Is Yamnaya overrated?

Four years after the publication of the seminal ancient DNA paper Massive migration from the steppe is a source for Indo-European languages in Europe by Haak et al., we're still waiting for some of its loose ends to be finally tied up with new samples. In particular...

- if the men of the Corded Ware culture (CWC) were, by and large, derived from the population of the Yamnaya culture, then where are the Yamnaya samples with R1a-M417, the main CWC Y-haplogroup?

- if the men of the Bell Beaker culture (BBC) were also, by and large, derived from the population of the Yamnaya culture, then where are the Yamnaya samples with R1b-P312, the main BBC Y-haplogroup?

- and, most crucially, if R1b-L51, which includes R1b-P312, and is nowadays by far the most important Y-haplogroup in Western Europe, arrived there from the Pontic-Caspian steppe, then why hasn't it yet appeared in any of the ancient DNA from this part of Eastern Europe or surrounds, except of course in samples that are too young to be relevant?

I'm certainly not suggesting that, in hindsight, the said paper now looks fundamentally flawed. In fact, I'd say that it has aged remarkably well, especially considering how fast things are moving in the field of ancient genomics.

But those loose ends really need tying up, one way or another. It's now time.

So someone out there, please, let us know finally if you have the relevant Yamnaya samples. And if you don't, that's OK too, just tell us what you do have. Indeed, it'd be nice know a few basic details about the thousands of samples that have been successfully sequenced in various labs and are waiting to be published. A lot of people would appreciate it.

See also...

Corded Ware as an offshoot of Hungarian Yamnaya (Anthony 2017)

Hungarian Yamnaya > Bell Beakers?

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Commoner or elite?

I recently started looking at the correlations between Y-chromosome haplogroups and social standing in ancient Europe, and was surprised by what I learned about the five currently sampled prehistoric Scandinavians belonging to Y-haplogroup R1b. I certainly wasn't expecting to uncover these stories about a mass human sacrifice, a bog body, and an Arctic circle warrior:

- The earliest Scandinavian in the ancient DNA record belonging to R1b comes from a grave site in what is now northern Norway (VK531, Margaryan et al. 2019). This individual has a genome-wide profile similar to that of local Mesolithic hunter-gatherers, but is dated to just ~2,400 BCE. During this time, Scandinavia was dominated by a "new" population associated with the Battle-Axe culture (BAC), with high levels of ancestry from the steppes of Eastern Europe. Since VK531 wasn't buried with any BAC grave goods, and indeed with no grave goods at all, it's possible that he may have been from a remnant forager population that was displaced and ultimately forced into extinction.

- R1b-U106 is today by far the most common R1b subclade in Scandinavia, but it's not yet clear how it managed to attain this status. Was it perhaps through elite dominance? The earliest ancient individual belonging to R1b-U106 is dated to 2275-2032 calBCE and comes from a Late Neolithic, likely post-BAC burial ground in what is now Sweden (RISE98, Lilla Beddinge, grave 49, southern skeleton, Allentoft et al. 2015). However, RISE98 wasn't buried in any way that would suggest he was an individual of high social standing. In fact, he was found in a mass grave, along with two other adults and two infants, possibly representing a human sacrifice. The only artefact in the grave was a bone needle. More details are available here.

- During the Nordic Bronze Age it became customary for Scandinavian elites to be laid to rest in richly furnished barrows, while commoners were buried in flat graves with few or no offerings. Human remains recovered from a "commoner" flat grave cemetery dated to the Early Bronze Age near the present-day city of Aalborg, northern Denmark, included the skeleton of a male belonging to Y-haplogroup R1b-M269 (RISE47, grave 3, skeleton 8, Allentoft et al. 2015). Keep in mind, however, that this might have been another case of an ancient Scandinavian R1b-U106 if not for missing data. A flint dagger was found alongside one of the skeletons in this cemetery, but RISE47 wasn't accompanied by any grave goods (see here).

- One of the most amazing archeological discoveries made in Scandinavia is the Trundholm Sun Chariot. Found in a peat bog on the island of Zealand, Denmark, in 1902, it's thought to be an Indo-European religious artefact dating back to the Nordic Bronze Age; a representation of a horse pulling the sun and perhaps also the moon in a spoked wheel chariot. Another important discovery in a peat bog near Trundholm dating to the Nordic Bronze Age was the body of a man belonging to R1b-M269 (RISE276, Trundholm mose II, bog find 1940, Allentoft et al. 2015). However, chances are slim that RISE276 was a charioteer or, say, a spiritual guru who accidentally drowned in the bog. Most Danish bog bodies are thought to have belonged to sacrificial victims or executed criminals.

- Interestingly, the earliest likely Scandinavian warrior belonging to R1b, and also R1b-U106, is from an early Iron Age burial in present-day northwestern Norway (VK418, Margaryan et al. 2019). This site isn't quite as far north as the grave of the above mentioned VK531, but it's still well within the Arctic circle. Apparently, VK418 was buried with some impressive weapons, potentially of "eastern origin", including a shield, spearheads and a sword. Who knows, he may even have been an elite warrior for his time and place?

The other two main Scandinavian Y-haplogroups, I1a and R1a, haven't yet been found in prehistoric Nordic remains from such, shall we say, depressing burials. That's not to say, of course, that they won't be sooner or later. RISE175, from Allentoft et al. 2015, is currently the only individual who fits the bill as a representative of the Nordic Bronze Age elite. He was buried in a barrow grave in what is now southwest Sweden and probably belongs to Y-haplogroup I1a. That's not much to go on, but perhaps it's a sign of things to come?

See also...

Isotopes vs ancient DNA in prehistoric Scandinavia

Who were the people of the Nordic Bronze Age?

They came, they saw, and they mixed

Viking invasion at bioRxiv

A new preprint featuring hundreds of Viking Age genomes has appeared at bioRxiv [LINK]. Titled Population genomics of the Viking world, it looks like a solid effort overall, although I'm skeptical about its conclusions. I might elaborate on that in the comments below, but I'll have a lot more to say on the topic if and when I get to check out the ancient genomes with my own tools. Details about the new samples, including their Y-chromosome haplogroup assignments, are available here. Below is the abstract, emphasis is mine:

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Margaryan et al., Population genomics of the Viking world, bioRxiv, posted July 17, 2019, doi: https://doi.org/10.1101/703405

See also...

They came, they saw, and they mixed

Who were the people of the Nordic Bronze Age?

Asiatic East Germanics

Asiatic East Germanics

Around a third of the ancient individuals in my dataset associated with East Germanic-speaking cultures show obvious ancestry from Central and/or West Asia.

This shouldn't be too surprising, considering, for instance, the well documented contacts between East Germanic tribes and the Avars, Huns, Sarmatians and other nomadic groups that streamed into Europe from the Asian steppes during the Migration Period. It's a topic that I've raised before at this blog (see here).

But the curious thing is that very little, if any, of this ancestry has percolated down to present-day Europeans.

The easiest way to show this is with a Principal Component Analysis (PCA) based on my Global25 data. The relevant PCA datasheet can be downloaded here. Basic details about the ancient samples in the analysis are available here.

Some of the Northeastern European populations, particularly the Uralic speakers, appear to be attracted to the Hunnic cluster. However, this is mostly an artifact of pre-Migration Period east to west population expansions in the far north of Europe, probably including those of the Proto-Uralians (see here).

So how is it that, despite ruling over vast areas of Europe for hundreds of years, the East Germanics appear not to have contributed significantly to the present-day European gene pool? My theory is that, much like the Avars and Huns, they were militarily and demographically overwhelmed by the ascending groups around them, such as the Slavs, and they simply went extinct.

To wrap things up, here's a basic qpAdm mixture model designed to test for Hunnic-related ancestry in a few Eastern and Northern European populations of interest. Note the significant slice of this type of ancestry in the likely early Goths of the Chernyakhiv culture. Is it real? Feel free to share your thoughts in the comments below.

UKR_Chernyakhiv
DEU_MA 0.863±0.038
Hun_Tian_Shan 0.137±0.038
chisq 12.525
tail prob 0.325466
Full output

Swedish
Baltic_EST_IA 0.126±0.078
DEU_MA 0.849±0.073
Hun_Tian_Shan 0.025±0.020
chisq 8.338
tail prob 0.595877
Full output

Ukrainian
Baltic_EST_IA 0.121±0.064
DEU_MA 0.857±0.060
Hun_Tian_Shan 0.022±0.017
chisq 11.458
tail prob 0.322956
Full output

Estonian
Baltic_EST_IA 0.597±0.069
DEU_MA 0.373±0.064
Hun_Tian_Shan 0.030±0.017
chisq 15.739
tail prob 0.107361
Full output

See also...

Conan the Barbarian probably belonged to Y-haplogroup R1a

More on the association between Uralic expansions and Y-haplogroup N

Uralic-specific genome-wide ancestry did make a signifcant impact in the East Baltic

Who were the people of the Nordic Bronze Age?

Ancient DNA has revealed that large scale migrations and population replacements have often accompanied major cultural changes in prehistoric Europe. But, for now, my opinion is that the formation of the archeologically ostentatious Nordic Bronze Age wasn't associated with any significant foreign gene flow into Scandinavia. I've tested this as best as I could with the few relevant ancient samples that are currently available.

For instance, below are among the most successful qpAdm mixture models that I was able find for various ancient Scandinavian groups dating back to the local Middle Neolithic (MN) period. The Nordic Bronze Age population is represented by three individuals labeled Nordic_BA. Unfortunately, the guy pictured above, from the famous Borum Eshøj barrow burial in what is now Denmark, didn't make the cut. For more details about my sampling and labeling strategies refer to the text file here.

Nordic_MN_B
CWC_CZE 0.822±0.059
POL_Globular_Amphora 0.178±0.059
chisq 14.478
tail prob 0.341086
Full output

SWE_Battle_Axe
CWC_Baltic_early 0.662±0.028
POL_Globular_Amphora 0.338±0.028
chisq 11.234
tail prob 0.591189
Full output

Nordic_LN
Nordic_MN_B 0.928±0.069
SWE_TRB 0.072±0.069
chisq 12.139
tail prob 0.516307
Full output

Nordic_BA
Nordic_LN 0.851±0.061
SWE_TRB 0.149±0.061
chisq 10.897
tail prob 0.619475
Full output

It's impossible to successfully model the ancestries of Nordic_MN_B and SWE_Battle_Axe simply with the populations that were living in Scandinavia before them. Therefore, it's likely that they were migrants or the recent descendants of migrants to Scandinavia. But there's nothing surprising about that, because they're archeologically associated with the Corded Ware culture (CWC), which has always been seen as intrusive to Scandinavia from the south and east.

Conversely, it's easy to produce statistically sound mixture models for both Nordic_LN and Nordic_BA exclusively with earlier Scandinavian populations. Indeed, based on the outgroups or right pops that I'm using, Nordic_LN is almost indistinguishable from Nordic_MN_B, and the same can be said of Nordic_BA in regards to Nordic_LN.

Of course, if I mixed and matched reference populations from across prehistoric Europe, I could probably come up with some spectacular statistical fits even without the need for any Scandinavians. Essentially that's because Nordic_LN and Nordic_BA are closely related to many earlier and contemporaneous peoples living all the way from the Atlantic facade to the Ural Mountains. My point, however, is that this isn't crucial, despite the dearth of ancient samples from Scandinavia.

This is how things look in a Principal Component Analysis (PCA) of Northern European genetic variation based on my Global25 data. Strikingly, Nordic_MN_B, SWE_Battle_Axe, Nordic_LN and Nordic_BA more or less recapitulate the cluster made up of present-day Swedish samples. The relevant datasheet is available here.

Granted, two of the Nordic_BA samples sit just south of the Swedes, no doubt due to their slightly higher ratios of Neolithic farmer (SWE_TRB-related) ancestry, but this is also an area of the plot that many present-day Danes call home (not shown, because I don't have any suitable academic Danish samples to run).

I'll eat my hat if it turns out that Scandinavia experienced a major population shift (say, more than a collateral ~10%) during the LN and/or BA periods. And I'll post a clip of it online too.

Update 27/08/2019: Four of the samples from the recent Frei et al. paper on human mobility in prehistoric southern Scandinavia are in my Global25 datasheets. So I thought it might be interesting to check whether their strontium isotope ratios correlated with their genomic profiles.

In the Principal Component Analysis (PCA) below, RISE61 is a subtle outlier along the horizontal axis compared to the other three Nordic ancients, as well as a Danish individual representative of the present-day Danish gene pool. Also note that RISE61 shows the most unusual strontium isotope ratio (0.712588). The PCA was run with an online tool freely available here.

To help drive the point home, here's a figure from Frei et al., edited by me to show the positions of RISE47, RISE61 and RISE71. If RISE276 was also in this graph, he'd be sitting well under the "local" baseline, in roughly the same spot along the vertical axis as RISE47.

Interestingly, RISE61 belongs to Y-chromosome haplogroup R1a-M417, while RISE47 and RISE276, who appear to have been locals, both belong to R1b-M269. My guess is that RISE61 was a recent migrant from a more northerly part of Scandinavia dominated by the Battle-Axe culture (BAC). The BAC population was probably rich in R1a-M417 because it moved into Scandinavia from the Pontic-Caspian steppe via the East Baltic. This is what Frei et al. say about RISE61 and his burial site:

The double passage grave of Kyndeløse (Fig 1, S1 File) located on the island of Zealand yielded 70 individuals as well as a large number of grave goods, including flint artefacts, ceramics, and tooth and amber beads. We conducted strontium isotope analyses of seven individuals from Kyndeløse encompassing a period of c. 1000 years, indicating the prolonged use of this passage grave. The oldest of the seven individuals is a female (RISE 65) from whom we measured a “local” strontium isotope signature ( 87 Sr/ 86 Sr = 0.7099). Similar values were measured in five other individuals, including adult males and females. Only a single individual from Kyndeløse, an adult male (RISE 61) yielded a somewhat different strontium isotope signature of 87 Sr/ 86 Sr = 0.7126 which seems to indicate a non-local provenance. The skull of this male individual revealed healed porosities in the eye orbits, cribra orbitalia, a condition which is possibly linked to a vitamin deficiency during childhood, such as iron deficiency.

By the way, RISE47 was buried in a flat grave, which suggests that he was a commoner. RISE276 was found in a peat bog in Trundholm, where the famous Trundholm sun chariot was discovered (see here). He may have been a human sacrifice.

Citation...

Frei KM, Bergerbrant S, Sjögren K-G, Jørkov ML, Lynnerup N, Harvig L, et al. (2019) Mapping human mobility during the third and second millennia BC in present-day Denmark. PLoS ONE 14(8): e0219850. https://doi.org/10.1371/journal.pone.0219850

See also...

They came, they saw, and they mixed

Children of the Divine Twins

The mystery of the Sintashta people

On the association between Uralic expansions and Y-haplogroup N

Almost all present-day populations speaking Uralic languages show moderate to high frequencies of Y-chromosome haplogroup N. I reckon there are two likely explanations for this:

- the speakers of Proto-Uralic were rich in N because they lived in an area, probably somewhere around the Ural Mountains, where it was common, and they spread it with them as they expanded from their homeland

- Uralic languages often came to be spoken in areas of North Eurasia where N was already found at moderate to high frequencies

The major exception to this rule are Hungarians, whose language belongs to the Ugric branch of Uralic. Their frequency of N is close to zero and they don't differ much in terms of overall genetic structure from their Indo-European-speaking neighbors in East Central Europe.

This is an issue that has generated much debate over the years about the nature of Uralic expansions, who the Hungarians really were, and how the Hungarian language came to be spoken in the heart of Europe.

But I never understood what the fuss was about, because based on historical sources alone it seemed rather obvious that Hungarian was introduced into the Carpathian Basin during the Middle Ages by a relatively small number of invaders from the east, probably from somewhere around the Ural Mountains, who imposed it on local Indo-European-speaking populations.

As far as I can remember, this has always been the academic consensus, and the results from one of the first ancient DNA studies of human remains soundly corroborated it. Back in 2008, Csányi et al. reported that two out of four skeletons from elite Hungarian conqueror graves dating to the 10th century carried the Tat C allele, which meant that they belonged to Y-haplogroup N (see here).

We've since had to wait over a decade to get a more comprehensive look at the Y-chromosome haplogroups of medieval Hungarians. The most useful effort to date, a manuscript courtesy of Neparáczki et al., was posted this week at bioRxiv (see here).

The results in the preprint suggest a much more complex picture than simply a migration of an obviously Uralic-speaking population rich in Y-haplogroup N into the medieval Carpathian Basin. But they do confirm the presence of N in Hungarian conqueror elites, and, in fact, of very specific subclades of N that link them to the present-day speakers of Uralic languages from around the Ural Mountains. Here are some pertinent quotes from the prepint:

Three Conqueror samples belonged to Hg N1a1a1a1a2-Z1936, the Finno-Permic N1a branch, being most frequent among northeastern European Saami, Finns, Karelians, as well as Komis, Volga Tatars and Bashkirs of the Volga-Ural region. Nevertheless this Hg is also present with lower frequency among Karanogays, Siberian Nenets, Khantys, Mansis, Dolgans, Nganasans, and Siberian Tatars 23.

...

It is generally accepted that the Hungarian language was brought to the Carpathian Basin by the Conquerors. Uralic speaking populations are characterized by a high frequency of Y-Hg N, which have often been interpreted as a genetic signal of shared ancestry. Indeed, recently a distinct shared ancestry component of likely Siberian origin was identified at the genomic level in these populations, modern Hungarians being a puzzling exception 36. The Conqueror elite had a significant proportion of N Hgs, 7% of them carrying N1a1a1a1a4-M2118 and 10% N1a1a1a1a2-Z1936, both of which are present in Ugric speaking Khantys and Mansis 23.

...

Population genetic data rather position the Conqueror elite among Turkic groups, Bashkirs and Volga Tatars, in agreement with contemporary historical accounts which denominated the Conquerors as “Turks” 38. This does not exclude the possibility that the Hungarian language could also have been present in the obviously very heterogeneous, probably multiethnic Conqueror tribal alliance.

Indeed, a large proportion of the 44 males from elite Hun, Avar and Hungarian Conqueror burials analyzed in the study belonged to Y-haplogroups that can't be plausibly associated with the earliest Uralic speakers, but rather with those of various Indo-European languages, such as I1 and R1b-U106 (these are Germanic-specific markers), I2a-L621 and R1a-CTS1211 (obviously Slavic) and R1a-Z2124 (largely Eastern Iranian).

If most of these results aren't due to contamination, then it's likely that both the early Hungarian commoners and elites were, by and large, derived from Indo-European-speaking populations. No wonder then, that present-day Hungarians are basically indistinguishable genetically from their Indo-European-speaking neighbors and, like them, show hardly any Y-haplogroup N.

See also...

Hungarian Conquerors were rich in Y-haplogroup N (Fóthi et al. 2020)

More on the association between Uralic expansions and Y-haplogroup N

Ancient DNA confirms the link between Y-haplogroup N and Uralic expansions