January 26, 2011

X-linked haplotype of Neandertal origin in non-Africans

This seems like a very good case for the presence of something (B006 haplotype) clearly non-African and Neandertal-related in non-Africans.

What I find most interesting, however, is the presence of African-specific haplotypes that seem quite divergent from the most common human haplotypes.

For example (Table 1), haplotype B006 differs from the modal Eurasian haplotype B001 (which is common to Eurasians and Africans) at 13 sites, and B007 (which is African-specific) differs from B001 at 11 sites. It seems to me that B007 might represent archaic African admixture.

It is also not clear why the common haplotype in Neandertals and Eurasians cannot be due to modern human admixture in Neandertals.

An X-linked haplotype of Neandertal origin is present among all non-African populations

Vania Yotova et al.

Abstract

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of H. sapiens who left Africa between 80 Kya and 50 Kya to colonize the rest of the world. Here we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

Link

31 comments:

German Dziebel said...

I've always considered the B0006 haplotype as the best genetic evidence (apart from the overwhelming linguistic and kinship data) for a non-African origin of all modern humans. This study only confirms this further. The authors suggest the Neanderthal admixture scenario because of the peer pressure to keep the mainstream out of Africa theory alive. Needless to say, they didn't find B0006 in Neanderthals. They simply attribute it to Neanderthals.

What is most interesting is that, according to the map, B0006 is much more frequent in the Americas, where there are no Neanderthals. Neanderthals may have wandered as far as South Siberia but if it were truly a neanderthal admixture event at the very beginning of an out of Africa journey we would never end up having this introgression at such high frequencies in the New World.

The Out of America scenario explains the data much better. B0006, as Dienekes correctly points out, is more divergent from B0001 than the African-specific B0007.

The authors detected the same "Neanderthal admixture" in East Africa among the Maasai and suggested a back-migration. Most likely, it's the founding migration of non-Africans into Africa, with South Africans either picking up archaic lineages in sub-Saharan Africa as they expanded from East Africa or evolving a few homoplasies with chimps in a surprising historical turnaround.

Finally, Y-DNA has always contained strong evidence of a back-migration into Africa represented by haplogroup E. This is consistent with the present X chromosome results. From the mtDNA perspective, hg M1 (part of the huge Asian-Amerindian M macrohaplogroup) is also found in East Africa and has also been interpreted as representing a trace of a back migration into Africa.

b said...
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terryt said...

"supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans".

I have always considered that to be the default position, and I've always wondered why nearly everyone has always been so opposed to such a possibility. I guess it's a product of the general human belief that we are somehow 'special', and different from the rest of biology. Ultimately it's a product of religious belief. God created a single pair of every 'kind'. Surely if any species derives from a very small population inbreeding would rapidly become a huge problem.

eurologist said...

It is also not clear why the common haplotype in Neandertals and Eurasians cannot be due to modern human admixture in Neandertals.

My understanding is that the authors refer to the fact that B006 is much less derived than any other haplotype. This would not be expected of one of several types migrating ooA, when it (or similarly ancestral types) don't survive, there.

Also, B007 has 5 mutations that are extremely common, and that B006 does not have - so it seems way younger. Even B002 has three common mutations shared by almost everyone - but only one of those shared with B006. Thus, B002 seems old, but not quite as old. Within Africa, it is of course almost impossible to say whether such diversity was part of the "founder" population, or acquired in later migrations. Also, given what we know about human migrations world-wide over the past 50,000 years, I have a hard time believing that much substructure persisted in Africa from before, say, 200,000 years ago.

Needless to say, they didn't find B0006 in Neanderthals. They simply attribute it to Neanderthals.

Well it and only it matches Neanderthal exactly - where that one is known. B006 has only three changes, and two of those are matched, the third is unknown (but common to almost all extant haplotypes).

As I have mentioned before, such admixtures could also be from late heidelbergensis - there is no reason to attribute it to Neanderthal, specifically.

German Dziebel said...

"Also, B007 has 5 mutations that are extremely common, and that B006 does not have - so it seems way younger."

Eurologist, how can B006 be younger than B007? B006 is the most underived, or the least derived among human X-linked haplotypes. Take a look at this tree here, p. 76: http://books.google.com/books?id=X88O8C3ZHvMC&pg=PA76&lpg=PA76&dq=B006+X+chromosome&source=bl&ots=mjmS0yOA-c&sig=obJLojUsaH6w2of8RALh5QqGMIo&hl=en&ei=MkhETaDPPInbgQePy7S8AQ&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBsQ6AEwAQ#v=onepage&q=B006%20X%20chromosome&f=false

What it means, if translated into mtDNA or Y-DNA phylogenies, is that haplotypes that are usually considered most derived, e.g. Y-DNA P (Q,R) may, instead, show special affinity with Neanderthal sequences, which obviously predate human MRCA.

TruthPlease said...
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TruthPlease said...
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eurologist said...

Eurologist, how can B006 be younger than B007?

Of course not.

Perhaps what I wrote can somehow interpreted the wrong way:

"Also, B007 has 5 mutations that are extremely common, and that B006 does not have - so it seems way younger."

B007 is the subject of the sentence, so "it" consequently refers to that.

German Dziebel said...

""Also, B007 has 5 mutations that are extremely common, and that B006 does not have - so it seems way younger."

B007 is the subject of the sentence, so "it" consequently refers to that."

Got it. Thanks for the clarification. Now we're in full agreement.

German Dziebel said...

@TruthPlease

"i'm considering foregoing the study of genetics all together..."

Please do so asap.

"and now you want to claim all people desended from south america because theres 0 asian chromosomes left and mysteriously all the indians have very european looking and related ydna"

What a nonsense!

"im writing it here right now so years from now when they make the claim that all people came from the spanish of south america we can all know its a conspiracy."

TruthPlease is a spamming program.

"i know maju thinks the same."

Who's maju and why should anybody care what he thinks?!

Annie Mouse said...

Hmm...

From Figure 1 it looks like most of the B006 is in the Americas, mostly in areas associated with Native American populations. Not what I would have expected.

I could understand dilution effects from later African waves. But would still have expected most of the B006 to be in Western Europe.

Annie Mouse said...

Nothing in Papua New Guinea where the most recent archaic/modern contact occured.

As high in western India as in Western Europe.

Nothing much in Arabia where we believe there was significant early Neanderthal contact

I am just not buying this as archaic or Neanderthal, yet.

Annie Mouse said...

The map in figure 1 reminds me strangely of the distribution of mitochondrial Haplogroup X. I dont think this is neanderthal/archaic at all. Looks like a population flow out of North India that carried B006 (on the X chromosome) and Haplogroup X (on the mitochondrial DNA).

eurologist said...

@German Zwiebel:

Now we're in full agreement.

We would make a perfect couple. We agree on almost everything, except the prenuptial... ;) Thanks for the frenemy... ;)

TruthPlease said...
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German Dziebel said...

"I am just not buying this as archaic or Neanderthal, yet."

Me neither. Precisely for the same distributional reasons that you identified. If it were neanderthal admixture in West Asia we would have found B006 at high frequencies in West Asia, Western Europe and Southern Europe, with decreasing frequencies elsewhere as populations migrated outwardly from these original contact areas. The pattern of the data is the opposite from that.

http://blogs.discovermagazine.com/gnxp/2011/01/neandertal-admixture-revisiting-results-after-shaken-priors/

German Dziebel said...

@urologist

"We would make a perfect couple. We agree on almost everything, except the prenuptial... ;) Thanks for the frenemy..."

Just surrender, honey, and I'll let you begin another sizzling romance, with the likes of TruthPlease, for example.

@TruthPlease

"i got x2, do you want to hear my "oral tradition"?"

No, thank you. But Urologist very well may. Go to his site at http://eurologist.blogspot.com/ and speak your mind.

terryt said...

"the yanomamo amerindians in northwest brazil have up to 12 percent x2 mtdna, did you have that? i got x2, do you want to hear my 'oral tradition'?"

I get the feeling there is something you don't understand about all this. X mitochondrial DNA haplogroups has nothing to do with the X chromosomes.

"If the X-chromosome b006 is the sex chromosome from a neanderthal then it is common sense to consider a woman who has two of these x-chromosomes a different species with simply a high homo-sapien autosomal admixture percentage".

At the formation of the haploid sex cells, or meiosis, the genes on each of the X chromosomes in the mammalian female mix. So you cannot call any X chromosome 'Neanderthal' or 'modern'. If an individual woman had one X chromosome from a Neanderthal and one from a modern human her daughters' X chromosomes would be very much mixed. Basically the same for the mammalian male, although it has only one X chromosome. But as this is not passed to his sons his X chromosome becomes mixed with whatever X chromosome the mother of those sons posseses.

TruthPlease said...
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German Dziebel said...

"dziebel's conspiratorial claim"

I wanted to quit this string, but I keep laughing my ass of at this guy TruthPlease's opinions about me. Earlier, he called me "dziebel alemán" is Spanish. He must have interpreted my first name German as my nationality and hence he suspected that I'm brandishing some outrageous white supremacist bias. Truly, the web is a treasure trove of odd, bizarre and utterly deranged individuals.

Terry, BTW, he is your buddy Maju's buddy. Buyer beware!

terryt said...

"dziebel's conspiratorial claim that people came from south america and not africa"

I agree that the evidence against his theory outweighs the evidence in favour of it.

"the whole thing doesnt just scramble like eggs every time"

Not completely scrambled every time I'll grant.

"the fact that specific "diseases" and traits are continually passed on"

But they're mainly expressed in the male. Because they have only one X chromosome so any gene on that chromosome is expressed even though it may be recessive in the paired chromosome of the female.

terryt said...

"Terry, BTW, he is your buddy Maju's buddy. Buyer beware!"

Thanks for the warning. Maju has actually been quite nice to me lately.

German Dziebel said...

"I agree that the evidence against his theory outweighs the evidence in favour of it."

My odds are getting better fast. Don't miss the upturn, Terry. The recent papers on the Iban and the Ivatan seem to support my ideas about Austronesian prehistory, too. That's the magic of having two doctorates.

TruthPlease said...
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terryt said...

"terryt, does terryt stand for terry turner?"

No.

"The recent papers on the Iban and the Ivatan seem to support my ideas about Austronesian prehistory, too".

How so? I've been arguing with Maju as to whether the Iban paper proves a major pre-Austronesian human presence in Borneo. To me it doesn't. Almost any of the haplogroups listed could easily have been brought into Borneo by Austronesian-speaking people. The only possible exceptions are some of the mtDNA Ms and Y-haps F and K. But even these few haplogroups could be relativley recent introductions. I'm not familiar with the Ivatan paper.

German Dziebel said...

Terry:"How so?"

Here is why.

"Analyses of autosomal data indicate that the Iban are most similar to mainland Southeast Asian groups and suggest that gene flow from Taiwanese agriculturalists appears to be relatively minor in contrast to that from mainland Southeast Asians and Indonesians. The results of NRY and mtDNA haplogroup analyses complement the autosomal analyses by suggesting less gene flow from the agriculturalist expansion from Taiwan than has been previously claimed for ISEA populations." (Simonson, Ancestry of the Iban Is Predominantly Southeast Asian, 2011).

This minor demographic contribution from Taiwan - as suggested by a local but representative example - couldn't lead to the proliferation of 1200 or so Austronesian languages.

The Ivatan paper didn't find any evidence for the founding out of Taiwan migration in the Batanes and thge Orchid island:

"A close genetic relationship between Yamis and Ivatans was hypothesized by linguistic studies, since both groups of islanders belong to the Batanic sub-branches of the Malayo Polynesian language group found in the ISEA. Accordingly, such a relationship would indicate a northward migration from the Philippines via Batanes archipelago and Orchid Island toward Taiwan. Our study, using Y-SNP and mtDNA polymorphism at the macro haplogroup level, showed that a strong affinity between the Yamis and Ivatans was resulted from gene flow between Taiwan and Philippines. Each island population showed a higher affinity with the closest main island (i.e., Yami with Taiwan, or Ivatan with Philippines) than with each other. This suggests an early isolation of the population and little intermarriage among the islands. Only few traces of gene flow were found between Yami and Ivatan or between Yami and Philippines. The gene flow appear independent from the cultural development, suggesting that trading had small impacts on genetic exchanges but must have resulted the linguistic affinity observed today among Yami, Ivatan and Philippines.
The age estimates of the mtDNA or Y-STRs variations suggested settlements on the islands dated back to ~3,000 YBP. However, the archeological artifacts found on Orchid Island and Batanes were associated with the “Out of Taiwan” hypothesis, indicating a southward migration from Taiwan and an earlier settlement on the islands that might be 4,000 YBP. These conflicting observations suggested that our sampling may have been too small to reveal sufficient or significant markers that can support a unique southward gene flow." (Loo, Genetic affinities between the Yami tribe people of Orchid Island and the Philippine Islanders of the Batanes archipelago, p. 18).

terryt said...

The islands east of Taiwan and the Philippines first:

"the archeological artifacts found on Orchid Island and Batanes were associated with the 'Out of Taiwan' hypothesis, indicating a southward migration from Taiwan and an earlier settlement on the islands that might be 4,000 YBP".

So they hardly abandon the out of Taiwan hypothesis.

"The age estimates of the mtDNA or Y-STRs variations suggested settlements on the islands dated back to ~3,000 YBP".

That proves a point Dienekes is constantly bringing up. The age of the haplogroup's diversity does not necessarily coincide with the date of its arrival. On the small islands a single clade could easily come to dominate with time.

"Each island population showed a higher affinity with the closest main island (i.e., Yami with Taiwan, or Ivatan with Philippines) than with each other".

I think that's what we would expect. As far as I'm aware most people see the development of the early Austronesian language involved the Philippines as well as Taiwan. As shown by the authors' comment:

"Our study, using Y-SNP and mtDNA polymorphism at the macro haplogroup level, showed that a strong affinity between the Yamis and Ivatans was resulted from gene flow between Taiwan and Philippines".

So the Austronesian language still seems to have emerged from Taiwan, and then moved to the Philippines and to the islands immediately to the east. But tyhe closeness of the present languages is because although:

"trading had small impacts on genetic exchanges but must have resulted the linguistic affinity observed today among Yami, Ivatan and Philippines".

Now to the first one:

"Analyses of autosomal data indicate that the Iban are most similar to mainland Southeast Asian groups"

Suggests very strongly that the Iban's ancestors came from the mainland relatively recently. They're not Paleolithic arrivals.

"gene flow from Taiwanese agriculturalists appears to be relatively minor in contrast to that from mainland Southeast Asians and Indonesians".

But it's certainly not absent. Y-hap O1a is there, as are several mtDNA Bs. By the time the Austronesian-speaking people reached Borneo it's a fair bet that they had become mixed with other people they'd met along the way, such as members of Y-haps O2a and O3, as well as various mtDNAs. A paper you linked to recently suggested that the Sumatran and Bornean Austronesian languages demonstrated a substrate, presumably Austro-Asiatic. It also suggested the Borneo languages came mostly from Sumatra. So the 'minor demographic contribution from Taiwan - as suggested by a local but representative example -' could easily 'lead to the proliferation of 1200 or so Austronesian languages' of Borneo. Especially seeing as it is (was) mainly jungle-clad mountains.

So the Austronesian out of Taiwan hypothesis holds up.

terryt said...

"That proves a point Dienekes is constantly bringing up".

And here's his comment, from his blog 'Sailing across the Pacific to settle Polynesia':

"The common founder of a set of lineages may postdate the colonization event, if the number of colonists was small enough so that attrition was high enough, and a founder that lived long after the colonization effect contributed most of the present-day population"

Michele said...

Dienekes, before you dismiss German's ideas entirely, you should check out THE PLEISTOCENE COALITION website started by Virginia Steen Mcintyre and other reputable geologists who dated stone tools and extinct megafauna fossils in direct association in stratified sites (Valesequillo and others) in central Mexico by three accepted dating techniques commonly used at ancient sites in Africa to around 200,000 years old.Also, a skull fragment from central Mexico evaluated at Texas A&M university was reported to be very similar to that of Asian Homo erectus from China.Also, Dr. Barbara Purdy (prof. emeritus U.of Fla.) reported in her latest book "Florida's People During The Last Ice Age" the finding of stone tools made using Levallois techniques at the C.C.A. site in North Central Florida from pre-Clovis levels in stratified contexts and dated by thermoluminescence and patination studies to 25-28000 years old. I have personally recovered Levallois cores and tools here in South Georgia USA which support her finds, and the archeologist Blaine Ensor has reported similar tools from the Capps and Shelly sites in Alabama which he calls epi-Levallois from surface collections, which display reduction characteristics he claims are distinct from Clovis or later cultures. I became interested in this subject after personally finding Levallois cores and tools which i could not find illustrated in mainstream North American archeological literature, but upon reading Bordes "Typologie" which describes Western European Neanderthal lithics the same cores and tools were described.So, it seems there is indeed evidence of pleistocene occupation by pre-Clovis hominids in the America's long before Clovis, but this information has been largely dismissed out of hand by mainstream archeologists in spite of stratified sites excavated by well credentialed archeologists and geologists.Mark

German Dziebel said...

Mark, I've noticed the intriguing comments regarding Levallois style points in the New World that you made on several websites. Also, thank you for leaving a note on my Anthropreneur which has been idle for a while. We can take it offline and discuss it further. In the light of recent genetic research, e.g., the high frequencies of B006 in America and its matches with Neanderthals (more here http://blogs.discovermagazine.com/gnxp/2006/11/neandertal-humans-introgression/), yours and Barbara Purdy's findings make lots of sense.
Please send me an e-mail to discuss.

Vin said...

Hi folks, I find the discussion very interesting, although way to technical for me. I just have two question.

Is it more likely that humans arose from Neanderthals("archaics" and "moderns") and these fellas entered Africa.

Also could modern Eurasians, most of them anyway, have come from archaic populations.

Thanks for your insightful discussions :)