May 11, 2010

Direction of gene flow (to or from Neanderthals, or ...?)

In my first post on Green et al. (2010) I bring up a couple of red flags to the tale of Neandertal admixture that has appeared in the media:
  1. The uniformity of alleged Neandertal admixture outside Africa is suspect, given that Neandertals were a West Eurasian species
  2. The observed pattern of Neandertals being closer to non-Africans than to Africans can be well explained by structure in Africa itself, a point which the authors concede (as their Scenario 4), but which has received zero play in the media which -as usual- have jumped on the more easily digestible ("caveman sex") explanation.
Now I want to address another major red flag that I hinted at before, namely the direction of gene flow, if gene flow did in fact occur between modern humans and Neandertals.

The authors reject that gene flow into the Neandertals took place; I immediately got suspicious of this claim because it is not consistent with what we know from historical cases of contact.

Whether it is Europeans meeting Native Americans, Yayoi meeting Jomon, or Bantu farmers meeting Pygmy hunters, the story is always the same: the dominant intrusive population ends up with admixture from the native one, but admixture goes both ways.

If modern humans and Neandertals interbred, then there is absolutely no reason to think that "we" got Neandertal genes, but "they" didn't get ours. To think that requires extra assumptions, e.g., that modern-Neandertal kids were shunned by Neandertal societies, i.e., that Neandertals were a sort of prehistoric Samaritans that practiced strict endogamy. I find that hard to believe.

There is an alternative explanation for why no modern admixture in Neandertals would be detected, namely the early age of the bones tested in the paper, which are from Europe and date from the Early Upper Paleolithic, when modern humans had not yet arrived in Europe. It is worthwhile to consider this explanation:

If admixture occurred primarily in Europe itself, then we would expect Neandertal admixture to be higher in modern Europeans or Caucasoids. But we don't see that at all, so, unless we postulate that Papua New Guinean and Chinese ancestors reached their final destination with a detour through Europe after 40ky or so, we can safely conclude that Neandertal-modern admixture was earlier and occurred in the Middle East.

So, we have a population of moderns and Neandertals mixing in the Near East. According to the authors' scenario, episodes of admixture between the two species gave "us" enough Neandertal admixture that was carried by our (modern) ancestors throughout the world, creating a fairly uniform (but small) component of "Neandertal" ancestry.

But, why wouldn't the (modern) admixture in Near Eastern Neandertals also be carried a couple of thousand km into Europe? In short: we are supposed to think that Neandertal admixture in modern humans made it to the ends of the earth, but modern admixture in Neandertals could not move a short distance from West Asia into Europe. The explanation of pristine European Neandertals presented in the paper just doesn't fly in the context of the authors' broad model.

It is also worthwhile to consider the actual genetic argument for no modern-to-Neandertal introgression. This goes something like this: we observe closer proximity between modern non-Africans and Neandertals than between modern Africans and Neandertals. This can be explained by either Neandertal-to-non-African gene flow or vice versa.

The authors observe that modern non-Africans are closer to Yoruba than to San. They argue that if Neandertals had modern non-African admixture, then they would also be closer to Yoruba than to San. But, they observe that they are about equidistant to Yoruba and San. Ergo, they couldn't have substantial non-African admixture.

The error in this syllogism is the equation of modern non-Africans (who are closer to Yoruba than to San) with ancient non-Africans for which this was not necessarily the case.

Perhaps a case could be made that this was true for late Out-of-Africans, as these split off from other moderns after the Yoruba-San split. But, the late Out-of-Africans were not the only anatomically modern humans who left Africa, and we have good evidence of anatomically modern humans outside Africa before the exodus that gave rise to modern Eurasians (at sites like Qafzeh).

Note that this observation nicely addresses the argument presented by John Hawks on the young coalescence dates between some Neandertal and Eurasian DNA, which supposedly disqualifies the African structure scenario I presented (and which the authors labeled as "Scenario 4" in their paper). These young coalescence ages can be easily explained as modern-to-Neandertal gene flow within the context of the African structure model.

Finally, I want to remind readers of a very interesting paper I blogged about last year. Here are the relevant quotes:
Our data on neighbors and variability is unsupportive of the strict forms of a single-origin model but does not conflict with another approach, the model of ‘‘isolation by distance,’’ which predicts that genetic and phenotypic dissimilarity increases with geographic distance (24, 29–31). The metapopulation framework would predict the same because frequency and magnitude of genetic exchange would follow the likelihood of 2 populations to meet, which declines with geographical distance from the early AMH epicenter in Africa. Our fossil AMH data, however, suggest that before there was isolation by distance from Africa, there already existed (at least temporally) isolation by distance within Africa during the Pleistocene.

Seemingly ancient contributions to the modern human gene pool (36) have been explained by admixture with archaic forms of Homo, e.g., Neanderthals. Although we cannot rule out such admixture (37), the clear morphological distinction between
AMH and archaic forms of Homo in the light of the proposed ancestral population structure of early AMH to us suggests another underestimated possibility: the genetic exchange between subdivided populations of early AMH as a potential source for ‘‘ancient’’ contributions to the modern human gene pool (9, 36).
I won't present the reasoning behind these conclusions (the paper is open access anyway), but they have an important implication: seemingly "ancient" contributions to modern humans need not have been acquired by either Neandertals or other archaic (pre-sapiens) populations, but they could also have been acquired by admixture with different branches of anatomically modern humans.

Given that anatomically modern humans appear on the record ~200ky ago, so they probably existed at an even earlier date, while extant sapiens populations trace their earlier split much later (the authors date the Yoruba-San split at most 164ky or as late as 67ky), we can reasonably assume that there were anatomically modern sapiens populations that are not ancestral to any modern humans, and which may have contributed seemingly "ancient" genes to our expanding ancestors.

There you have it: structure in Africa, modern-to-Neandertal admixture, or even sapiens-to-sapiens admixture, there are plenty of alternatives to the story dominating the media.

37 comments:

onur said...
This comment has been removed by the author.
onur said...

Whether it is Europeans meeting Native Americans, Yayoi meeting Jomon, or Bantu farmers meeting Pygmy hunters, the story is always the same: the dominant intrusive population ends up with admixture from the native one, but admixture goes both ways.

I know this is off the topic but doesn't that imply that Greeks (especially Anatolian Greeks), Armenians and non-Turkic speaking NW Iranian populations should have Turkic admixture (mostly Turkmen/Oghuz) due to Turkic invasions and migrations to their lands beginning from the early Seljukid times?

German Dziebel said...

"There you have it: structure in Africa, modern-to-Neandertal admixture, or even sapiens-to-sapiens admixture, there are plenty of alternatives to the story dominating the media."

Not to mention the possibility that existing phylogenies of modern human mtDNA, Y-DNA, etc. sequences that "attest" to the origin of modern humans in Africa are trees growing upside down. If we look at the original paper on mtDNA by Johnson et al. 1983 as well as several subsequent publications, the ancestral "morph" was found at higher frequencies in America, Asia and Europe than in Sub-Saharan Africa.

onur said...

the ancestral "morph" was found at higher frequencies in America, Asia and Europe than in Sub-Saharan Africa

What do you mean by "ancestral "morph""? Could you elucidate your point?

Dienekes said...

I know this is off the topic but doesn't that imply that Greeks (especially Anatolian Greeks), Armenians and non-Turkic speaking NW Iranian populations should have Turkic admixture (mostly Turkmen/Oghuz) due to Turkic invasions and migrations to their lands beginning from the early Seljukid times?

Not really, as the Turkic conquest was not demographic. Modern Turks have little original Turkish DNA. If we used them as an analogy, Europeans would almost be completely Neandertal, which is simply not the case.

German Dziebel said...

In those days they didn't have haplotypes yet. They had "morphs" formed by "restriction sites." The method was very superficial and resulted in only 35 types/morphs but the topology of the resulting tree was very similar to all the subsequent ones. Africans were clearly different from everyone else, but not because they were the oldest population but because they were most derived from the ancestral "morph."

Take a read:
Johnson MJ, Wallace DC, Ferris SD, Rattazzi MC, Cavalli-Sforza LL.
Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns // J Mol Evol. 1983;19(3-4):255-71.

See also Excoffier L, Langaney A. Origin and differentiation of human mitochondrial DNA. Am J Hum Genet. 1989 Jan;44(1):73–85; Excoffier et al. Genetics and History of Sub-Saharan Africa // Yearbook of Physical Anthropology 30 (1987).

Excoffier later migrated over to the "out of Africa" side but those early results have never been refuted, only forgotten.

Regarding Dienekes's point about "substructure," one of the earliest criticisms of the out of Africa model of human evolution was centered precisely around the notion of the structure of the ancestral population. Out of Africa assumes that mating in this ancestral population was random, but in all "ethnographically" attested examples (e.g., small Amazonian demes) a population is always already subdivided and Fst is high. (See Neel, Estrutura populacional dos amerindios e algumas interpretacoes sobre evolucao humana // Origens, Adaptacoes e Diversidade Biologica do homem nativo da Amazonia. 1991.

Good old stuff,eh?

Dragon Horse said...

Dienekes, your friend responded to your argument:

http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/african-population-structure-neandertal-mixture-2010.html

Daniel said...

WHat comes to my mind in all that "Homo Sapiens Sapiens" - "Homo Sapiens Neandertalis" INtermixture Scenario:

What about non-sexual genflow?

I recall a guy who got a nobel prize for "proving" (by model only) that for example flu viruses can transport genes from one human to another human without sexual intercourse.
And that it even could transport genmaterial between different species, like dogs to humans.

I recall that it was said, "this will totaly revolve the idea of evolution!"

BUt I havent heard about this theory recently. HAve they already thrown it overboard?

I mean, this theory claims that there is non-sexual genflow between lifeforms that just happen to live in the same region long enough. If there is any thruth to this theory, its totaly normal that there was geneflow with neandertalians.

Well, of course the calculated chance for horizontal genflow is 0.000'000'000'001%. And so its unlikely to reach values of 4% with a transfer speed like that....
But still....

Marnie said...

non-sexual gene flow . . . flu viruses . . . gene flow direction . . .

what will you guys think of next?

really, the oil spill sounds more interesting.

face it. There must have been a few good looking Neanderthal women. Men often aren't very discriminating. And even if the Neanderthal women looked a little odd, their kids probably looked more or less normal.

Please! My head hurts.

Stop it!

pconroy said...

As regards Neanderthal or archaic hominins mating with modern humans, let's remember the curious story from Abkhazia about Zana the wild woman and her son Khwit:

http://www.isogg.org/ancientdna.htm

http://www.bigfootencounters.com/articles/zana.htm

http://www.hominology.narod.ru/zanai.htm

princenuadha said...

@ Daniel, you contradict yourself...so I'm not sure why you brought it up. I would like to read that article; where is it? Though, as a means of complex organism evolution I don't think. I don't know much about genetics or developmental biology but considering the mechanisms of both I don't think it would happen in humans.

The chain is too hard to even imagine. The virus must somehow pick up another species DNA. Then it must maintain its stability, with new DNA, and transport to another species. then it must still be able to it inject DNA as it normally does and inject the new DNA. Presumably it must invade only the gamete producing sites. Then against all odds must be absorbed into the gamete dna. Then that gamete must be able to function still. Then the fetus must be healthy and lastly pass the new gene to his or her gamete/offspring. lastly a monkey must fly out of maju's anus to complete this beautiful statistical anomaly.

@ dienekes The Greeks probably have a very small amount of old Turkish so the rule (above) would be followed

@ marnie in some ways men aren't discriminating and in some ways they are. Just consider how much less men go for fat women if not fat themselves (if fat it is a social thing), women older than them, 14 year old girls who are biologically ready but..., but maybe most notably in tall women. Guys in practice dont care much that much about race (black/white) but are still be impeded over what can be petty things. women have been turned on by bonobos having sex and I'm sure men would have too if they had less awareness/control.

Maju said...

Point by point Dienekes:

1. "The uniformity of alleged Neandertal admixture outside Africa is suspect, given that Neandertals were a West Eurasian species".

This is no problem if the admixture episode happened in West Asia prior to the Eurasian Expansion as such.

2. "The observed pattern of Neandertals being closer to non-Africans than to Africans can be well explained by structure in Africa itself, a point which the authors concede (as their Scenario 4)"...

Were not you claiming that your hypothesis is not scenario 4 and that this scenario has to be discarded for parsimony reasons (I see more than just parsimony against it: it would contradict the very L2"6 and specifically L3 and Y-DNA E expansion in Africa).

2. ... "another major red flag that I hinted at before, namely the direction of gene flow"...

This is only logical: Eurasian H. sapiens would soon after experience a massive expansion but West Asian Neanderthals never seem to have back-migrated to Europe. Even if the flow was truly bi-directional, we would never be able to know of it by looking at Croatian Neanderthals most likely.

2b. "... why wouldn't the (modern) admixture in Near Eastern Neandertals also be carried a couple of thousand km into Europe?"

Why would it? Neanderthals had expanded from Europe to West and Central Asia but they never went really far, either into Asia or into Africa. Neanderthals were short-legged and carried lots of body weight (pure muscle) requiring of specially ample lungs and torso to keep their demanding metabolism working. It is well documented that they exploited much smaller territories than our species and in general they show no expansive drive. I see absolutely no reason to have Palestinian or Iranian Neanderthals back-migrating to Europe, much less as there was already competence in those areas, as was the case.

3. "But, the late Out-of-Africans were not the only anatomically modern humans who left Africa, and we have good evidence of anatomically modern humans outside Africa before the exodus that gave rise to modern Eurasians (at sites like Qafzeh)".

Unless they are the same. I have for long considered the possibility that the OOA happened at that period, the Abbassia Pluvial, which was humid enough to favor trans-Saharan and trans-Arabian flows. This situation would not happen again until 50,000 BP, too late for the OOA.

4. "Finally, I want to remind readers of a very interesting paper I blogged about last year".

Not sure what to think. If there was such a divide and its impact is understood as 2% Neanderthal admixture, that probably means, within your hypothesis, a 10-20% or more of that Northern distict group instead (as they are obviously more closely related with H. sapiens in any case). Where are their haploid lineages then? Why would they impact an OOA population via, probably, South Arabia and not the bulk of the pre-OOA population at the Nile and Red Sea coasts, which also was expanding to other regions of Africa?

I don't make much sense of this on light of our knowledge of human population genetics, we should see such a strong signal even in the haploid pool, at least mtDNA. We don't.

Dienekes said...

Dienekes, your friend responded to your argument:


This post is a reply to that, unless I'm missing something.

Dienekes said...

Why would it? Neanderthals had expanded from Europe to West and Central Asia but they never went really far, either into Asia or into Africa. Neanderthals were short-legged and carried lots of body weight (pure muscle) requiring of specially ample lungs and torso to keep their demanding metabolism working.

Lol, you can walk from Syria to Europe even if your "legs are short". Neandertals were hunters, so they weren't exactly crippled. Besides, you don't even have to walk, you need only mate with your neighbor.

Your other points are either irrelevant, wrong, or addressed in the text.

German Dziebel said...

"1. "The uniformity of alleged Neandertal admixture outside Africa is suspect, given that Neandertals were a West Eurasian species".

This is no problem if the admixture episode happened in West Asia prior to the Eurasian Expansion as such."

After having successfully replaced anatomically modern humans in West Asia, as archaeological evidence seems to indicate, Neandertals proceeded to contribute their genes to the next generation behaviorally modern humans who apparently barely escaped the encounter and stampeded all the way down to Australia. And all this for the sake of helping some 21 century savants make their "theories" work.

Maju said...

Good point. It is still perfectly possible anyhow that European and West Asian Neanderthals were distinct populations because there are barriers between Syria and Croatia and population density was low enough to allow for no contacts in very long periods.

Briggs 2009 did notice a structured population among European Neanderthals with the Caucasus specimen (Mezmaiskaya 1) being markedly distinct from the rest. I understand from that that the West Asian and Central Asian Neanderthal populations must be at least that distant and probably quite more.

Mezmaiskaya is not farther from Vindija than Syria but they are clearly members of two different populations. Vindija clusters with other European lineages and Mezmaiskaya does not.

Hence there was surely a marked population structure among Neanderthals, which was no doubt less dynamic than ours (legs and metabolism again).

Dienekes said...

Briggs 2009 did notice a structured population among European Neanderthals with the Caucasus specimen (Mezmaiskaya 1) being markedly distinct from the rest. I understand from that that the West Asian and Central Asian Neanderthal populations must be at least that distant and probably quite more.

Briggs et al. found that Neandertals had one third our mtDNA diversity. Going by your logic, modern humans that have population structure have not experienced gene flow with each other.

Note that most modern humans are a few tens of thousands of years away from each other based on mtDNA. It will take more than "short legs" to explain why admixture taking place in the Near East c. 100ky would not find itself into Europe 50ky later.

It doesn't make any sense either that Neandertals would be a partitioned population across 2,000km or so within a single latitude/climate zone, but Africans AMH were not across triple the distance and across several ecological zones.

You can't talk Neandertal partition while at the same time affirming an African panmictic species.

Maju said...

(part 2)

"It doesn't make any sense either that Neandertals would be a partitioned population across 2,000km or so within a single latitude/climate zone, but Africans AMH were not across triple the distance and across several ecological zones".

How come Africans were not a partitioned population! They were with all likelihood, specially regarding Khoisan peoples. The rest, excepting Pygmies (another pretty much isolated branch), were surely quite concentrated at the OOA time in the Eastern Sudan/East Africa region. Yes, the fossil North African group may well have been a fourth distinct population but we are not aware of which genetic legacy it may have left, if any, and it's extremely unlikely that it'd be a Neanderthal legacy.

I really don't understand either why you seem to think that Croatia would be better connected with Syria than with the Caucasus.

"You can't talk Neandertal partition while at the same time affirming an African panmictic species".

Nobody is saying that about Africans. Khoisans are a very good example of how radically divided Africa was, even with no major barriers in between and with Sapiens legs and metabolism.

In fact it's the very ancient division of Africans before the OOA which allows us to make comparisons. We know that the ancestors of Yorubas and Eurasians were part of the same population (Y-DNA E) or the same two very closely related populations (mtDNA L3 and L2) and instead we find they are closer in this (and only in this) to Khoisans.

That pretty much sums it up.

Maju said...

(part 1)

"Briggs et al. found that Neandertals had one third our mtDNA diversity. Going by your logic, modern humans that have population structure have not experienced gene flow with each other".

Not sure what you mean. Modern humans before Neolithic and specifically sailing and horse and camel domestication (not tomention globalization in the last 500 years) were more structured than today almost without doubt and had much less gene flow between all levels of regions and populations.

A 'huge' back-flow from West Asia could have an impact, let's be adventurous, of 5% in Croatia, which would mean (at 2% admixture level with H. sapiens in West Asia) that the Croatian Neanderthals would get 0.1% of those H. sapiens genes (everything else equal). This tiny amount would not really be easily detectable at the level that the Paabo team seems to be working.

Of course the gene flow might well have been ultimately unidirectional for a vast array of possible accidental reasons (small accidents in a small population have a huge effect) but I see no reason to think that it was not bidirectional on light of the present data. We'd need West Asian Neanderthal DNA to get a better idea, really. I wonder if Mezmaiskaya 1 will provide us with some answers in this regard in the near future.

"It will take more than "short legs" to explain why admixture taking place in the Near East c. 100ky would not find itself into Europe 50ky later".

For exactly the same reason it's not in Africa. Even the actual large backflow from Eurasia only made a minor impact in Africa and there was never a second OOA migration which caused any major impact in Eurasia either.

Whatever flows between European and West Asian Neanderthal populations must have been limited because they were the same kind of animal with very similar techno-cultural level preventing each other from having a free ride in their lands. This was not apparently the case when Neanderthals colonized West and Central Asia nor when Sapiens colonized Africa and later Asia-plus.

We need to understand that demic movements are affected by patterns very similar to fluids' mechanics and that demic pressure itself is a barrier to penetration, which instead spreads much easier where there is no such pressure (i.e. in virgin land or scattered H. erectus' territories).

So we'd need something more than wishful thinking to allow for Neanderthal back-migration to Europe after the Neanderthal 'OOE'. And, even then, the impact would be too low to allow for H. sapiens genes to be detected.

(continues)

Maju said...

Btw, Dienekes: just found that there is a copy of this post of yours, without any attribution, at this site. I imagine you'd like to know.

Dienekes said...

Nobody is saying that about Africans. Khoisans are a very good example of how radically divided Africa was, even with no major barriers in between and with Sapiens legs and metabolism.

If you are not saying that about Africans, then you have to concede that admixture in a structured African population is every bit as good an explanation as admixture with Neandertals.

Actually it's better, because I still don't see how Out-of-Africans following the coastal route to Asia would end up with the same "Neandertal" admixture as Western Eurasians whose ancestors co-existed with Neandertals far longer.

For exactly the same reason it's not in Africa. Even the actual large backflow from Eurasia only made a minor impact in Africa and there was never a second OOA migration which caused any major impact in Eurasia either.

You should say "not in Yorubans and San", rather than not in Africa. We'll see how this research holds up when East Africans are sampled.

The Neandertal-admixture scenario would predict "no Neandertal" admixture in East Africans (because of demography and location of admixture outside Africa). My scenario predicts pseudo-"Neandertal" admixture in East Africans.

We'll see who's right.

princenuadha said...

@Daniel

OMG you dumb mfer there actually is some substance to what you were saying. "gene lateral transfer" is something I literally came across today by accident in a science blog/ news. Its not just a prediction but has been observed.

The article was talking about how a fish species has contains 15 genes that were transferred to it from a parasitic worm. The scientist notes, as I suspected, that it is especially rare for this transfer to happen in multicellular animals.

I'm not sure how the transfer took place though. as far as how it relates to this blog one must consider the rarity of the transfer, the amount, and the fact that a parasitic worm is in having a lot of exchanges with its host, and probably some co-evolution, unlike humans and Neanderthals. (no DS jokes either!). You would be right in saying this mechanism must make us rethink evolution.

Dienekes said...

If you posted a comment on this yesterday it may have been lost in a moderation accident. Unfortunately I have had to start moderating comments because of the appearance of certain trolls, but I deleted a bunch of comments by accident when I meant to delete a single one. So, if it's not too much trouble, post your comment again.

Maju said...

(part 1)

I think I was affected by that accidental deletion. Let's see if I can re-create my reply.

"If you are not saying that about Africans, then you have to concede that admixture in a structured African population is every bit as good an explanation as admixture with Neandertals".

There is some deep structure in Africa but it divides Khoisans (population A hereafter) from the rest, including Eurasians (pop. B1). To a lesser extent it also affects Pygmies (pop B2).

That structure does not justify your theory but rather debunks it because Yorubas are as B1 as Eurasians.

You'd be hypothesizing a third pop. C in North Africa and Palestine. While this may be justified by the archaeological record, it is not by the genetic one. In other words: there's no trace of any such pop. C in modern day humans.

If this hypothetical distinct population C is at the source of the Neanderthal admixture or noise (false admixture signal), Eurasians should have much more than 1-4% of them (as this is identified unmistakably as Neanderthal-specific), maybe 20 or 40%. That high level of admixture between populations B1 and C should have left some other genetic trace but that does not seem to be the case.

So I conclude that these C people either went totally extinct or were just a subgroup of the main population B1, from which both Yorubas and Eurasians stem.

"Actually it's better, because I still don't see how Out-of-Africans following the coastal route to Asia would end up with the same "Neandertal" admixture as Western Eurasians whose ancestors co-existed with Neandertals far longer".

We don't know for sure if the migrant OOA population took the South Arabian route or if it did so exclusively. In fact, this bit of Neanderthal admixture at the very root of Eurasians adds some weight in favor of the Crescent Fertile route, though as I have mentioned elsewhere, it may well be just a parallel route or the admixture event could have happened not in Palestine but rather towards Iran.

Also we don't know for sure that early West Eurasians lived side by side with Neanderthals for longer than the migrant group. For instance: between L3 (Africa) and M (South Asia) there are three CR mutations, while from R (South Asia) to H (rapid expansion in Europe) there are 4 coding mutations. This tells me that the times of the OOA migration and the West Eurasian colonization were probably similar (some 10-20 Ka).

Additionally, there could have been a second migrant group, probably surviving from the Skhul/Qahfez migration and intense interaction with Neanderthals, who were the ones to interbreed and would have been absorbed by the main migrant group. If they were at levels of 12% Neanderthal admixture, the apportion between the merging groups would have been of 4-1, if they were at levels of 25%, of 8-1, etc.

Of course the simplest explanations would be either (1) that the whole migration happened via Fertile Crescent or (2) that South Arabian migrants met 'sexy' Neanderthals in Iran but it's not necessarily the correct one. In any case, we lack of archaeological evidence to support either hypothesis and genetics is of little help here.

(continues)

Maju said...

(part 2)

"You should say "not in Yorubans and San", rather than not in Africa."

Yorubas are pretty much a good representative of the B1 population from which proto-Eurasians spawned. If this B1 population was "Neanderthalized" in Africa that should be evident among Yorubas.

"The Neandertal-admixture scenario would predict "no Neandertal" admixture in East Africans"...

Genuine East Africans like Dinka or Hadza for sure, less clearly for those populations affected by the Eurasian back-flows like most Ethiopians and such.

We'll see, of course. But Yorubas are sufficiently 'East African' genetically (Y-DNA E, mtDNA L2"6... or L3 if you are nit-picky) for that structure you hypothesize about to be present in them at very noticeable levels, if not fully. Yorubas, as close cousins of Eurasians are, so far, excellent evidence that Neanderthal admixture and not any hypothetical structure is the answer. Both are essentially derived from that B1 population I mentioned before.

terryt said...

"then you have to concede that admixture in a structured African population is every bit as good an explanation as admixture with Neandertals".

But much of ther admixture in Africa is a result of the Bantu migration, relativley recent.

"The Neandertal-admixture scenario would predict 'no Neandertal' admixture in East Africans (because of demography and location of admixture outside Africa)".

It's quite possible there's a lot of Neanderthal admixture in east Africa. Movement from Eurasia into East Africa is shown by the Eurasian haplogroups present there. And what about Y-hap R1b as far as West Africa?

"Unfortunately I have had to start moderating comments because of the appearance of certain trolls"

Unfortuante all right. The rapid conversations possible on your blog have made the commnets section fascinating.

Dienekes said...

There is some deep structure in Africa but it divides Khoisans (population A hereafter) from the rest, including Eurasians (pop. B1). To a lesser extent it also affects Pygmies (pop B2).

The point is about structure between AMH populations, or even AMH and non-AMH Homo within Africa. It's about deeper structure, i.e., remnants of Homo in Africa that were separate from our main ancestral population.

Yorubas are pretty much a good representative of the B1 population from which proto-Eurasians spawned. If this B1 population was "Neanderthalized" in Africa that should be evident among Yorubas.

The point isn't that the Neanderthalized but rather that they admixed with other Homo in Africa that didn't belong in the sapiens-Neandertal clade.

Genuine East Africans like Dinka or Hadza for sure, less clearly for those populations affected by the Eurasian back-flows like most Ethiopians and such.

There are ways to determine whether chunks of "Neandertal" DNA are due to recent admixture or to admixture taking place tens of thousnads of years ago. If East Africans have "Neandertal" DNA chunks that share recent (as in a couple thousand years) origins with East Eurasians, then you can dismiss it as backflow.

Maju said...

"The point is about structure between AMH populations, or even AMH and non-AMH Homo within Africa. It's about deeper structure, i.e., remnants of Homo in Africa that were separate from our main ancestral population".

Food? ;D

Seriously: there's nothing to support any such structure. It's a mere speculation.

"The point isn't that the Neanderthalized but rather that they admixed with other Homo in Africa that didn't belong in the sapiens-Neandertal clade".

The whole point of the issue is that we, Eurasians, differ from Yorubas much less in the overall genome than in these few specific 'Neanderthal' blocks.

If Yorubas were admixed with some other species/subspecies of Homo, the difference would be smaller or even inverted. So such hypothetical Yoruba admixture would have to:

1. Be impossible to detect using Neanderthal-specific alleles (as this hypothetical other species would be equally distant from Sapiens and Neanderthals, or closer to Sapiens but never to Neanderthals).

2. Be exactly the same between Yoruba and San but smaller among Eurasians, in spite of these and Yorubas being more closely related than the San.

Think about it because it's really indefensible. You are building on thin air.

Marnie said...

Regarding the chunks of Neandertal DNA and their age:

We're waiting.

I think there's not point in debating this. If there is a way to look at this, in East African populations, in Middle Eastern population, in Asian populations, etc., then I hope and expect that someone is doing that.

Andrew Oh-Willeke said...

"The Neandertal-admixture scenario would predict "no Neandertal" admixture in East Africans (because of demography and location of admixture outside Africa). My scenario predicts pseudo-"Neandertal" admixture in East Africans."

Honest question. How could one distinguish back migration into East Africa (which has been documented by other means to be statistically significant at a population genetic level) statistically from your scenario?

Dienekes said...

Honest question. How could one distinguish back migration into East Africa (which has been documented by other means to be statistically significant at a population genetic level) statistically from your scenario?

The so-called "Neandertal" DNA would have recent common ancestors in East Africans and West Asians (long chunks of identical or near-identical sequence at regions identified as candidates for Neandertal introgression).

In my scenario, however, in addition to such sequences (due to back-migration from West Asia), you would have older common ancestors which won't be explainable by West Asians crossing the Red Sea a few thousand years ago, thus evidence for "Neandertal" DNA that is a feature of native East Africans.

If that is the case, then we will know that it's not really of "Neandertal" origin.

German Dziebel said...

"The point is about structure between AMH populations, or even AMH and non-AMH Homo within Africa. It's about deeper structure, i.e., remnants of Homo in Africa that were separate from our main ancestral population."

Why would these remnants be located in Africa if the existence of this "deep substructure" is attested in Eurasian populations?

John said...

"We need to understand that demic movements are affected by patterns very similar to fluids' mechanics and that demic pressure itself is a barrier to penetration, which instead spreads much easier where there is no such pressure "

Yes but even small to macerate colonies can and do overwhelm native populations when other factors cause the native populations to be reduced or eliminated. that has occurred many times.

terryt said...

"but even small to macerate colonies can and do overwhelm native populations when other factors cause the native populations to be reduced or eliminated. that has occurred many times".

But don't forget, so has mixing. Many times.

Maju said...

"Yes but even small to macerate colonies can and do overwhelm native populations when other factors cause the native populations to be reduced or eliminated".

But such other factors, such as supervolcano catastrophes, are not common. I'd ask for specific evidence of such catastrophic decline that so far I can only conceive, if anything, in relation to Toba and Campania super-volcanoes (74 and 40 Ka ago respectively).

Marnie said...

This thought is kind of peripheral to the whole discussion on Neandertals, but it does have new relevance in light of the recent findings:

Why do While People Smell Like Wet Dogs When They Come Out of the Rain?

http://www.amazon.com/
White-People-Smell-Like-Dogs/dp/0967597102

If you're white, try smelling your kids' hair sometime.

Skorpion said...

http://www.newscientist.com/article/mg20627603.600-neanderthals-not-the-only-apes-humans-bred-with.html