October 11, 2010

Deep ancestors of human DNA compatible with structured African population

(Last Update Oct 13)

This is a wonderful paper as it directly deals with the old coalescence times of human autosomal DNA and their presumed incompatibility with the Out of Africa model:
A genome-wide frequency distribution of the TMRCAs has been reported by curating
the literature (Garrigan and Hammer 2006) but no systematic and consistent analysis has been performed in a single genome-wide data set. We report the fi rst genomewide estimation of the TMRCAs of anatomically modern humans, and we investigate if diff erent scenarios of human evolutionary history are supported by this estimate.
The four scenarios considered by the authors are seen schematically in the following figure from the paper:

The Recent out of Africa: Single Origin Population model is the simple model that has found support in the shallow coalescence times of human Y-chromosomes and mtDNA and has made the jump to popular culture. In this model, humans are a young species that underwent a bottleneck, and Eurasians are descended from a group of Africans that left the continent. This model has been criticized for its perceived inability to explain deep divergence times in autosomal DNA.

The Recent out of Africa: Multiple Archaic Populations is the model I have advocated over the years (check out the "Palaeoafrican" label of the post for my past writings on the subject). It agrees with the previous model in the recent African origin of modern Homo sapiens but it states that the African population was structured and not panmictic: divided into fairly isolated long-standing subpopulations, and that Eurasians are descended from a single one of these African subpopulations (which I have termed "Afrasians").

The existence of a structured African population makes easy work of deep divergence times, as the variants that have such deep origins are presumed to have evolved separately in different African subpopulations, and then to have found themselves in the modern gene pool after the breakdown of this structure.

The Multi-Regional: Recent Admixture model is the one advocated by those seeing Neandertal and/or Homo erectus introgression in Eurasia. Like the previous two models, it agrees on the recent African origin of modern humans, but it sees a place for long isolated pre-existing Eurasian hominids, who contributed some of their mtDNA to modern humans.

Like the previous model, deep divergence times are no problem, as two variants with deep common ancestry are presumed to stem from the separated Eurasian and African Homo. This model has found recent support by analysis of the Neandertal genome but as the authors of that study and myself have stressed, the evidence for 1-4% Neandertal introgression into Eurasians has an alternative explanation consistent with the previous (Multple Archaic Populations in Africa) model.

Finally, the Multi-Regional: Long Standing Admixture model sees no special place for Africa, except as the point of origin of human Y chromosomes and mtDNA. Humans are descended from Homo populations from around the world that have always maintained gene flow between them. This model obviously explains deep divergence times, but has a difficult time explaining the African origin of the uniparental markers, the palaeoanthropological evidence for an emergence of anatomical modernity in East Africa and the genetic evidence for a diminution of genetic variation in Eurasia with increasing distance from East Africa.

The authors seem to propose a fifth model, Ancestral Bottleneck which is noted as a bottleneck 150,000 years ago in a possibly ancestral structured population. This model doesn't get its own figure, but can be seen in the Single Origin Population model as "Potential bottleneck 150,000 years ago".

This model seems to combine elements of the first two ones: it is an essentially single origin model for extant humans, but it keeps the possibility of structure in Africa prior to the bottleneck, and pushes the breakdown of this structure before the bottleneck.

Here is what the distribution of TMRCAs for autosomal DNA, mtDNA, and Y-chromosomes:

The authors observe that really old most recent common ancestors are predicted by all four models, so they are no reason to discount the Single Origin Population model. However, it is plain that the variance of TMRCAs observed for actual human autosomal DNA is great (the black curve is "flat"). Here is what they write:
The variance of the empirical TMRCAs is larger than the variance predicted by three of the four different models of human evolution (see Figure 2 and Supplementary Table 3), and this large variance has been interpreted as the result of archaic sub-structure in Africa (Harding and McVean 2004). Indeed, the Multiple Archaic Populations' (scenario 2) shows similar variance of TMRCAs as the empirical data, but the inflated variance of the empirical TMRCA estimates can also be due to variation in mutation or recombination rate across the 40 sequence-regions (McVean et al. 2004).
In other words, the variance is great (more young and old TMRCAs than expected), either because of variation in mutation and recombination rates (i.e., different genomic regions evolve at different paces), or because of the multiple archaic populations idea. Unfortunately, the paper does not attempt to show how e.g., a variable genome-wide mutation rate might serve to flatten the TMRCA variance of the three models that fail to reproduce the data.

When we look at uniparental markers (mtDNA and Y-chromosomes), all four models predict older ancestors than observed. Here is what they write:
The models of human evolution typically predict older TMRCAs compared to the estimated 170,000 years for mtDNA (Ingman et al. 2000) and the upper estimate of 100,000 years for the Y-chromosome (Tang et al. 2002; Wilder et al. 2004; Shi et al. 2010). For mtDNA, a TMRCA of 170,000 years is within the range of values predicted by the `Multiple Archaic Populations' scenario (P(TMRCA less than 170,000) = 0.21), but the mitochondrial TMRCA estimate is diffi cult to reconcile with the remaining three scenarios (P less than 4x10-2). For the Y-chromosome, a TMRCA of 100,000 years is clearly at odds with three of the models (P less than 6x10-4), but for the `Multiple Archaic Populations' scenario with archaic African admixture, the proportion of simulated gene trees with TMRCAs younger than 100,000 years is larger than for the other three models, albeit quite small (P = 1.5x10-2).
Thus, while all four models can perhaps account for old autosomal TMRCAs (The "multiple archaics" on its own, the other three with help from variable genome-wide evolution), none of them can account for the young ages of human Y-chromsomes and mtDNA, with "multiple archaics" again coming on top, being consistent with "mitochondrial Eve", and coming closer (but not quite) to consistency with "Y-chromosome Adam".

There are ways to reconcile all four models with the uniparental markers, however. For the Multiple Archaic Populations model, they acknowledge that the Y-chromosome problem would go away if they increased the number of these populations from their current 3, while for the rest they invoke selection to account for the recency of human mtDNA and Y-chromosomes.

The effective population size tug of war

Parenthetically, it is important to note here the problem of the effective population size, as it has fueled quite a lot of sensationalistic media stories and documentaries (of the "humans were at the brink of extinction, and then a small band of them survived and went on to conquer the world" kind).

Here are some useful observations:

High effective population size => old TMRCAs
Low effective population size => young TMRCAs
Directional selection => young TMRCAs
Balancing selection => old TMRCAs
Structured population => old TMRCAs

In order to account for the recency of human Y-chromosomes and mtDNA, scientists came up with very low population sizes for our ancestors ("the endangered tribe" meme).

Unfortunately, this has the side-effect of predicting very low ages for autosomal DNA, lower than observed! To fix one problem, another one is created.

Can we have our cake and eat it too? An idea is to invoke balancing selection in autosomal DNA, i.e., the persistence of two variants at a given locus because they confer different advantages/disadvantages and an equilibrium between them exists, not allowing one or the other to reach its destiny of fixation.

Another idea is to invoke directional selection in Y-chromosomes and mtDNA. In directional selection, competing alleles are weeded out not by the winds of fortune, but by the supremacy of the successful alleles (Adam and Eve in our case) which push them to the side.

A different idea is to invoke ancient population structure. This immediately adds time to the TMRCA (since the different sub-populations became separated), and can thus explain old divergence times.

A fourth idea is to invoke "technical" things like variable mutation rate across the genome, or see problems in the standard age estimations for Adam and Eve. That way you can explain why there are more old autosomal TMRCAs than your model predicts, or why Adam and Eve are younger.

No wonder that there is no consensus among experts!

Conclusion

This paper certainly shows that the multiple archaic African populations model that I have advocated is a strong contender for being close to what actually happened. A priori, I think that the ecological and climatic variation in Africa -especially due to its north-south geometrical orientation-, and the long-established presence of Homo in the continent, make it unlikely that a single population of Homo survived there at the expense of all others.

In short, I think that: humans were never endangered in Africa, never dwindled to small numbers (inferred ancestral effective population sizes in the paper are 8k for Multiple Archaic Populations and 14k for Ancestral Bottleneck), and were not a single panmictic population spanning ecological niches and climate zones.

Rather, there were always separate populations in Africa, and climatic change (and more lately behavioral/subsistence change) has resulted in an ever-present process of population fusions and fissions. One of these sub-populations, living somewhere in East Africa, accumulated enough biological advantages to become extremely successful, populating Eurasia on the one hand where some admixture with archaic Eurasians may have taken place, but, also, successfully populating the rest of Africa, where it absorbed other subpopulations of Homo in the continent itself.

UPDATE (Oct 13): Some discussion of the paper and my own theories in Gene Expression, wherein Chris Stringer, a leading proponent of the "Recent out of Africa: Single Origin Population" says that:
My new book covers all this, and your recent work, but I do agree with Dienekes on the importance of deep African population substructure to the story..
While Gregory Cochran thinks I'm wrong:
Dienekes is wrong about the Neanderthal interbreeding results being explained by African population substructure, , but there are a lot of indications that there was significant substructure. A lot of this involves work that is not yet published: I look forward to seeing the details. Some of what I hear is remarkable.
For myself, I'm waiting to see data on native east Africans on segments of "Neandertal" ancestry. Let's look at native groups from Somalia, Kenya, Ethiopia, Tanzania with limited Caucasoid admixture and let's see how much "Neandertal" ancestry they have. If they don't have any, then "Neandertal" genes must have a Eurasian admixture explanation. If they have too little, then it can be explained by Caucasoid admixture in more recent times. But, if they have much more "Neandertal" admixture than Caucasoid admixture can explain, then the obvious solution is African population substructure.

Mol Biol Evol (2010) doi: 10.1093/molbev/msq265

Deep divergences of human gene trees and models of human origins

Michael GB Blum and Mattias Jakobsson

Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago, and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates – between 100,000 and 200,000 years – of the most recent common ancestors for the mitochondrion and the Y-chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosomal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X-chromosome on the other hand.

Link

18 comments:

terryt said...

Perhaps the most interesting aspect of the information here is the separation in TMRCAs of Y-haps and mtDNA, as shown in graph C. Surely that difference is significant. Maju has often bleated on to me about what men or women the first haplogroup into a particular region could have bred with. I look forward to hearing what he has to say as to the men the mtDNA L women bred with before the modern Y-haps appeared. Y-haps, and mtDNA, have obviously been replaced, and disappeared completely, at times.

We know that Y-hap distribution generally seems to be younger than mtDNA. Quite possibly this has always been the case. But the simplest explanation for the evidence offered in this post is 'directional selection in Y-chromosomes and mtDNA', but not necessarily genetic.

We can be fairly sure that both technology and culture have become important factors in human evolution. Perhaps have always been, since the first tools appeared. My guess would be that mtDNA spreads with culture and Y-haps spread with technology.

In that case the ancient TMRCAs of X chromosome and autosomal DNA presents no problem at all. We have the 'Multiple Archaic Populations model', but not necessarily confined to Africa. Then the main apparent problem with the 'Multi-Regional: Long Standing Admixture model' dissappears: the 'diminution of genetic variation in Eurasia with increasing distance from East Africa'. It possibly goes back to the emergence of Homo erectus. Humans have been a widespread, continuously evolving species over the last 1.5 million years. The curve is 'flatter' than expected because of the population movement from Africa that accompanied the haplogroups.

The 'Recent out of Africa: Multiple Archaic Populations model' is not really satisfactory, in that it's extremely unlikely that the African population was completely isolated from the Eurasian population over the whole 1.5 million years.

Andrew Oh-Willeke said...

"it's extremely unlikely that the African population was completely isolated from the Eurasian population over the whole 1.5 million years."

True, the African population wasn't completely isolated. But, the interaction genetically with the Arabian Peninsula and North Africa was quite modest for most of that time period and never became a majority impact. (There are also a couple of notable instances where the genetics point to a strong likelihood of back migration to Africa in the pre-colonial era.)

The influence beyond that region is pretty much entirely attributable to second order effects of Arabian and North African people with African genetics who participated in trade in the Mediterranean from about the Bronze Age until the fall of the Roman Empire, and from the presence of those same people in reasons that became part of the Islamic empire from around 700 CE to 1500 CE, with a couple of historically well documented exceptions (e.g. a military unit whose member settled where they were deployed in South Asia). By the Neolithic, gene flow may have been mostly into Africa, not out of it as Neolithic cultures better defended their space and expanded.

Still, there are virtually no traces of any L haplotype mtDNA in East Asia, the Americas, South Asia, Central Asia or Europe (beyond the Balkans), that is not clearly attributable to European Colonial era migrations, despite the fact that they are predominant in Africa. And, the same can be said of almost all of the predominant African Y-DNA haplotypes. Aside from a few E subtypes in the Near East and Mediterranean basin (and I would argue possibly Y-DNA haplotype T), there are virtually no genetic traces of Africa in Eurasia.

It could be that the Upper Paleolithic hunter-gatherer genome was more African and that there is now little trace of that population in because it was largely replaced close to Africa, and the places where the Upper Paleolithic genome wasn't replaced (e.g. Native Americans, Aboriginal Australians) also happened to be the places with the least subsequent room for contact with Africa.

Andrew Oh-Willeke said...

I would appreciate a little more fleshing out of what a "Multiple Archaic Populations" scenario would look like. In other words, which physical anthropological and genetic populations are we talking about and when, at least as examples of what the scenario would look like?

Is the notion that this would parallel the apparent genetic breakdown in modern humans between Khoisan, Pygmy, L2 "black African," L3 "black African" and a proto-Eurasian offshoot of L3 that went on to form M and N on the mtDNA side (with parallel divisions on the Y-DNA side)?

Or, is the notion that there were various subtypes of pre-Cro-Mags such as Neanderthals, Homo Erectus, H. Heidlerberg, etc. which would have shared genes to a limited exchange with each other and early Cro-Mags?

Or have I got it entirely wrong and there is some other breakdown all together?

Ponto said...

There is way too much emphasis on haplogroups. It seems unlikely that various human groups were on one haplogroup in their founder populations. Western Europeans may be high in R1b today but the founders of those populations most likely contained many haplogroups now lost in the same method stated in the extinction of surnames some time ago by Dalton?. Produce no sons, your Y chomosome haplogroup and your surname is extinct. Women without daughters do not pass on their haplogroup with any chance it will be passed on by those daughters to their daughters. Haplogroups E, Y chromosome, and L, mitochondrial, may simply have died out in Europe but were present in reasonably numbers in the founding populations of Europe.

terryt said...

"But, the interaction genetically with the Arabian Peninsula and North Africa was quite modest for most of that time period and never became a majority impact".

We don't really know that to be so, although it certainly seems to be so since the development of modern haplogroups. But that's only for the last 150,000 years at most. There could have been major earlier immigrations, such as of the Dmanisi-type H.erectus, or whatever you care to call it. The separation between H. erectus and H. ergaster may be the result of some sort of back-movement too. The Acheulean may indicate some sort of major exchange between Africa nad Eurasia as well. And the Levallois.

"Is the notion that this would parallel the apparent genetic breakdown in modern humans between Khoisan, Pygmy, L2 'black African,' L3 'black African' and a proto-Eurasian offshoot of L3 that went on to form M and N on the mtDNA side (with parallel divisions on the Y-DNA side)?"

That gives five sub-populations. Dienekes quotes the article as saying, 'For the Multiple Archaic Populations model, they acknowledge that the Y-chromosome problem would go away if they increased the number of these populations from their current 3'. I find it difficult to imagine many more populations than just the three in Africa at any one time. To me it is most likely that the extra populations required would have to be extra-Africa, so to speak.

onur said...

Haplogroups E, Y chromosome, and L, mitochondrial, may simply have died out in Europe but were present in reasonably numbers in the founding populations of Europe.

The so-called "African-specific" haplogroups can still be found in Eurasians in very small numbers and have probably been part of the Eurasian gene pool since the colonization of Eurasia, thus they are probably nothing to do with any Negroid admixture in Eurasians except a portion of them in nearby (to Sub-Saharan Africa) territories like North Africa and Arabia.

Insightful said...

Dienekes, Gregory Cochran says on Razib Khan's blog that you are wrong about Neanderthal interbreeding results being explained by African population substructure. He commented here:

http://blogs.discovermagazine.com/gnxp/2010/10/daily-data-dump-monday-21/#comments

Dienekes said...

Well, he says:

Dienekes is wrong about the Neanderthal interbreeding results being explained by African population substructure, , but there are a lot of indications that there was significant substructure. A lot of this involves work that is not yet published: I look forward to seeing the details. Some of what I hear is remarkable.


Not much to say as there isn't any information there. We shall see...

I am still waiting to see if there are so-called "Neandertal" DNA segments in native East Africans.

If there aren't then my theory suffers a terrible blow; if there are, then the theory of Neandertal introgression suffers a terrible blow.

Maria Lluïsa said...

"I am still waiting to see if there are so-called "Neandertal" DNA segments in native East Africans. "

Why East Africans and not North Africans or Central Africans? I suspect that if they (Pääbo et al) would have analyzed East Africans and South Africans instead of West Africans and South Africans as they did, you'd be saying: "I am still waiting to see if there are so-called "Neandertal" DNA segments in native West Africans".

They didn't analyze East Africans, right; they didn't analyze North Africans, native americans nor middle easterners either; as for the waited Neandertal DNA segments in East Africans, I'm not sure, but apparently Jeffrey Long analyzed about 2.000 persons from around the world (possibly also East Africans):

http://www.nature.com/news/2010/100420/full/news.2010.194.html

and they came to the same conclusions as Green et. al. These were his words:

"They found exactly what we saw in our study":

http://blogs.monografias.com/sistema-limbico-neurociencias/2010/05/07/migrating-humans-interbred-with-neanderthals-after-leaving-africa/

Dienekes said...

Why East Africans and not North Africans or Central Africans?

North Africans are principally Caucasoid, so if the "Neandertal genes" were found in them, then they could be explained by backflow from (Neandertal-admixed) Eurasians.

If "Neandertal genes" turn up in Central Africans, then that will really kill the "Neandertal admixture" theory, as there is no plausible scenario in which such genes would turn up there. People can seemingly swallow the Japanese having the same fraction of "Neandertal ancestry" as Caucasoids (as the data shows), but it would take quite a leap of faith to explain THAT in Central Africans.

I am waiting for native East Africans, of course, because my theory depends on a recent common ancestor between Homo sapiens and Homo Neandertalensis, and admixture of this clade with other archaic Homo in Africa. It is in East Africa that Homo sapiens emerged most likely, and if he shared DNA with Neandertals, then it would survive in East Africans. If, however, as the other theory holds, the DNA was picked up in Eurasia from Neandertals, then "Neandertal DNA" will not turn up in East Africa, or it will turn up at the minimum levels allowed for by Caucasoid backflow into East Africa.

Dienekes said...

m not sure, but apparently Jeffrey Long analyzed about 2.000 persons from around the world (possibly also East Africans):

The best I could find on this is that it is based on microsatellites and I could not find a reference.

I am talking about the specific estimate of 1-4% admixture based on full sequencing carried out by the Paabo group

http://www.sciencemag.org/cgi/content/full/328/5979/710

which explicitly used Yoruba as representatives of Africa. This group found that Neandertals were closer to Eurasians than to Africans (Yoruba). I want to see if the same holds if native East Africans are used instead of Yoruba, and to what degree, and what is the estimate of "Neandertal admixture" in Somalis, Maasai, and so on.

eurologist said...

I have stated this before - the "no gene flow" theory between west Eurasians and Africans is about as likely as Saturn being the only planet with rings. First you see just one and believe in the uniqueness, but later and with better instrumentation/analysis you see it is common.

Antecessor=heidelbergensis had ample opportunity to mix with African populations in the Mediterranean region and in the near East every 50,000 to 100,000 years, based on climatic cycles.

Based on fossil evidence I believe it is quite clear that erectus, on the other hand, evolved separately and separated from African and European populations for about 1.5 million years.

And any admixture in Asia different from the "single, early Neanderthal event" would be more likely from heidelbergensis groups that are known to have ventured all the way to China.

Only when climate more drastically changed for the worse and Neanderthal features start to develop ~300,000-400,000 years ago does it seem plausible that contact was extremely limited, if not non-existent until about 120,000 years ago. (Climate was close to Mediterranean in Central Europe, before then).

Between ~1.4 million and 300,000-400,000 years ago, there is a close relation and similar progression between African and European finds - supporting relative easy, and likely bi-directional, gene flow.

Thus, it is not difficult to understand why some of the Neanderthal genome indicates a fairly late complete separation (~400,000 years ago).

So, not only were there likely 3-5 African populations (SA/SWA bush, SA coast, EA, NA), they also likely had a different degree of admixture from European/middle East populations. More or less final sapiens perhaps emerged when AMH SA populations with low admixture merged with EA populations with higher admixture.

The difficulty of course is to keep it all separate: there is clearly ancient autosomal material that is native African as there is some that is native (i.e., 0.5 to 1.5 million years old) European - and likely present to some degree in both populations from both sources.

terryt said...

The study actually supports what many geneticists have been trying to tell everyone for years. Each individual gene in a species has its own individual origin. Genes advantageous for the survival of the particular species move through that species like ripples through a pond. Of course individual genes are often carried through the species by the expansion of a subspecies, carrying the relevant gene as well as another particular combination of genes.

"There is way too much emphasis on haplogroups".

The haplogroups behave in much the same way as diploid genes do. Advantageous versions travel through the species, in a wave.

Maria Lluïsa said...

"I am waiting for native East Africans, of course, because my theory depends on a recent common ancestor between Homo sapiens and Homo Neandertalensis, and admixture of this clade with other archaic Homo in Africa. It is in "East Africa that Homo sapiens emerged most likely, and if he shared DNA with Neandertals, then it would survive in East Africans. If, however, as the other theory holds, the DNA was picked up in Eurasia from Neandertals, then "Neandertal DNA" will not turn up in East Africa, or it will turn up at the minimum levels allowed for by Caucasoid backflow into East Africa."

I'm not an expert, but apparently Khoisans, and not East Africans, hold the most ancient lineages on Earth (they were the first group to split off from others). There are many population structures within Africa, but individuals of West African origins seem to have also East African ancestry, so if East Africans had or still have any pseudo-neandertal DNA I'd expect to find a bit of it in West Africans, but apparently they have the same levels (about 0%) as Khoisanids. Giving the fact that West Africans and East Africans are more closely related to Europans/Asians than Khoisanids, I find it quite illogical that this fraction of neanderthal DNA was lost in some African lineages but mantained in the group who left Africa and met the neanderthals.

"I want to see if the same holds if native East Africans are used instead of Yoruba, and to what degree, and what is the estimate of "Neandertal admixture" in Somalis, Maasai, and so on."

Some East Africans have variable levels of admitxture with non-African groups, so it's likely to find a bit of neanderthal DNA in them. If that's true, I'd be very hard to tell if the neanderthal DNA was already present in East Africans or it's due to recent admixture with non-Africans.

There are some problems with the neanderthal theory, like: why can't we detect any modern human admixture in neanderthals? or: why all non-African groups seem to carry the same amount of neanderthal DNA, if neanderthals and modern humans met various times at different places?
But I still consider it much more likely than the African-structure theory, giving the fact that neanderthals are very closely related to H.sapiens and the two coexisted for a long time.

Dienekes said...

Some East Africans have variable levels of admitxture with non-African groups, so it's likely to find a bit of neanderthal DNA in them.

I prefer numbers. For example, I've quantified Caucasoid admixture in Maasai as 3.2% or 5%.

What's 5% of 4%? It's 0.2%. So, if we see that Maasai have 0.2% "Neandertal genes" or thereabouts, then that's explained by Caucasoid backflow. If we see that they have much more and are more similar to Eurasians, then Caucasoid backflow can't explain how they got "Neandertal genes".

I'd expect to find a bit of it in West Africans, but apparently they have the same levels (about 0%) as Khoisanids.

You have to realize that the 0% estimate is predicated on the acceptance that so-called "Neandertal DNA" was picked up by Eurasians outside Africa.

What scientists have done is to see that Eurasians are a little bit (4% worth of a little bit) closer to Neandertals than Yoruba are. Thus, they set Yoruba to 0% and Eurasians to 4%.

My theory tells the converse, that Yoruba have +4% worth of Palaeoafrican that predates the Neandertal-sapiens split, and rather than thinking of Eurasians "moving away" from Africans because of Neandertal admixture, we are thinking of Yoruba "moving away" from Eurasians because of Palaeoafrican admixture.

Maria Lluïsa said...

"What scientists have done is to see that Eurasians are a little bit (4% worth of a little bit) closer to Neandertals than Yoruba are. Thus, they set Yoruba to 0% and Eurasians to 4%."

Yes, but Yorubans and Khoisanids show the same levels of neanderthal DNA, either if they have 0% or 20%. If East Africans and non-Africans have similar levels of neanderthal DNA, which are higher than those of other Africans, then I'd expect to see some levels -or at least, some differences- in the amount of neanderthal DNA in West Africans, because as I said above, they have East African ancestry, so I'd expect maybe a 1 or 2%. That's not what we see, but on the contrary, all analyzed Africans show the same levels of neanderthal DNA.

"My theory tells the converse, that Yoruba have +4% worth of Palaeoafrican that predates the Neandertal-sapiens split, and rather than thinking of Eurasians "moving away" from Africans because of Neandertal admixture, we are thinking of Yoruba "moving away" from Eurasians because of Palaeoafrican admixture."

I find this to be an extremely complicated model without with no evidence at all. I'm not an expert, but as far as I know, mtDNA, Y-chromosome and autosomal DNA point out that Khoisanids, not Yorubas nor East Africans, have the oldest clades and split off the first, then west africans, and then East africans + non-Africans.
Your scenario seems to imply a Yoruban + Khoisanid branch and another branch comprising East Africans + non-Africans + Neandertals. If I get it right, the two branches had to split off before neanderthals separated from East Africans + non-Africans, that is, more than 400.000 years ago (others say more than 1.000.000). I find it extremely unlikely. There's no evidence of such a structure within Africa, as far as we know.
There's another thing: divergence. While by most genes neanderthals and all humans analyzed diverged 300-400.000K, another fraction of genes show a much younger coalescence times (less than 100.000) which can't be explained if they separated from East Africans + non-Africans much earlier.

Dienekes said...

There is nothing complicated about my model. I'm not going to speculate on what we will see in East Africans, until we actually see it.

The "Neandertal" model makes a prediction: "Neandertal" admixture in Africa should be equal except in those populations (such as North Africans and East Africans) that have non-African admixture, and in proportion to that admixture.

My model makes a prediction: "Neandertal" admixture in Africa should vary in proportion to the relative contribution of the archaic African component and if East Africans turn up with more "Neandertal" admixture than back-migration from West Eurasians can explain then evidence for it is added.

as far as I know, mtDNA, Y-chromosome and autosomal DNA point out that Khoisanids, not Yorubas nor East Africans, have the oldest clades and split off the first, then west africans, and then East africans + non-Africans.

So what? Splitting off first has no bearing whatsoever on whether or not they have admixed with archaics.

Your scenario seems to imply a Yoruban + Khoisanid branch and another branch comprising East Africans + non-Africans + Neandertals

Incorrect. All humans belong to the same branch, which may, however, have picked up some archaic (Neandertal in W Eurasia or pre-Neandertal African in Africa) DNA.

If we look at extant E Africans, and exclude their Eurasian and non-E African elements from other places of Africa then the two models make different predictions.

E Africa is special because that is where our species is said to have -originated so we expect E Africa to have been home to the ancestors of Eurasians rather than to other populations in a structured Africa scenario.

another fraction of genes show a much younger coalescence times (less than 100.000) which can't be explained if they separated from East Africans + non-Africans much earlier.

These younger coalescence times are due to admixture from the expanding moderns INTO the Neandertal gene pool.

http://dienekes.blogspot.com/2010/05/direction-of-gene-flow-to-or-from.html

German Dziebel said...

"There are some problems with the neanderthal theory, like: why can't we detect any modern human admixture in neanderthals?

Maybe for the same reason that we don't find French borrowings in Latin? Homo sapiens sapiens descended from a Neanderthal-like population. Only 1-4% of original genes survived in Homo sapiens sapiens, the rest were selected against or lost through drift. Naturally, non-African humans are closer to non-African Neanderthals. African populations are further removed from the Neanderthal ancestor than non-African populations because they went through a greater number of bottlenecks as they re-populated Africa.

"or: why all non-African groups seem to carry the same amount of neanderthal DNA, if neanderthals and modern humans met various times at different places?"

This could just be the effect of limited sampling. American Indians, for instance, were not part of the the sample in Green et al. 2010. Judging by the fact that American Indians have such traits attested in Neanderthals as blood group O and shovel-shaped incisors at higher frequencies than any other continental population (with decreasing frequencies in Africans), their fraction of Neanderthal ancestry may end up being higher than 1-4%.

"My theory tells the converse, that Yoruba have +4% worth of Palaeoafrican that predates the Neandertal-sapiens split, and rather than thinking of Eurasians "moving away" from Africans because of Neandertal admixture, we are thinking of Yoruba "moving away" from Eurasians because of Palaeoafrican admixture."

I like this idea. Very thought-provoking. But I don't think you need to place the origin of humans in this case in East Africa. East Africans may just as well have diverged from Eurasians because of Paleoafrican archaic introgression.