Wednesday, May 1, 2013

Some Important Open Issues In Human Prehistory

1. When and where did Neanderthal admixture take place?

One, two and three admixture event scenarios are all plausible (and, of course, more complex scenarios are also possible).

The simplest model assumes that admixture took place ca. 100 kya to 75 kya at a time when the archaeology shows the two species overlapping in the Levant and the effective population size would have been smallest, and not thereafter. But, this would mean that a schism into West Eurasian and East Eurasian populations would have had to happen very early on to prevent the admixed Neanderthal genes from coming closer to fixation between the proto-West Eurasians and proto-East Eurasians than differences in which Neanderthal genes are found in each population reflect.

Another one admixture model puts the date closer to 50-75 kya when the modern human population is at a post-Toba low point after an initial Out of Africa surge, perhaps in an Arbian or Persian Gulf refugium. This reduced effective population size, and allows for a sustained period of declining population during which genetic drift can loose some of the Neanderthal inheritance and give rise to Founder effects not likely to be seen in a rapidly expanding population that has reached fixation.

In a simple two event model, West Eurasians and East Eurasians split before admixture takes place and Neanderthal admixture takes place in parallel processes that produce similar overall levels of admixture in each clade of Eurasians in different places - perhaps one in Anatolia, and another in Arabia, Persia or South Asia. This also has the virtue of driving down effective population sizes in each source population.

A three event model combines these two models, which some admixture taking place early on and pre-schism and some taking place later in parallel.

An example of a more complex model would be one with a common admixture event, additional East Eurasian admixture, and then additional West Eurasian admixture that is diluted in the Upper Paleolithic to Neolithic transition by West Asian populations that did not experience the additional West Eurasian admixture experienced by Europeans with prolonged co-existence with Neanderthals.

2. Were there cases of archaic admixture in Africa?

Preliminary population genetic analysis and possibly one Y-DNA haplogroup A00 that looks older than the species make this look plausible and may have happened in two or three separate cases there quite recently.

The case for Neanderthal and Denisovan admixture where observed is in my opinion rock solid and not adequately explained by any other mechanism (such as deep population structure in Africa within modern humans).

The window of time in which additional non-African, non-Neanderthal, non-Denisovan admixture could be discovered in modern humans alive today hasn't completely closed but is well on its way to doing so. It is quite clear that this isn't present outside modern relict populations of Eurasia and the Americas.

3. It is clear that there was a major modern human population genetic transition in Europe between the Upper Paleolithic and the early Iron Age. How much of this transition in any given part of Europe took place:
* during the Mesolithic era on the eve of the Neolithic revolution;
* when the first farmers arrived with the Neolithic revolution;
* in the mid- to late Neolithic (i.e. the Copper Age and early Bronze Age);
* in the early Iron Age.

Two subquestions here are particularly unclear.

First, were Y-DNA Haplogroup R1b and mtDNA haplogroup H, respectrively which expanded from Iberia during the Neolithic era and Bronze Age indigeneous haplogroups in continuity with the Paloelithic era, or did they arrive with folk migrations in the Mesolithic, the early Neolithic, or the Bell Beaker people?

Tenatively, I favor an arrival of R1b predominantly with the Bell Beaker people, and an arrival of mtDNA haplogroup H in Iberia mostly in the Mesolithic or with the Bell Beaker people. But, there is no ancient Y-DNA evidence old enough to definitively resolve the question, mutation rate based dates are too uncertain to resolve the issue, and the ancient mtDNA evidence is thin. Publically available data from France on this point is particularly thin.

Second, what were the relative contributions to the expansion of Y-DNA Haplogroup R1b and mtDNA haplogroup H, respectrively which expanded from Iberia during the Neolithic era and Bronze Age of the first farmer early Neolithic megalithism culture and the Bell Beaker expansion?

I suspect that R1b and H expansions in Western Europe are predominantly Bell Beaker rather than Megalithic, but the eivdence is not yet secure enough to be sure.

This goes hand in hand with the question of whether the Bell Beaker expansion gave rise to language shift from previous languages of the first farmers of that region. I suspect that it did, but resolution of this prehistoric genetic question would go a long way towards shoring up or undermining that assumption.

On the other hand, many points are fairly settled.

In my mind, there is increasingly little reason to doubt that linguistically Indo-European didn't arrive in Western Europe until at least the Urnfield culture, and that prior to that point almost the entire maximal range of Bell Beaker influence had at some point been linguistically Vasconic.

In my mind, it is all but settled that the Indo-European Iron Age tweaks to the gene pool of Western Europe were quite modest.

It is also likely all but settled in my mind that mtDNA H was at the very least confined to far Southern regions in Europe until the Neolithic at the earliest, and that mtDNA H bearers did not participate materially in the repopulation of Europe immediately after the retreat of the glaciers after the Last Glacial Maximum. This in turn implies that this was probably not an important mtDNA component of refugia populations that participated in this repopulation and were probably rare in, or absent from Southern Europe until at least the Mesolithic (e.g. as a pilot wave from the Fertile Crescent and vicinity in advance of the first farmers on the eve the Neolithic revolution).

4. What were the geographic and archaeological culture sources for the first wave Neolithic populations of Europe and the Bell Beaker peoples?

Modern Europe is to a crude approximation a composite of a West Asian, Mediterrean and Northeast Asian signal. New ancient DNA data from Central Europe makes it an unlikely Bell Beaker source population. A region roughly stretching from the Balkans to Anatolia to the Caucasus to the Zargos Mountains and Western Persia to the remainder of the Fertile Crescent are the most plausible candidates. But, some of these areas are blanks in the ancient DNA map, we don't have a perfectly solid sense of how the ancient populations of these regions differed from the modern ones other than to be forewarned that there has been a lot of historic and late prehistoric era population. It is also possible that at least one signal from a first wave Neolithic population (most likely the LBK) has been so obscured that it can no longer be distinguished from noise in modern populations.

The emerging notion of LBK as "the Neolithic revolution wave that failed" is looking more plausible.

Data from the Ukraine, Central Asia and Iran are particular thin.

5. Are the outlier dates for modern humans in the New World from 20,000 years ago and older valid or not?

There is good reason to scrutinize this data as explained in a previous post, but the evidence is what it is and if there is really no methodological flaw then we have to explain it. The possibility that outlier sites could represent archaic hominin populations that made the trip before modern humans but left a very modest footprint because their lithic technology was less advanced and they were less ecology distrupting top predators is particularly intriguing if the evidence becomes strong enough to force us to fit the theory to it.

6. What archaic hominin species is Denisovan DNA associated with?

Denisovan DNA was found in a Siberian cave. Denisovan admixture is found from roughly the Wallace line and beyond. At least two know archaic hominin species were present in between: Homo Erectus, in most of that region, and Homo Florensis on Flores and perhaps a couple of neighboring islands only. Theories about the existence as a separate species and range of Homo Heidlebergus is also sketchy.

There is no solid indication of Neanderthals beyond South Asia, but they aren't entirely ruled out, particular via a Northern route to the Denisovan cave. Some clade analysis of the Denisovan DNA suggests a clade shared with Neanderthals apart from Homo Erectus.

7. When did modern humans make it from South Asia to Southeast Asia?

The window admitted by archaeology is approximately 100,000 years ago to 45,000 years ago, with a time frame of 65,000 to 75,000 most strongly favored by the evidence, but not very conclusively established.

8. How many waves of mass migration were there to Asia in the Upper Paleolithic and when did they take place?

There is little evidence of prehistoric mass population genetic transfer between East Eurasia and West Eurasia (with a couple of notable exceptions, e.g., for Uralic populations and in the case of mtDNA haplogroup X) prior to the historic era after this initial first order split of Eurasians after leaving Africa.

The data is probably a better fit to several waves of pre-Neolithic migration, rather than just one (although the major Neolithic waves need to be understood to parse the earlier waves from the genetic data). But, the timing and paths of these waves is subject to reasonable dispute.

9. How did Homo Erectus go extinct?

While the evidence is very thin indeed on this point, extinction due to warfare and/or inability to complete for food and territory with modern humans upon first contact, outside of Flores where a cooperative mode emerged, possibly boosted by the Toba erruption or a climate shift seems most plausible.

10. When, if ever, did Homo Florensis go extinct?

The earliest possible date for the extinction is about 10,000 years ago, which is the date of the oldest skeletal evidence, but there is good reason to think that they persisted even after first contact with Europeans and that there may even be a tiny population of this species extant on one known part of one Indonensian island.

11. Is the Inuit language linguistically related to the Uralic languages as part of a transpolar language family?

There is some scholarly evidence to suggest that this might be the case, but it is not widely accepted at this point.

12. Was the Na-Dene a separate migration wave to the New World separate from the Paleo-Eskimo Dorsett, or do they represent admixture of Dorsett and first wave indigeneous American populations?

Historically, these have been treated as two separate post-first wave indigeneous population events, but some suggestive ancient DNA analysis points to collapsing them into one wave. This population is the only one strongly linked to an old world Paleo-Siberian population lingustically to date.

13. To what extent can known historical cultures of the New World in the last several thousand be properly said to be derived from each other? What is the sequence of historical cultures in North America?

There is accumulating evidence that a lot of separate archaeological cultures in the New World can all be traced back to an early one near Monroe, Louisiana.

14. What are the linguistic origins of Japanese?

The Yayoi people came from Korea and the evidence strongly favors one of the languages of Korea at about that time as a source, but there is not agreement on which one. There is likewise dispute over whether Korean and Japanese languages are related to the Altaic languages with some evidence, particularly statistical analysis of lexemes, favoring that position.

15. Is the Dravidian language family indigeneous or did it have an outside source, and if so which one?

Multiple theories exist. I tend to favor an Afro-Dravidian hypothesis with a source language not that different from early Swahili, although distinct from it. This is because the South Asian Neolithic involved a heavy component of Sahel African crops. Some archaeological evidence suggests that it could be that these crops were brought to South Asia, domesticated by the Harappans or related populations, and then returned to Africa.

16. How did Y-DNA haplogroup T end up in the western EASTERN part of South Asia?

This distribution is suggestively similar to the expansion of the Dravidian language and South Asian Neolithic. But, the resolution of the Y-DNA haplogroup T data collected so far is not high enough to discern its source (and possibly with it a source for Dravidian crop transfer).

11 comments:

terryt said...

"Tenatively, I favor an arrival of R1b predominantly with the Bell Beaker people"

I've come to that conclusion too, after long assuming R was Paleolithic. I see Maju is claiming a pre-Neolithic presence of R1b1a2a1a1b-S116 in Iberia but note its long series of numbers and letters and so its very downstream nature. And its spread coincides reasonably well with megalithic distribution. The other widespread European R is R1b1a2a1a1a-U106 which to me looks perhaps part of Indo-European's spread into Europe. Both are relatively recent into at least Western Europe I suspect.

"mutation rate based dates are too uncertain to resolve the issue"

I agree. But Dienekes has listed R1b1a2a1a1a5-S264 at 6500-7000 years. Fits.

"there is increasingly little reason to doubt that linguistically Indo-European didn't arrive in Western Europe until at least the Urnfield culture, and that prior to that point almost the entire maximal range of Bell Beaker influence had at some point been linguistically Vasconic".

Agreed. I suspect that Indo-European was first spread by R1a haplogroups, but the language spread far beyond the haplogroup expansion.

"The possibility that outlier sites could represent archaic hominin populations that made the trip before modern humans but left a very modest footprint because their lithic technology was less advanced and they were less ecology distrupting top predators is particularly intriguing if the evidence becomes strong enough to force us to fit the theory to it".

Those archaic Americans may have comprised such a small gene pool that inbreeding prevented expansion, or perhaps even their eventual extinction. It was only with the arrival of greater numbers that the population was able to expand considerably and leave its mark on the environment. There is evidence for something similar having happened in New Zealand with evidence of man-induced fires perhaps a thousand years before the definite evidence of human arrival. By the way, have you seen the paper regarding colonising numbers in Australia? Here it is:

http://www.nature.com/news/first-australians-may-have-been-migrants-rather-than-drifters-1.12865

One thousand people. Not accidental arrivals.

"There is no solid indication of Neanderthals beyond South Asia"

As far as I'm aware there is actually no evidence for Neanderthals anywhere within South Asia apart from some disputed presence in the far northwest.

"How did Y-DNA haplogroup T end up in the western part of South Asia?"

I strongly suspect it originated there. It is 'brother' to L which is definitely a South Asian haplogroup.

"How did Homo Erectus go extinct?"

I think that technically it didn't become extinct. Collectively we probably have many genes picked up by 'modern' humans as they passed by and mixed with Homo erectus populations.

terryt said...

At the risk of annoying you as much as I annoyed Maju I'd like to draw your attention to this little gem:

http://cuevadelapileta.blogspot.co.nz/2013/05/clues-to-southeast-asian-civilisation.html

Maju will hate it because:

"The discovery tells us that the Con Co Ngua people are likely descendants of the original colonisers of Southeast Asia and Australia. In fact, putting flesh back on their bones would reveal people that looked a lot like modern day indigenous Australians and Melanesians".

What maju got most annoyed with me about was my insistence that the 'Mongoloid' phenotype of modern SE Asians is the product of later movement into the region. He doggedly maintained the Mongoloid phenotype was indigenous to the region. But here we have research showing that the 'Melanesian' phenotype survived in North Vietnam until at least 'sometime between 5,000 and 6,000 years ago'.

andrew said...

The methods in the nature.com article are very flimsy and make important unreasonable assumptions (e.g. population bust from LGM, steady rate of growth otherwise rather than logistic curve, assumption of linear relationship between tool production and population), and the haplogroup evidence of Papuans and Aboriginal Australians just screams out for tiny population sizes. A hundred is probably close to the mark (and the notion that you can fit an exponential equation over 1,550 generations with the requisite level of precision to get a factor of ten right when the number of generations itself is probably variable to +/- 100 generations or so, is absurd.

Re: Y-DNA haplogroup T - it is Eastern South Asia, not Western, which is why it is so odd. You see it in Mesopotamia, Ethiopia, early Neolithic Europe, Semitic populations in Africa, and eastern South Asia - hopping over an L region. It is probably Mesopotamian in origin and doesn't belong in the high frequency geographically tiny area where it is found unless it is a recent arrival.

I am defining extinct to mean "cease to exist as a separate species if the resulting species is predominantly the other part of the hybrid." Also, it doesn't appear that there was any admixture in mainland Asia where most H. Erectus must have lived. They went completely extinct in most of their range.

terryt said...

"the haplogroup evidence of Papuans and Aboriginal Australians just screams out for tiny population sizes".

That is not entirely correct. Australia has two basal M haplogroups (M14, M15) as well as the derived M42a, four basal N haplogroups (N13, N14, S and O) as well as one basal R haplogroup (P) and the derived R haplogroup R12. Although New Guinea has no basal N haplogroups it has three entirely different basal M haplogroups (M27, M28 and M29'Q) as well as R14 (shared with the Lesser Sunda Islands) and several P-derived haplogroups (presumably from Australia). That doesn't exactly 'scream' tiny population sizes, especailly not for Australia.

"Y-DNA haplogroup T - it is Eastern South Asia, not Western"

Are you sure of that? I used to be convinced it was so but now I'm not so sure. The reason I originally thought it was so is because at that time it was still part of what is now called MNOPS, which is definitely from east of South Asia. But now it has been shown to be separate I accept it formed along the route from Africa to SE Asia.

"and doesn't belong in the high frequency geographically tiny area where it is found unless it is a recent arrival".

I think it is certainly a recent arrival, in the sense of around 10-12,000 years ago, through much of the western regions where it is found today.

"it doesn't appear that there was any admixture in mainland Asia where most H. Erectus must have lived. They went completely extinct in most of their range".

I actually believe our evolution has been far more complicated than the simple story usually presented.

andrew said...

Re Y-DNA T see the maps here: http://dispatchesfromturtleisland.blogspot.com/2011/10/evidence-regarding-dravidian-linguistic.html

terryt said...

Very interesting comments about Y-DNA T. Perhaps it did coalesce further west along the route to SE Asia than I have so far considered likely. That would place JT as forming around the Anatolian plateau, LT somewhere in southern Iran and MNOPS in SE Asia. But that leaves South Asia suspiciously blank, only F haplogroups.

andrew said...

FWIW, I think that LT probably has Mesopotamian origins with L breaking off from T with the proto-Harappans and the T staying in Mesopotamia and then expanding from there with early Neolithic expansion.

terryt said...

"6. What archaic hominin species is Denisovan DNA associated with?"

I don't know if you've noticed John Hawks' latest post, but just in case you haven't here it is:

http://johnhawks.net/weblog/reviews/denisova/biology-of-genomes-pennisi-update-2013.html

Some interesting aspects:

"And the comparison revealed another surprise: Four percent of the Denisovan genome comes from yet another, more ancient, human—'something unknown,' Pääbo reported".

So we have yet another ancient Homo species that could interbreed at least with another species that could interbreed with 'modern' humans. In fact the whole thing gets even more complicated:

"With all the interbreeding, 'it's more a network than a tree,' points out Carles Lalueza-Fox"

On another matter, that Maju gets extremely worked up about, this article on mammoth extinction was published in a local paper recently:

http://www.nzherald.co.nz/world/news/article.cfm?c_id=2&objectid=10884722

Quote:

"Among late-surviving mastodons he has studied, Dan is finding examples of females losing calves (where one pregnancy is immediately followed by another, rather than by two years of lactation) and of males going into musth early (just as young bull elephants do in Africa, when mature males are poached out). Dan had also found examples of mammoths dying in the autumn, a time of year when they should have been in peak condition. Autumn deaths argued for an extrinsic cause of death. For Dan, all this could be pinned on one such cause: overhunting by humans".

Note: 'just one cause'. I dare you to bring this to Maju's attention!

terryt said...

Sorry. I left this bit out:

"But it's hard to argue from those isolated cases that humans were responsible for wiping out entire species. Far from rampaging across the continent, killing every large mammal in sight, it seems ancient hunters may have had a more subtle, but no less terminal impact. Over thousands of years, the level of hunting was just enough to be unsustainable for these huge, slow-breeding behemoths of the ice age".

andrew said...

Whether the mechanism was directly due to overhunting of megafauna or was more subtle and indirect, it is very hard to argue I think with the overwhelming circumstantial evidence pointing to the arrival of modern humans as the proximate cause and tipping point of megafauna extinction. The fact that it occurs in both continents of the Americas, in Northern Asia, in Australia, and in New Zealand, all very close in time to the arrival of modern humans and that almost every single one of dozens of species of megafauna go extinct at this moment of first contact in each of these places, despite the timing of first contact being different in different places, argues very strongly for modern human arrival being the tipping point. And, the fact that megafauna faired better in Africa and South and Southeast Asia where contact with archaic hominins may have "inoculated" local megafauna by allowing them to co-evolve with hominins is a case of the exceptions proving the rule.

Re the Denisovan admixture with yet another unknown archaic hominin species (i.e. not modern human and not Neanderthal), this really is exciting and mysterious. Fitting two non-Neanderthal, non-modern human archaic species into Eurasia (presumably pre-OOA), is not an easy task. I am inclined to think that one of Asian H. Erectus (probably Denisovan) and the only other real candidate I can come up with as the second archaic hominin species would be H. Ergaster (sometimes called African H. Erectus and believed to be ancestral to all known Eurasian hominin species), or Homo heidelbergensis aka Homo rhodesiensis which was antecedent to Neanderthals in essentially the same range and were probably antecedent to modern humans in Africa. There is no attested instance of H. Ergaster outside Africa, although arguably this is due to geography influenced taxonomy since not everyone agrees that H. Ergaster and H. Erectus are the same species.

If Denisovans are a late evolutionary phase of H. Erectus that first admixed with H. Heidelbergensis to the west of their range and then late admixed with Neanderthals who replaced them to the west of their range (at least amongst N. Asian Denisovans) (with H. Flores being a pygmy species of H. Erectus due to island dwarfism that probably lacked Neanderthal or H. Heidelbergensis admixture), then you start to have a pretty coherent story.

The plot would really thicken if the trace unidentifical archaic admixture in the Denisovans and the trace archaic admixture in either certain Khoisan or certain pygmies in Africa were a match - pointing strongly to the possibility that there were relict populations of H. Heidelbergensis both in and outside Africa through the Upper Paleolithic (with the other of the two separate unaccounted for archaic admixture in African populations possibly being a trace of H. Ergaster (I'd guess Ergaster for the Khoisan and Heidelbergensis for the Pygmies in light of the probably archaic admixed Y-DNA haplogroup found in West Africa near Pygmy territory and based on the need for Heidelbergensis to be closer to Eurasia than Ergaster - also we know that Ergaster's range extended to Southern Africa based on fossil evidence but have no evidence of Ergaster in jungle settings - perhaps due to preservation conditions, but perhaps because they never lived there). If H. Heidelbergensis evolved north of the Congo and never migrated to Southern Africa, then H. Ergaster would be the most evolved archaic hominin species in Southern African upon first contact with modern humans and might have survived for some time as a relict population in marginal environments that the Khoisan would eventually themselves being pushed into.

terryt said...

"it is very hard to argue I think with the overwhelming circumstantial evidence pointing to the arrival of modern humans as the proximate cause and tipping point of megafauna extinction".

Exactly. It is possible to claim alternative causes for individual cases but considered as a whole the evidence is pretty compelling.

"Fitting two non-Neanderthal, non-modern human archaic species into Eurasia (presumably pre-OOA), is not an easy task".

I don't see a problem there. After all Denisovans and Neanderthals were very close neighbours, leaving a considerable amount of Eurasia for other species.

"the only other real candidate I can come up with as the second archaic hominin species would be H. Ergaster (sometimes called African H. Erectus and believed to be ancestral to all known Eurasian hominin species)"

My vote goes towards an East Asian separate species, perhaps descended from 'Pekin Man'. When the information on the EDAR370 variant came out the authors suggested one possibility was introgression from some unknown East Asian species as well as a possible mutation within Homo sapiens. I thought the former scenario quite likely.

"If Denisovans are a late evolutionary phase of H. Erectus that first admixed with H. Heidelbergensis to the west of their range and then late admixed with Neanderthals who replaced them to the west of their range (at least amongst N. Asian Denisovans) (with H. Flores being a pygmy species of H. Erectus due to island dwarfism that probably lacked Neanderthal or H. Heidelbergensis admixture), then you start to have a pretty coherent story".

Possible. But I think you are hugely influenced by your desire to fit the Australasian Denisova genetic trace with SE Asian Homo erectus. At this stage we have no evidence at all that SE Asian H. erectus had any significant genetic connection to Denisovans in the Altai. That is a huge distance and for most species with the apparent limited mobility of pre-modern humans would be sufficient to give rise to separate species. The distance involved certainly seems sufficient to have given rise to separate species within other genera.