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Saturday, May 30, 2015

Another strange paper from the Wellcome Trust


I often don't agree with what Greg Cochran has to say (for instance, see here). However, his last post, a damning critique of the recent Pagani et al. paper on the Out of Africa exodus, was simply awesome:

I’ve been complaining about researchers being too narrow. This article is a spectacular example. But it’s not just the lead author: everyone whose name is on the paper must be assumed to be equally ignorant and incurious – as well as the reviewers, and editors, and for that matter anyone who doesn’t stay up all night laughing at them.

This is actually the second paper in only a matter of weeks from Wellcome Trust scientists that defies reason. Last month Ayub et al. claimed that the Kalash people of the Hindu Kush were an ancient north Eurasian population isolated from their neighbors for ~12,000 years. Check out my befuddlement here.

75 comments:

Krefter said...

I'm going to send them my Dogs DNA, and see what they say. Maybe they can tell us the route humans took out of Africa.

truth said...

It's so bad to mix politics with science. I mean, they are pretty much agreeing with Afrocentrism (Ancient black egyptians until the arab conquest).

Hélio de Vasconcelos said...

Afrocentrists must be having the day of their lives. Big party ensues!

ZI Alt said...

Huh? They say "We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes...".

They also point to the modern Egyptian admixture results as being diluted from a number >80% down to 80% with a recent (750ya) influx of African genomic material in Table S2 and more directly with ref.14 - "These sub-Saharan ancestries appear to be a recent introduction into North African populations, dating to about 1,200 years ago in southern Morocco and about 750 years ago into Egypt, possibly reflecting the patterns of the trans-Saharan slave trade that occurred during this period".

Not much cause for afrocentric celebration there, unless they are illiterate...big party ensues!

Roy King said...

You guys are meshuga in your obsession about "race". The article merely tests a hypothesis about whether "Out of Africa" passed through Egypt or directly from Ethiopia. It has nought to do with outmoded 19th century racial classifications. The article should stand or fall based on the reasonableness of its conclusions from its data. Grow up!

capra internetensis said...

It is pretty underwhelming, but if you look at the references they don't seem to be proposing any kind of wild Afrocentric scenario.

They note that the "affinity of the Egyptian African component with the modern East and West African populations could be due to either a continuity of human presence in the area or recent gene flow from neighboring African regions resulting from demographic processes and slave trade over the last two millennia." The reference for this sentence is a Lancet article about sickle cell disease, which states that the sickle cell haplotype found in North Africa originates in Benin and is thought to have arrived from West Africa via the slave trade. (Kind of an odd choice.)

The reference for the admixture date of Egyptians 750 years ago (Henn et al 2012) ascribes it to the arrival of sub-Saharan ancestry into Egypt at that time, primarily Maasai-like (Nilotic), with a small Luhya-like (Bantu) contribution.

This new paper is really a refinement of an analysis from Pagani's 2012 study on Ethiopia. In that one they mention that "the 'African' component of the Ethiopian genomes may also result in part from recent migrations into Ethiopia from other parts of Africa, a possibility that we have not examined here."

So I don't think they are unaware of the complications, they just don't seem to be addressing them.

Krefter said...

@Roy Kind,
"The article merely tests a hypothesis about whether "Out of Africa" passed through Egypt or directly from Ethiopia. It has nought to do with outmoded 19th century racial classifications."

I agree. People assumed the authors were assuming modern Egyptians come mostly from Arab conquest.

Davidski said...

Look, what they're basically saying is that if they mask the Eurasian segments in an Egyptian's genome then they'll be looking at genetic variation in Egypt going back 60,000 years or so.

This is idiotic.

Maju said...

I an also skeptic (the article is poorly written and does not go to any depth in the explanation of the analysis performed, so I thought: this is hard to accept unless they write it all over and explain properly, preferably supporting it with some haploid genetics if possible) but the criticisms I read here are bad.

Let's assume that effectively the Egyptian "African" genetic component is "recent", or at least partly so. How does it matter the actual geography of this component at the OoA IF they are still right on that Egyptian-African component being closer to Eurasianness than the Ethiopian-African one? IF they have actually discovered that, it is important in itself, regardless that the component(s) might have originated in other parts of Africa, like Sudan maybe.

What I question is that they fail to demonstrate that altogether, that the demonstration is not convincing, that the choice of reference population (only one?) for "Africanness" is meaningless, and that they do not even bother explaining their method well enough to result convincing and that they do not address the issue of haploid genetics, which IMO is much more clear-cut when it comes to such deep ages (and rather seems to favor an Arabian route if anything).

But I did find the Kalash paper convincing instead. The methodology was better and so was the exposition.

Lemniscate said...

I agree with your analysis of the paper. However, please don't refer to these papers as coming generally from the 'Wellcome Trust'. They have come from Chris Tyler-Smith's group at the Wellcome Trust Sanger Institute at Hinxton in Cambridgeshire. There is another Wellcome Trust genetics institute at Oxford, the Wellcome Trust Centre for Human Genetics, which had nothing to do with these papers.

Davidski said...

Okay, thanks, I'll make a note of that.

andrew said...

Worth noting that this is basically a four component comparison:

The Levant, South Arabia, Ethiopia and Egypt are compared. The analysis assumes that if (Levant - recent admixtures) is closer to (Egypt - recent admixture) than (South Arabia - recent admixture) and (Ethiopia - recent admixture) then Sinai migration, else Gate of Tears migration.

But, the continuity problems that are particularly obvious in Egypt are also present in the other three regions at that time depth.

One thing we know about the population genetics of the Out of Africa population(s) that is (are) ancestral to modern Europeans is that it (they) had a couple of clades of mtDNA L3 (which are called mtDNA M and mtDNA N) that are sister clades to the other basal L3 clades (L3a, L3b'f, L3c'd'j, L3e'i'k'x, L3h) all of which have strong ties to East Africa and/or Ethiopia, but only a couple of which have ties to Egypt, often restricted to secondary branches of those clades.

We also know that the most of the predominant Y-DNA and mtDNA clades of Southern Arabia are highly derived in phylogenies with likely roots outside of Southern Arabia.

So, the ancestors of modern Eurasians were probably more like modern Ethiopians than modern Egyptians in mtDNA, and Southern Arabians are probably a near total replacement of the first modern humans to live there. But, we don't know enough from modern DNA data at all to say anything intelligent about the route taken.

Krefter said...

@Andrew,
"that are sister clades to the other basal L3 clades (L3a, L3b'f, L3c'd'j, L3e'i'k'x, L3h) all of which have strong ties to East Africa and/or Ethiopia"

So, is Ethiopian's African mtDNA and Y DNA closer in relationship to Eurasians than other Africans? I know Ethiopians are Eurasian-admixed, so I'm talking about their non-Eurasian lineages.

Kristiina said...

Last week I checked Eurogenes K12 results of Yemenites and Egyptians. Here is a new comparison with Amharas with some K10 results added.
Egyptians
Transcaucasian 0.27-0.32
Northeast African 0.25-0.32
EEF-WHG 0.25-0.31
Sub-Saharan 0.06-0.11
Pygmy 0.00-0.02

LBK 0.42-0.47 (K10)
Euro Hunter Gatherer 0.00-0.03 (K10)

Yemenites
Transcaucasian 0.22-0.31
Northeast African 0.25-0.32
EEF-WHG 0.18-0.22
Sub-Saharan 0.08-0.24
Pygmy 0.01-0.03

LBK 0.32-0.46 (K10)
Euro Hunter Gatherer 0.00-0.01 (K10)

Amhara Ethiopians
Transcaucasian 0.04-0.14
Northeast African 0.49-0.55
EEF-WHG 0.03-0.12
Sub-Saharan 0.17-0.24
Pygmy 0.05-0.13

LBK 0.08-0.17 (K10)
Euro Hunter Gatherer 0.00-0.02 (K10)

Egyptians have very little Sub-Saharan and Pygmy! Instead, they seem to consist in three components in equal shares: Transcaucasian, Northeast African and EEF-WHG. We would need ancient DNA from the Near East to sort out the relationship between EEF and Transcaucasian and their geographic origin. In any case, the share of LBK in Egyptians is even 47%! I would think that in part it is shared ancestry of first farmers and in part later Mediterranean contacts. I do not think that Northeast African component is a result of slave trade, but it must be an autochtonous component in Egypt from the palaeolithic times.

Compared with Egyptians, Yemenites are slightly more African, but their LBK portion is still very high.

Ethiopians are clearly more African, but it means Northeast African, which must be the autochtonous component in the area.

Maju, do you know when and where there are archaeological cultures in Northern Africa that have their origin in the Near East (or Europe)?

The very old admixtures are even more interesting, e.g. if yDNA E and mtDNA L3 originated outside of Africa and if L3 is part of N. I hope we will be wiser in the future.

andrew said...

@ Krefter

The mtDNA evidence suggests that the Out of Africa basal Eurasian population(s) must have had origins in Ethiopia and/or East Africa, but doesn't tell us how they got from Africa to Eurasia, although geography and common sense gives us only two choices of route - the Gate of Tears or up the Nile and across the Sinai.

I think that it is likely that modern Southern Arabia and Egypt are totally unlike Upper Paleolithic Southern Arabia and Egypt in population genetics.

The archaeology strongly favors an association of the oldest archaeological remains in Arabia with contemporaneous Nubian complex archaeology in Africa around 100 kya to 130 kya, while still not providing definitive guidance on a route of travel. http://dispatchesfromturtleisland.blogspot.com/2012/10/evidence-mounts-for-out-of-africa-100.html

@Kristiina N is a subclade of L3. L3 is not a subset of N. L3 almost certainly originated in Africa, and the evidence strongly favors an African origin of Y-DNA E as well.

Mike Thomas said...

Andrew

I'd agree; but DE* probably arose in near East.

Kristiina

I'd need to get back to you about specific details of specific periods, but essentially North africa is a population sink. Fossil and archaeological data is scarce for the earliest AMH periods. Later on (eg Holocene) much of Egypt, eg, was scantily populated during fluctuations in rainfall.

This means multiple periods of local extinctions and re-colonization.

Kristiina said...

Andrew, two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ~106,000 years ago, so humans must have left Africa at least 110 years ago (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028239). The age of mtDNA L3 is only 70 000 which means that it could not have been in Oman at that time. According to this new paper, Egyptians and Ethiopians split from non-African populations 55,000 and 65,000 years ago, and according to Rieux et al. 2014 (http://mbe.oxfordjournals.org/content/31/10/2780.full), the U5 and U6 split is estimated at 50 000 years, i.e. that would be the time frame of a Eurasian back migration to Africa.

In practice, this would mean that Arabian mtDNA went extinct and a new migration followed c. 60 000 years ago, but it was very rapid as the age of mtDNA P in Sahul is 60 000 and U5 and U6 split only 10 000 years later, i.e the evolution L3-N-U-U5/U6 took only 10 000 years.

Of course, there are many uncertainties about age estimations but there are also uncertainties about the phylogenetic structure of haplogroups. It is true that I am not entirely satisfied with this dominant theory.

Ebizur said...

Kristiina wrote,

"The very old admixtures are even more interesting, e.g. if yDNA E and mtDNA L3 originated outside of Africa and if L3 is part of N. I hope we will be wiser in the future.

...

Of course, there are many uncertainties about age estimations but there are also uncertainties about the phylogenetic structure of haplogroups. It is true that I am not entirely satisfied with this dominant theory."

The generally accepted phylogeny of human mtDNA has N and M as separate branches of a greater L3 haplogroup, alongside other branches named L3a, L3b'f, L3h, etc.. According to several published papers that I have seen, it may actually be the case that some or all of the L3(xM, N) clades are more closely related to haplogroup M than they are related to haplogroup N (i.e. L3 would bifurcate into M'L3a'b'c'... vs. N as opposed to a multifurcation into M vs. N vs. L3a vs. L3b'f vs. L3h, etc.). I have never seen a phylogenetic tree in which this polytomy is resolved so that any L3(xM, N) clade might be more closely related to haplogroup N than to haplogroup M.

An M'L3a'b'c... vs. N bifurcation would dovetail nicely with my hypothesis regarding correlations between certain mtDNA haplogroups and certain Y-DNA haplogroups. On the basis of the modern distribution of these haplogroups, I have inferred that mtDNA haplogroup M'L3a'b'c... should originally have been associated with Y-DNA haplogroup DE, and mtDNA haplogroup N should originally have been associated with Y-DNA haplogroup CF.

Kristiina said...

Thank you Ebizur, I agree entirely with you! I hope that we will soon see papers, including ancient DNA, that tackle these issues.

Although M and N are still placed as sister braches, this graph is interesting in order to compare ages of M, N and several L branches.
http://mbe.oxfordjournals.org/content/31/10/2780/F1.large.jpg

Kristiina said...

Thank you Mike! I agree with you on multiple local extinctions and re-colonizations. However, am I right that at some point of time Sahara was much more hospitable than it is now, so when it dried up there must have been migrations around the area. Then, we have that Iberomaurusian culture in North Africa during the LGM.

Kristiina said...

Ebizur, now I go back to my comments last week when I was astonished to see the huge difference between continental Eurasians such as Ust Ishim and modern Near Easterners. To me, it looks like those Ust Ishim like Eurasians were harbouring yDNA K/C and mtDNA R haplogroups while it is possible that the so called Basal that was located in the palaeolithic Near East harboured yDNA E and mtDNA L3.

I am also hoping to see some ancient N that is not R popping up somewhere to clear the picture.

Mike Thomas said...

Kristiina

See
"Climate-Controlled Holocene
Occupation in the Sahara:
Motor of Africa’s Evolution"

"Desert Environment and Origins of
Agriculture in Egypt"

"The Nile Corridor
and the Out-of-Africa
Model: An Examination of the
Archaeological Record" by Philip Van Peer

"Out of Africa: from an Egyptian point of view". Pierre Vermeersch

Mike Thomas said...

another very interesting paper

http://www.antiquityofman.com/LatePleistocene_technocomplexes.pdf

Maju said...

@Kristiina: for whatever is worth, I run the 1000GP Egyptian sample vs. regional controls in January 2012. Both samples are from the Delta, although they are somewhat different from each other anyhow.

Their East African (Masai-like) component was around 10% (8.3% and 11.2%). Most other components are of West Eurasian affinity (estimated by Fst distance between the components). The exceptions are the "Berber" component (which in this run shows relatively low distances to the East African one but also to West Eurasian components, suggesting it represents a mixture) and a component labeled "Arab2", which shows very high Fst distances to everybody else and MIGHT be an OoA residue of the "Basal Eurasian" typology (would need independent confirmation). This "Arab2" component is very notable among Saudi Arabs (11.2%) and one of the Egyptian samples (11.8%) but not the other (2.8%). Notice that it cannot be Lazaridis' "Basal Eurasian" because it shows very low scores among Palestinians and Kurds (0.4-0.5%) or Spaniards as well (negligible).

Kristiina said...

Mike, thank you! I skimmed through the articles or read the abstracts.

When I look at the map of the Nubian Complex occurrences in Northeast Africa and Arabia, I see that the oldest site ”Sodmein Cave”, 119 kya, is very near Sinai, so one would postulate that people crossed over to Eurasia there, although with this I do not exclude Bab el-Mandeb exit. In fact, according to Wikipedia, Skhul Layer B has been dated to an average of 81,000-101,000 years ago with the electron spin resonance method, and to an average of 119,000 years ago with the thermoluminescence method.

In any case, Rose et altri note that ”As the late Nubian Complex at Aybut Al Auwal is dated to MIS 5c, slightly earlier than the late Nubian Complex in Africa, we remain open to the possibility that the late Nubian Complex originated in Arabia, and subsequently spread back into northeast Africa.”.

Maju, thank you for the complementary map. I agree with your interpretation, but there is also the yellow component that looks like a native Egyptian component. I understand that the c. 30% Northeast African component in Egyptians in Eurogenes K12 should correspond to the light blue Maasai component and the yellow Egyptian component together. The two green Saudi components are also interesting as they are not frequent in Palestinians, Turks etc. and are clearly more frequent in African groups. As you said, these components could harbour OoA elements but with ancient Eurasian admixtures. Then, I would also like to know when and in which archaeological context U6 arrived in Africa and what was the yDNA. It could also be related to these Saudi components.

In any case, people must have been crossing from Egypt to Asia and back for tens of thousands of years, so the prehistory of that area is far from simple.

Maju said...

"I would also like to know when and in which archaeological context U6 arrived in Africa and what was the yDNA".

Nobody knows for sure. The only thing clear re. U6 is that it is derived from U and hence from R and N, being necessarily of Eurasian origin. The mystery lays in two contradictory facts:

1. The UP arrived to Northeast Africa (but not yet to NW Africa) around the time it does to Europe, Central Asia, etc. Being therefore of West Asian origin most likely and hence a good candidate to carry Eurasian lineages like U6, X1, etc. In NW Africa however the first UP is of European origin most likely (Oranian or Iberomaurusian culture) and has a quite late date (LGM). So far there is nothing suggesting an UP arrival to NW Africa before these dates (only to Cyrenaica: Dabba industry, but not farther West).

2. U6 highest basal diversity is unmistakably in Morocco, next come Canary Islands and the Iberian Peninsula, as if to intently underline the "westernness" of U6 as a whole. Only U6a could have a more eastern origin (total or partial). BUT there is no precursor of U6 other than U itself, so it is totally unclear how the U6 founder got to Morocco.

One could well imagine a European route, as it makes archaeological sense, however another similarly Morocco-centered lineage, and with a distribution very similar to that of U6 (for example in the Western Iberian Peninsula), is Y-DNA E1b-M81, and this one does not look European or Eurasian at all but is clearly of African derivation. So question mark: open answer.

"It could also be related to these Saudi components".

The "Arab2" component is not found in NW Africa (they have another small component that also looks very old, very distant, but different from the "Arab2" one in my run, as this one does not show in NW Africans nor the old NW African one, Aterian?, shows up in Egyptians or Arabs - see: HERE). For whatever my runs are worth, these are two different ancient components showing up in different exercises, even if they do seem to have in common that they are very distant from everything else (Fst distances to other components that correspond to "intercontinental" values). In the case of the NW African one it might be Aterian residue (most common in Southern Morocco, where physical anthropologists have often spotted "pseudo-Khoisanid" tendencies in looks), in the case of Egypt and Saudi Arabia it might be OoA residue but hard to say without further research. I don't discard it's just a strange fluke, of course, as I haven't researched the matter any further, but the "ancient" components would in any case be two: one for NW Africa and another for the Red Sea area. These are of course two very different regions, separated by a vast desert, that have got no obvious direct connection (archaeologically speaking) between the OoA era and the Epipaleolithic, what amounts to some 80-90,000 years.

...

Maju said...

...

"In any case, people must have been crossing from Egypt to Asia and back for tens of thousands of years, so the prehistory of that area is far from simple".

Agreed in general terms. But in concrete terms we can discern some very specific periods of interaction:

1. The OoA era (Abbasia Pluvial), with flows to Palestine (c. 125 Ka BP?) and Arabia by land (c. 90 Ka BP - notice that these happened AFTER the seemingly coastal flows c. 125 Ka BP via Southern Arabia).

2. The UP/LSA era (Mousterian Pluvial), with probable flows from Asia to NE Africa (the matter still requires clarification but this is my main work hypothesis).

3. The Epipaleolithic (Neolithic Semi-Pluvial), with flows of microlithist type from Egypt/Sudan to the Levant (as well as, for the first time that we can discern, to NW Africa: Capsian culture). This is probably the time of the main spread of Northern Afroasiatic languages.

4. The Neolithic: plausible but not well demonstrated flows from West Asia to the "Green Sahara".

5. Historical flows, whose nature seems mostly political-military rather than demographic, although they may have included some people movements also, notably Semitic pastoralists of the Hyksos type, whose impact would have been mostly limited to the Eastern Desert and maybe some specific settlements in the Delta.

terryt said...

"According to several published papers that I have seen, it may actually be the case that some or all of the L3(xM, N) clades are more closely related to haplogroup M than they are related to haplogroup N"

Is anyone else unable to scroll through the mt-DNA N page on Phylotree? It certainly doesn't work for me yet the other pages are quite alright.

"only two choices of route - the Gate of Tears or up the Nile and across the Sinai".

Technically it is 'down the Nile' isn't it?

"so humans must have left Africa at least 110 years ago"

I tend to agree. At that time the climate was deteriorating from a particularly warm period and so it may have been even earlier. We also have difficulty explaining the fact that 'eastern' Neanderthals appear to be much more similar to modern humans than are western Neanderthals. That surely requires some sort of early gene flow in the eastern region.

Maju said...

"Is anyone else unable to scroll through the mt-DNA N page on Phylotree?"

Works for me.

terryt said...

"Works for me".

Thanks. Must be something funny on this computer.

terryt said...

I persevered and got it to work. I note a new basal N haplogroup is listed, N7, discovered in the Cambodian northeast. This adds yet another basal N haplogroup to the string that stretches all the way through China (north and south), along the SE Asian peninsula and out to Australia. This once more raises the interesting problem of why basal M and R haplogroups totally replaced basal N haplogroups in South Asia but multiple basal branches of all three survive together all through the East and Australia/New Guinea. Toba is unlikely to be the explanation as SE Asia is much closer to the eruption centre than is South Asia.

Mike Thomas said...

Terry

SEA is not my strong area; but could it have anything to do with

1) the direction of volcanic fallout ?
2) later, in situ and/ or west asian expansions into India which erased earlier signals. ?

Maju said...

It's a trap, Mike: he bites and does not release you. There's no need for an explanation because there was no N in South Asia, just some westward-migrating groups who were mostly basal R. Also there were, it seems plenty of M people already well established there, what limited the expansion of R and her "sisters".

But let it at this because it will go circular before you can blink.

terryt said...

"It's a trap, Mike: he bites and does not release you".

I don't release people who claim to know what they're talking about, but don't.

"There's no need for an explanation because there was no N in South Asia, just some westward-migrating groups"

Yes, no N in South Asia yet somehow it reached East Asia to become established there.

"Also there were, it seems plenty of M people already well established there, what limited the expansion of R and her 'sisters'".

There is no shortage of in South Asia. It is all over the place.

"the direction of volcanic fallout ?"

Possible, but it would have to have been a howling gale if its spread was narrow enough only to affect India.

"later, in situ and/ or west asian expansions into India which erased earlier signals. ?"

I think it is often accepted that Indian populations are largely a product of movement into the region from both east and west. That holds especially so for the languages at least:

http://www.unz.com/gnxp/agriculture-came-with-men-to-the-indian-subcontinent/

terryt said...

A paper I'm sure many will find interesting:

https://faculty.washington.edu/wjs18/Pop_Structure/Science-2011-Rasmussen-94-8.pdf

Quote:

"Rather than supporting a single early human expansion into eastern Asia, our findings support the alternative model of Aboriginal Australians descending from an early Asian expansion wave
some 62,000 to 75,000 years B.P. The data also fit this model’s prediction of substantial admixture and replacement of populations from the first wave by the second expansion wave, with a few
populations such as Aboriginal Australians, and possibly PNG Highlands and Aeta, being remnants
of the early dispersal"

The K-M526 the authors refer to is almost certainly the recently defined K2b1a1-P60.

Oh, and here's the paper regarding the ancient Cambodian mt-DNAs. It will explain much about SE Asia:

http://www.researchgate.net/profile/Bing_Su/publication/257753779_Analysis_of_mitochondrial_genome_diversity_identifies_new_and_ancient_maternal_lineages_in_Cambodian_aborigines/links/00b4952696afdcf9bd000000.pdf


Maju said...

@Terry: Note that in fig. 2 Papuans and other Melanesians are in the black arrow, shared with Europeans and Chinese and not in the brown one (exclusive of the Australian Aboriginal sample). This is consistent with associating the black arrow with the {Y-DNA K2 + mtDNA R} "clan" and the brown arrow with the {Y-DNA C + mtDNA M/N(xR)} "clan". If the conclusions of Rasmussen are correct, it'd just mean that the K2 clan expansion partly replaced the previous C (and D) clans in the Far East, before turning around to the Westward march that culminated in the early UP colonization of Western Eurasia by H. sapiens.

This data does not seem consistent with claiming that "possibly" (sic) Papuans and Aeta would be part of the first flow but rather should support their pertaining mostly to the second wave (too high in Y-DNA K2 and often also mtDNA R). Instead other high Y-DNA C/D and mtDNA M/N(xR) peoples such as Andamanese, Ainu/Jomon, proto-Tibetan, proto-Mongol, etc. might have belonged to the first wave to East Asia but later in some cases admixed with the second wave beyond recognition.

The problem is that Rasmussen uses an imperfect over-simplified and West-Asia-centric model of expansion of H. sapiens into Asia, which does not consider the need for the ancestors of West Eurasians to have gone all the way to SE Asia and back, at least in most cases. Also he assumes that Denisovan admixture means exactly that: admixture with the H. heidelbergensis of Denisova cave and not some undocumented "cousin" from Indonesia, as was surely the actual case.

The interest of the paper, if it can be deemed acceptable in its core findings, would be that it seems to support the notion of two successive waves to East (SE) Asia (and by extension Australia): (1) the early one(s) of the C and D "clans" and (2) the late one of the K2 "clan", which partly replaced the former and maybe pushed it to peripheral zones too.

Maju said...

The study on Cambodian aboriginal mtDNA is also of interest, thank you.

terryt said...

"the black arrow with the {Y-DNA K2 + mtDNA R} 'clan' and the brown arrow with the {Y-DNA C + mtDNA M/N(xR)} 'clan'".

True.

"If the conclusions of Rasmussen are correct, it'd just mean that the K2 clan expansion partly replaced the previous C (and D) clans in the Far East, before turning around to the Westward march that culminated in the early UP colonization of Western Eurasia by H. sapiens".

But the K2 clan did not replace C and D in the far East yet it did so in South Asia. Strange. And neither M nor R replaced N in East Asia but did so in South Asia. Also strange.

"This data does not seem consistent with claiming that 'possibly' (sic) Papuans and Aeta would be part of the first flow but rather should support their pertaining mostly to the second wave (too high in Y-DNA K2 and often also mtDNA R)".

Agreed. The paper is a few years old and the main point the authors are making is that there is evidence for two expansions. I would say it is unlikely to be from two expansions within Africa but two from just outside it somewhere.

"Instead other high Y-DNA C/D and mtDNA M/N(xR) peoples such as Andamanese, Ainu/Jomon, proto-Tibetan, proto-Mongol, etc. might have belonged to the first wave to East Asia but later in some cases admixed with the second wave beyond recognition".

I think it is pretty obvious that mt-DNA M moved north from (possibly) somewhere near Cambodia, or Myanmar/South China. But that could have been part of the Y-DNA K2a expansion, not necessarily involving C or D. I agree that C and D were probably part of the 'first wave'.

"The problem is that Rasmussen uses an imperfect over-simplified and West-Asia-centric model of expansion of H. sapiens into Asia"

Yes. The real situation is likely to be far more complicated than even the paper is suggesting.

"does not consider the need for the ancestors of West Eurasians to have gone all the way to SE Asia and back"

To be fair I'm pretty sure the Rasmussen paper came out before the phylogeny of Y-DNA K was resolved to the extent it now is.

"Also he assumes that Denisovan admixture means exactly that: admixture with the H. heidelbergensis of Denisova cave and not some undocumented 'cousin' from Indonesia, as was surely the actual case".

I keep changing my view on that admixture. Basically it seems East Asia and Australia/New Guinea has elevated levels of Neanderthal admixture too. The Denisova element may be from near Denisova cave. That just makes the whole story even more complicated.

"The interest of the paper, if it can be deemed acceptable in its core findings"

I think the date offered for Australian settlement also make it interesting ("We show that Aboriginal Australians are descendants of an early human dispersal into
eastern Asia, possibly 62,000 to 75,000 years ago"). That is too early to have involved K2b and so does tend to support the idea that C was the earlier Y-DNA into Australia. I was beginning to have difficulty in convincing myself of that.

Maju said...

K originated in South Asia, from F (also coalesced in South Asia). K2 (P1) in South Asia only replaced, partly if anything, its own F-derived "cousins". I don't see any reason to imagine C or D in South Asia before the K2 expansion, just F. I also see no reason to imagine mtDNA N in South Asia at any pre-Toba time. If there was anything like that, it must have been completely erased by the ash rain.

In other words, my model for the Asian expansion of our species, which you should know well by now is:

1. Founder effect {F+M} in South Asia
2. Founder effects {C/D+M/N} in East Asia (and Australia)
3. Mostly (but not only) {K2+R} secondary (but quite impacting) expansion, probably soon after Toba (exploiting the open niches) and culminating in the early UP and the related "conquest of the Neanderlands".

I explained in some finer detail and with cool maps HERE.

terryt said...

"I don't see any reason to imagine C or D in South Asia before the K2 expansion, just F".

That's how I see it too. C and D have to have both been in East Asia while F was in South Asia though.

"I also see no reason to imagine mtDNA N in South Asia at any pre-Toba time".

Or at any time.

"1. Founder effect {F+M} in South Asia"

Yes.

"2. Founder effects {C/D+M/N} in East Asia (and Australia)"

But C, D and N must have reached there by some route. They didn't just materialise.

"3. Mostly (but not only) {K2+R} secondary (but quite impacting) expansion, probably soon after Toba (exploiting the open niches) and culminating in the early UP and the related 'conquest of the Neanderlands'".

We agree on far more than we disagree. Although I think the K2+R expansion was probably no earlier than some 45 kya.

Krefter said...

"Post and Discuss New/Old mtDNA Data"

http://www.anthrogenica.com/showthread.php?4615-Post-and-Discuss-New-Old-mtDNA-Data&p=87553#post87553

Anything to do with Modern mtDNA. I'm almost done with studies with data from West Asia and Pakistan, and from Russia and Poland. Everything non-West Eurasian is open-game. There's a lot to discover there.

Mike Thomas said...

If the early SEA/Australian dispersal (followed by later further migrations) model is correct, then it might fit with the admittedly controversial findings from Mungo man- ie a discontinuity between him and the ancestors of current Aborigines..

terryt said...

"If the early SEA/Australian dispersal (followed by later further migrations) model is correct, then it might fit with the admittedly controversial findings from Mungo man"

Makes sense. A little bit of expansion on my earlier comments, as Maju is well aware I don't actually think there were two separate migrations from Africa. I think the difference is the result of two separate routes of migration. We have to wait for further research to either prove or disprove that idea but to me it explains the evidence as we have it better than does any other theory.

Mike Thomas said...

Which two routes, Terry ?

terryt said...

"Which two routes, Terry ?"

I think it is obvious that F-derived Y-DNAs moved east through South Asia. I also think the distribution of N-derived mt-DNAs suggests a movement east via Central Asia somehow. In other words the two routes east I envisage are south and north of the Tibetan Plateau. To me it appears as though both Y-DNA C and D were eliminated from Central Asia by extreme climate cooling but the two survived somewhere at the eastern end of the plateau. The case of mt-DNA M is more problematic. It seems to have had a huge spread centred on mainland SE Asia but that leaves the problem of which mt-DNA accompanied Y-DNA F east. To me that makes far more sense than proposing total replacement of particular haplotypes by other haplotypes. We know from many regions that total replacement is not particularly common. Older haplogroups often survive, if at a reduced proportion of a population.

Maju disagrees completely with the above scenario and says there is no evidence for modern humans through Central Asia until the Upper Paleolithic. But there is very little fossil evidence for what species of humans occupied Central Asia at any one time, and his complaint ignores the fact that the UP did not coincide with the OoA but postdates it considerably. As far as I'm aware the only real human fossil in the region is the Teshik-Tash individual. It has been shown to be Neanderthal through its mt-DNA, but until that was isolated there were all sorts of arguments as to what species it was. In any case it is nowhere near as 'Neanderthaloid' as specimens fro further west indicating to me it is some sort of hybrid. And what will it be called if its Y-DNA turns out to be modern human? Males tend to travel beyond any expandingmargin of human settlement as illustrated by most recent colonial expansions.

We can presume from the resent study of the early Aurignacian individual that hybridism between human and Neanderthal was reasonably common along the margin of modern human expansion. I presume such was the case throughout human expansion, and not just that of modern humans.

Mike Thomas said...

interesting

I fear it be decades before we know for sure- with the paucity of skeletal samples in asia

capra internetensis said...

@Terry

Did you see this yet?

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129839

terryt said...

@ capra internetensis:

No, I hadn't. What can I say? Stunning. Thanks very much. And the leading author is Spanish. I wonder what Maju thinks. Quote:

"Our phylogenetic and phylogeographic analysis of macrohaplogroup N in Eurasia supports the existence of an additional northern route out of Africa, not involving the Arabian Peninsula or the Indian subcontinent as previously envisaged"

The paper does offer far more than just that however, and kicks the Bab al Mandeb crossing into touch. A real mine of information. But to me the above has been reasonably obvious for many years. Of course it is great to see a detailed analysis. What we need now is for a group to analyse the M haplogroup, a much more difficult proposition I think.

I had a few more thoughts on the matter yesterday before I saw your link. It seems the population in Central Asia underwent considerable periodic change as we have the Neanderthal Teshik Tash at 70 kya, next the modern human Ust-Ishim at 45 kya and then the Denisova mysteriously appears at 41 kya. The situation was obviously quite complex.

Mike Thomas said...

Fascinating paper
I don't think it "kicks" the Red Sea crossing "into touch" because it clearly suggests that there might have been multiple acenues for ex africa. They correlate mtDNA Hg N with a Levant-Caucasus-East asia one; they still see Hg M as a possible southern route

capra internetensis said...

With the timing they propose there is another obvious possibility: they *did* travel through South Asia, but everyone who stuck around there had a really bad day when Toba blew.

terryt said...

"they still see Hg M as a possible southern route"

Possible. But basal M is even more noticeable for its absence in Saudi Arabia than is basal N.

"they *did* travel through South Asia, but everyone who stuck around there had a really bad day when Toba blew".

Again possible but Toba left M and R untouched. That is difficult to explain.

By the way Capra, I see the paper only came out on Monday last week. How come you were aware of it so quickly? Do you subscribe to PLOS one? Another by the way, I like the name 'internet goat'.

terryt said...

"they still see Hg M as a possible southern route"

They in fact say, 'This does not preclude the existence of a southern route across South Asia as proposed by ourselves [17,68] and others [4,75] based also on other mtDNA lineages'. But that deals only with South Asia.

Regarding M in Arabia they write, 'Seven per cent of the Arabian samples were assigned to macro-haplogroup M, of which 4% are members of the North African haplogroup M1, and the remaining 3% conform a miscellaneous group of sequences from South, Southeast and Eastern Asian origins and sole representatives of Melanesia (Q1), Madagascar (M32c) or Australia (M42). In particular, the rare Arabian M sample completely sequenced in this study (S3 Fig) belongs to the Indian M42b1 clade, sharing only transversion 95C with a Munda sequence (MUN22) at the same clade. A sister branch of the Indian M42b, with a coalescence time estimation around 55 kya, has spread in Australia [62]'. So no M basal haplogroups in Arabia either.

Another comment they make is, 'All these evidences points to a successful Paleolithic exit through the Sinai Peninsula during the last interglacial period (Fig 1A). Finally, as sea levels would be higher in that time than in glacial episodes, alternative routes involving crossing maritime straits as the Bab al Mandeb through Arabia or the Gibraltar through Iberia would have fewer possibilities of success'.

"they *did* travel through South Asia, but everyone who stuck around there had a really bad day when Toba blew".

However they write, 'This scenario [absence of basal N) strongly contrasts with the huge presence of autochthonous M [40,72] and R [31,59,60,73] lineages with deep coalescence ages in India. It could be alleged that primary autochthonous N lineages existed in India but became extinct due to genetic drift, but this hypothesis is in contradiction with the fast population growth detected in prehistoric southern Asia [74]'. Note, 'deep coalescence ages', presumably as deep as those of N elsewhere.

In fact they write, 'On the top of the common L3* trunk, macrohaplogroup N accumulated a stem of five mutations without any known bifurcation. From this fact, it can be deduced that, after the out-of-Africa, the bearers of this lineage seem to have had demographic difficulties and remained as a stagnate population for a long time'. M has only three mutations on its stem and so presumably originally expanded earlier than did N.

Mike Thomas said...

Terry
Do the results suggest that both M & N traveled northward ex africa; then M arrived and expanded from India; whilst N from E Asia ?

terryt said...

The paper Capra linked to alos has some interesting comments regarding the DEnisova genetic contribution. They suggest it is unlikely to have come from anywhere near Australia:

"It has been proposed that the geographic range of Denisovans when the introgression could happen was greater, reaching southeastern Asia [127]. However, against that supposition, it is the fact that the analyzed Altaian Denisovans had an extremely low genetic variation at around 70 kya [120], so that if a greater geographic range existed it would be too early to have admixed with modern humans in Southeast Asia".

That narrows down the options. Actually it is worth re-reading the Australian paper in the light of this recent one. It is simply a matter of shifting the brown line in fig. 2 up through Central Asia and down through East Asia and everything makes complete sense. Except for the slightly higher Denisova contribution to New Guinea rather than to Australia. However I'm sure an obvious explanation will appear some time.

terryt said...

"Do the results suggest that both M & N traveled northward ex Africa"

The authors barely mention M. My understanding is that only N went north, although they hint M may have reached the Caucasus. In any case they seem to suggest that M did not go through the Arabian Peninsula. They actually make no comment about M's route which is why I mentioned a few days ago that it provides another field of research. My own feeling is that M must have gone directly to, then through, South Asia and been held up in the hill region of Burma/NE India/S China for some time where it diversified considerably.

With regard to my suggestion a few days ago: the two mt-DNA haplogroups fit very the separate first (N) and second (M) migrations mentioned in the Australian paper.

Mike Thomas said...

I'll re-read it!
I was initially a little sceptical about such an old age (65 kya )- esp in light of controversies regarding to dating, genetics of Mungo man etc

terryt said...

"I was initially a little sceptical about such an old age (65 kya )- esp in light of controversies regarding to dating, genetics of Mungo man etc"

I do have doubts about the dating of Mungo Man but that does not mean I'm sceptical of early Australian dates. Humans most likely arrived at the northwestern edge of the continent and Lake Mungo is way to the southeast. Humans probably didn't expand rapidly across the whole of Australia. It is not as human-friendly as is North America. If humans arrived in Oz during a really arid period they could have been confined to the lusher regions in the northeast for quite some time. The comment in the Rasmussen paper that 'estimate that aboriginal
Australasians split from the ancestral Eurasian
population 62,000 to 75,000 years B.P.' fits entirely the mt-DNA N dating given in the Fregel (2015) paper.

Maju said...

Terry said: "I wonder what Maju thinks"

I did not have time to read it before but it's clearly a bunch of self-complacent fallacies:

(1) They say: "the inhospitable climatic conditions in Arabia at that time, the lack of pertinent fossil record along the trail, and the early colonization of Australia". Indeed these are serious problems to accept a 60-70 Ka OoA. But they are easily solved with a 125-100 Ka OoA, which is reasonably well documented. The problem is in the "molecular clock" and very particularly in its calibration. Not only Australia was colonized surely before 60 Ka but South and SE Asia were c. 100 Ka ago and Arabia/Palestine c. 125 Ka ago. There is a sufficiently good archaeological record for that today and should be used for calibration of the MC.

(2) Also there is zero archaeological support for any sort of H. sapiens migration via the North. Instead in a key regions like Altai is (every single Paleolithic Northern migration must have crossed it) the evidence supports Heidelbergensis (Denisovan) and Neanderthal successive occupation. H. sapiens is only apparent at the beginnings of the Upper Paleolithic.

(3) If we consider mtDNA not in isolation terms but associated with Y-DNA, we can see that there is no obvious partner for N. Instead all early Y-DNA macro-haplogroups were associated with mtDNA M, and only exceptionally with N. Hence (pre-)N must be seen as something that was associated to a dominant M but as minor partner, having only success at a late date surely and from a SE Asian coalescent geography.

(4) "There is no evidence of deep autochthonous N(xR) clades in the Arabian Peninsula". Ditto. Nobody expects it, save precisely those who claim (without any support) a Western origin for this lineage. It'd be interesting to study better the L(xM,N) lineages (L0, L3(xM,N), L4 and L6), which are the ones that can fit with an OoA persistence scenario, but that's still at a very early stage and requires first of all a much better understanding at the fine detail of African mtDNA genetics (otherwise it's hard to understand).

(5) "... recently, it was stated that the introgressed Neanderthal DNA in humans is more closely related to the Mezmaiskaya Neanderthal from the Caucasus than it is to either the Neanderthal from Altai in Siberia or to the Vindija Neanderthals from Croatia"...

That is consistent with a West Asia admixture scenario, which is the default scenario. It does not imply migration to Altai via the Caucasus, nor migration to Altai at all. It just suggests that Skhul 5 was probably a sapiens-neanderthal hybrid of some sort and directly related to the general Eurasian Neanderthal admixture episode: a West Asian early OoA migration event by all accounts.

...

Maju said...

...

(6) "Clearly, this scenario is in conflict with the hypothesis of a single dispersal out of Africa of modern humans through the Bab al Mandeb strait into Arabia, and a sole southern coastal migration through South Asia to southeastern Asia and Australasia".

No, it is not. It is only in conflict with the "molecular clock" the scholastic parrots are using. With archaeology on hand there were several 125-90 Ka BP migrations from Africa to Arabia and Palestine (and possibly to southern Iran as well), some of them across the Red Sea, some probably across the Sinai. The first MSA-like cultures in Arabia in any case arrived via the sea and are found not too far from the coasts, only the late 90 Ka migrations took place via inland routes. But this is trivial because, whatever the routes used to reach Arabia and Palestine, that was just a preliminary stage, the real OoA began when people (H. sapiens) moved from those areas to South and SE Asia and that is only documented since 100 Ka onwards. That's the time-frame when mtDNA M "exploded" in the most massive star-like structure of all the human lineage. The Arabian stage can only be thought as preliminary and within "African" lineages (L, as even M itself had not coalesced yet).

(7) "... it is difficult to explain why Eastern Asians have more Neanderthal DNA contribution than Europeans and South Asians".

Not all East Asians follow that pattern: neither Japanese nor "purest" Native Americans like Karitiana do. IMO it's a product of founder effect accidents and anyhow the differences are very minor and irregular.

Also if West Eurasians are essentially N and South Asians are essentially M, but East Asians are a mix, how can they correlate both things at all? Nonsense again.

In brief: not making sense at all. Terry should love it though because it's almost literally his obsessive theory.

capra internetensis said...

@Terry

Someone else posted the paper on another site and it was clearly relevant to the conversation!

I think N having a longer branch length from L3 than M does is just chance - IIRC most studies put the TMRCA of M later than that of N, usually close to that of R. In this study N is dated to 60 (plus or minus 15) kyo and M to 48 (plus or minus 6) kyo, while R is 54 (plus or minus 10) kyo.

But the mtDNA clock ticks very unsteadily indeed, so I don't trust any of the date estimates much.

The expansion of M and R would be post-Toba and from the east.

Maju said...

Capra: you have faith in "studies" and "molecular clock", I tell you: look at the facts implicit in them, it's much easier with mtDNA (you can count the mutations yourself: no mystery anywhere). And what you will see is that it's a methodology problem: MCH methods work averaging branches, so lineages accumulating more mutations since split appear younger than their siblings who are "conservative". Hence N appears older than M and U appears older than R0.

That's an illusion: on one side mere drift will tend to preserve the conserved original haplogroup, suppressing the mutants by mere statistics, unless the effective population tends to minimal numbers of the kind of Ne=2 or at least Ne<10. On the other side mutations are not neutral: they are errors in the copy and therefore mostly deleterious to a greater or lesser extent, being selected against except in very rare occasions, this adds up to the previous process: novel mutations tend to be eliminated unless the affected population is tiny. Again, in mtDNA, with a very short DNA chain and being fundamental for metabolism, i.e. the most basic function of the cell and body, this "evolutionary" issue must be most seriously taken into consideration.

So you do have to count from the root down and not average branches. You can only do that between two calibration points, the calibration cannot be circular MCH reasoning (someone estimated this, causing someone else to estimate that and now I use those estimates to build my own: that's junk-in:junk-out) but actual archaeological data points.

terryt said...

@ Capra internetensis:

"Someone else posted the paper on another site and it was clearly relevant to the conversation!"

Thanks very much for doing so.

"I think N having a longer branch length from L3 than M does is just chance"

I agree. It was just that the authors brought the matter up. However I do think the Zhang et al Cambodia paper I linked to above does confirm M was already present in mainland SE Asia by the time N reached there.

"But the mtDNA clock ticks very unsteadily indeed, so I don't trust any of the date estimates much".

You are absolutely correct. And it seems from the N and M papers that Y-DNA chronology is way out. Looks as though the standard estimates should be roughly doubled. I suspect the calculated coalescence dates are minimum dates at best. A particular haplotype can remain isolated in a particular region for a considerable time before it is able to expand on its own accord.

"The expansion of M and R would be post-Toba and from the east".

We would need time depths for M in India to be sure of that. M certainly seems to have reached Cambodia before Toba erupted. And India certainly contains multiple basal M haplogroups which conflicts with the idea of a Toba extinction.

terryt said...

@ Maju:

"it's clearly a bunch of self-complacent fallacies"

Just because you disagree with it?

"IMO it's a product of founder effect accidents and anyhow the differences are very minor and irregular".

You are behind the times. The authors mention that concept:

"However, the detection of a putative autochthonous N5 lineage in India [31] was enough to reinforce the single southern migration hypothesis, with the important additional assertion that all the three mtDNA founder lineages in Eurasia (M, N, R) travelled together in a unique main expansion".

As you know, I call that 'The Garden of Eden Syndrome', the wish to see modern humans as having arisen instantly in a single source population and having spread rapidly from that region. Surely you realise it was far more complicated than that scenario.

"Indeed these are serious problems to accept a 60-70 Ka OoA. But they are easily solved with a 125-100 Ka OoA, which is reasonably well documented".

They actually agree with you there, as you would have seen if you were not so frightened to read the paper.

"H. sapiens is only apparent at the beginnings of the Upper Paleolithic".

That is only so if you totally accept the UP as being the defining marker of H. sapiens presence. Surely everyone agrees that the UP developed after, and probably considerably after, modern humans had left Africa.

"If we consider mtDNA not in isolation terms but associated with Y-DNA, we can see that there is no obvious partner for N".

There is an obvious partner if you disregard the molecular clock dates for Y-DNA. Why do you insist the molecular clock is accurate when it comes to Y-DNA?

"Hence (pre-)N must be seen as something that was associated to a dominant M but as minor partner, having only success at a late date surely"

You're proposing here that a haplotype with a very minority presence survived as part of a single population during a protracted movement all the way from Africa to SE Asia, and then suddenly expanded on its own in Australia? Wow.

"Nobody expects it, save precisely those who claim (without any support) a Western origin for this lineage".

You are now proposing that N miraculously jumped from Africa to SE Asia before it even coalesced?

"It'd be interesting to study better the L(xM,N) lineages (L0, L3(xM,N), L4 and L6), which are the ones that can fit with an OoA persistence scenario"

The authors did that, and what they found was a young coalescent age for them all, and that they were obviously post original OoA arrivals from Africa.

"It does not imply migration to Altai"

But the Denisovan is almost impossible to explain without such a migration.

"With archaeology on hand there were several 125-90 Ka BP migrations from Africa to Arabia and Palestine (and possibly to southern Iran as well), some of them across the Red Sea, some probably across the Sinai".

If you actually were prepared to read the paper, instead of refusing to because it conflicts with your preconceived ideas, you would see they claim the OoA occurred '125-90 Ka BP' and, at that time, sea level would have been too high for an easy crossing of the Red Sea. They actually do not rely very much on your 'molecular clock' except as supporting information.

"Also if West Eurasians are essentially N and South Asians are essentially M, but East Asians are a mix, how can they correlate both things at all? Nonsense again".

It makes perfect sense, except if it doesn't fit your Garden of Eden concept. The pattern was obviously N to the north, M to the south, the two meeting in SE Asia where R formed from N, R then moving both north and west from SE Asia. Explains everything adequately.

terryt said...

Sorry. A third, short, comment. Maju, your stance contrasts with that of Eurologist. Here's what he said about the Fregal paper:

"great paper by open-minded authors".

Amazing how differently people see things.

Maju said...

Terry I'm not going to get embroiled in a discussion with you of the kind:

You: "The authors mention that concept"...

Me: "No, they don't, you're talking about something else".

You: "They actually agree with you there"...

Me: "No, they don't, you're talking about something else".

You: "You are now proposing that N miraculously jumped from Africa to SE Asia before it even coalesced?"

Me: Sure, that's been my thesis for many years, just remove the term "miraculous" and replace it by "absolutely normal". Ah and it was not yet N but L3 (pre-N), your sloppiness with the nomenclature is so annoying! I bet you enjoy doing that.

You: "Denisovan is almost impossible to explain without [Altai]".

Me: Deni-what? It's just old good H. heidelbergensis. Maybe you need to redesign your route and force it via Atapuerca? I can show you the way, it's not far from here. Nah, just kidding, the admixture event was actually in Flores (or whatever). What I mean is that it's very possible to explain, yeah, but we have discussed this many times earlier.

You: "you would see they claim the OoA occurred '125-90 Ka BP'"

Me: I did read the paper. Did I miss some footnote? Care to quote the exact paragraph?

You: "Garden of Eden"

Me: Yeah, I'm the snake of that kids tale... or whatever.

END OF DISCUSSION


terryt said...

"Me: I did read the paper. Did I miss some footnote? Care to quote the exact paragraph?"

You didn't miss a footnote. You failed to read the paper:

"In addition, it has to be mentioned that, using a revised genome-wide mutation rate [108], the split between non-African and African populations was situated in a range of 90 to 130 kya. These ranges overlap with the presence of modern humans in the Levant, as attested by the fossil evidence retrieved from the Qafzeh and Skhul caves [109]. It also coincides with a wet climatic period that would facilitate a sub-Saharan Africa northward spread to the Mediterranean shores across the present-day Saharan desert, not only through the Nile Valley but also across Libya and the Maghreb [110–112]. In the same temporal window is the Aterian stone industry that extended overall in North Africa and the Sahara desert, from the Atlantic coast to the Nile Valley and outward into the Levant [113]. Of paramount importance is the evidence that Aterian presents hints of modern human behavior as suggested by the inclusion of ornamental shell beads in their African and Levantine assemblages, and the technological advantage of their stem tools, suitable for hafting [114,115]. Furthermore, affinities between Aterian skulls and Levantine earlier Homo sapiens have been reported [116], as well as cranial morphometric affinities between Levantine and later Pleistocene/early Holocene human populations from Australia [117]. All these evidences points to a successful Paleolithic exit through the Sinai Peninsula during the last interglacial period (Fig 1A). Finally, as sea levels would be higher in that time than in glacial episodes, alternative routes involving crossing maritime straits as the Bab al Mandeb through Arabia or the Gibraltar through Iberia would have fewer possibilities of success".

"Me: Sure, that's been my thesis for many years, just remove the term 'miraculous' and replace it by 'absolutely normal'.

So it's absolutely normal for groups of humans to leap across thousands of kilometres of land. Great.

"Ah and it was not yet N but L3 (pre-N), your sloppiness with the nomenclature is so annoying!"

Pre-N? How come we have basal N haplogroups in western Eurasia? Or did they leap thousands of kilometres from East Asia after pre-N had jumped thousands of kilometres east some time before that? Nothing you say makes any sense.

"It's just old good H. heidelbergensis".

Is it? And you know that because? You do realise there is no evidence for a H. heidelbergensis presence in SE Asia don't you?

"the admixture event was actually in Flores (or whatever)".

Making things up yet again.

terryt said...

I doubt you realise how stupid this idea of yours is:

"it was not yet N but L3 (pre-N)"

What you are proposing here is that some sort of 'L3*' moved all the way from very near Africa to SE Asia yet failing to diversify in the slightest along the way. In fact some 4-5 times being reduced to not much more than a single female, thus developing its tail of five mutations. All this while being part of a growing and diversifying group of M haplogroup women. What is even more unbelievable once this diverse M and single now-developed N reach SE Asia a small group of N women, again perhaps not much more than a single woman, moves back through South Asia. Once more failing to diversify along the route yet diversifying considerably once it emerges from the western margin of South Asia. This last without resulting in the formation of a single unified branch in contrast to the numerous, reasonably diversified group of N women left behind in SE Asia.

That scenario is surely so unlikely as to be not worth considering for a moment.

Maju said...

Alright, I did miss that part. I did read the section though but missed the detail. They still use it, ignoring all the relevant findings in Yemen (Nubian complex) and the United Arab Emirates (other MSA of Rose and Armitage), which seem to imply a crossing of the Red Sea or Bab-el-Mandeb, as well as the later dated (c. 90 Ka) "trailblazers" (of Petraglia) across Arabian inlands. Their whole argumentation is based on Mediterranean archaeology only (Aterian and Skhul/Qafzeh remains - they seem aware of the latest revisions of these sites but they seem ignorant of the new Arabian sites altogether). Hence their thesis in favor of a land-only migration is clearly flawed.

What is informative is that there is one revised mutation rate Durbin 2012 (pay per view) that fits the Abbasia Pluvial window and is therefore most likely the correct one.

"What you are proposing here is that some sort of 'L3*' moved all the way from very near Africa to SE Asia yet failing to diversify in the slightest along the way".

That is directly derived from the fact that there is no known derived branch between the L3 and the N node: that means that 4 coding region mutational steps (equivalent to time lapses in the molecular clock paradigm, quite long ones in mtDNA) took place between the L3 node and the coalescence of N. N was in other words a small lineage, a trickle, between these two expansion nodes (L3 and N).

It's not just N, it is the same with M, just that there are only 2 sterile intermediate SNPs and not 4 (i.e. half the time). And it is the same with other lineages through the human genome, of course.

We have discussed this a zillion times: do not pretend to be surprised, Terry. I find really annoying that you make me explain this again for third parties, when you know exactly all this.

What happened to those potential branches that weren't? They were pruned either because the population was small all the time (main thesis) or because of catastrophic causes (for example Toba event). The two first steps are shared by both M and N, so they obviously correspond to the OoA process through Arabia/Palestine, where they left no legacy. The two later steps only are found in N, i.e. M was quickly expanding while pre-N was not (or was in areas that were later destroyed in terms of population survival). It does not matter much: the fact is that pre-N must have remained small until it found an opportunity to expand in SE Asia, which is the super-clear origin of this haplogroup.

...

Maju said...

...

"You do realise there is no evidence for a H. heidelbergensis presence in SE Asia don't you?"

There is one piece of indirect evidence: the so-called "Denisovan" admixture, which is the same among certain "N peoples" like Australian Aborigines and "R peoples" like Papuans, so it's not directly related to mtDNA lineage and only seems to be explained by geography, i.e. the crossing into Australasia. Heidelbergensis therefore had almost certainly arrived to SE Asia back in the day and for some reason its admixture only affected in significant amounts to the populations who crossed Wallacea and not those who remained behind.

We also have other indirect piece of indirect evidence in the Flores hominin, who was obviously able to navigate through the island chain and may be related somehow. There is also the Solo (Ngandong) hominin from Java, who has been so far described as "H. erectus" but displayed a very advanced technology (and seems craniometrically close to Flores hominin per Peter Brown). As H. heidelbergensis is clearly not anymore possible to relate to H. neanderthelansis in any way (as was thought until a few years ago) all Asian H. erectus remains could well be Denisovan cousins and be therefore source of "Denisovan" admixture in modern Homo sapiens. Many of them could also get reclassified as H. heidelbergensis at any moment, mind you.

But the most important piece of evidence is in any case the geographic restriction and lack of phylogenetic correlation of Denisovan admixture: Papuans are R-dominated and quite close to West/South Eurasians in Y-DNA too (K2b) and yet they are as "Denisovan" as Australian aborigines, while West/South Eurasians are in the opposite extreme. The conclusion must therefore be that only those populations crossing to Australasia really got admixed (although minor backflow to some East Asians is likely too, maybe at the original dates or maybe at later dates). The evidence points to Flores, really.

terryt said...

At least you are being civil here.

"That is directly derived from the fact that there is no known derived branch between the L3 and the N node: that means that 4 coding region mutational steps (equivalent to time lapses in the molecular clock paradigm, quite long ones in mtDNA) took place between the L3 node and the coalescence of N. N was in other words a small lineage, a trickle, between these two expansion nodes (L3 and N)".

However it is extremely unlikely that such a 'small lineage, a trickle' would have survived the long trip to SE Asia as part of a rather large eastward-moving population. As a rule minority haplotypes tend to be eliminated quite quickly. As well as that problem you're also proposing a similar trip back westward once the N lineage had become fully formed.

"It's not just N, it is the same with M, just that there are only 2 sterile intermediate SNPs and not 4 (i.e. half the time)".

Quite. But we don't have the problem of absent lineages along the route from Africa. In fact we have quite a large number of branches along any postulated route.

"I find really annoying that you make me explain this again for third parties, when you know exactly all this".

I keep bringing it up because I believe your proposed scenario is impossible.

"They were pruned either because the population was small all the time (main thesis)"

We know it wasn't 'small' It produced a large number of M haplogroups. And M in the east is as ancient as is N as we see from the Zhang paper:

http://www.researchgate.net/profile/Bing_Su/publication/257753779_Analysis_of_mitochondrial_genome_diversity_identifies_new_and_ancient_maternal_lineages_in_Cambodian_aborigines/links/00b4952696afdcf9bd000000.pdf

"because of catastrophic causes (for example Toba event)"

Which had minimum effect on the M haplogroups, and possible the R ones as well.

"M was quickly expanding while pre-N was not"

Difficult to fit with your proposed scenario where you evidently have M and N moving east as part of a single population.

"There is one piece of indirect evidence: the so-called 'Denisovan' admixture"

We cannot even be sure that admixture occurred in SE Asia. let alone was from heidelbergensis in the first place, and so it is hardly evidence, indirect or not, for heidelbergensis presence there.

"We also have other indirect piece of indirect evidence in the Flores hominin, who was obviously able to navigate through the island chain and may be related somehow".

Probably not related. It is far more erectus than heidelbegensis for a start.

"There is also the Solo (Ngandong) hominin from Java, who has been so far described as "H. erectus" but displayed a very advanced technology"

I agree that is a far more likely candidate than is Flores. But:

"all Asian H. erectus remains could well be Denisovan cousins"

I think the author's comments regarding the very restricted genetic diversity in the Denisova population make it very unlikely it was a widespread population.

"The conclusion must therefore be that only those populations crossing to Australasia really got admixed (although minor backflow to some East Asians is likely too, maybe at the original dates or maybe at later dates)".

The remnant element in East Asia is more likely to be that, a remnant. That is what the authors propose. The Denisove level was reduced through the expansion of M and even R. The Y-DNA connection is confusing but that is the only problem I see with the authors' hypothesis and presumably has a logical explanation.

capra internetensis said...

I actually think the Y DNA clock is more trustworthy than the mtDNA clock. mtDNA is tiny (4 kilobytes! - the size of a small text file), leading to frequent back-mutations, and many mutations (as Maju says) are likely to be under selection. NRY is incomparably larger and far more neutral. (In fact you can lose huge chunks of your Y chromosome containing multiple genes involved in sperm production without losing fertility in the slightest.)

I do not have complete faith in either clock by any means, but rather I think they give us windows of time which are the best place to start looking. If in fact they are way off, we will find out sooner or later when we get Paleolithic aDNA which falls outside of the expected region of the phylogenetic tree.

Uniparental lineages need not coalesce at the time of the original expansion. AMHs may have spread through Eurasia well before the time of the most recent common ancestor of all surviving patrilineages.

I don't see a problem with one lineage (N) remaining minor while another (M) expanded. That is perfectly normal; consider I1 and I2, for instance.

terryt said...

"Uniparental lineages need not coalesce at the time of the original expansion".

Exactly. In fact the Rasmussen paper makes that obvious. The Australian population split from the rest as much as 75 kya yet the oldest mt-DNA in Australia is dated at 43 kya in the Fregel paper. Of course the 'Australian' population may not have actually been present in Australia at 75,000 but may have spent some time hanging round in SE Asia before being able to cross from Timor. Interestingly 46 kya. is the date usually claimed for megafauna extinction in Australia.

"I do not have complete faith in either clock by any means, but rather I think they give us windows of time which are the best place to start looking".

I certainly do not take them too seriously. The aDNA clock, as used in the Rasmussen paper, is likely to be much more reliable.

"AMHs may have spread through Eurasia well before the time of the most recent common ancestor of all surviving patrilineages".

True. In fact I have long suggested that the non-African mt-DNA and Y-DNA lineages need not even have left Africa together.

"I don't see a problem with one lineage (N) remaining minor while another (M) expanded".

But it is most unlikely that the lineage that remains minor is moving anywhere at all. It is usually an indication it has remained isolated geographically for the time it remained minor. It is especially unlikely in the case that the minor lineage remained minor while moving in company with a lineage that is expanding and diversifying.

"That is perfectly normal; consider I1 and I2, for instance".

Are you talking mt- of Y-DNA there. As far as mt-DNA goes I is in effect N1a1b2, and splits into I1, I2'3, I4, I6 and I7. Sure, some spread more than others but I don't see any problem with that. It is widespread and obviously some would have been able to exploit any new region they arrived in while other lineages will be more restricted geographically. Y-DNA forms I1 and I2 but both expanded widely.

capra internetensis said...

Sorry, I meant Y haplogroup I. Both expanded, but while I2 began expanding (gradually) before the LGM, I1 did not expand until about 5000 years ago. And they have overlapping distributions.

terryt said...

Thanks for the clarification, Capra.

"while I2 began expanding (gradually) before the LGM, I1 did not expand until about 5000 years ago. And they have overlapping distributions".

I don't see a problem. I'm not very familiar with Y-DNA I but I would guess the two branches originated in separate regions within the I* distribution. Perhaps representing separate movements from the core region (Turkey/Iraq?). I2 perhaps entered a more comfortable environment and was able to gradually expand, perhaps more southerly centred. While I1 became restricted geographically until 5000 years ago. The overlapping distribution would be the product of expansions since that 5000 years. You would presumably more easily be able to analyse the situation than I am and I would be very interested to read your conclusions. You will need to consider the present geographic distribution of as many clades as possible.

capra internetensis said...

Well I am no expert on it, but it looks like I1 spread from somewhere in the vicinity of Germany, while I2 is all over the place, including West Asia and even North Africa. I'd guess it was already in a few different places before the LGM, but who knows. (Actually I1 first shows up in Neolithic aDNA from Hungary *before* its expansion, so it is possible it actually came in with farmers from SE Europe or even the Near East.)

It is indeed possible that I1 was stuck in one refuge area for 20 000+ years and never got a chance to expand.

I think to really answer this question you'd need to run some kind of coalescence simulation. Maybe someone has already done so, I don't know.