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Wednesday, March 26, 2014

The story of R1a: the academics flounder on


There's been a lot of horseshit published over the years about Y-chromosome haplogroup R1a, which just happens to be my haplogroup. That includes academic papers in journals like PLoS ONE and Nature. My advice is, take all of that stuff with a very large pinch of salt and just look here for updates.

Indeed, a new paper on the phylogeography of R1a appeared at the Nature website today: Underhill et al. 2014. It's actually a much better effort than anything else on the topic at academic level thus far, but certainly not without issues.

For instance, the authors failed to include two well known and very important R1a subclades in their analysis: the Northwest European-specific R1a-CTS4385 and the East and Central European-specific R1a-Z280. As a result, the former is lumped with R1a-M417* and the latter with R1a-Z282*. In fact, Z280 is shown to be above Z282 in the topology of R1a-M420 (see Figure 1 here), which is plain wrong. These are major oversights and mean that this study is not a very useful resource as far as the phylogeography of European R1a is concerned.

But the paper does show a couple of interesting things. For instance, the maps below offer the best illustration to date of the dichotomy between the European-specific R1a-Z282 and Asian-specific R1a-Z93.



However, these are very closely related subclades, sharing the Z645 mutation (unfortunately not mentioned in the paper), and both reaching high frequencies among Indo-European speakers. It's therefore plausible that groups carrying these markers expanded to the west and east from a zone between their current hotspots, possibly the Volga-Ural region, rather recently.

Indeed, these migrations had to have happened after 4800-6800 YBP, which is the age of R1a-M417 reported by Underhill et al., and backed up by estimates from genetic genealogists using, among other things, complete R1a sequences (see here). In other words, the rapid expansions of R1a-Z282 and R1a-Z93 appear to have taken place from more or less the same region during the generally accepted early Indo-European timeframe, making them excellent candidates for paternal markers of the early Indo-European dispersals.

At the same time, the paucity of R1a-Z93 and derived lineages in Europe, including Eastern Europe, suggests that historic migrations originating in East and Central Asia, like those of the early Turks, had a negligible effect on the paternal ancestry of modern Europeans. This shows very clearly on the PCA in Figure 4 (see here).

Citation...

Underhill et al., The phylogenetic and geographic structure of Y-chromosome haplogroup R1a, European Journal of Human Genetics, advance online publication, 26 March 2014; doi:10.1038/ejhg.2014.50

See also...

R1a-Z93 from Bronze Age Mongolia

Afghan Hindu Kush: a genetic sink

30 comments:

Daniel Szelkey said...

I also have R1a, I belong to R1a-z280.
The study found that the Kazan Tatars are dominated by the European branch of R1a rather then the Asian branch. It also showed that the Greeks and Crete have far more Europe R1a than Asian R1a. The study verified that Asian R1a, is the dominate kind in Azerbaijan and all of the Caucasus except the Nogays. No data was available before this study. European R1a was verified at a very low frequency in Afghanistan, and Iran. The strangest thing however was the 14% European R1a among the Beduoins, who are these?.

Daniel Szelkey said...

In addition to this the study is the first high resolution study of R1a in the Chuvash and the Komi. Clearly finno-ugric languages are associated with European R1a, rather than asian R1a. It also proved that the Altai, and Turkic speaking Siberiais dominated by Asian R1a,with around 1% European R1a something that was not known before this study.

Davidski said...

The high frequency of Z282* among the Bedouin is very likely due to a recent founder effect.

I'd say that this lineage did come from Europe, but probably a long time ago, like the Bronze Age. It's now found at very low frequencies across West Eurasia.

But as per above, the major problem with this study is that it basically ignores Z280, which is the most common form of Z282 in Eastern Europe. In fact, for some bizarre reason it shows Z280 to be ancestral to Z282, M458, and Z284. Crazy.

vooruit said...

Ha ha!
I didn't dream, did I?
They've tested the R1a in Altai/south Siberia and it so happens they are Z93*, right?

People that we KNOW arrived from south Russia in the chalcolithic time (common morphology and light pigmentation (known via aDNA), eaaly yamnaya potteries, cult objects and axes, kurgan, west female lineages and almost fully R1a male lineages in aDNA, copper and silver metallurgy, pastoralmism, etc...) had Z93*.

This yells Kurgan theory validation!
Am I right or am I right? :)

אחיקם גדליהו ישעיהו בן הלל said...

The phylogenetic analysis is naive and wobbly but the maps clearly highlight the Z92-Z282 dichotomy in Eurasia.

I will take this as validation of the Kurgan theory and the Yamna culture's association with PIE.
I have little doubt that R1a was the driving force in this process, and that R1b-L51 hopped on board at some point.

All is needed is aDNA to invalidate years of nonsensically biased articles positing West Asia or the Indian subcontinent as R1a's cradle.

barakobama said...

You forgot to mention plenty of ancient DNA evidence(or prove) that R1a1 was mostly spread with Indo Europeans.

About Time said...

What's the Z282* in Bedouin? Did it piggyback with any other Euro clades and does it show up anywhere else in Mideast?

אחיקם גדליהו ישעיהו בן הלל said...

"The Kurgan theory can no longer be denied for a number of reasons"

Linguistically, it's the best explanation out there.
No other tops it, everything points to it as the PIE Urheimat.

We're really dealing with a paradigm here, where Genetics, Historical Linguistics and Archeology seem to lead to the same conclusion.

Davidski said...

About Time,

It's very difficult to figure out what those supposedly Z282 lineages are among the Bedouin in this paper. But Z282 and the downstream Z280 have been found in the Middle East before. They appear to be a subset of European Z282 diversity.

http://i129.photobucket.com/albums/p217/dpwes/Z282-Z283.jpg~original

http://i129.photobucket.com/albums/p217/dpwes/Z280.jpg~original

Source:

https://www.familytreedna.com/public/r1a/default.aspx?section=results

About Time said...

@Davidski, definitely an interesting (and IMO surprising) distribution map.

It's too bad the samplers didn't ask the Bedouin their genealogy. Arabs tend to keep tabs on that stuff, even in the cities. They are like the Irish/Scottish or the Cohens/Levites in that regard.

There is a guy on the FTDNA R1a group who is Al Sheibi Al Quraishi (not clear to me which Quraysh clan his family claims descent from), but I think he's Z93. Where did those Z282s come from? Looks like N Europe honestly.

Davidski said...

There were many population movements from Europe and the Eurasian steppe to the south that could explain the occasional presence of Z282, Z280 and even M458 across West and Central Asia. The early Indo-European dispersals for one, but also later Indo-European migrations like those of the Scythians, Sarmatians and Cimmerians, and the Russian expansion into Central Asia and even Iran, among others. Also don't forget that hundreds of thousands of slaves were taken from all over Europe by the Ottomans and others, and many Mamluks (slave mercenaries) came from Eastern Europe. These Mamluks were often very powerful politically, and I wouldn't be surprised if they fathered quite a few descendents in the Middle East.

barakobama said...

Davidski, what does IBS mean? Because the results for MA-1 don't make sense.

Davidski said...

IBS means Identical-by-State. See here...

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002287

And yeah, the results for MA-1 make sense. They're very similar to the drift stats from the Raghavan paper, but with South Asians higher on the list.

http://img811.imageshack.us/img811/4151/zubo.png

barakobama said...

MA-1 is much more related to for example Lithuanians than to native Americans, who have possible as much as 70% WHG-ANE ancestry. So that is why the results made no sense to me.

Davidski said...

Native Americans are 30-40% ANE (MA-1 like), while Lithuanians only about 17%.

The fact that WHG and ANE are closely related clades, and Lithuanians over 60% WHG + ANE, isn't enough to make Lithuanians more similar overall to MA-1.

barakobama said...

Whatever, it's just some people still think MA-1 was not west Eurasian. Some think he was an intermediate Eurasian, and just because he is so related to WHG does not mean he is closely related to west Eurasian forms in the middle east.

Can't wait what the 45,000 year old Siberian will tell.

Davidski said...

MA-1 isn't the link between West and East Eurasians because he's 0% East Eurasian. I'm not sure why some people aren't getting this?

West Eurasians and Amerindians are the ones who are mixed, with the African-like Basal Eurasian and East Asian ancestry, respectively.

I'm guessing that 45K year-old Ust-Ishim sample will turn out to be ancestral to MA-1, La Brana-1, Loschbour and Motala12. So in other words, he'll look like the first of the Mammoth Steppe hunters who, one way or another, contributed 50-60% ancestry to our genomes.

barakobama said...

I can't read Underhill et al., 2014 because it costs money, and i am wondering did they mention Indo Europeans at all in their paper? A 2 year old could notice the similarity between the distribution of R1a Z282 and Copper age Corded ware culture, and it just happens that there have already been two R1a1 samples found from the Corded ware culture.

https://www.google.com/search?q=corded+ware+culture&espv=210&es_sm=122&tbm=isch&tbo=u&source=univ&sa=X&ei=mfg6U_dqiPHbBd6fgLAC&ved=0CEsQsAQ&biw=1024&bih=667

Supposed bronze age iron age Indo Iranians in Asia were also full of R1a1, probably had more than any modern people. The R1a M417 Indo European theory makes alot of sense. I can't believe the ignorant retard who wrote this paper previously theorized the Indus valley as the home of R1a. When that is one of many areas Indo Iranians(who were full of R1a1) conquered during the bronze age.

I know that R1a1 samples from proto Indo European cultures of the Pontiac steppe will be published soon, maybe then the authors of this paper will realize Indo Europeans are the source of most modern R1a.

Davidski said...

Yes, they suggest that the spread of Z282 was linked to the spread of the Corded Ware Culture. They also mention the Copper Age R1a samples from Eulau, eastern Germany, to support their case. But they don't say that the Corded Ware Culture was Indo-European.

They also don't appear to notice that the generally accepted Proto-Indo-European homeland near the middle Volga is located in between the present-day hotspots of Z282 and Z93, which are two very closely related subclades sharing the Z645 mutation (which they didn't even test).

So they basically say that R1a first expanded from Iran (which is unlikely, because R is probably an ANE marker of the steppes), and then for some unknown reason M417 exploded out of nowhere during the Copper Age, began to mutate, and ended up dominating two regions with long histories of Indo-European speech and culture.

Ryan said...

"So they basically say that R1a first expanded from Iran (which is unlikely, because R is probably an ANE marker of the steppes), and then for some unknown reason M417 exploded out of nowhere during the Copper Age, began to mutate, and ended up dominating two regions with long histories of Indo-European speech and culture."

I wouldn't discard this out of hand. The Zagros mountains area had very savanna-like vegetation at the LGM. I would think that would be a pretty favourable environment for people used to hunting herds of large mammals on the steppe. There doesn't seem to be any ancient DNA available from the region thanks to 30 years of strife, but would it really be that implausible if the Zarzian culture turned out to have a great deal of affinity to steppe hunters?

In terms of an unknown reason for the expansion, I'd point out that the location and time of R1a's expansion put forward in this paper is more or less exactly where goats were domesticated. I would think the first pastoralists would have expanded pretty widely.

Then, when one of those groups of pastoralists domesticated horses, there is a second wave of expansion.

It would rather elegantly reconcile both the Anatolian and Kurgan hypotheses.

I don't think it would be a stretch to attribute some role in domestication to descendants of steppe hunters. It's not exactly a huge leap to go from following herds, to managing herds, to outright domestication. I know researchers have suggested the climate change following the LGM as a catalyst to this too. In open savanna there's little danger of hunting an area out, as you need to be constantly moving to follow the herds anyways. With the shift to more forested terrain, the danger of overhunting of deer and wild goats becomes much more real.

Maybe I'm explaining this badly... does that make some sense?

I'd point out that similar conditions would have existed in the Altas mountains as the Zagros. Perhaps that area could have acted as an incubator for R1b as the Zagros did for R1a?

Davidski said...

I find it very difficult to believe that R1a and MA1-related ancestry (so called ANE) didn't fist appear in the Near East with the arrival of early Indo-European groups like the Hittites and Indo-Iranians, the latter of which are said to have rode in on their "mountain donkeys", in other words horses, named as such because they first appeared in the east of Iran during the Iron Age, coming down from the Iranian Plateau, where I suspect both R1a and ANE peak today in the country. Almost the same thing happened across much of Europe during the Copper and Bronze Ages.

This fits perfectly with all of the data we've seen of late. All other theories seem like attempts to put Anatolia, Iran and/or India into the Proto-Indo-European picture. But these really look like lost causes at this stage.

About Time said...

@Ryan, sounds reasonable to me. When people have a choice, warm is better than freezing/cold. Siberia is a super harsh nasty place to live.

Some people move out of temperate zones when they get too crowded/congested with all the resulting social pathologies (crime, freeloaderism, loss of early egalitarianism, etc).

Also, I tend to think Basal/EEF were part of kurgan expansion and were more the "brains" of the operation. "ANE" were IMO more the brawn + had more coherent cultural pattern. Hunter bands are typically simpler and more egalitarian among themselves. Brainy people tend to be a little individualistic and socially incoherent in practice.

But put 2 together in right circumstances (necessity) and you can get synergy. For a while.

Ryan said...

You posted this a while back but I can't track down the original source. Do you know where it's from? http://img18.imageshack.us/img18/5406/qcu6.png

The arrow showing the spread of microblade technology from Mongolia to Tepe Guran in the Zagros is what I'm referring to. I'm not suggesting that the Zarzians were overwhelming ANE or that they had a huge demographic impact on the first Indoeuropeans. I'm just suggesting that they had some ANE affinity, that they had a decent amount of R1*, and that they were the vector by which R1a spread to Volga region.

I agree with you that R is likely an ANE marker, but I don't think it follows that every population that contains it must have HUGE levels of ANE. The Ouldeme in Cameroon are overwhelmingly R1b and I don't think anyone would accuse them of being particularly Siberian.

Most ANE in Indoeuropeans would still come from the people indigenous to the Volga area. The mDNA from early Kurgan sites were mostly C4a'b'c and its descendants, which suggests a pretty clear Siberian origin to me.

""I find it very difficult to believe that R1a and MA1-related ancestry (so called ANE) didn't fist appear in the Near East with the arrival of early Indo-European groups like the Hittites and Indo-Iranians"

Well, what I'm suggesting is that the Zarzians in the Zagros mountains weren't really part of the Near East from a purely Y DNA standpoint. The genetic and archaeological evidence for the domestication of goats happening in the Zagros mountains seem pretty solid. I doubt those goats spread to the Pontic Steppe without some people accompanying them.

" the Iranian Plateau, where I suspect both R1a and ANE peak today in the country."

How would the Y-DNA of the Kalash fit into this? In particular the Y-DNA reported as R* and R1* in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588664/

If I'm right, the Kalash could be descended (mostly) from a parallel migration of ANE groups at the same time as other ANE groups were moving to both the Zagros mountains. The high amount of genetic drift in the Kalash would suggest their ANE heritage must have originated prior to the Indo-Aryan migrations into the area doesn't it? They certainly received inputs from Indo-Aryan and South Asian neighbours too, but the older ANE remained the dominant component. Or am I way off base here?

"This fits perfectly with all of the data we've seen of late. All other theories seem like attempts to put Anatolia, Iran and/or India into the Proto-Indo-European picture. But these really look like lost causes at this stage."

I agree 100% there. I'm not suggesting Indo-European originated anywhere but the Pontic Steppe.

I'm just suggesting that the data used to support the Anatolian hypothesis has actually misclassified some terms as Indo-European that really came from an earlier sprachbund, which has thrown off the computer models and biased them towards an origin in Anatolia.

Am I out to lunch here or...?

About Time said...

@Ryan, remember Kura-Araxes was key in Mallory's main kurgan model. Remember big things can have small beginnings.

Just because the IEs "made it big" doesn't negate that maybe they started out in a compressed space (like Kura-Araxes - near the Mede center ny the way) where their toolkit came together as an integrated package.

Also just because they were a Proto-culture doesn't mean their origins were not hybrid. Or even dual origins that kept some dustinctiveness, like Vedic castes. Brahmins and Kshatriya - alternatively supporting each other in a cultural symbiosis or destructively fighting each other for dominance.

Don't forget Central Asia was less arid in the past. Even the Aral Sea has shrunk in recent years due to Soviet irrigation projects.

Davidski said...

Ryan,

I was referring to R1a, not R1b or R2.

The latter two might well have moved into the Near East before the Proto-Indo-European dispersals. That's possibly why we now see R1b in Africa without any appreciable levels of ANE there.

Also, it's likely that R2 was present in South Asia prior to the arrival of the Indo-Aryans in the sub-continent. Indeed, a lot of the R* lineages reported in old studies from South Asia are actually R2, while the R1* are often R1b. Keep in mind also that some results might just be lab errors.

In any case, I'm not aware of any verified cases of R* or R1* anywhere.

Ryan said...

A, fair enough. Is it really that big a contradiction between your position that R1a is a purely Indo-European marker and this paper's position that the purely Indo-European markers are just a couple of mutations downstream from R1a?

Yah, I took another look at that paper, and it looks like they didn't bother testing for R1b, so those R1* individuals would likely just be R1b.

The R* individuals are M173 positive and negative for M17 PK5 and M124. The frequency seems implausibly high for Greece.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588664/figure/F1/ Not sure how that fits in but if it's just an error in labeling or something that wouldn't surprise me.

Do you have any guess as to where/when/how R1 split up?

Davidski said...

I think R1 split at around the time when Mal'ta boy was alive, or even a little earlier. That's what complete sequences of R1a and R1b suggest, including when they're analyzed together with Mal'ta boy's R* sequence.

I'd say this probably happened in North Eurasia, most likely somewhere between the Urals and Lake Baikal.

Indeed, I really don't think anymore that the Near East had much of a role in the history of R1a. To me it looks like a sink for various movements from the north and east, which managed to leave minor signals there and not elsewhere, probably because this region has been less susceptible to large scale population replacements through migrations and massive in-situ expansions, like the steppe and Eastern Europe, respectively. That might have something to do with its topography, which is obviously more varied than that of the steppe and forest steppe to the north.

Grey said...

"The strangest thing however was the 14% European R1a among the Beduoins, who are these?."

Both Egypt and Persian empires imported steppe mercenaries. If they were stationed on the borders of Arabia by various empires - which would make sense - I wonder if steppe pastoralists could adapt to desert pastoralism relatively easily and if there were any mass desertions at any time?

#

"MA-1 isn't the link between West and East Eurasians because he's 0% East Eurasian. I'm not sure why some people aren't getting this?"

I think it's because East Asian descended peoples dominate those regions now and displaced the original population that had originally stretched from France to America.

#

"So they basically say that R1a first expanded from Iran (which is unlikely, because R is probably an ANE marker of the steppes)"

It depends where in the sequence you start from. Say the sequence was:

1) Northern Eurasia (mammoth steppe)
2) Iran (pushed south by LGM)
3) Northern Eurasia again (return after the LGM)
4) One population of R* domesticate horses in one part of the steppe and expand out from there

Then "first expansion" depends on what is being talking about. If it's specifically IE then it has to be step (4) but if it's small groups with different clades of R1a moving back and forth then it could be a lot more debatable.

Also if ANE and R* covered the mammoth steppe from LGM times then that is a very large area. If so the IE wouldn't so much have spread R1a as spread *their clades of R1a*.

Brent Doe said...

Hey David,

I've been looking over the underhill spatial frequency distribution maps of M458. I just want to make sure I am reading this right... It says most of Southern/Central Sweden is 5-20% m458?? Am I reading that right?

Thanks!

Davidski said...

Swedes from Malmo (the only Swedish sample in this study) show 11.3% of R1a, and 2.1% of that is M458 (three people out of 141). The frequencies are in this table...

http://www.nature.com/ejhg/journal/vaop/ncurrent/extref/ejhg201450x5.xls

I'm fairly sure that M458 reaches higher frequencies in other parts of Sweden and Denmark, like perhaps Bornholm, but we need some samples to verify this.