A comedy of errors

A couple of years ago, the authors of a paper about a group of Iron Age nomads from the site of Shirenzigou, in the eastern Tian Shan, made a mistake. They wrongly assigned two of these nomads to Y-haplogroup R1b-M269.

This faux pas made them believe that the Shirenzigou nomads were closely related to the M269-rich population associated with the Afanasievo culture.

Indeed, since the Afanasievo culture was often credited with the spread of Tocharian languages to the Tarim Basin, these authors, led by Chao Ning, also concluded that the Shirenzigou nomads were potentially the missing link between the Afanasievo culture and the Tocharians (see here).

Moreover, Ning et al. used formal statistics to argue that the Shirenzegou nomads harbored Afanasievo-related genome-wide ancestry, rather than Sintashta-related genome-wide ancestry, despite the fact that the latter ancestry was widespread in the Tian Shan and surrounds during the Bronze and Iron ages. Soon after, another group of authors, led by Chuan-Chao Wang, also went out of their way to link the Shirenzigou nomads to the Afanasievo people with genome-wide DNA using formal statistics (see here).

Interestingly, one of the Shirenzigou nomads belongs to Y-haplogroup R1a-Z93, which is an obvious Sintashta-related lineage. Both Ning et al. and Wang et al. missed this important fact.

They also missed the key fact that the R1b lineage found in the Shirenzigou nomads actually belongs to an Inner Asian subclade, which is only very distantly related to the originally Eastern European R1b-M269.

Now, formal stats are a very useful tool for studying genome-wide ancestry. But they're not infallible, and that's actually something of an understatement. Indeed, if you don't run sanity checks when using formal stats, you're likely to come to some unusual, even arse about face, conclusions. Uniparental markers, like Y-chromosome haplogroups, can provide a robust sanity check when running formal stats on genome-wide data.

One problem with formal stats is that Sintashta-related ancestry often looks very much like Afanasievo-related ancestry when it's mixed with indigenous Central Asian ancestry. Basically, the reason why this happens is that the Central Asian ancestry dampens the Early European Farmer (EEF) signal in the Sintashta-related ancestry.

This is an artifact that once caused scientists at Harvard to believe that Central Asian Scythians and present-day South Asians lacked Sintashta-related ancestry.

Unfortunately, since the publication of the Ning et al. paper, a consensus has emerged in academia that the Shirenzigou nomads are indeed the missing link between the Afanasievo culture and the Tocharians. But, let's be objective and honest here, it's a consensus based on nothing more than a comedy of errors.

On the other hand, me and most of the commentators at this blog have formed opinions about the Shirenzigou nomads that are totally at odds with the academic consensus, that:

- they're a complex mixture of Sintashta-related, indigenous Central Asian and Tibetan-related ancestries, with no clear, unambiguous signal of Afanasievo-related ancestry

- they weren't the speakers of Proto-Tocharian or even related in any specific way to the Tocharians

- they were probably the speakers of a now extinct Indo-Iranian language, and, at least based on geographic proximity, possibly related to the Yuezhi.

Feel free to make up your own mind. But for me, the question of how Tocharian languages ended up in the Tarim Basin remains wide open. I admit though, I'm currently quite partial to the idea floated here by commentator Copper Axe that the Chemurchek culture may have had something to do with it.

See also...

Don't believe everything you read in peer reviewed papers

The great shift

Here's a Principal Component Analysis (PCA) featuring some of the ancients from the recent Saag et al. paper at Science Advances. To see an interactive version of the plot paste the Global25 coordinates here into the relevant field here.

Note that the Fatyanovo culture agropastoralists, who are rich in Y-haplogroup R1a and steppe ancestry, cluster with present-day Eastern Europeans. On the other hand, the Volosovo culture singleton sits near the European hunter-gatherer cline that no longer exists.

This Volosovo individual belongs to Y-haplogroup Q1a. However, most of the Volosovo males whose genomes are soon to be published belong to Y-haplogroup R1b.

Thus, in much of Eastern Europe during the Bronze Age, agropastoralists rich in R1a and steppe ancestry replaced hunter-gatherers rich in R1b and with no steppe ancestry. Of course, that's not where the story ends, but I'll get back to that later this year.

By the way, the relatively high coverage Fatyanovo Y-chromosome sequences are being analyzed at YFull. You can check out the results here.

See also...

Fatyanovo as part of the wider Corded Ware family (Nordqvist and Heyd 2020)

There's a new archeological paper about the Fatyanovo culture at the Proceedings of the Prehistoric Society [LINK]. It includes this quote on page 18:

In the traditional narrative, the Fatyanovo people – like the CWC populations in general – are regarded as Indo-European, representing the pre-Balto-Slavic (-Germanic) stage (Carpelan & Parpola 2001, 88; Anthony 2007, 380; also Gimbutas 1956, 163; Tretyakov 1966, 109) in the spread of Indo-European languages.

That's correct, but considering the latest ancient DNA research on the Fatyanovo people, the traditional narrative is probably wrong. Fatyanovo males were rich in Y-haplogroup R1a-Z93, which is found at very low frequencies in Balto-Slavic populations (see here). It's actually much more common nowadays in Central and South Asia, where it often reaches frequencies of over 50% in Indo-Iranian speaking groups.

Balts and Slavs are rich in R1a-Z282, which is a sister clade of R1a-Z93 that has been found in Corded Ware and Corded Ware-related samples from west of Fatyanovo sites. That is, in present-day Poland and the Baltic states.

Therefore, the origins of the Balto-Slavs should be sought somewhere west of the Fatyanovo culture, probably in the Corded Ware derived populations from what is now the border zone between Poland, Belarus and Ukraine.

Indeed, in my view the Fatyanovo people are more likely to have spoken Proto-Indo-Iranian rather than anything ancestral to Baltic or Slavic (see here).

Nordqvist and Heyd, The Forgotten Child of the Wider Corded Ware Family: Russian Fatyanovo Culture in Context, Proceedings of the Prehistoric Society, online 12 November 2020, DOI: https://doi.org/10.1017/ppr.2020.9

See also...

The oldest R1a to date

The oldest R1a to date

My popular map of the oldest instances of Y-haplogroup R1a in the ancient DNA record has a new entry: PES001 from the recent Saag et al. preprint. PES001 comes from a burial site in what is now northwestern Russia and is dated to a whopping 10785–10626 calBCE.

Indeed, I'm not aware of any R1a samples older than PES001 among the treasure trove of thousands of ancient samples waiting to be published. So it's likely that this individual will remain the oldest member of our R1a clan for some years to come.

See also...

Y-haplogroup R1a and mental health

Like three peas in a pod

The mystery of the Sintashta people

On the exotic origins of the Hungarian Arpad Dynasty (Nagy et al. 2020)

Hungarians speak a Uralic and Finno-Ugric language. However, the founders of the Medieval Hungarian state, the Arpad Dynasty, probably had Irano-Turkic paternal origins. There's a very interesting new paper on this topic at the European Journal of Human Genetics (see here). From the paper, emphasis is mine:

The phylogenetic origins of the Hungarians who occupied the Carpathian basin has been much contested [40]. Based on linguistic arguments it was proposed that they represented a predominantly Finno-Ugric speaking population while the oral and written tradition of the Árpád dynasty suggests a relationship with the Huns. Based on the genetic analysis of two members of the Árpád Dynasty, it appears that they derived from a lineage (R-Z2125) that is currently predominantly present among ethnic groups (Pashtun, Tadjik, Turkmen, Uzbek, and Bashkir) speaking Iranian or Turkic languages. However, their closest kin, the Bashkirs live in close proximity with Finno-Ugric speaking populations with the N-B539 haplogroup. A recent study shows that this haplogroup is also found in modern Hungarians [41]. Intriguingly, the most recent separation of the N-B539 derived lineages found in Hungarians and Bashkirs is estimated to have occurred ~2000 years before present [42]. This would suggest that a group of people consisting of a Turkic (R-SUR51) component and a Finno-Ugric (N-B539) component left the Volga Ural region about 2000 years ago and started a migration that eventually culminated in settlement in the Carpathian Basin.

Citation...

Nagy, P.L., Olasz, J., Neparáczki, E. et al. Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third. Eur J Hum Genet (2020). https://doi.org/10.1038/s41431-020-0683-z

See also...

Hungarian Conquerors were rich in Y-haplogroup N

On the association between Uralic expansions and Y-haplogroup N

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

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

Fatyanovo males were rich in Y-haplogroup R1a-Z93 (Saag et al. 2020 preprint)

I'd say that thanks to this preprint we're now a lot closer to solving the mystery of the Sintashta people. Over at bioRxiv at this LINK. From the preprint:

Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 28 individuals from the territory north of this source area - from the under-studied Western part of present-day Russia, including Stone Age hunter-gatherers (10,800-4,250 cal BC) and Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900-2,050 cal BC). We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around 10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming - the Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry and thus likely originating from a fast migration towards the northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these ancestries coexisted from around 3,000 BC.

...

Interestingly, in all individuals for which the chrY hg could be determined with more depth (n=6), it was R1a2-Z93 (Table 1, Supplementary Data 2), a lineage now spread in Central and South Asia, rather than the R1a1-Z283 lineage that is common in Europe [38,39].

Saag et al., Genetic ancestry changes in Stone to Bronze Age transition in the East European plain, BioRxiv, Posted July 03, 2020, doi: https://doi.org/10.1101/2020.07.02.184507

See also...

Like three peas in a pod

Like three peas in a pod

One of the most interesting questions still waiting to be answered by ancient DNA is where exactly did the ancestors of the present-day European and South Asian bearers of Y-haplogroup R1a part their ways? Indeed, the answer to this question is likely to be informative about the place and time of the split between the Balto-Slavic and Indo-Iranian language families.

I was doing some reading today and discovered that the peoples associated with the Bronze Age Fatyanovo-Balanovo and Unetice archeological cultures shared strikingly similar metalwork, despite being separated by well over two thousand kilometers of forest and steppe. Apparently, this similarity is especially pronounced in the metalwork of the Unetice culture from what is now Slovakia (see Ancient Metallurgy in the USSR: The Early Metal Age, page 136).

S11953 is currently the only sample from Slovakia associated with the Unetice culture (Sirak et al. 2020). There are no Fatyanovo-Balanovo samples available yet. However, as far as I can tell, I0432 from Samara, Russia, should be a decent stand in (Mathieson et al. 2015).

Of course, both S11953 and I0432 belong to Y-haplogroup R1a. Moreover, S11953 belongs to a typically Balto-Slavic subclade of R1a, while I0432 belongs to a closely related subclade that is dominant nowadays among the Indo-Iranian speakers of Asia.

S11953 is younger than I0432, but this doesn't necessarily mean that his ancestors arrived in East Central Europe from deep in Russia during the Bronze Age. Indeed, the opposite is more likely to be true. That is, I0432 is probably the recent decedent of migrants from somewhere near the North Carpathians, because he shows elevated European Neolithic farmer ancestry compared to earlier ancients from the Samara region (see here).

Below is a Principal Component Analysis (PCA) showing how S11953 and I0432 compare to each other in the context of ancient West Eurasian genetic variation. Obviously, they're sitting in the same part of the plot, which suggests that they harbor very similar ratios of ancient genetic components and probably share relatively recent ancestry. The relevant PCA datasheet is available here.

I've also highlighted myself, Davidski, on the plot. That's because I share the same Balto-Slavic-specific subclade of R1a with S11953 and, in terms of overall ancestry, I'm similar to both S11953 and I0432. Moreover, I'm the speaker of Polish, which is a Balto-Slavic language. What are the chances that we're dealing here with a remarkable string of coincidences? Indeed, was the North Carpathian region perhaps the homeland of the language ancestral to both Balto-Slavic and Indo-Iranian?

However, please note that there's nothing unusual or remarkable about my ancestry. The vast majority of people of Central, Eastern and Northern European origin - that is, mostly the speakers of Balto-Slavic, Germanic and Celtic languages - would also land in this part of the plot.

See also...

On the doorstep of India

Y-haplogroup R1a and mental health

The mystery of the Sintashta people

The Abashevo axe did it (Mednikova et al. 2020)

Open access at the Journal of Imaging over at this LINK. From the paper, emphasis is mine:

A massive bronze battle axe from the Abashevo archaeological culture was studied using neutron tomography and manufacturing modeling from production molds. Detailed structural data were acquired to simulate and model possible injuries and wounds caused by this battle axe. We report the results of neutron tomography experiments on the bronze battle axe, as well as manufactured plastic and virtual models of the traumas obtained at different strike angles from this axe. The reconstructed 3D models of the battle axe, plastic imprint model, and real wound and trauma traces on the bones of the ancient peoples of the Abashevo archaeological culture were obtained. Skulls with traces of injuries originate from archaeological excavations of the Pepkino burial mound of the Abashevo culture in the Volga region. The reconstruction and identification of the injuries and type of weapon on the restored skulls were performed. The complementary use of 3D visualization methods allowed us to make some assumptions on the cause of death of the people of the Abashevo culture and possible intra-tribal conflict in this cultural society. The obtained structural and anthropological data can be used to develop new concepts and methods for the archaeology of conflict.

...

Human skeletal remains from excavations of the Pepkino burial mound bear many traumatic wounds on the skulls and postcranial bones (Figure 4). The primary hypothesis is that young men of the Abashevo culture fell at the hands of enemies, which were the representatives of another tribe or culture [14,16]. After their discovery in the XX century, the skulls of killed people of the Abashevo culture were restored using anthropological paste, including beeswax.

...

A simple explanation for obtaining such injuries is the conclusion that the victim stood face to face with their assaulter and tried to back away from the battle axe, but fell and received other lethal wounds. The superficial trauma by the battle axe as well as serious damage to a bone structure and deep cracks in the skull are visible in the upper part of the model.

...

The comparison of the real bronze axe with the model obtained from molds indicates their complete identity and the belonging of these axes from different archaeological sites of the Abashevo culture to the same cultural group. This conclusion may indicate intra-cultural conflict among the Abashevo people. As a final note, the presented results of quite diverse imaging methods indicate a new direction in the archaeology of conflicts and the applicability of 3D modeling methods to identify both weapons technologies and the specifics of the use of these weapons to injure humans.

Citation...

Mednikova et al., The Reconstruction of a Bronze Battle Axe and Comparison of Inflicted Damage Injuries Using Neutron Tomography, Manufacturing Modeling, and X-ray Microtomography Data, J. Imaging 2020, 6(6), 45; https://doi.org/10.3390/jimaging6060045

See also...

An early Mitanni?

I've updated my Global25 datasheets with most of the ancients from the new Skourtanioti et al. paper. Here's a Principal Component Analysis (PCA) based on the data. It was produced with the Vahaduo PCA tools freely available here and the text file here.

Note that one of the Bronze Age females from Alalakh, labeled ALA019, appears to have ancestry from Turan and the Eurasian steppe. She may well have been a Mitanni of Indo-Aryan origin.

Interestingly, a Copper Age male from Arslantepe, ART038, belongs to Y-haplogroup R1b1a2 aka R1b-V1636. This is an unusual find, because R1b hasn't yet been reported in any Copper Age or earlier samples from outside of Europe and the Eurasian steppe.

As far as I can tell, this individual doesn't harbor any genome-wide ancestry from north of the Caucasus. However, R1b-V1636 is a rare lineage that is first attested in Eneolithic samples from the North Caucasus Piedmont steppe, so ART038's Y-chromosome might be the first evidence of the presence of steppe ancestry in Copper Age Anatolia.

I've also added most of the ancients from the new Agranat-Tamir et al. paper to the Gobal25 datasheets. The PCA below is based on the text file available here.

The Megiddo samples include a trio of interesting outliers dated to 1600-1500 BCE with significant ancestry from the steppe. One of these individuals is a male, I2189, who belongs to Y-haplogroup R and probably R1a. So he might also be of Indo-Aryan origin.

Another Megiddo male, S10768, belongs to R1b-M269 and probably shows a few per cent of steppe ancestry. I've already discussed how R1b and steppe ancestry may have ended up in the Bronze Age Near East in a couple of my previous posts:

R1b-M269 in the Bronze Age Levant

How did steppe ancestry spread into the Biblical-era Levant?

R-V1636: Eneolithic steppe > Kura-Araxes?

Of horses and men #2

Fascinating stuff courtesy of Fages et al. at the Journal of Archaeological Science: Reports (emphasis is mine):

Abstract: The domestication of the horse and the development of new equestrian technologies have had a far-reaching impact on human history. Disentangling the respective role that horse males and females played during this process is, however, difficult based on iconography and osteological data alone. In this study, we leveraged an extensive ancient DNA time-series to determine the molecular sex of 268 horses spread across Eurasia and charted the male:female sex ratio through the last 40,000 years. We found even sex ratios in the Upper Palaeolithic and up until ~3900 years BP. However, we identified a striking over-representation of horse males in more recent osseous assemblages, which was particularly magnified in funerary contexts but also significant in non-ritual deposits. This suggests that the earliest horse herders managed males and females alike for more than one thousand years after domestication at Botai, but that the human representation and use of horses became gendered at the beginning of the Bronze Age, following the emergence of gender inequalities in human societies.

...

The time period around ~3900 years ago marked a drastic shift in male:female sex ratios inferred from excavated remains, after which the horse osteological record comprises approximately four males for every female (Fig. 2). This over-representation of horse males was maintained when disregarding those animals excavated from ritual burial sites (77/25 ~ 3.08 males for every female) and even more pronounced in the animal bones found in funerary contexts (66/14 ~ 4.71 males for every female). This indicates that the status of male and female horses dramatically changed during the Bronze Age period. This is in line with archaeozoological evidence from the Late Bronze Age cemeteries of the Volga-Ural region associated with the Sintashta, Potapovka and Petrovka cultures, that suggest a domination of male horses in funerary rates (Kosintsev, 2010). Interestingly, this pattern somehow mirrors that observed in humans, for whom a clear binary gender structure ubiquitous across all funerary practices, clothing, personal ornaments and representations is not observed during the Neolithic but became the norm from the transition between the Neolithic and the Bronze Age onwards (Robb and Harris, 2018). In addition, the prevalence of male horses in funerary contexts throughout the past three millennia is in line with archaeological evidence from burial sites (Bertašius and Daugnora, 2001, Taylor, 2017) and suggests that stallions (or geldings) were more prized for sacrificial rituals. This is possibly due to symbolic attributes then-associated with masculinity, mounted warriors and chariotry, such as power, protection and strength (Frie, 2018). In particular, petroglyph images associated with vehicles, characterized by two wheels with spokes, became typical by the late third – early second millennium BCE (Jacobson-Tepfer, 2012). They are generally associated with male warriors and the emergence of mobile warfare (Anthony, 2007) or ritual needs, in particular the passage to the after-life land (Jones-Bley, 2000). This suggests an essential ideological role of stallions and their use in elite warfare and ritual practices (Drews, 2004, Kelekna, 2009, Novozhenov and Rogozhonskiy, 2019).

...

Future research should focus on assessing the molecular sex of horses from Early and Middle Bronze Age Pit Grave and Catacomb cultures, which do show evidence for social inequality, but for which sex inequalities remain to be investigated.

Fages et al., Horse males became over-represented in archaeological assemblages during the Bronze Age, Journal of Archaeological Science: Reports Volume 31, June 2020, 102364, https://doi.org/10.1016/j.jasrep.2020.102364

See also...

Of horses and men

Inferring the linguistic affinity of long dead and non-literate peoples: a multidisciplinary approach

The mystery of the Sintashta people

Latest on Sintashta-Petrovka chariots (Lindner 2020)

Open access at Antiquity at this LINK. As far as I can tell, several individuals from the graves analyzed in this paper are in my ancient DNA dataset and the Global25 datasheets. Sample I1064 from the Kamennyi Ambar 5 cemetery comes to mind. Here's the abstract:

In Eastern Europe, the use of light vehicles with spoked wheels and harnessed horse teams is first evidenced in the early second-millennium BC Sintashta-Petrovka Culture in the South-eastern Ural Mountains. Using Bayesian modelling of radiocarbon dates from the kurgan cemetery of Kamennyj Ambar-5, combined with artefactual and stratigraphic analyses, this article demonstrates that these early European chariots date to no later than the first proto-chariots of the ancient Near East. This result suggests the earlier emergence of chariots on the Eurasian Steppe than previously thought and contributes to wider debates on the geography and chronology of technological innovations.

See also...

The mystery of the Sintashta people

Y-haplogroup R1a and mental health

I've updated my map of pre-Corded Ware culture R1a samples with a couple of new entries from Central and South Asia (the original is still here). However, before any of you get overly excited, please note that these samples aren't older than the Corded Ware culture. The reason I added them to my map is to counter the ongoing absurd claims online that South Asian R1a isn't derived from European R1a.

Just in case the map can't be viewed in all of its glory in some devices, here's what the fine print says:

The oldest example of R1a in ancient DNA from Central Asia is dated to 2132-1940 calBCE (ID I3770, Narasimhan 2019). Moreover, this sequence is closely related to much older R1a samples from Central, Eastern and Northern Europe, and phylogenetically nested within their diversity. Thus, it must surely represent a population expansion from Europe to Central Asia. Indeed, it's also associated with the Bronze Age Andronovo archeological culture, which is usually seen as an offshoot of the Corded Ware culture (CWC) of Late Neolithic Europe. The vast majority of present-day R1a lineages in Central Asia are closely related to that of I3770, and so must also ultimately derive from Europe.

The oldest instance of R1a in ancient DNA from South Asia is dated to just 1044-922 calBCE (ID I12457, Narasimhan 2019). This sequence, as well as the vast majority of present-day South Asian R1a lineages, are closely related to much older R1a samples from Central, Eastern and Northern Europe, and phylogenetically nested within their diversity. Thus, they must surely represent a population expansion from Europe to South Asia via Central Asia, in all likelihood during the Bronze Age. Even if R1a existed in South Asia before the Bronze Age, which is extremely unlikely, because it's found in samples from indigenous European hunter-gatherers, the vast majority of present-day R1a lineages in South Asia must be ultimately from Europe.

The idea that most, if not all, South Asian R1a is derived from European R1a seriously scares a lot of people. This is obvious in many online discussions on the topic. I suspect they're so frightened by it because, in their minds, it has the potential to encourage discrimination and even racism, perhaps by re-defining the colonization of much of the world by European nations in the recent past as the natural order of things?

In any case, clearly we're dealing with some sort of mass phobia here. I've got advice for those of you suffering from this problem: if you're honestly worried that the geographic provenance and expansion history of some Y-haplogroup is going to negatively impact on your life in any meaningful way, then it's time to find yourself a quality mental health professional. All the best with that.

See also...

The mystery of the Sintashta people

The Poltavka outlier

Yamnaya isn't from Iran just like R1a isn't from India

On the surprising genetic origins of the Harappan people (Shinde et al. 2019)

The long awaited paper with ancient DNA from the Indus Valley Civilization (IVC) site of Rakhigarhi has finally arrived. Courtesy of Shinde et al. at Current Biology:

An ancient Harappan genome lacks ancestry from Steppe pastoralists or Iranian farmers

The bad news is that the paper features just one low coverage IVC genome, and it belongs to a female, so there's no Y-haplogroup. However, importantly, this individual is very similar to genetic outliers from Bronze Age West and Central Asia known as Indus_Periphery. So much so, in fact, that they could easily be from the same gene pool.

This, of course, gives strong support to the idea that Indus_Periphery is a useful stand-in for the real IVC population (see here).

Surprisingly, despite being largely of West Eurasian origin, the IVC people possibly didn't harbor any ancestry from the Neolithic farmers of the Fertile Crescent or even the Iranian Plateau.

That's because, according to Shinde et al., their West Eurasian ancestors separated genetically from those of the early Holocene populations of what is now western and northern Iran around 12,000 BCE. In other words, well before the advent of agriculture.

This surely complicates matters for those arguing that Indo-European languages may have arrived in the Indian subcontinent with early farmers via the Iranian Plateau. The more widely accepted theory is that Indo-European languages spread into South Asia with Bronze Age pastoralists from the Eurasian steppes. See here...

Update 05/09/2019: I had a quick look at the ancient Rakhigarhi individual with qpAdm, just to confirm for myself that she was indeed largely of West Eurasian origin and practically indistinguishable from Indus_Periphery. The genotype data that I used are freely available here.

IND_Rakhigarhi_BA
IRN_Ganj_Dareh_N 0.711±0.065
Onge 0.232±0.067
RUS_Tyumen_HG 0.057±0.059
chisq 13.251
tail prob 0.0392147
Full output

Indus_Periphery
IRN_Ganj_Dareh_N 0.674±0.015
Onge 0.237±0.014
RUS_Tyumen_HG 0.090±0.012
chisq 14.877
tail prob 0.0212326
Full output

Indus_Periphery
IND_Rakhigarhi_BA 0.946±0.074
Onge 0.054±0.074
chisq 10.358
tail prob 0.169152
Full output

This does appear to be the case, although it's also obvious that my models are missing something important because their statistical fits are rather poor. I'm guessing the main problem is trying to use the Onge people of the Andaman Islands as a proxy for the indigenous foragers of the Indian subcontinent.

See also...

Y-haplogroup R1a and mental health

A surprising twist to the Shirenzigou nomads story

Remember those potentially Afanasievo-derived and Tocharian-related Shirenzigou nomads from the Ning et al. paper? Well, in my opinion, they're probably neither. The genotypes and other data for these Iron Age individuals from the eastern Tian Shan are available here.

Below are a few successful and not so successful qpAdm mixture models for them. Note that I tried to use a wide range of relevant "right pops", but also retain a lot of markers, specifically to be able to discriminate between different types of steppe and steppe-derived sources of gene flow (refer to the full output). Admittedly, the Shirenzigou nomads can be modeled with Afanasievo-related ancestry, but...

CHN_Shirenzigou_IA
KAZ_Botai 0.161±0.023
KAZ_Wusun 0.490±0.023
NPL_Mebrak_2125BP 0.349±0.019
chisq 5.793
tail prob 0.926172
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.143±0.022
NPL_Mebrak_2125BP 0.295±0.019
Saka_Tian_Shan 0.562±0.024
chisq 6.796
tail prob 0.870794
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.185±0.023
NPL_Mebrak_2125BP 0.428±0.021
RUS_Sintashta_MLBA 0.270±0.026
TJK_Sarazm_En 0.117±0.027
chisq 11.351
tail prob 0.414345
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.032±0.027
KAZ_Zevakinskiy_LBA 0.567±0.025
NPL_Mebrak_2125BP 0.401±0.019
chisq 15.157
tail prob 0.232961
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.452±0.031
RUS_Afanasievo 0.435±0.025
RUS_Okunevo_BA 0.114±0.049
chisq 19.808
tail prob 0.0708003
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.409±0.031
RUS_Okunevo_BA 0.173±0.050
Yamnaya_RUS_Caucasus 0.418±0.026
chisq 20.453
tail prob 0.0589872
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.464±0.033
RUS_Okunevo_BA 0.104±0.053
Yamnaya_RUS_Samara 0.432±0.027
chisq 27.189
tail prob 0.0072566
Full output

Both the Wusun and Saka are generally accepted to have been the speakers of Indo-Iranian languages. So it's possible that the Shirenzigou nomads were Indo-Iranian speakers too, or at least derived from such peoples.

Surprisingly, NPL_Mebrak_2125BP was the key to obtaining the best statistical fits. This is a trio of samples, roughly contemporaneous with the Shirenzigou nomads, from a burial site high up in the Himalayas in what is now Nepal (see here).

To be honest, I'm not quite sure why the Himalayan ancients work so well in my models. Perhaps they're just a really good proxy for an Iron Age population from the northern edge of the Tibetan Plateau?

By the way, most of the Shirenzigou nomads made it into the latest Global25 datasheets (see here). They can be analyzed in a variety of ways described in this blog post: Getting the most out of the Global25. Below is a screen cap of me comparing the effectiveness of Afanasievo, Sintashta and Wusun samples as proxies for the steppe ancestry in the Shirenzigou nomads with an online tool freely available here. As expected, the algorithm picks Sintashta ahead of Afanasievo, and the Wusun ahead of both.

See also...

They mixed up Huns with Tocharians

Some myths die hard

The mystery of the Sintashta people

The PIE homeland controversy: August 2019 status report

Archeologist David Anthony has a new paper on the Indo-European homeland debate titled Archaeology, Genetics, and Language in the Steppes: A Comment on Bomhard. It's part of a series of articles dealing with Allan R. Bomhard's "Caucasian substrate hypothesis" in the latest edition of The Journal of Indo-European Studies. It's also available, without any restrictions, here.

Any thoughts? Feel free to share them in the comments below. Admittedly, I found this part somewhat puzzling (emphasis is mine):

It was the faint trace of WHG, perhaps 3% of whole Yamnaya genomes, that identified this admixture as coming from Europe, not the Caucasus, according to Wang et al. (2018). Colleagues in David Reich’s lab commented that this small fraction of WHG ancestry could have come from many different geographic places and populations.

I think that's highly optimistic. It really should be obvious by now thanks to archeological and ancient genomic data, including both uniparental and genome-wide variants, that the Yamnaya people were practically entirely derived from Eneolithic populations native to the Pontic-Caspian (PC) steppe. So, in all likelihood, this was also the source of their minor WHG ancestry.

Indeed, they clearly weren't some mishmash of geographically, culturally and genetically disparate groups that had just arrived in Eastern Europe, but the direct descendants of closely related and already significantly Yamnaya-like peoples associated with long-standing PC steppe archeological cultures such as Khvalynsk and Sredny Stog. I discussed this earlier this year, soon after the Wang et al. paper was published:

On Maykop ancestry in Yamnaya

I hope I'm wrong, but I get the feeling that the scientists at the Reich Lab are finding this difficult to accept, because it doesn't gel with their theory that archaic Proto-Indo-European (PIE) wasn't spoken on the PC steppe, but rather south of the Caucasus, and that late or rather nuclear PIE was introduced into the PC steppe by migrants from the Maykop culture who were somehow involved in the formation of the Yamnaya horizon.

Inexplicably, after citing Wang et al. on multiple occasions and arguing against any significant gene flow between Maykop and Yamnaya groups, Anthony fails to mention Steppe Maykop. But the Steppe Maykop people are an awesome argument against the idea that there was anything more than occasional mating between the Maykop and Yamnaya populations, because they were wedged between them, and yet clearly distinct from both, with a surprisingly high ratio of West Siberian forager-related ancestry (see here and here).

Despite all the talk lately about the potential cultural, linguistic and genetic ties between Maykop and Yamnaya, including claims that the latter possibly acquired its wagons from the former, my view is that the Steppe Maykop and Yamnaya wagon drivers may have competed with each other and eventually clashed in a big way. Indeed, take a look at what happens after Yamnaya burials rather suddenly replace those of Steppe Maykop just north of the Caucasus around 3,000 BCE.

Yamnaya_RUS_Caucasus
RUS_Progress_En_PG2001 0.808±0.058
RUS_Steppe_Maykop 0.000
UKR_Sredny_Stog_II_En_I6561 0.192±0.058
chisq 13.859
tail prob 0.383882
Full output

Yep, total population replacement with no significant gene flow between the two groups. Apparently, as far as I can tell, there's not even a hint that a few Steppe Maykop stragglers were incorporated into the ranks of the newcomers. Where did they go? Hard to say for now. Maybe they ran for the hills nearby?

Intriguingly, Anthony reveals a few details about new samples from three different Eneolithic steppe burial sites associated with the Khvalynsk culture:

The Reich lab now has whole-genome aDNA data from more than 30 individuals from three Eneolithic cemeteries in the Volga steppes between the cities of Saratov and Samara (Khlopkov Bugor, Khvalynsk, and Ekaterinovka), all dated around the middle of the fifth millennium BC.

...

Most of the males belonged to Y-chromosome haplogroup R1b1a, like almost all Yamnaya males, but Khvalynsk also had some minority Y-chromosome haplogroups (R1a, Q1a, J, I2a2) that do not appear or appear only rarely (I2a2) in Yamnaya graves.

As far as I can tell, he suggests that they'll be published in the forthcoming Narasimhan et al. paper. If so, it sounds like the paper will have many more ancient samples than its early preprint that was posted at bioRxiv last year.

For me the really fascinating thing in regards to these new samples is how scarce Y-haplogroup R1a appears to have been everywhere before the expansion by the putative Indo-European-speaking steppe ancestors of the Corded Ware culture (CWC) people. It's basically always outnumbered by other haplogroups wherever it's found prior to about 3,000 BCE, even on the PC steppe. But then, suddenly, its R1a-M417 subclade goes BOOM! And that's why I call it...

The beast among Y-haplogroups

At this stage, I'm not sure how to interpret the presence of Y-haplogroup J in the Khvalynsk population. It may or may not be important to the PIE homeland debate. Keep in mind that J is present in two foragers from Karelia and Popovo, northern Russia, dated to the Mesolithic period and with no obvious foreign ancestry. So it need not have arrived north of the Caspian as late as the Eneolithic with migrants rich in southern ancestry from the Caucasus or what is now Iran. In other words, for the time being, the steppe PIE homeland theory appears safe.

Update 20/12/2019: A note on Steppe Maykop

See also...

Is Yamnaya overrated?

The PIE homeland controversy: January 2019 status report

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

They mixed up Huns with Tocharians

I don't yet have the genomes from the recent Ning et al. paper on the Iron Age nomads from the Shirenzigou site in the eastern Tian Shan. But I do have most of the previously published data featured in the paper, including the Damgaard et al. 2018 Hun and Saka samples from the western Tian Shan.

After reading the Ning et al. paper between the lines and running a few analyses of my own, it's clear to me that most of the supposedly Tocharian-related Shirenzigou individuals actually share a very close relationship with the Tian Shan Huns, and indeed may have been their ancestors.

For instance, Ning et al. found that a large part of the ancestry of the Shirenzigou ancients could be modeled with the Tian Shan Huns, which was an anachronistic approach because the former are older than the latter. They also found that Ulchi-related ancestry was a key part of the genetic structure of eight out of the ten Shirenzigou individuals, and this likewise appears to be an important part of the genetic structure of the Tian Shan Huns.

Note the strong statistical fits in the Global25/nMonte and qpAdm mixture models below, respectively, which characterize these Huns as a two-way mixture between the Ulchi and the earlier Tian Shan Saka. And keep in mind that the Saka also harbor significant Ulchi-related ancestry.

Hun_Tian_Shan
Saka_Tian_Shan,92
Ulchi,8
distance%=1.2553

Hun_Tian_Shan
Saka_Tian_Shan 0.928±0.009
Ulchi 0.072±0.009
chisq 4.409
tail prob 0.992464
Full output

Moreover, the Shirenzigou males belong to Y-haplogroups Q1a and R1b (two instances of each), and they share the latter with one of the Tian Shan Huns. Judging by the data from the relevant BAM files, it's also possible that the Shirenzigou males share a very rare subclade of R1b with the Hun, defined by the PH155 mutation (see here). The Y-haplogroup assignments for the other Tian Shan Huns end at R and R1, but that's almost certainly due to missing data.

On the other hand, two Tian Shan Sakas belong to Y-haplogroup R1a but none to R1b, which fits with the pattern from currently available ancient DNA that R1a was more common than R1b in Saka-related groups, such as the Scythians and Sarmatians (see here).

This is all very interesting, because the Huns replaced the Saka in the western Tian Shan, and, considering their R1b and excess Ulchi-related ancestry, very likely moved into the region from the direction of Shirenzigou. Indeed, in my opinion a strong argument can now be made that the Iron Age population from the Shirenzigou region took part in the formation of the Hunnic confederacy.

So where does that leave the theory presented by Ning et al. that the Shirenzigou ancients may have been closely related, and perhaps even ancestral, to the Tocharians, simply because they packed a lot of Yamnaya-related and possibly proto-Tocharian Afanasievo ancestry, and were living close to the Tarim Basin, where Tocharian languages were subsequently first attested?

I'm not sure, but I now find it difficult to reconcile this theory with the fact that they were closely related, and probably ancestral, to the Tian Shan Huns. As far as I'm aware, Huns cannot be linked to Tocharians in any meaningful way.

Of course it's possible that different Afanasievo-derived groups were living in the Tarim Basin and surrounds, and, as some merged with new populations pushing into the region from the east and adopted non-Indo-European languages, others retained their Tocharian speech and eventually split into communities speaking Tocharian A, B and apparently also C (see here).

But this has to be demonstrated directly with ancient DNA from archeological sites where Tocharian languages were attested. Till then, I'll keep thinking that Ning et al. wrote a paper about Tocharians that really should've been a paper about Huns.

Here's a famous wall painting of Tocharian princes from the cave of the sixteen sword-bearers in the Tarim Basin, dated to 432–538 AD. They don't look like guys with a lot of Ulchi-related admixture to me, but I might be wrong. Feel free to let me know what you think in the comments below.

Update 08/17/2019: The Shirenzigou nomads are now in my dataset. Below are a few successful and not so successful qpAdm mixture models for them. Note that I tried to use a wide range of relevant "right pops", but also retain a lot of markers, specifically to be able to discriminate between different types of steppe and steppe-derived sources of gene flow (refer to the full output). Admittedly, the Shirenzigou nomads can be modeled with Afanasievo-related ancestry, but...

CHN_Shirenzigou_IA
KAZ_Botai 0.161±0.023
KAZ_Wusun 0.490±0.023
NPL_Mebrak_2125BP 0.349±0.019
chisq 5.793
tail prob 0.926172
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.143±0.022
NPL_Mebrak_2125BP 0.295±0.019
Saka_Tian_Shan 0.562±0.024
chisq 6.796
tail prob 0.870794
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.185±0.023
NPL_Mebrak_2125BP 0.428±0.021
RUS_Sintashta_MLBA 0.270±0.026
TJK_Sarazm_En 0.117±0.027
chisq 11.351
tail prob 0.414345
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.032±0.027
KAZ_Zevakinskiy_LBA 0.567±0.025
NPL_Mebrak_2125BP 0.401±0.019
chisq 15.157
tail prob 0.232961
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.452±0.031
RUS_Afanasievo 0.435±0.025
RUS_Okunevo_BA 0.114±0.049
chisq 19.808
tail prob 0.0708003
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.409±0.031
RUS_Okunevo_BA 0.173±0.050
Yamnaya_RUS_Caucasus 0.418±0.026
chisq 20.453
tail prob 0.0589872
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.464±0.033
RUS_Okunevo_BA 0.104±0.053
Yamnaya_RUS_Samara 0.432±0.027
chisq 27.189
tail prob 0.0072566
Full output

Both the Wusun and Saka are generally accepted to have been the speakers of Indo-Iranian languages. So it's possible that the Shirenzigou nomads were Indo-Iranian speakers too, or at least derived from such peoples.

Surprisingly, NPL_Mebrak_2125BP was the key to obtaining the best statistical fits. This is a trio of samples, roughly contemporaneous with the Shirenzigou nomads, from a burial site high up in the Himalayas in what is now Nepal (see here).

To be honest, I'm not quite sure why the Himalayan ancients work so well in my models. Perhaps they're just a really good proxy for an Iron Age population from the northern part of the Tibetan Plateau? By the way, most of the Shirenzigou nomads made it into the latest Global25 datasheets (see here).

See also...

Almost everything you ever wanted to know about the Xiaohe-Gumugou cemeteries

The mystery of the Sintashta people

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

Afanasievo people may well have been proto-Tocharian speakers (Ning et al. 2019)

Update 17/08/2019: A surprising twist to the Shirenzigou nomads story

...

During the Early Bronze Age, around 2,900 BCE, a population associated with the Yamnaya archeological culture migrated from the Pontic-Caspian steppe in Eastern Europe deep into Asia, as far as the Minusinsk Basin in South Siberia.

This rapid, long-range expansion was likely to have been the first significant migration of a Yamnaya-related group far to the east of the Ural Mountains, and it resulted in the formation of the Afanasievo archeological culture (see here).

The appearance of Tocharian languages in the Tarim Basin, in what is now western China, is often associated with the Afanasievo culture, mainly because of the confirmed presence of European-related populations in the Tarim Basin during the Bronze Age, as well as the likely highly divergent position of the Tocharian node in the Indo-European language phylogeny.

But the Afanasievo people were separated by considerable distance in space and time from the Tocharians, and can't yet be reliably linked to them with archeological or genetic data. So even though the inference that the former are linguistically ancestral to the latter is quite plausible, it's far from certain.

However, thanks to a new paper at Current Biology by Ning et al., at least we now know that a population with significant Yamnaya/Afanasievo-related ancestry was living in the eastern Tian Shan Mountains just a few hundred years before Tocharian languages were attested nearby [LINK]. Below is the paper summary, emphasis is mine:

Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1, 2, 3, 4, 5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6, 7, 8, 9, 10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. 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.

Ning et al., Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan, Current Biology, July 25, 2019, DOI: https://doi.org/10.1016/j.cub.2019.06.044

See also...

It was always going to be this way

The mystery of the Sintashta people

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

Inferring the linguistic affinity of long dead and non-literate peoples: a multidisciplinary approach

Ancient DNA has treated us to many surprises in recent years. But it has also uncannily corroborated some well established hypotheses that were formulated decades ago from historical linguistics and archeological data. One such hypothesis is that the population associated with the Late Neolithic Corded Ware culture (CWC), and its myriad offshoots, spoke early Indo-European languages and spread them across much of Europe and into the Indian subcontinent.

Below is a series of figures in which I explain why the CWC and its likely close relative, the Sintashta culture, are widely regarded as early Indo-European-speaking cultures, even though their languages aren't attested. To view the images at their maximum size, right click on the thumbs and choose "open link in a new tab".

It's a damn shame that we still don't know where the modern domesticated horse lineage ultimately came from. I'm pretty sure that it came from the Pontic-Caspian steppe, but I was hoping this would be confirmed in the latest paper on horse genomics published today at Current Biology: Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Nope, the topic wasn't even covered, and no wonder, because the sampling strategy in the paper didn't allow it to be. What we desperately need are samples associated with such archeological cultures as Khvalynsk, Repin, Sredny Stog and Yamnaya. Maybe next time, eh?

See also...

Some myths die hard

Ancient DNA tells us that the Bronze Age wasn't kind to the indigenous populations of Central Asia. It seems to have wiped them out totally. Indeed, Central Asia might well be the only major world region in which native hunter-gatherers failed to make a perceptible impact on the genetics of any extant populations.

Before the Neolithic transition, much of Central Asia was home to hunter-gatherers closely related to those of nearby western Siberia. During the Neolithic, agriculturalists and pastoralists from the Near East gradually moved into the more arable parts of southern and eastern Central Asia, eventually giving rise to the Bactria Margiana Archaeological Complex, or BMAC, and other similar communities.

It's not clear what their relationship was like with the native hunter-gatherers in these areas. But they did mix with them in varying degrees. This is obvious because genome-wide genetic ancestry characteristic of the Botai people, who hunted and eventually domesticated horses on the Kazakh steppe during the 4th millennium BCE, and were probably the archetypal Central Asians for their time, is found at significant levels in a number of later samples from Central Asian farmer and pastoralist sites, such as Dali, Gonur Tepe and Sarazm.

Thus, even though the Neolithic transition did have a big impact on Central Asia, and clearly led to large scale population replacements in some parts of the region, this was just the beginning of these population shifts. Moreover, in some cases the expanding farmer and pastoralist populations seem to have acquired significant indigenous Central Asian ancestry and spread it with them.

The precise geographic extent of the relatively unique Botai-related ancestry in prehistoric Eurasia is still something of a mystery. But to give you a general picture of where it was found from around 6,000 BCE to 2,000 BCE, here's a map with info about samples with significant levels of this type of ancestry from a wide range of sites in space and time.

Going by this map, I'd say it's safe to infer that the Botai-related ancestry was a major feature of practically all forager populations living between the Caspian Sea and the Altai Mountains. It was also present in the Early Bronze Age (EBA) pastoralist population associated with the Steppe Maykop archeological culture of Eastern Europe, so it may have already been in Europe as early as 3,800 BCE, because that's when the Steppe Maykop culture first appeared.

It's an interesting question where the ancestors of the Steppe Maykop herders came from. I once simply assumed that they were closely related to the Maykop people who lived in the Caucasus Mountains. But it's now clear that the populations associated with these two similar cultures were starkly different, with the Maykop people being basically of Near Eastern origin and lacking any discernible Botai-like ancestry. My guess for now is that the Steppe Maykop herders were in large part the descendants of the Kelteminar culture population from just east of the Caspian Sea, but we'll see about that when more ancient DNA comes in.

The other great mystery is what eventually happened to the Steppe Maykop people. Around 3,000 BCE, their culture vanished from the archeological record and their particular genetic signature disappeared from the steppe ancient DNA record. Where did they go? Did they migrate back east?

I don't know, but at about that time other Eastern European steppe herders, those associated with the Yamnaya and Corded Ware archeological cultures, began to stir and migrate in big numbers in basically all directions, including into Steppe Maykop territory. Indeed, unlike the Steppe Maykop population, these groups weren't closely related to any contemporaneous or earlier Central Asians. But they ended up moving into Central Asia, and in a big way too.

Their impact all the way from the Ural Mountains to what are now China and India was profound. For instance, not only did they end up totally replacing the Botai people, but also their horses. For more details on this topic check out the Youtube clip here. I have a strong suspicion that the same sort of thing happened to the aforementioned Steppe Maykop people. In other words, they may have been forced out from the Eastern European steppe, and perhaps sought shelter in the Caucasus Mountains?

Admittedly, I'm not offering anything new here. I just wanted to emphasize a few key points, because I'm still seeing some confusion online about the population history of Central Asia, and especially how it relates to the population history of Europe, and also the Proto-Indo-European homeland question. Make no mistake, thanks to the ancient DNA already available from Central Asia, we can confidently infer the following:

- the chance that the ancient European populations associated with the Yamnaya, Corded Ware and other closely related archeological cultures formed as a result of migrations from Central Asia is zero

- the chance that the Proto-Indo-European homeland was located in Central Asia is zero

- the chance that present-day Europeans, by and large, derive from any ancient Central Asian populations is zero

See also...

Central Asia as the PIE urheimat? Forget it

The Steppe Maykop enigma

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

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