February 20, 2016

Are living Africans nested within Eurasian genetic variation (?)

The picture on the left (source) shows quite nicely that according to current understanding, Africans are nested within Eurasian genetic variation. The modern humans have the following structure:

(Early modern human lineage detected as admixture in the Altai Neandertal, ((Asians, Europeans), Africans)),

and then there are two deeper layers of Eurasian hominins (Neandertal/Denisovans) and the "Mystery hominin" that mixed into Denisovans.

Africans are thus just a leaf of the Eurasian family tree, casting serious doubt -if this model is to be believed- to the position that H. sapiens originated in Africa and are descended from people who never left the continent. It seems much simpler to derive them from an early migration (~200kya?) from Asia which would nicely explain why the continent's first sapiens populations appear tentatively in the northeastern corner, and why they do not replace archaic hominins for most of the 200 thousand years until today. In a reversal of perspective it is not Skhul/Qafzeh that are the "migration that failed", but rather the Omo 1 outlier is.

One might argue that this is just a consequence of the fact that lots of ancient genomes have been published from Eurasia, but none from Africa. So, there are all these branches of deep archaic Eurasians simply because there are no genomes of deep archaic Africans.

But, this explanation does not really work. If Africans had any significant ancestry deeper than the split of "Early modern human lineage", then this lineage would be closer to (Asians, Europeans) than to Africans. However, Kulhwilm et al. assert that it is "equally related to present-day Africans and non-Africans". If they had any ancestry deeper than ((Denisovans, Neandertals), H. sapiens), then (Denisovans, Neandertals) would be closer to non-Africans than to Africans. Well, they are, but this is now satisfactorily explained by admixture from (Denisovans, Neandertals) into non-Africans, thanks to genomes like Ust Ishim, K14, and Oase which have big chunks of Neandertal ancestry that can't be explained any other way. No need to invoke any such lineage when a simpler well-documented alternative exists.

The presented phylogeny negates the possibility of the existence of collateral archaic African kin of the extant Africans that admixed with them, and leads to the conclusion that Africans are nested within Eurasian variation because they really are. This is, of course, incompatible with the statistically inferred archaic introgression into Africans which indeed postulates the existence of such archaic Africans and their contribution to extant ones.

I don't see any obvious flaw with Kulhwilm et al. but if its model is right, then it does lead to some rather extreme conclusions. It contradicts the evidence for archaic introgression; if Hsieh et al. is wrong (and I don't seen any evidence for that either), then Kulhwilm et al. can be saved, but only if Africans are really nested within several layers of Eurasian variation and did not admix at all with the morphologically diverse archaic Africans of the paleoanthropological record. This also doesn't seem right now that we know that sapiens-archaic admixture was a common occurrence in Eurasia. The reversal of perspective alluded to above may help here by removing the opportunity for admixture, but that too is, of course, an extraordinary claim.

In sum, I am rather convinced that the latest discoveries have muddled the origin story of our species and some major rethink is needed to evaluate the totality of the evidence.

32 comments:

Grogard said...

I've thought for a while now out of africa is bunk, but I will turn this even further on its head.

An intermediate population that is half african and half eurasian from which they both split is never something that made any sense.

We have to either speak of mixing or speak of evolution, not speak of some convoluted third option of anti-mixing. That is we either came from mixing various ancient groups together, or came from evolving (which is multi-regionalism). Out of Africa is really a mixing hypothesis with "rare, infrequent" evolution that can be all but discounted. Multiregionalism is an evolution+diffusion and hypothesis - but migrations are not discounted, either.

So as a mixing scenario like out of africa, a blended modern human that has all the DNA of all the races together doesn't make any sense. That is an end result not a basis for a starting point.

So if we see this while I don't think it totally discounts out of africa or validates multiregionalism, what it really implies is that there's already two separate populations at this point which are not mixed together and that the eastern neanderthals are in between them. One eurasian population that provides a lot of the genes we have today outside of africa and one separate one probably already in africa which is more african-like - with the eastern neanderthals in contact with both.

Which would seem to support multiregionalism or perhaps even out of east asia

cosasdehombres said...

Mistery hominid is not anymore just a theory, but a fact:
http://meeting.physanth.org/program/2016/session13/prufer-2016-the-high-quality-genomes-of-a-neandertal-and-a-denisovan.html
In the high quality genome of Altai they found it, the admixture with a highly divergent hominid.
Also good is to see the european genome in China-Mongolia at 2BC!! (supporting the theory of proto-aryan origin in mongolian plateau):
http://meeting.physanth.org/program/2016/session40/rogers-2016-genetic-variation-between-the-population-of-the-ancient-xiongnu-and-modern-populations-in-central-mongolia.html
The time of the Wide Genomes as the "golden parameter" of archeology is arrived and it brings a lot of presents

terryt said...

"Africans are thus just a leaf of the Eurasian family tree, casting serious doubt -if this model is to be believed- to the position that H. sapiens originated in Africa and are descended from people who never left the continent".

I have never seen any reason why humans are descended from some H. erectus species that had never left Africa. The evidence uncovered in the last few years shows our evolution was far from simple. In fact an unbiased look at the mt-DNA evidence suggests that the humans who relatively recently left Africa descend from a population that had earlier entered it. Otherwise we have Denisovans' ancestors leaving Africa, followed by Neanderthals' ancestors, followed by modern humans' ancestors. Surely a more parsimonious interpretation of the mt-DNA shows Denisovans and Neanderthals separating somewhere in western Eurasia, then Neanderthals and modern humans separating when modern human ancestors entered Africa from Eurasia. I don't think there is any doubt that the surviving mt-DNA have a deep origin in Africa, probably dating to 200,000 years ago. However we know nothing yet of the ancestry before that time. In fact the surviving mt- and Y-DNA lines need not have entered Africa together, not left it together.

German Dziebel said...

Good job, Dienekes! You learned your lesson when I lectured you on the origins of Indo-Europeans and scored an easy win. You are finally coming to your senses when it comes to modern human origins and voicing my ideas. But don't forget to properly reference the true pioneers of your thinking.

Ross said...

I would have thought that the Y chromosone distribution (Dienekes March 14 2015) shows significant African influences from 100kya to the present for Eurasians. Certainly there is some gene flow through interbreeding incidents shown in the diagram as (1) then (4) then (3), but this seems to be relatively minor across the genome.

That is, I am suggesting there must have been some mutation along the lower blue to purple line in the diagram that has produced significant changes from what was in the higher purple line (Early modern human), Neanderthal or Denisovan, that has enabled the mitochondrial and Y chromosone dominance of recent (within say 60kya) Africans. We need some ancient African genomes.

eurologist said...

"In sum, I am rather convinced that the latest discoveries have muddled the origin story of our species and some major rethink is needed to evaluate the totality of the evidence."

I agree. But I also think one should pursue more analyses of extant Eurasian whole-genome sequences, similar to the African studies.

For example, shouldn't it be possible to study Eurasian and African genomes to see what the chunk size is at SNP positions of these very early AMHs inferred from the Altai Neanderthal? What I am driving at is that it appears to be very difficult to trace who was where and when. So it would be very interesting to see who has the larger chunks of these regions, and what is the estimated TMRCA (with the usual 20% to 30% salt of grain, in the best case scenario, of course).

Such an analysis may be able to answer whether early (200,000 - 100,000 ya) ooA AMHs are still genetically reflected in Eurasians.

Awale Abdi said...

So your proposition is that the earliest ancestors of AMH originated in Africa (last I checked the earliest archaeological evidence of our species and its predecessors seems centered in Africa) then they left Africa for Eurasia then they returned and left again (this "last" exodus being representative of the exit responsible for current "Eurasians")?

Sounds over-complicated. I prefer the idea that AMH were always mainly nestled in Africa but a very early expansion (or expansions) out of the continent occurred and that is responsible for the people whom those Eastern Neanderthals owe their AMH ancestry to but these peoples seemingly mostly died out before or sometime after the later dispersal (or dispersals) out of Africa responsible for current Eurasians who seem firmly nestled within "African diversity" in terms of Y-DNA, mtDNA and auDNA. AncientDNA has so far only been making the recent Out-of-Africa hypothesis look more and more solid.

andrew said...

The entire hypothesis hinges on the continental affinities of the modern human component (a 1%ish portion) of a sample size of one (a single Altai genome) that supports step 1 of the diagram above.

This evidence is far too thin to support a paradigm shift of that magnitude. It is entirely plausible that there is no affinity to African v. non-African modern humans in that component simply because the part that remains in the Altai Neanderthal genome is shared by all humans (as much of the modern human genome is) while the portion of the human genome that is informative with regard to ancestry was lost over the tens of thousands of years between the admixture event and the death of the individual whose genes were measured - an event that is not just possible but likely.

themgt said...

As someone who knows nothing about genetics or anthropology, I had a thought.

What if 1000->100kya Africa had a large population of widely-interbreeding archaics, well-adapted and evolving slowly, essentially one big species. Then small founder populations fork off and rapidly adapt/evolve into Neanderthals, Denisovans, etc and interbreed and then backmigrate to Africa.

Point being, would the already present/large/stable archaic population in Africa mean that all variability from interbreeding with that population would look paradoxical, that Africans would have "significant ancestry deeper than the split" but it would be difficult to show with statistical inferences because the variability of the archaics they interbred with was contained within other human lineages, whereas interbreeding w/ the small founder populations would be much more obvious.

Mark Moore (Moderator) said...

I never really got an answer on the other thread so I thought I would give it a go here. Are the mysterious "Basal Eurasians" linked to this other mystery population of basal type humans who admixed with the Altai N. in any way? I seem to remember them as also being described as "African-like but not African" in their genome.

Also, east Asians are known to have a somewhat higher amount of Neanderthal DNA than Europeans, but the chart shows only one such admixture event. I thought the most parsimonius explanation was that East Asians had a second injection of such genes. That is not shown on the diagram. An oversight or is there another more accepted explanation?

jehoneycutt said...

I am both facinated and lost. My apologies for being off topic, but I would very much like to take some classes that would allow me to keep up with your blogs without my head spinning. Could you point me in the right direction? Or even to the starting line?

andrew said...

Another possible methodology issue is that a lot of continental ancestry informative markers are less than 100,000 years old. If admixture took place ca. 100kya to 125kya in the window where archaeology supports that possibility consistent with the Altai genome, then almost by definition, very few non-African ancestry markets will have had time to come into being. It will look basal to African and non-Africans because it is literally sampling from the moment of their divergence.

But, the statistical tests of continental affinity are being done with modern genomes. Almost all of the non-African ancestry informative genes in modern non-Africans are the result of post-Out of Africa mutations (almost by definition). Before that, there is just one population and there has not been enough time for these non-African mutations or for that matter many African ancestry indicators to have mutated into existence yet. So, compared to modern populations, of course it is going to look basal to both which have differentiated in the last 100,000 years.

Add the issue of purging of ancestry informative genes with no selective fitness effects in my previous comment, and the informative power of the data to support the all human variation is nested hypothesis, and you've really got nothing statistically significant left.

Dienekes said...

The entire hypothesis hinges on the continental affinities of the modern human component (a 1%ish portion) of a sample size of one (a single Altai genome) that supports step 1 of the diagram above.

No, because there is also no evidence for Africans having ancestry pre-dating the AMH-Neandertal split. But it would definitely weaken the case if the "Early modern human lineage" didn't exist or has some other interpretation.

So your proposition is that the earliest ancestors of AMH originated in Africa (last I checked the earliest archaeological evidence of our species and its predecessors seems centered in Africa) then they left Africa for Eurasia then they returned and left again (this "last" exodus being representative of the exit responsible for current "Eurasians")?

I don't think there's any strong evidence that AMH originated in Africa from physical anthropology. Sure there's Omo 1 but later specimens like H. sapiens idaltu are more archaic. It's hard to argue priority based on isolated finds from a region whose geology favors preservation. If Omo 1 had been found in west Africa or south Africa maybe there'd be a better case, but one can easily imagine that he was part of a population that came from Asia.

Ryan said...

If Omo 1 had been found in west Africa or south Africa maybe there'd be a better case, but one can easily imagine that he was part of a population that came from Asia.

The argument on West Africa seems a bit specious. Correct me if I'm wrong here, but aren't there a grand total of 0 hominin fossils from West Africa? The absence of evidence isn't the same as the evidence of absence. I don't think anyone is arguing that West Africa had 0 hominins until the Upper Paleolithic, but as far as I know there's no fossil record to show that presence.

terryt said...

"We have to either speak of mixing or speak of evolution"

I very strongly suspect evolution is always a product of mixing. It doesn't make sense that it is the product of genetic change in a small, isolated population which then expands. That would produce excessive inbreeding depression. On the other hand I'm sure genetic change always occurs in a small, isolated population, but the survival of such genetic change depends on the population's ability to breed with a wider population. In other words evolution is the result of the interaction of both inbreeding and hybrid vigour.

"it really implies is that there's already two separate populations at this point which are not mixed together and that the eastern neanderthals are in between them".

I think it indicates we have a series of clines, just as we have today.

"the Y chromosone distribution (Dienekes March 14 2015) shows significant African influences from 100kya to the present for Eurasians".

It does indicate exactly that. But we know that haploid DNA can be surprisingly independent of diploid DNA. In fact basically each gene has its own independent evolution and history.

"there must have been some mutation along the lower blue to purple line in the diagram that has produced significant changes from what was in the higher purple line (Early modern human), Neanderthal or Denisovan, that has enabled the mitochondrial and Y chromosone dominance of recent (within say 60kya) Africans".

It may not have involved genetic change at all. I consider that Y-DNA is usually spread by expanding technology (passed usually from father to son, or at least close male relations) and mt-DNA is spread by expanding culture. Nothing to do with genetic change.

"there is also no evidence for Africans having ancestry pre-dating the AMH-Neandertal split".

That fits the mt-DNA evidence that neither Denisovans nor Neanderthals formed from any immediately previous movements out of Africa, and certainly not from separate ones. It was the ancestors of modern humans who moved into Africa, resulting in the split between Neanderthal and modern mt-DNA lines.

"then they left Africa for Eurasia then they returned and left again"

If the mt-DNA evidence can be taken at face value we have H. erects moving out of Africa nearly 2 million years ago, then much more recently the ancestors of modern humans moving back into Africa and then some 60,000 years ago of those Africans moving back out again. Not really very complicated at all.

terryt said...

Further to my comment regarding modern human clines. Here's an illustration of the modern mt-DNA regional centres for those who may not have seen it. I would presume that the geographic boundaries acting here would also have been active for virtually all of our evolution:

http://mtdnaatlas.blogspot.co.nz/2016/02/asia-has-five-mtdna-gene-pools.html

David Jacobson said...

The part of the thousand genome data that I looked at had many more sequences of linked variants that were specific to Africa then anywhere else.

Gundisaluus Menendiz said...

I really can't understand, what the problem is. Just like the evolution of haplogroup R1b in Africa, is the same way haplogroup E evolved thousands of years earlier.
Ancient Africans (A and B) have a deep ancestry with Archaic populations and as new arrivals migrated into Africa, they admixed with these ancient populations that already had archaic admixture in them for the last 200K years.
This video just about sums it up.
https://www.youtube.com/watch?v=BiF0U8tPouo

ΔΙΗΝΕΚΗΣ said...

Well, if they are three ancient populations that with evolution produce

Neanderthal> europeans
Denisovans> asians
"ancient africans"> modern africans

it is rational?

Unknown said...

back in the early 90s when i earned my degree in anthroplogy, i was taught and accepted the ooa theory without question. at the time, even though it had arisen out of a paper submitted in the ate 1980s based on snp variation in modern africans walked back by the majority of its authors less than 5 years later, and was based on nothing. snp variation in biology is known to be based on disease load, not genetic time-depth--no place on earth has a higher human disease load than africa.in fact, the majority of human snp studies are carried out to understand, predict, and combat diseases, such as cancer. it's embarrassing anthropologists ignore this to cling to a theory.

i believe now that ooa's quick and near universal adoption was based on 4 things: the knowledge that race is a biologic falacy, and thus the that regionalism was clearly unnacceptable so we came from one place, the discovery of lucy and the lack of "missing link"-esque species outside africa, the african genetic adam and eve discovery, also contepororanenous with the first ooa theory, and latent racism that africans are primitive, esp. the san.

the theory has been dogmatictically clung too despite growing contradictory evidence, i believe, due to the fact that most people embrace the comfort and safety of cognitive disonance and a reluctance to challenge the status quo.

i also majored in philosophy with a focus on the philosophy of science and logic, and began seeing serious flaws with the theory soonn after graduation, that has grown steadliy as more and more as new evidence has been discovered.

all evidence points to us being a eurasian species, including that all of our closest homo cousins are eurasian species. i do believe homo likely originated in afric, but i think that hom was erectus, not sapiens.

where something is currently has no bearing on where it orinated. the cheetah, camel, and horse originated in the americas. even african adam and eve, could abosulty have lived somewhere else.

a large wrench is about to be thrown into works, a 50,000 yo mammoth cache was uncovered recently in colorado, the bones show unmistakable cut marks of stone tools, it is being painstakingly excvated and studied by the university of colorado, knowing the revolution it will cause in paleoanthropology.

while absence of evidence, such as exists in africa and seemingly existed in the americas, is not proof of absence, Africa's lack of evidence should have been treated the same way as the american lack of evidence.

Grogard said...

Andrew, that is not correct we have some very ancient markers for bonobos and neanderthals in human population. We can't know how old something is til we find it in ancient DNA and it can always go backwards more.

But even things like blood types are markers as well. And everyone in africa seems to have O+ with the rest being due to relatively recent introgression. We KNOW these are many millions of years old!

I won't say this paper is game over for out of africa but even if your claim were true, it wouldn't make any difference to this paper anyway.

mooreisbetter said...

I like the fact that Dienekes is asking questions. Questions come from humility and a little bit of skepticism toward the orthodoxy, and both are good; both advance science.

The theory would be pretty simple: A population of modern HS expanded from Asia. The earliest wave went into Africa. Africa acted as a cul-de-sac. The rest of the world acted as a crossroads.

The remaining humans in the Asian origin point retained features comparable to those of Africans, but their DNA (for example, their Y line) mutated a couple steps to what we call subjectively a new Haplogroup (in this case, C).

Far from unprecedented. Look at who retains Denisova DNA and how far they are from their origin. Look at who retains purported Steppe Haplogroups at highest frequency, and how far they are from their origin.

This theory must be respectfully considered at least.

Joyce said...

If humans still carry 20% of Neanderthal genes after tens of thousands of years, that should definitely give the mainstream a pause about their fanatic belief in "out of Africa", especially recent OOA 50-60 kya. OOA was initially based on Darwin's belief that humans must have evolved where the great apes residing, but there are living apes in Asia too and now everybody knows that a lot of ancient creatures have become extinct. Besides, primates are believed to have originated in Asia. Humans have no fur, so we probably evolved in warm zone and that makes Africa, south Asia and south America all possible candidates (warm and large non desert area). It is comical that OOA contributes every similar pre human species found outside Africa as something evolved in Africa and then migrated out of Africa, so it has been "out of Africa" again, again and again but never entered Africa. From my limited reading, H. Erectus seems widely accepted as one of pre human ancestors which existed in Eurasia about 2 mya. The Java man dated 1.8 mya had brain volume over 1000cc (within modern human range, almost 6 foot tall, the average height of modern man). The Peking men dated 700 kya had brain volume over 1,200 cc (close to average brain size of modern man) who must have some ability to deal with not so temperate climate. There is no reason why Peking man could not have come from America or gone to America. "out of America" should not be completely dismissed either, so experts can be open minded to potential evidence.

Joyce said...

There are two massive maternal haplogroups, M and N, outside Africa. Pardon my ignorance, how do they decide that there are more diversities in Africa when there are more mtDNA markers outside Africa? It seems that M and N branched out from India to all directions. I do not understand why part of L3 branch in Africa got out of Africa to a region with similar climate but changed differently. How do you prove that L3 in Africa was not a daughter branch of M or N? "maternal eve" is very arbitrary to me.

Joyce said...

"Genetic clock" has been partially based on assumption that humans and chimps diverged about 5 mya and now it seems more like 10 mya according new fossils. The clock should have been questioned long ago because humans have been mutating fast compared to chimps by the clock. Some pro OOA commenters seem to agree that OOA was earlier than previously thought, but then back again. Well, Africa is not every tribe's safe house and the tribe could just go back when it got tough outside even if the tribe was anywhere near the "door". Humans left Africa earlier (if OOA true) and already established significant population before last glacial (around 120,000 kya)and the "bottle neck" was from the wild climate swings. Earlier OOA and back flow would make the "maternal eve" more arbitrary and ice age related southward movement no doubt would have triggered fight and population replacement.

eurologist said...

Again I would like to remind everyone that besides the genetic evidence, it is important to look at both the archaeological (fossil) and paleoclimate record. We know that late African erectus (ergaster) is very similar to European erectus, and evidence suggests that heidelbergensis evolved from the European branch, and Neanderthal from that - but most likely not without exchange with Africa (there are continuing transcontinental anatomical resemblances). I have to find the mtDNA paper that seemed to suggest Neanderthal mtDNA is much closer to AMHs than Denisovan's (heidelbergensis?) is - which could indicate one such admixture event from Africa around 400,000 - 450,000 ya. Remember that the corridor between SE Europe / SW Asia and Africa is open every ~50,000 - 100,000 years, with sporadic longer interruptions. So, I would have no problem with the idea that AMH's ancestor derived from that interaction of these groups - but with the reservation that after about 300,000 ya there was little to no interaction, and from ~230,000 - 190,000 there were very good living conditions for humans in many parts of Africa, while just thereafter conditions were horrible in Europe and parts of SW Asia. To me, that indicates that most likely AMHs started to thrive in Africa during this time period, and any more modern humans not resembling Neanderthals, heidelbergensis, or erectus didn't make it in that corner area or anywhere else ooA.

Next, stone tools, fossils, and the climatic record tell us that AMHs with tools similar to those in the Nile region again lived in SW Asia, some time 125,000 - 100,000 ya, during a climatically favorable period. To me, the most pressing question is, can we find genetic evidence of this (early or perhaps only, after ~300,000 ya) ooA in current ooA populations, keeping in mind that DNA timing estimates are often 20%-30% off, sometimes even by a factor of two or more (too short)?

Keep in mind that an ooA after ~100,000 ya is almost impossible until ~50,000 ya, due to strong climatic difficulties, while AMHs suddenly appear in Australia, the Levant, and in or close to Europe and Siberia ~50,000 ya. There is absolutely no way that a few thousand people migrate out of tropical Africa and conquer almost the remainder of the world with all its different climate zones and different habitats, fighting off well-adapted "natives," in a very few thousand years, developing the technologies required to cross deserts, high deserts, high mountains, broad rivers and ocean passages, and the tundra all the way to Australia and the arctic sea.

terryt said...

"I have to find the mtDNA paper that seemed to suggest Neanderthal mtDNA is much closer to AMHs than Denisovan's (heidelbergensis?) is - which could indicate one such admixture event from Africa around 400,000 - 450,000 ya."

Not necessarily so. If the Neanderthal/Modern line split from Denisovan outside Africa it could well be that the split between Neanderthal and modern was the result of the modern ancestor having moved into Africa. It doesn't automatically mean the split was the result of Neanderthal ancestor having moved out of Africa.

"There is absolutely no way that a few thousand people migrate out of tropical Africa and conquer almost the remainder of the world with all its different climate zones and different habitats, fighting off well-adapted 'natives,' in a very few thousand years, developing the technologies required to cross deserts, high deserts, high mountains, broad rivers and ocean passages, and the tundra all the way to Australia and the arctic sea".

Correct. That has always been a problem for the recent OoA theory.

Poise & Pen said...

There's nothing blocking off Africa today I don't know where on earth people get such crazy ideas. You can walk from the tip of south africa all the way to norway without spending much time, taking a coastal route. And that is in one person's lifetime, not over thousands of years. And this is a very warm period where things would be the least accessible. People do exactly that and migrate all the way from subsaharan africa even today!

It also doesn't take millions or thousands of people moving. Ultimately it only requires two. Two is enough to completely replenish the whole population of earth so long as there are no hard and fast population limits to contend with.

So out of africa is very possible in that respect, with no limitations on time. That is not really what the theory is about, though. The idea is that some magic advantage evolved, generally believed to be speech. Since that is out the window now because of genetics and since it seems there's tons of other hominids in the human line it would seem this idea is completely wrong.

terryt said...

"Ultimately it only requires two. Two is enough to completely replenish the whole population of earth so long as there are no hard and fast population limits to contend with".

Not so. The problem with inbreeding depression would become an extremely limiting factor. In fact outbreeding seems to have considerably helped human migration outside (and within) Africa.

"The idea is that some magic advantage evolved, generally believed to be speech. Since that is out the window now because of genetics and since it seems there's tons of other hominids in the human line it would seem this idea is completely wrong".

Agreed.

Poise & Pen said...

As I said already, a bottleneck is required to cause problems. A bottleneck is not a population reduction but an upper limit. Without the upper limit there is no bottleneck.

If you put 1000 people onto an island that can support just 1000 people then over time they will die out due to inbreeding issues. Whether you put two or two million onto the island initially doesn't matter, it's the long term drift that causes genetic problems.

If you put 1000 people onto Africa or Eurasia in good conditions then the upper population limit is so gigantic that this won't come into play at all. That's what a founder effect looks like - a whole large population that looks very much like some tiny population.

Ironically Out of Africa argues the opposite, it argues for a drift scenario where the differences in people today come from genetic drift from a common original population. Somehow people came to eurasia and were kept in small bottlenecked populations for a great deal of time before they really did much settling. Which is more or less the opposite of what you would expect in that situation, or what most people think of when they talk about Out of Africa.

eurologist said...

Well, (one of) the paper(s) on mtDNA estimates a TMRCA of 400,000 to 800,000 ya and is:

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing; Richard E. Green at al., Cell, Volume 134, Issue 3, p416–426, 8 August 2008


and now we have a paper on y-DNA with a similar time estimate (450,000 to 800,000 ya)

http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7
http://www.cell.com/ajhg/pdfExtended/S0002-9297%2816%2930033-7

terryt said...

I think the information has been available for some time now to place the modern/Neanderthal split at around half a million years as a working date. These papers bear that date out very well. I also think we have a fairly reliable date for the modern/Neanderthal and Denisovan split at around one million years.