May 28, 2008

Y chromosomes and mtDNA from Siberian Khanty and Mansi

European Journal of Human Genetics doi: 10.1038/ejhg.2008.101

Northwest Siberian Khanty and Mansi in the junction of West and East Eurasian gene pools as revealed by uniparental markers

Ville N Pimenoff et al.


Northwest Siberia is geographically remote territory, which has been settled by indigenous human populations probably since the Upper Paleolithic. To investigate the genetic landscape of Northwest Siberians, we have analyzed mitochondrial and Y chromosome DNA polymorphisms of 169 unrelated individuals from Khanty and Mansi ethnic groups in Northwest Siberia. In addition, HVS-I sequences (N=3522) and Y chromosome SNP data (N=2175), obtained from the literature, were used to elucidate the genetic relationships among the North Eurasian populations. The results show clinal distributions of mtDNA and Y chromosome haplogroups along East–West axis of Northern Eurasia. In this context, the Ugric-speaking Khanty and Mansi appear as unique intermediate populations carrying Upper Paleolithic and more recent haplotypes typical for both West and East Eurasian gene pools. This admixture indicates that the Khanty and Mansi populations have resided in the contact zone of genetically distinguishable eastern and western Eurasia.



Kosmo said...

I learned something recently which has rocked both my faith of mtDNA as an indicator of migration, and my confidence that I know what I'm talking about when I discuss anthropology. Since I'm an avid reader of this site, I did a search to see if it's ever been discussed here, and I see it hasn't. So I've been biding my time, hoping to bring it up when a related topic is posted. This post on Siberian mtDNA is close enough. (At least I hope so) If not, I beg your apologies.

Anyway, here's what I'm hoping to get other people's learned opinion on: Lake Mungo Man is considered by all to have fully modern anatomy, and has been dated to around 40kya. This is something I already knew. What I didn't realize until recently was that they'd extracted DNA from the bones, and it turns out that the mtDNA from Mungo Man derives from an even deeper clade than L0. The split between Mungo and the rest of humanity is even deeper than the split between the deepest clades of the Khoisan. This seems to be in direct conflict with the premise that all beyond-Africa modern humans are a subset of African genetic diversity.

So here are the facts:

1.) The oldest bones of modern humans are found in Africa.

2) The oldest mtDNA clades which can be found in living humans are found in Africa.

3) The oldest mtDNA clades which can be found in bones which are agreed to be modern are found in Australia.

This presents several obvious problems.

Dienekes said...

Do you have a source for this information?

AP said...

Dienekes said...

40,000 year old mtDNA from a study published in 1995 seems suspect to me. There has been enormous progress since then, especially understanding contamination and DNA degradation, so I don't really have much faith in that finding.

Kosmo said...

Dienekes, I'm actually quite relieved that you hadn't heard of this study either. I considered myself up-to-the minute on paleometagenomics, yet this study had slipped under my radar. I think this study has slipped under a lot of people's radar, because it is just so difficult to believe.

Here's one source:

The key finding:

"Simon Easteal, an evolutionary geneticist at ANU, then set about analysing the sequence [from Mungo Man]and comparing it with sequences of the same gene from nine other early Australians - ranging in age from 8,000 to 15,000 years - as well as 3,453 contemporary people from around the world, chimpanzees, bonobos and two European Neanderthals.

According to Easteal's evolutionary tree, the line that led to the most recent common ancestor of contemporary people, includes the ancient Australians but excludes Mungo Man."

---So this would mean Mungo Man is not a maternal descendant of mitochondrial eve! (I think the exclamation point is warrented) Another article placed Mungo man's mt clade intermediate to the split between Neanderthal sequences and the deepest Khoisan/non-Khoisan split.

I haven't been able to find any follow-up studies which overturn this finding, so that makes me suspect it still stands. The New Scientist article is from 2001.

Kosmo said...

The quick and dirty interpretation I've seen applied to this case in order to try to make sense of the data is that a chance loss of mitochondrial diversity has occured since early anatomically modern populations first developed in Africa. While I'm certain, mt diversity can be lost over time, that explanation doesn't satisfy me in this specific case because it would require that both the early AM population of Africa and the early AM population of Australia would have to lose, by chance, the exact same older mt types. It would also require that those same older mt types be lost from the various population refugia left in route between Africa and Australia.

To me, trying to explain this problem away with "chance loss" reminds me of when geneticists throw lethals into their punnett squares in order to make them work. It's a cheat.

Most australians are N, with a smattering of M thrown in. Not only is Mungo man not an N or M, he's not even L3. In fact, he's not L2, L1, or L0. He's pre- "L"

On an interesting side-note, he was also 6'4" with a gracile skeleton and doesn't really look much like later Australians. Who was this guy? I'm fascinated.

Dienekes said...

I explained my skepticism about the accuracy of the sequence, but assuming that it's true, it's not very surprising. "Our" mitochondrial Eve isn't necessarily the same as the mitochondrial Eve of people living 40Ky ago, or of those that will live in the future. If an asteroid destroys the Khoi-San tomorrow, then mtDNA-Eve of living mankind will suddenly become a lot younger. By definition we have a subset of the genetic diversity of our ancestors.

Kosmo said...

While I agree with the general principle you're espousing (and even acknowlege that several prominent anthropologists have taken a similar interpretation), I still don't believe it is a logical explanation for the data in this specific instance. Let me give you my reasons, and then you can tell me if you agree with my reasoning.

While the mitochondrial Eve of modern people shouldn't necessarily be the same mitochondrial Eve of anatomically modern people 40kya, under the current out-of-Africa model, one shouldn't expect to find evidence of the deepest clade division at the far end of our species' advancing edge.

In the current model, if Mungo Man's mt haplotype arrived in Australia via that first wave of modern man to cross the Red Sea, then that would mean his mt haplotype was present, at some frequency, in not only that first population to leave Africa, but also in the African population of which it was a subset. This is why genetic diversity decreases with distance from Africa, and why geneticists agree Africa is the homeland of our species. Each step along the path of a migration route produces new populations which are genetic subsets of the populations from which they derive.

So lets think about this. This would logically require that in addition to being present in Africa, Mungo man's halplotype would also have to be present at both the very root of the out-of-Africa expansion AND, at the very least, every single step along the migration route to Australia. Even given a skipping-stone view of this migration, one is left to wonder why M and N left genetic signals along the way, but Mungo's mt did not.

Kosmo said...

What I wrote in the above post is the reason that, while I agree with the principle of haplogroup diversity loss over time (Such loss occuring as haplotypes are lost through chance in the ancestral population), I absolutely disagree with it being an explanation for Mungo's deep-rooted mt haplotype . Such a scenario would require the independent loss of Mungo's halpotype from every population of modern man in the world at a point after which those populations were already spread across the globe.

You said that if the San were destroyed by an asteroid, humanity would suddenly look a lot younger-- and I agree. But keep in mind the reason this is so. It is so, because the San are the people who STAYED. They're the ones who aren't a subset of anything. They live not far from the place our species began-- not the other side of the world from it.

You said the Mungo's mtDNA haplotype, if true, isn't that surprising, but I completely disagree. It is shocking and can't be explained by the current out of Africa model.

There is only one way to explain it.

Dienekes said...

We also need to consider the possibility of selection; such a sweep might have reached the edge of human habitation later than the central regions. Also, we simply don't have any data on how variable modern humans were in terms of their mtDNA back then.

Kosmo said...

Selection is a possiblity in this case, though I'm reluctant to invoke it. Once you raise the specter of mitochondrial selection, everything starts becoming suspect. Again, it seems a little like putting lethals in your Punnette squares to make them work. Of course, that doesn't mean it's wrong. But still.

As far as data on how variable human mtDNA was in the past, I think we can safely assume it was more variable than today. And I also think we can safely assume it was most variable in the geographical area where modern man first arose. Finally, I think it is safe to assume that a mitochondrial haplotype that is present at the very root of multiple expansions into multiple continents is very unlikely to be be independently lost from all those populations.

Yet Mungo Man's mtHaplotype is found nowhere other than in him. Hence Mungo Man's mt could not have been present at the root of modern man's expansion into multiple continents. It couldn't have been a part of the same population that spread M and N across the world, or we'd see it.

How do we reconcile this?

I think the reason Mungo's mtDNA left no trace in any of the deep clade modern African populations, or in the broad out-of-African expansion, is because it is not an African halpotype at all. At least not in the sense that it was carried out of Africa in the cells of anatomically modern Homo Sapiens. I think the most likely explanation is that it is the smoking gun for regional mixture with Homo erectus during man's migration through SE Asia into Australia.

terryt said...

Kosmo. There is the argument that Mungo Man's mtDNA may have been contaminated, and this allows the "out of the Garden of Eden theory" to survive. But I agree with you, "I think the most likely explanation is that it is the smoking gun for regional mixture ... during man's migration through SE Asia into Australia". I'd disagree that it was SE Asian H.erectus though. Mungo Man doesn't look anything like contemporary SE Asian H. erectus. Remember they died out possibly as recently as 30,000 years ago. Mungo Man is probably from somewhere else in Asia.

However, you may not be aware of it, but fossils of a more recent type, known as "Kow Swamp", have also been found in Australia. Dating to no earlier than 20,000 years and probably more recent. Their mtDNA is Eve's but even the most ardent "out of the Garden of Eden theory" concede they do look "somewhat similar" to later SE Asian H. erectus. Of course the difference in appearance is downplayed, they could just represent variation in a single population. No explanation for how this might have happened on such a small continent though. Again perhaps "it is the smoking gun for regional mixture".

Kosmo said...

Terry, I didn't know they'd typed the mtDNA of one of the Kow swamp specimens. Thanks for that information.

The peopling of Australia has developed into quite an enigma, hasn't it? There's the anatomically modern Mungo, who has inexplicably ancient and divergent mtDNA-- and then we have the Kow swamp specimen, with modern mtDNA, but hints of a premodern phenotype.

If one were to predict what you'd expect to find if early regional mixture DID take place, this is exactly it-- the shuffling and mismatching of phenotype and mtDNA haplotype.

And then there's the Flores issue.

It must be an exciting time to be an Australian anthropologist.

terryt said...

Kosmos. Here's the paper dealing with mtDNA in prehistoric Australians:

Here's my take on the ancient peopling of Australia:

It's the end point of a series of essays, starting with Polynesia and moving back in time to explain the pattern of migrations through Wallacea.

Kosmo said...

Thanks Terry. I found your take on the peopling of Australia to be very well thought out-- and I suspect you're right on just about everything you said. Thanks again.

terryt said...

Thanks for those comments of support Kosmos.