BC (query from the Digital Atlas of Innovations). The data points to an early peak in the expansion of this innovation at the turn of the 4th–3rd millennium BC, while direct evidence supports a radical increase from around the mid–3th millennium BC until the early 2nd millennium, coinciding with the expansion of East Bell Beakers and related European Early Bronze Age cultures. Data and image modified from Klimscha (2017).

    EDIT (3 MAY 2019): A recent reminder of these parallel developments by David Reich in Insights into language expansions from ancient DNA:

    • Yamna expansion to the west “with horses and wagons”, with a more homogeneous ancestry in modern Europeans due to later migrations from the east (and north):

    • “Descendants” of Yamna (once the culture was already “dead”), expanding to the east mainly with Corded Ware ancestry:

    Another recent open access paper on horse domestication is The horse Y chromosome as an informative marker for tracing sire lines, by Felkel et al. Scientific Reports (2019).

    Related