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

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

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...

The resistance crumbles

Over the years some scientists from the Estonian Biocentre have been among the staunchest opponents of the idea that Bronze Age pastoralists originating in the steppes of Eastern Europe had a significant genetic and linguistic impact on South Asia (for instance, see here).

But this week they put out a review paper titled The genetic makings of South Asia [LINK] featuring the figure below. It's a nice visualization of the current state of understanding of the peopling of South Asia, and does acknowledge the major role that the said steppe pastoralists had in this process.

However, there's not a single mention of Y-haplogroup R1a in the review. This is surprising, considering the once common, but now no longer valid, claims that this paternal marker may have originated in India. I guess the grieving process will continue for a little longer for some.

My long-held opinion about the claims that R1a was native to India, Iran, Central Asia, or, indeed, anywhere but its actual homeland, which is certainly Eastern Europe, can be summarized as such: LOL!

See also...

On the doorstep of India

One of the most remarkable discoveries in the recent Narasimhan et al. 2018 preprint has to be the presence of what are essentially Eastern European migrant populations within the Inner Asian Mountain Corridor (IAMC) during the Middle to Late Bronze Age (MLBA). Remarkable for so many reasons, but seemingly under-appreciated by a lot of people, judging by the online discussions that I've seen about the preprint, and even, I'd say, the authors themselves.

Narasimhan et al. labeled these groups as belonging to the "forest/steppe MLBA" complex (for instance, see the main figure from the preprint here). This is indeed what they are in terms of their genetic structure, but certainly not geography, because the IAMC is well south of the steppe. Thus, in my Principal Component Analysis (PCA) I'm going to label them as part of the "post-steppe herder expansion Turan" complex.

Strikingly, most of these people cluster with Bronze Age Eastern Europeans, and even some Bronze Age Central Europeans. They're also sitting very close to the more easterly present-day Slavic-speakers from Russia and Ukraine, and indeed closer to the bulk of the European cluster than some present-day Turkic and Uralic groups from the Volga-Ural region. Even I never predicted such an outcome. Sure, I was expecting to see ancient genomes from South Central Asia with some very heavy steppe influence, but not this. The relevant datasheet is available here.

Two of the MLBA IAMC individuals are from Kashkarchi in the Ferghana Valley, in what is now Uzbekistan, and basically on the doorstep of the Indian subcontinent. I've made special mention of them on the plot, and I've also highlighted a pair of individuals from the Bronze Age Central Asian sites of Gonur Tepe and Shahr-i Sokhta, who are, in all likelihood, unadmixed migrants from the Indus Valley (for more on that, see here).

It's surely not a coincidence that the ancient and present-day South Asians on the plot (including those from Pakistan's Swat Valley dated to the Iron Age) form an almost prefect cline between these two pairs of individuals. It's also surely not a coincidence that the MLBA IAMC groups are rich in Y-haplogroup R1a-M417, and in particular its R1a-Z93 subclade, which is today an especially frequent marker in Indo-European-speaking South Asians.

Forget about the pre-MLBA populations from the forests, steppe, or IAMC, like those represented by Dali_EBA; they're practically irrelevant to this story. How do I know? Because they have little to no impact on the above mentioned cline. And this can be easily verified with mixture models based on multiple Principal Components (PCs) and formal statistics (for instance, see here).

Clearly, many populations in South Asia, particularly those speaking Indo-European languages, derive the bulk of their steppe-related ancestry from the peoples of the MLBA IAMC, and/or their very close relatives. And if you do believe that this inference is just based on coincidences, then I'm sorry to say this, but obviously a new, much less mentally challenging, hobby or profession beckons. All the best with that.

Just to help put all of this in a geographic perspective, here's a topographical map of Eurasia. I've marked the location of the Ferghana Valley. The close relatives of Kashkarchi_BA most likely skirted their way around those winding high mountains and slipped into India via the Khyber Pass, which I've also marked on the map.

And the rest, as they say, is history, including the history described in the ancient Indo-Aryan Sanskrit texts known as the Vedas. I'm sure we'll soon be learning about these events in great detail when many more ancient samples from Pakistan and, hopefully, the first ancient samples from India, are published.

Citation...

Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

See also...

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

The Poltavka outlier

Anyone who still thinks that Y-chromosome haplogroup R1a originated in South Asia should burn this map into their brains. It'll come in useful over the next few years as we learn from ancient DNA about the conquest of the Indian subcontinent, and indeed much of Asia, by pastoralists from the western Russian and Ukrainian steppes.

X marks the spot of the burial site of Poltavka sample I0432 from the Mathieson et al. 2015 dataset. This individual belongs to Y-chromosome haplogroup R1a-Z93(Z94+), which today accounts for well over 90% of the R1a lineages in Asia and peaks in frequency at over 60% in the northern parts of South Asia.

Moreover, the dating of his burial site, 2925-2536 calBCE, suggests that he lived not long after the Z93 and Z94 mutations came into existence. That's because Z93 doesn't appear to be much older than 5,000 years based on full Y-chromosome sequence data (see here and here, including the comments).

So I0432 could well turn out to be a crucial piece in the puzzle of the peopling of South Asia.

Interestingly, this individual was flagged as an outlier in the Poltavka sample set by Mathieson et al., hence his other moniker: the Poltavka outlier. However, this wasn't because of any ancestry from South or even Central Asia. In fact, it was because he was too western.

Principal Component Analyses (PCA) featuring a wide range of present-day and ancient samples from Europe and Asia, like the one below, show that Poltavka outlier clusters further west than most Corded Ware individuals from Germany. Right click and open in a new tab to view full size.

In the past, using qpAdm, I modeled Poltavka outlier as 63.7% Yamnaya Samara and 36.3% German Middle Neolithic. This is probably not very far from the truth, but qpAdm offers a supervised mixture test in which the results are heavily reliant on the choice of outgroups, so I thought I'd revisit the issue with TreeMix, which allows an unsupervised analysis.

In a dataset including seven relatively high coverage Copper Age (CA), Early Bronze Age and Middle Neolithic (MN) European genomes, TreeMix picked out Poltavka outlier as the most likely sample to be admixed, showing a mixture edge of 33% from the base of the branch leading to the Iberian MN individual to that of Poltavka outlier.

This outcome is very similar to my qpAdm model, but it suggests an even more western source of admixture in Poltavka outlier. Could this admixture actually be from Iberia? I wouldn't discount this possibility, considering the presence of Bell Beaker communities, possibly of Atlantic or even Iberian origin, as far east as present-day Poland. Indeed, according to Cassidy et al. 2015, German Beakers show high affinity to MN and CA Iberians (see page 51 in the supp info here).

I double checked my TreeMix result with D-stats, and yep, when placed in a clade with Poltavka or Samara Yamnaya, Poltavka outlier shows the strongest signal of admixture from the Iberia MN individual.

At the same time, however, the signal from the Early Neolithic (EN) Iberian fails to reach significance (Z=<3), which suggests that, in fact, TreeMix and D-stats might be seeing the Iberia MN sample as the most attractive mixture source due to her high level of Western European hunter-gatherer (WHG) ancestry, which Poltavka outlier also has plenty of, rather than anything specific to Iberia.

In any case, it's clear enough that Poltavka outlier was the result of mixture between Yamnaya-related western steppe pastoralists and the descendants of Middle Neolithic Europeans with a high ratio of WHG ancestry. Where this admixture actually took place and which archaeological cultures were involved will have to be resolved with further sampling of ancient remains from Central and Eastern Europe.

However, it's already impossible to place the origin of Poltavka outlier anywhere in Asia, which suggests that both Z93 and Z94 are also from well inside the generally accepted borders of Europe.

This obviously has implications for the origins of the Indo-Iranians, because the widespread presence of these mutations in Asia gels very nicely with the idea, and indeed academic consensus, that Indo-Iranian languages expanded rapidly from the Eurasian steppe into Asia during the Bronze Age.

Considering that Poltavka outlier came from a Kurgan burial, and was therefore an individual of some social standing, he might be the direct ancestor of many millions of present-day Asians. If so, this won't be very difficult to prove in the near future as ancient DNA research revs up a few notches.

On a related note, apparently there's a paper on the way with ancient DNA results from Rakhigarhi, a Harappan site in Haryana, northern India (see here). As far as I know, the results will include Y-chromosome haplogroups of three males, but I don't think we'll see any decent genome-wide data at this stage. However, hopefully I'm wrong and the paper will come out with full ancient genomes.

Feel free to post your predictions in the comments. I'm tentatively expecting a couple of instances of J2 and maybe an L or H. Razib made basically the same prediction recently so I'm not being original. What I do know is that we won't see any R1a-Z93. The only way that might happen is if, say, someone coughed or sneezed on the Harappan remains.

Data source and reference...

Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians, Nature, 528, 499–503 (24 December 2015), doi:10.1038/nature16152

See also...

The beast among Y-haplogroups