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Thursday, December 31, 2009

The ongoing debate on the molecular clock in human mtDNA


You may already know that I am highly critical of the often too generalized assumption that molecular clock based age estimates have any strong validity. Way too many people just assume that if geneticists say that certain lineage has this or that age, that is almost the equivalent of C14 datations, which are quite accurate and repeatedly proven. That is not just not true at all. Molecular clock theory is only very weakly proven and critical variables such as the exact mutation rates, the effective population sizes involved, the influence of factors such as weak selection and the validity of the mathematic constructs used to evaluate these ages are all too poorly understood in fact.

So I want to raise your attention on the recent spat of research papers on this matter, with contradictory results but all interesting to read in any case. They are:


Each of them has as co-author one or several "big names" on the field of human population genetics. Soares' paper is the oldest by some months and hence cited by the others, albeit critically, and is backed by Oppenheimer, McAulay and Richards. Loogväli's paper has Thomas Kivisild as co-author, while Endicott's research is co-signed by Mait Metspalu.

As said before, they each reach to different conclusions though they are complex enough that I'd shy a bit of analyzing them in depth myself here. Suffice to say, as illustrative example, that Soares concludes that mtDNA N is older than M (and that South Asian M is more recent than East Asian M - an artifact of their method in my opinion), while Loogväli concludes exactly the opposite, assigning to M an estimate age of c. 77,000 years and to N of 68,000 years. Meanwhile Endicott is much more cautious and makes instead a critical review of the most important literature on the matter, along with the archaeological data in a very comprehensive manner. However he seems persuaded that, contrary to Oppenheimer's catastrophist hypothesis, the deep origin of Eurasians is in South Asia.

In fact, while finding interesting the other papers too, more Loogväli's than Soares' (who seems to fall in too much in the errors generated by statistical artifacts and relies heavily on similarly controversial Pan-Homo divergence estimates), I am surely more in agreement with Endicott's caution in this highly complex and controversial matter. Hence I will reproduce here his concluding remarks (adding my emphasis in bold type), demanding greater rigor:

Further research is needed to improve our confidence in molecular estimates of human evolutionary timescales. First, the most reliable calibrations within the human tree need to be identified. For mitochondrial DNA, this depends on finding well-defined haplogroups that can be precisely associated with dated palaeoanthropological evidence [17]. Second, the variation in observed rates across different timescales needs to be accurately quantified [16–18]. Third, these patterns of rate variation need to be investigated for nuclear data, including the Y-chromosome and short tandem repeats.

The chief recommendation arising from the current state of knowledge in the field is for a movement away from reliance on the human-chimpanzee calibration; instead, calibrations within the human tree are preferred (but see [14]). There are several recent examples of estimates made using archaeological calibrations [15–17,35], extending the efforts of earlier authors [3,60]. Considering recent advances in phylogenetic methodology, there is now a compelling motivation to employ statistical models that take into account rate heterogeneity among sites and among lineages, that correct for multiple substitutions (saturation), and that incorporate directly the uncertainty in the ages of calibrations used. Some methods also allow the statistical evaluation of competing demographic models, which can have an important influence on estimates of rates and timescales [17,23].


Important update (Jan-1-2010):

I just realized I had missed what seems to be a very important paper on the debate on the molecular clock applied specifically to human mtDNA also published in 2009:

Brenna M. Henn et al., Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates. Oxford Journals - Molecular Biology and Evolution, 2009 (open access).

I am still finishing it but it seems a most crucial and balanced analysis on the debate (within the molecular clock hypothesis) between the phylogenetic and pedigree mutation rates' camps.

As far as I can tell, Henn and colleagues largely respond (several months in advance) to some of the recommendations made by Endicott in his paper, using in fact archaeological calibrations to estimate the reality of the mutation rates. They conclude that while pedigree rates (decreased by 33% to fit with the realistic generation span of 30 years) are almost identical to reality for the last 5000 years, they are totally unrelated with the actual behaviour of lineages before c. 15,000 BP, when the phylogenetic rates become the only reliable ones. The lapse between these two dates behaves anomalously (rather sudden but irregular change from one model to the other) leaving a gray transitional zone, difficult to work with.

Notably (as some of the hottest debates are about the age of mtDNA haplogroup H), they conclude that H3 probably has an age of c. 18,000 BP, while H1 could be even quite older. This is totally consistent with the fact that North African H (including specially these two subclades) appears derived from Iberian mtDNA and with this haplogroup having been found in aboundance in ancient pre-Neolithic DNA in both Morocco and Portugal.

64 comments:

manju said...

Me too. Me too. I have told long back mtDNA clock is imperfect. It has to be calibrated properly by other means(I think I was responding to Ibra at Quetzalcoatl).

So, if M is older than N (I think we discussed this long back considering control region or coding region mutations... old calculation nothing new), what does that tell about relative ages of M in East Asia and South Asia?I couldn't find it in the study.

But I'm seeing consistency in M in East Asia being older than that in South Asia. Only Northern Route no Coastal Route.

Maju said...

Loogväli's paper does not discuss whether M is older in either place. However it does have some age estimates for many different sublineages in the supplementary material. As this paper was mentioned at Dienekes' a couple of days ago, I already mentioned there some of the inconsistencies of such age estimates, for example:

- Two R sublineages are given ages of 75 and 78 Ky, much older than their ancestor N even after considering the rather timid standard deviations.

- H1 (or a sublineage of it, can't recall now) is given an age of more than 30 Ky, while in the paper the authors suggest at some point that even the age of c. 18 Ky found in several recent papers for all H would be maybe too old.

So it's the same story as with all these erudite speculations: inconsistencies abound and make the whole matter of any MC calculation quite incredible.

One thing that Endicott criticizes is the high dependence of all these estimates on an statistical factor called rho, which he argues is highly misleading.

So it's not just calibrations but there are way too many issues with the method as a whole. Of course, M must be necesarily older than M1, M2, etc., that we know for sure, but how much older is very difficult to discern, much less based only on genetic data.

So, if M is older than N (I think we discussed this long back considering control region or coding region mutations...

I made an exercise in this blog using that kind of measuring (and another one in private using only control region mutations) but I acknowledge that is highly imperfect because most M sublineages have less mutations than most N-derived ones, suggesting a faster mutation rate in the N branch (however the one leading to H for instance is quite short so maybe it should be looked lineage by lineage - in any case a total mess of nearly unbearable complexity, even for the most daring and knowledgeable of scientists).

Whatever the case, I imagine that's why Soares and Oppenheimer have argued for M being slightly younger than N. However Oppenheimer believes that there was some sort of huge bottleneck after the intial spread (Toba eruption) affecting South Asia much more strongly than the East, so these kind of conclusions are kind of consistent with his model and therefore he's going to back preferably researchers that reach conclusions in that line.

Maju said...

But I'm seeing consistency in M in East Asia being older than that in South Asia. Only Northern Route no Coastal Route.

I don't. M must be equally older for all the planet, what may be older or younger locally is its spread or rather the spread of its sublineages. I have argued elsewhere that Soares' regionalization of the main sublineages creates a statistical artifact that causes that the more dominant a macro-clade is in a region, the younger it looks. Soares does not provide an age for N in West Eurasia but I am almost sure that this was an ex-post-facto decision and that, using his method, N would look oldest here, just because it's more dominant and its sublineages have expanded through a wider range of time.

I understand that relying on diversity is so far the most accurate method of determining the likely origin of a haplogroup and in that sense South Asia is clearly the origin of M. So it must be older there, even if only slightly so. Inversely N appears to have expanded from SE Asia after what I understand was a localized founder effect of the second phase of the expansion.

I totally discard the Northern route whatever the case: it is totally illogical (cold, aridity, unprecedented in the H. erectus spread and archaeologically not documented at all) and inconsistent with the much greater diversity rates found in the south. Of course you can't know what happened between the L3 and the M and N nodes, as the population was small necesarily in that phase but I only consider two possibilities:

1. The coastal route via Yemen and Oman into South Asia and beyond (usually dubbed "rapid coastal migration").

2. The route through the Fertile Crescent, which would have happened c. 100-90,000 BP and which requires an explanation for the erasure of this early Western population in the form of much increased aridity and Neanderthal expansion (the same explanation that applies for the "extinction" of the peoples of Skuhl/Qafez and North African Aterian, regardless of whether they are ancestral to Eurasians or just went totally extinct).

My two cents anyhow.

terryt said...

"because most M sublineages have less mutations than most N-derived ones, suggesting a faster mutation rate in the N branch"

Why do yoy choose a 'faster mutation rate' explanation over the more obvious one?

"Soares' regionalization of the main sublineages creates a statistical artifact"

But surely most sublineages are in fact largely confined to particular regions.

"I understand that relying on diversity is so far the most accurate method of determining the likely origin of a haplogroup"

Not really. Especially if the haplogroup has undergone a period of selection in that region. This would reduce its diversity, perhaps considerably. And M's diversity in India may be the result of its arrival in a virtually unoccupied subcontinent. One of your own comments even tends to support the idea: 'Oppenheimer believes that there was some sort of huge bottleneck after the intial spread (Toba eruption) affecting South Asia much more strongly than the East'.

"I totally discard the Northern route whatever the case: it is totally illogical (cold, aridity, unprecedented in the H. erectus spread and archaeologically not documented at all)"

Maju. I've provided a myriad of links proving that humans existed right across Central Asia from the Altai Mountains to the Upper Amur River long before modern humans had even first appeared. What's more, the occupation across the region seems to be continuous over the period of change to modern human.

"but I only consider two possibilities"

Number 1 is completely out. I've managed to convince many people, other than you, of that. The Yemeni coast has never been easily passable. Extreme aridity and cliffs dropping shear to the sea, even at times of lowered sea level. Apart from any consideration of whether humans actually had any sort of boating ability that long ago able to cross the extremely treacherous Bab al Mandab.

As for number 2:

"the erasure of this early Western population in the form of much increased aridity and Neanderthal expansion"

By the time the Western population was 'erased' in the Levant they could have moved almost anywhere on earth, certainly into what is now Iran and perhaps northern India. Aridity could well have moved them out of the Levant, but surely the same aridity would preclude them from moving along the Yemeni coastline. The Neanderthals were genetically adapted to colder conditions than were modern humans so their arrival is not a surprise at all.

Maju said...

Please, notice the update: I had missed a quite interesting 2009 paper on this matter.

Maju said...

@Terry:

Why do yoy choose a 'faster mutation rate' explanation over the more obvious one? -

Which more obvious one? If you have a haplogroup with two sublineages, one of which has 20 mutations and the other only 12, logically the first one has a faster mutation rate in fact: accumulating more mutations in less time.

This should not bother you anyhow because it would make N older than just counting the mutations at the stem, as they would represent each shorter periods than in sister clade M.

But never mind because I do not have a clear opinion anyhow.

But surely most sublineages are in fact largely confined to particular regions.

Yes. But Soares does create "false subclades" of M-SouthAsia and M-EastAsia, which are not true sublineages but arbitrary (geographical) sets of many different ones. M is M and its subclades are each of its sublineages, not any arbitrary set of them.

Not really. Especially if the haplogroup has undergone a period of selection in that region.

Not credible for me.

Maju. I've provided a myriad of links proving that humans existed right across Central Asia from the Altai Mountains to the Upper Amur River long before modern humans had even first appeared.

If I recall correctly, you have provided references of Neanderthal presence in Altai at about the time of H. sapiens spread in tropical Asia and of cultural spread within H. sapiens cultural types and dates towards Mongolia and North China.

But whatever: living in Southern Siberia is not the normal behaviour of the naked ape, much less before the invention of the needle (which should not be much older than the MP-UP transition).

Number 1 is completely out. I've managed to convince many people, other than you, of that. The Yemeni coast has never been easily passable.

Do you recall a critical former British colony called Aden and Hadramaut (later Popular Republic of South Yemen)? It includes the excelent harbour of Aden. The coast of Arabia towards the Indian Ocean is not at all as you say, and anyhow all you say on this sounds to me what in Spanish is said "buscar tres pies al gato" (looking for the three legs of the cat), i.e. overly complicated arguments on something that is very simple for the common of mortals.

I was just yesterday discussing on this same matter with another person who argued that fresh water would have been a major problem for the founder migrants because, as we all know, seawater can't be drunk. I had to bother quoting a couple Wikipedia articles on how those regions are out of the Arabian Desert even in the rather arid conditions of today and how they even provided most of the grain for the British army of Iraq in the colonial period.

And not even a "ok, you're right, thanks" after that. Sometimes is like "why bother?"

Your far-fetched "reasoning" (wishful thinking) is the same kind of self-complacent speculation.

Maju said...

(cont.)

Apart from any consideration of whether humans actually had any sort of boating ability that long ago able to cross the extremely treacherous Bab al Mandab.

Well, this other person was arguing for "seagoing vessels" and sails instead to sort the distance between Djibouti and Pakistan, go figure!

There's absolutely nothing against the coastal migration as possibility. Whether it is the correct explanation or not is something that will be most difficult to tell (unless further archaeological evidence clarifies the matter).

By the time the Western population was 'erased' in the Levant they could have moved almost anywhere on earth...

I agree but "could" is not the same as "did". And the evidence is not sufficiently clear.

... but surely the same aridity would preclude them from moving along the Yemeni coastline.

Depends largely on when it happened and on whether they depended more or less on land fauna, which would not be the case if they were mostly fishermen and seafood gatherers, as proposed by the, pretty much mainstream, "rapid coastal migration" theory.

Even in very arid conditions the Indian Ocean strip of Arabia surely had enough adapted vegetation including much water resources in them, like coconut palm trees, cactuses, etc. If food could be gathered from the sea because of cultural adaptation then they could at least survive much like Bushmen in the Kalahari do.

Don't look for the three legs of the cat... I'm pretty sure it has four.

Ibra said...

“Loogväli concludes exactly the opposite, assigning to M an estimate age of c. 77,000 years and to N of 68,000 years”

This is not part of their conclusion but rather from an older (1996) estimate of M and N based on the HVS1 region. Check citation e for this study’s own revised calibration of Kivisild et al. (2006).

“Soares concludes that mtDNA N is older than M”

As do most papers. This could be explained if M and R arose around the same time (say 2-3kyr after N) and experienced a stronger initial growth phase afterwards. This explains the diversity of M and R compared to N elsewhere. The younger South Asian haplogroups may be an independent situation of M expanded in the late paleolithic rather than during OOA otherwise M would equal the diversity in South East Asia.

manju said...

Maju:
Will you agree if N is older than M then it should be Northern Route?

Think about American route. Even that route is difficult. But still that didn't become a barrier. But if you observe Native American density was in the South (sub-tropical or tropical regions) and not in the North. If it was Coastal Migration, nobody would have left India and moved SE Asia.

Maju said...

Hi, Ibra. Lon no see.

This is not part of their conclusion but rather from an older (1996) estimate...

Well, it's part of the paper. They do seem to think it is correct or they would have not otherwise published it.

“Soares concludes that mtDNA N is older than M”

As do most papers. This could be explained if M and R arose around the same time (say 2-3kyr after N) and experienced a stronger initial growth phase afterwards
.

I make absolutely no sense of this.

M and N are sister clades and the stem of M is clearly shorter 3 to 5 if we consider only CR mutations. M also shows a clear signal of explosive growth (star-like sturcture with almost 40 distinct branches) that can only be explained if they were the pioneers in Asia (or the clearly dominant group within them).

Instead R is more like N, with less than 20 top-tier sublineages and clearly minor in South Asia, where it must have originated attending to diversity. If M and R expanded simultaneously, R should be quite more important numerically in South Asia and M and R should be coupled nearly everywhere, which is not the case.

For me M represents the early Eurasian expansion and N just a minor branch of it. However some N and most R could have been involved in a secondary East to West flow, maybe associated to the expansion Y-DNA MNOPS.

The younger South Asian haplogroups may be an independent situation of M expanded in the late paleolithic rather than during OOA...

That would not be M anymore but specific sublineages within it. Otherwise is trying to describe N based on whatever U6 did.

Maju said...

Maju:
Will you agree if N is older than M then it should be Northern Route?
-

No. Even if N is older, pre-N carriers surely followed the tropical route. The Northern route makes no sense whatsoever.

Think about American route. Even that route is difficult. But still that didn't become a barrier.

But we are talking of much more recent dates. Claiming that Altai would have been populated before India is like claiming that Beringia would have been populated before SE Asia.

I really don't understand what do you guys see in such far-fetched theories.

Maju said...

If it was Coastal Migration, nobody would have left India and moved SE Asia.

Why?

First they were clearly nomadic in their lifestyle.

Second they probably had some kind of boats that they used for that mobility, as well as for regular foraging.

Third why would not they cross into SE Asia, having about the same climate and conditions as South Asia?

Fourth, with such a population explosion as the M starlike signature so strongly suggests, demographic pressure would quickly increase, leading those groups in the edges to move further into the virgin lands, most of which were towards the East.

Only when the East was similarly dense would the demic pressure become balanced in Tropical Asia, causing the two regions to split more and more due to that geographic funnel around Bangla Desh. It is precisely at that time when we see (according to my earlier flirtations with the MC) increased pressure towards the edges: NE Asia and West/Central Eurasia, which were less immediate targets for expansion in the early stage.

Maju said...

Notice that N and its R derivative are only found in significative figures at the edges of the expansion scenario. That is, IMO, because they had no (or not much) room to expand where M had become dominant early on, but they were more successful at the frontier areas.

Maju said...

By the way a quote for Ibra and Manju from Endicott's paper:

The lacuna in South Asia appears to be even greater because there is sound genetic evidence that population expansion in modern humans commenced here substantially before other regions outside of Africa [35].

Reference #35 is: Atkinson, Q.D. et al. (2008) mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human
prehistory. Molecular Biology and Evolution 25, 468–474

Which I have not read (I believe) but you may want to anyhow.

Maju said...

Oh, yeah. I have read it: pretty impressive...

terryt said...

"If you have a haplogroup with two sublineages, one of which has 20 mutations and the other only 12, logically the first one has a faster mutation rate in fact: accumulating more mutations in less time".

Not logically so at all. Older is more logical, although the number of mutations on a line is presumably a function of how many novel mutations have actually survived to in turn produce more novel mutations.

"M is M and its subclades are each of its sublineages, not any arbitrary set of them".

True. But because M is not a European or Jewish clade it has not been asigned so many separate letters, unlike N. Nor have the basal connections been studied so intensely.

"living in Southern Siberia is not the normal behaviour of the naked ape, much less before the invention of the needle"

Yet 'primitive' Neanderthals managed it. And interestingly all the papers I provided claimed it was very difficult to say when modern humans actually replaced Neanderthals through the region. Just using the arrival of microlithic technology as a marker is completely inadequate. Australian Aborigines did not have such a technology when they first entered Australia, yet no-one seriously claims they were not 'modern'.

"The coast of Arabia towards the Indian Ocean is not at all as you say"

Take a look at these links:

http://en.wikipedia.org/wiki/Bab-el-Mandeb

Quotes: 'The Bab-el-Mandeb ... meaning "Gate of Tears" in Arabic ... derives its name from the dangers attending its navigation' Hardly an ideal crossing for anyone without sophisticated boating technology. Unless you believe there were no tides in those days.

And this picture of the Yemeni coast:

http://www.visualgeography.com/pictures/yemen_5_3.html

Ideal shellfish gathering environment I'd say. And don't go claiming that lowered sea level provides a four lane highway along the coast. It doesn't.

"M also shows a clear signal of explosive growth (star-like sturcture with almost 40 distinct branches) that can only be explained if they were the pioneers in Asia"

I agree. Probably post Toba. The fact that N doesn't seem to have partaken of that expansion argues that it wasn't actually even there. It was somewhere else. On the other hand R was able to expand through India at some later date, probably because of some new method of exploiting the environment. Your comment, 'Notice that N and its R derivative are only found in significative figures at the edges of the expansion scenario' further suggests N was not involved in M's expansion in India. Otherwise it would also be relatively common there.

"However some N and most R could have been involved in a secondary East to West flow, maybe associated to the expansion Y-DNA MNOPS".

Ahh. Now we're getting somewhere.

Maju said...

Not logically so at all. Older is more logical, although the number of mutations on a line is presumably a function of how many novel mutations have actually survived to in turn produce more novel mutations.

We are considering lineages as they exist in present day people. "Older" does not apply: all must be equally old. But accumulated mutations are in fact different in almost any two individuals, specially if they belong to two different sublineages.

But because M is not a European or Jewish clade it has not been asigned so many separate letters, unlike N. Nor have the basal connections been studied so intensely.

That was surely true in the past but nowadays, with so many Asian researchers involved, and the growing curiosity about the role and details of M in general, this is not true anymore.

Except for the letters thingy, of course - but remember that A, B, C and D were named so because they were found among Native Americans. Not sure what's the story behind this curious detail though. Sincerely, I would not mind some radical rationalization of the mtDNA nomenclature, as it was done with Y-DNA nine years ago.

Yet 'primitive' Neanderthals managed it.

Some people still think they were very hairy. I would not be too surprised... otherwise how do you explain that they occupied areas that our species could only occupy after the invention specialized multilayer clothing? Try living in Altai or Russia today without proper clothes! Even here is practically impossible...

And interestingly all the papers I provided claimed it was very difficult to say when modern humans actually replaced Neanderthals through the region. Just using the arrival of microlithic technology as a marker is completely inadequate.

Blade technology. Microliths belong to a later period (even in South Asia, that has the oldest dates.

If you first have Neanderthals with Mousterian and then Sapiens with pseudo-Aurignacian, well, the conclusion is just automatic, unless you are obsessed with something. It's just like Chatelperronian and true Aurignacian where I live: cultural change and species change must have been the same process.

It's not blade tech as such but the cultural change associated to remains of two different species. We could have more evidence, I guess, but the one we have is clearly sufficient.

Take a look at these links.

Selecting what you want to hear. I could argue that sea levels were much lower, that the strait is scattered with islands, that you are chosing the rocky areas in the photos and not the beaches, that they crossed by further north in the Red Sea, that after all crossing into Australia is much more challenging... but you have your pre-made opinion and won't listen, so why bother?

Maju said...

Probably post Toba.

Or pre-Toba or who knows. Jawalpuram continuity shows clearly that Toba was not any absolute barrier nor caused the death of nearly everybody.

The fact that N doesn't seem to have partaken of that expansion argues that it wasn't actually even there. It was somewhere else.

In Yemen or Oman maybe, just that it was not N yet but pre-N (L3*). Maybe it arrived just a few generations later or...

It was close enough to take part and even play a major role in the second part of the expansion, but along with M. But anyhow there could have been other L3 or just L lineages involved that do not exist anymore too. Drift happens.

On the other hand R was able to expand through India at some later date...

R expanded FROM South Asia, not "through". This means that some N sublineages had arrived there before (and apart of R, there is N1'5, N2...)

Your comment, 'Notice that N and its R derivative are only found in significative figures at the edges of the expansion scenario' further suggests N was not involved in M's expansion in India.

I am of that opinion, yes. But I would not argue for N-carriers bearing any special ability necesarily, after all it could only cause a minor impact in the already densely populated South Asia, while, if being somehow more fit, its impact should have been much greater, I imagine.

In general I tend to reject the vision of M and N as signs of two different populations: it's naive. They did not make genetic tests back then, you know.

"However some N and most R could have been involved in a secondary East to West flow, maybe associated to the expansion Y-DNA MNOPS".

Ahh. Now we're getting somewhere
.

Where? I'm not so sure what this means in the fine detail: just a backflow.

terryt said...

"R expanded FROM South Asia, not 'through'".

You don't 'know' that. You just assume it because it fits your theory.

"it could only cause a minor impact in the already densely populated South Asia"

Even today the population of South Asia is not evenly distributed through the subcontinent. Perhaps the particular environment N and/or R was able to move into was unoccupied.

terryt said...

"Not sure what's the story behind this curious detail though".

The first work was done by North American researchers so they looked first at their indigenous people. Less controversial (and fewer lineages) than looking at Europeans.

"Some people still think they were very hairy. I would not be too surprised... otherwise how do you explain that they occupied areas that our species could only occupy after the invention specialized multilayer clothing?"

Hair covering hasn't let any other apes move so far north so I doubt that hair alone would heve let Neanderthals do so. I suspect they had skin coverings of some kind and certainly so for their dwellings. The change from Neanderthal to modern is far more complicated than usually assumed.

"I could argue that sea levels were much lower"

No more than 100 metres lower, at which level the coast would still look much the same, perhaps with even fewer beaches.

"that the strait is scattered with islands"

Still a horrendous rip, perhaps even more than at present because of the narrowed channel.

"you are chosing the rocky areas in the photos and not the beaches"

They would still have to move past those extremely steep rocky areas.

"they crossed by further north in the Red Sea"

If they did that why on earth would they then move south to the Yemen coast?

"after all crossing into Australia is much more challenging"

By then they'd had plenty of time and reason to produce a functional boating ability.

"but you have your pre-made opinion and won't listen, so why bother?"

That's what we call the pot calling the kettle black.

Maju said...

I KNOW (as far as knowledge is possible) because of the much greater basal diversity of R in the subcontinent. MtDNA R coalesced in South Asia almost for sure.

Maju said...

You just assume it because it fits your theory.

"Cree el ladrón que todos son de su condición", Castilian saying that translates: "the thief believes that all are like him". ;)

I don't generally have theories which I would try to make the data fit in. I generally try to look at the data on its own merits and draw my hypothesis and theories from it. It's much more serious.

Maju said...

Hair covering hasn't let any other apes move so far north so I doubt that hair alone would have let Neanderthals do so...

Some monkeys do live quite far north, in Japan. They have thick furs, naturally. However, unlike macaques, Neanderthals used fire with normality. But we have absolutely no evidence that they were able to produce efficient clothes.

Having evolved in Ice Age Europe, unlike our species, it is only logical to suspect that they had some good biological adaptations to cold since the time of H. erectus and H. heidelbergensis.

No more than 100 metres lower. I've read that as much as 200 but 100 meters can be a lot anyhow.

They would still have to move past those extremely steep rocky areas.

If these were at the coast back then. Anyhow we humans are good climbers and can walk as well as navigate. I don't see the problem: Basque coasts also have such kind of rocky coast but we have been mariners since "always" (and by "always" I mean at least Magdalenian times). Yemenis have also traditionally practiced navigation and Aden was a most important harbour, though there were others.

You just have a problem of selective blindness: does not fit with my theory, hence I fight it by all means I can imagine. They are silly counter-arguments anyhow that lack much weight.

If they did that why on earth would they then move south to the Yemen coast? -

Why not? It's an inhabitable area, unlike the Arabian Desert to the north of it. I imagine that some small groups were crossing and even settling there since soon after the L3'4'6 split, as L6 looks more Yemeni than properly African.

By then they'd had plenty of time and reason to produce a functional boating ability.

And earlier too. In fact they had much more time between mtDNA Eve and the L3 split than between L3 and the M and N spread that characterize that peripheric migration into Sahul. The apportion is 36 basal mutations to the L3 node to 4/5 mutations to M and N. In the simplistic assumption that mutations reflect homogeneous time spans, it's 9 to 1 and 7 to 1 respectively. And we know that H. sapiens was living in the Horn area some 160,000 years ago (at least!)

terryt said...

"I imagine that some small groups were crossing and even settling there since soon after the L3'4'6 split, as L6 looks more Yemeni than properly African".

Imagine, yes. I wouldn't place too much emphasis on the L6 evidence, especially when we turn to the Y-hap evidence. The downstream haplogroup J seems to be the earliest in the southern Arabian peninsular, and the first to cross the water to Socotra.

"And we know that H. sapiens was living in the Horn area some 160,000 years ago (at least!)"

True. But no evidence whatsoever that they were living on the other side of the Red Sea so far south.

"Basque coasts also have such kind of rocky coast but we have been mariners since 'always' (and by 'always' I mean at least Magdalenian times)".

Magdalenian is a lot more recent than the times we're talking about here, and I have no doubt at all that boats were widespread by Magdalenian times.

"And earlier too".

But in Wallacea humans had the opportunity and an ideal environment in which to experiment safely with open water travel. Many closely spaced islands spread through relatively sheltered seas. This environment doesn't really exist elsewhere in the world.

Maju said...

True. But no evidence whatsoever that they were living on the other side of the Red Sea so far south.

True but do you think that there has been much archaeology in the area as of late? Or just in general?

Lack of evidence as such is not evidence of lack.

Magdalenian is a lot more recent than the times we're talking about here, and I have no doubt at all that boats were widespread by Magdalenian times.

Well, I'm of the opinion that whatever existed in Magadalenian times, also existed in Gravettian and Aurignacian times. I have already mentioned more than once how it seems most likely that people crossed Gibraltar strait in large numbers c. 20,000 BP.

Like in Yemen we find little or no Y-DNA evidence of such crossing but the mtDNA speaks volumes.

And Magdalenian is nothing but a slightly refined Aurignacian anyhow. In fact their difference is mostly a matter of mere radiocarbon dating, not really typological. So probably the early colonists of Europe already knew of boats and most of what is found at the late UP.

But in Wallacea humans had the opportunity and an ideal environment in which to experiment safely with open water travel.

That is nothing but a hypothesis. You don't build anything on mere speculations.

terryt said...

"That is nothing but a hypothesis. You don't build anything on mere speculations".

I don't know if you've ever been boating, or even involved in any sport at all. But you have to have the opportunity to perfect your technique to achieve anything in either activity. To become good at boating it is necessary to be able to travel short distances for practice to start with. And there has to be a motive to do so. There's no way anyone would be able to launch out into something like the Bab al Mandab in a boat without perfecting his technique elsewhere.

Refering back to one of your earlier comments regarding Austronesians giving up farming and taking up hunting and gathering. I mentioned to my brother I'd been having an internet discussion with someone who claimed it was unlikely anyone would give up farming to take up hunting just because prey was easily available in a new region. His comment was that it was obvious the person had never been either farming or hunting.

Maju said...

I have a permit and I have used small boats for profesional reasons in the past.

I have also suggested that the crossing of the Red Sea might have happened further north or whatever. Eritrea and Somalia are very arid regions that have nevertheless first quality fishing areas. Fishing and related activities has always been a productive activity in the area and also further in Africa, at the Great Lakes and rivers and along all the coast. I see absolutely no reason why "magically" they would be excluded from having boats and, instead, a few generations later, their descendants in Wallacea, also full of weirdo currents and risky atolls, would suddenly come up with the bright idea just because it pleases your imagination.

Sorry but I don't have to swallow that story: it's all in your mind. Even if you'd be right, you would not be able to produce any evidence in either sense.

So the possibility remains and is perfectly realistic.

terryt said...

"Fishing and related activities has always been a productive activity in the area and also further in Africa, at the Great Lakes and rivers and along all the coast".

Always? And in boats? What evidence can you provide?

"Wallacea, also full of weirdo currents and risky atolls"

What?

Maju said...

I can't provide any conclusive evidence for boating in the remote past, the same you can't either.

What? -

It's a meeting point between two Oceans, what do you think happens there?

I recall that Heyerdal had a very rough landing in that area and could not control the Kon Tiki direction after an otherwise very safe oceanic journey. And that's far more advanced than the usual canoe.

I really don't have any idea why would you think that the Malay Archipelago waters, with the many narrow straits connecting large bodies of water, would be safer than Bab el Mandeb or Gibraltar strait. Logically interoceanic flows are serious forces to take in account.

Though maybe you are an experienced sailor who has all his life navigated through Indonesia: a modern and real Sandokan, are you?

terryt said...

"Logically interoceanic flows are serious forces to take in account".

'Interoceanic flows' are not involved at all.

"I recall that Heyerdal had a very rough landing in that area"

You're confused there. The Kon Tiki expedition never got anywhere near Wallacea. From memory it finished in the Austral Islands, south of Tahiti.

"It's a meeting point between two Oceans, what do you think happens there?"

Again you're confused. What two oceans? The region consists of relatively sheltered seas: The Banda, the Celebes, the Sulu and the larger South China Sea. Even the Molucca Sea is fairly sheltered, and all were probably much more sheltered during times of lowered sea level. As for islands, Indonesia has over 17,000:

http://en.wikipedia.org/wiki/List_of_islands_of_Indonesia

I can't be bothered counting the number of islands in Malaysia:

http://en.wikipedia.org/wiki/List_of_islands_of_Malaysia

As for the Philippines, 7000 odd:

http://en.wikipedia.org/wiki/List_of_islands_of_the_Philippines

Plenty of opportunity to practice voyaging between islands.

"I can't provide any conclusive evidence for boating in the remote past, the same you can't either".

Sorry. People could not have reached Australia/New Guinea other than by boat. To argue that H. erectus could only have reached Flores by boat is incorrect. Elephants reached there also and I doubt they had boats. Wallaces Line is not a very thin, precise line. Apart from birds creatures from Sunda and Sahul did manage to move a little way into Wallacea but not right across it.

Maju said...

You are right about the Kon Tiki. It arrived to Tuamotu.

What two oceans? -

The Indian and Pacific oceans, of course. There are zillion of currents that travel along the many islands and channels as result of this. Maybe there are some sheltered areas but I know that there are also very strong currents.

Sadly Wikipedia is not to informative on the matter. I have searched but no info in either sense, just some maps showing that there are in fact currents between both oceans.

I know from memory that coral "seeds" generated there can reach very remote areas just because of those currents. But I can't detail at this moment how dangerous are the Indonesian waters (except for a long list of shipwrecks).

I also know that interoceanic flows in South African coasts make the region quite tricky to sail.

But don't desperate: Riel-Salvatore mentions today a new paper (paywall surely) that, among other stuff, shows that early Japanese (proto-Ainu?) already crossed open bodies of water:

"... the importance of watercraft use and island colonization as important innovative behaviors, and their discussion of the human settlement of the Japan archipelago to illustrate this is quite good, drawing on both 'paleobathymetric' data and obsidian sourcing studies that show that obsidian traveled across open bodies of water to reach several Upper Paleolithic Japanese sites".

Paraphrasing the Italian astronomer (or rather his legend): "e pur si navigate!"

Maju said...

Also Terry, digging in my bookmarks, I've found an interesting site that is clearly apologetic of the coastal route and people living "since always" at mangroves and other coastal areas.

Mangroves: "Mangrove forests may not be suitable for pleasant afternoon country walks, but many very sane people choose to live in the midst of them.

Where else could you find freeway for your boat (your major transport), free takeaway sewage services, fresh food for the taking, and no mosquitoes?"

No mosquitoes? I did not know that. Sounds good. :)

terryt said...

"No mosquitoes? I did not know that".

The reason you didn't know it is because it's not true:

http://medent.usyd.edu.au/fact/saltwet.htm

I'm not at all convinced by the arguments in your link praising life in the mangroves. If life in them was so luxurious how come the world's mangrove forests are virtually uninhabited today?

"The Indian and Pacific oceans, of course".

The main exchange between those two oceans occurrs south of Australia. Those waters are in fact very dangerous.

"early Japanese (proto-Ainu?) already crossed open bodies of water"

And you're surprised by that? I've been telling you for years that there seems to be an ancient connection between Australia and the Sea of Japan. At times of lowered sea level the Sea of Japan becomes even more land-locked than it is today. And the Yellow and East China Seas become dry land, or at least island-dotted, bounded on the seaward side by the expanded Ryukyus. At such times Taiwan provides the connecting link between the South China and East China Seas.

So, back to the connections between the Sea of Japan and Australia. For a start many people imagine some sort of connection between the Ainu and the Aborigines.

Turning to Y-chromosomes: C1 in Japan, related C4 in Australia. Providing a continuity between them we find C6 in New Guinea, C2 in Wallacea and various C*s around the South China Sea. What date do you see for their diversification?

Now mtDNA: Y/N9 around the Sea of Japan, especially at the northern end, and related S in Australia. Does their diversification coincide with that of Y-hap C's? Providing a continuity between mtDNAs Y and S we find R, in the form of P, B/R11 and F/R9/etc. (although many mtDNA R lines seem actually to be associated with the expansion of Y-hap SMKNOP).

This cosy little pattern suggests that Y-hap C/mtDNA N were the first to live along Eurasia's eastern coastal margin. Further, it looks as though members of Y-hap F/mtDNA M expanded independently into South/SE Asia through the forested hill country from India, mixing with the earlier inhabitants and eventually themselves crossing Wallace's line to reach the forested hill country of New Guinea (in the form of Y-haps S and M, and mtDNA Q, along with a few other M-derived mtDNA lines).

Maju said...

Your link does not say is not true. It seems to be a problem specific of the high tides areas and not of the regular tide mangrove marshes.

Mangroves are not ideal for civilization but they do provide excellent habitats for nomadic peoples it seems to me. Tidal marshes are among the most productive environments on earth as far as I can tell.

The main exchange between those two oceans occurrs south of Australia. Those waters are in fact very dangerous.

But it also occurs in Indonesia. Of course more water will go through the wider passages but more pressure (and hence stronger currents) will exist at the narrow passages of Indonesia and Malaysia.

This is only logical if you think about it.

And you're surprised by that? -

I am not! You with your Wallacean theories is the one who should be.

For a start many people imagine some sort of connection between the Ainu and the Aborigines.

Imagine... Data, hard facts, is what we need. And there is no such connection at least in genetics.

Turning to Y-chromosomes: C1 in Japan, related C4 in Australia.

Meh, that's like saying G in Caucasus, S in Australia. By that logic all can be related at some level (i.e. OoA and subsequent Eurasian expansion).

Now mtDNA: Y/N9 around the Sea of Japan, especially at the northern end, and related S in Australia.

Or related I in Denmark or J in Morocco. What the heck: all is N!

Does their diversification coincide with that of Y-hap C's? -

Can't say. But I know all them are Eurasian lineages that spread soon after the OoA most likely.

It's impossible to reason with you because you have a pre-determined idea that conditions all others. It's the "lightbulb over the head" syndrome. :(

terryt said...

"I am not!"

Why did you feel it necessary to mention it then? Surely once humans in East Eurasia had boating technology to reach Australia moving around islands just to the north near Japan would present no problem.

"But I know all them are Eurasian lineages that spread soon after the OoA most likely".

It's most unlikely they all spread at the same time. That's like saying all Y-hap R haplogroups spread at the same time. For some reason you believe that ancient haplogroup dispersal was completely different to that of more recent times. Surely it is over to those who claim such a fundamental difference to provide evidence, rather than it is for those who claim much the same processes have always occurred. The present is the key to the past is a basic concept in geology, and can be expanded to most, or all, other sciences.

Y-haps C1 and C4 obviously have a closer ancient connection to each other than either does to any member of Y-hap F. The same with early mtDNA haplogroups.

Maju said...

Why did you feel it necessary to mention it then? -

Because they are unrelated to Wallacea precisely.

Surely once humans in East Eurasia had boating technology to reach Australia moving around islands just to the north near Japan would present no problem.

Or vice versa. I have absolutely no reason to think that the colonization of Japan is more recent than that of Australia. In fact in the past mini-analysis of mtDNA in this blog, Japan appeared to have colonized before Sahul.

It's most unlikely they all spread at the same time. That's like saying all Y-hap R haplogroups spread at the same time. For some reason you believe that ancient haplogroup dispersal was completely different to that of more recent times.

No, no and no. No to each of the sentences above.

Whatever the case, we are not going to be able to solve the age of Y-DNA C with the few data we have now. That's the main reason why I really don't work anymore with Y-DNA for anything: because mtDNA is easier to understand in its totality and is much less dependent on research geographic biases.

Y-haps C1 and C4 obviously have a closer ancient connection to each other than either does to any member of Y-hap F.

I don't think so: F and C are brother lineages and hence F basal sublineages and C basal sublineages are cousins. If anything, I'd dare forecast that C sublineages will eventually be shown to be grouped geographically, i.e. C1'3 and C2'4. It's only logical when you have an idea of the general genetic landscape, where East Asian/American and Australasian/Negrito branches are "opposite", divergent, rather than specially related.

terryt said...

"I'd dare forecast that C sublineages will eventually be shown to be grouped geographically, i.e. C1'3 and C2'4".

Possibly so. But the Cs separated from the Fs at some stage, and have a common origin of some kind. Well, CF broke into C and F to be more exact. You claim that the breakup occurred while CF was still in India, and then both C and F expanded together. Founder effect is responsible for the current geographic distribution. I suspect the Cs and the Fs expanded at separate times. And quite possibly from separate regions. And this is responsible for the current geographic distribution.

"I have absolutely no reason to think that the colonization of Japan is more recent than that of Australia".

That puts the occupation of Japan at 50,000 years. Possible.

"Or vice versa".

Actually that agrees with what I've suggested at times. And fits the haplogroup evidence, as I pointed out earlier. The very first Australians (Y-hap C and mtDNA N) moved down the coast from further north. The next lot were the ones whose ultimate origins lie in India, the F-derived Y-haps and M derived mtDNAs.

"Because they are unrelated to Wallacea precisely".

If we've been correct in saying that the origin of the first Australians lies to the north then people round the Sea of Japan and in Australia are both quite intimately connected to Wallacea.

terryt said...

Sorry to take up more space on your blog but I'd like to sort out your envisaged scenario for ancient human migration. Please correct the elements of the following that are incorrect:

You hypothesise that at some time before the Toba eruption of 70,000 years ago modern humans crossed the Red Sea in primitive boats. Whereupon they migrated along the forbidding Yemen coastline. They crossed the Persian Gulf near the Strait of Hormuz and then proceeded along the equally forbidding Makran coast.

At the mouth of the Indus they immediately adapted to life in the incredibly productive mangrove forest, an idyllic environment which, for some obscure reason, humans have since largely abandoned. And, interestingly and incredibly, no humans remained behind anywhere along this route between Africa and India.

These humans of the Indus mangroves next again rapidly adapted to a new environment and spread through Pakistan/India some time before Toba erupted, remaining restricted to that subcontinent for at least the next 20-30,000 years. But around 40-50,000 years ago they suddenly expanded further again, but in no more than just two groups, one moving east and the other west, each containing a wide variety of haplogroups.

The western group moved onto the so far unoccupied Iranian Plateau, and from there ultimately reached Central Asia and Europe. The other group was able to move east through the highly desirable mangrove swamps of what is now Bangladesh (Again subsequently abandoned until humans were able to more recently clear the mangroves and farm the region).

From the mangroves of Bangladeash humans were able to next reach Australia/New Guinea and Japan, and most points in between (including the Andamans).

The modern haplogroup distribution is simply the result of founder effects established during these two rapid expansions out of India.

Am I correct? Is that how you see it?

terryt said...

Sorry. One more thing.

"It's only logical when you have an idea of the general genetic landscape, where East Asian/American and Australasian/Negrito branches are 'opposite', divergent, rather than specially related".

But that divergence may be only a little more than 50,000 years old.

Maju said...

You claim that the breakup occurred while CF was still in India.

I really don't know. In what regards to me it might even have happened in Africa before the OoA, just that there were drifted out by the spread of E. Or it might have happened in West Asia if the OoA went that way, or might have happened in India too. I just can't say.

What I know is that D and C look like minor localized founder effects with a spread center in SE Asia, what makes them parallel to mtDNA N probably.

That puts the occupation of Japan at 50,000 years. Possible.

Or 100,000 maybe. I really can't say at this stage of research.

If we've been correct in saying that the origin of the first Australians lies to the north...

I have not said that. Certainly I don't think Australian Aborigines originated in Japan nor anywhere as far north. At best, both early Japanese and Australians would have a common origin in mainland SE Asia, a corridor they must have passed by at some point in their journey from Africa.

Sure SE Asia is north of Australia but quite south of Japan. I know how you like to use ambiguous phrases like these ("to the north") to bring the discussion into confusion and I think it's dishonest.

You hypothesise that at some time before the Toba eruption of 70,000 years ago modern humans crossed the Red Sea in primitive boats.

I don't know, man. But I understand that it's a fairly reasonable possibility that can't just be rejected upfront as you do.

They crossed the Persian Gulf near the Strait of Hormuz.

I understand that there was no Persian Gulf at that time: it's a post-glacial feature.

... and then proceeded along the equally forbidding Makran coast.

This is almost unavoidable, yes, unless they sailed all the way from Oman to Sindh, which was probably beyond their possibilities. It'd be also unavoidable if they went through inland routes because further inland it's even much worse.

But no warm coast is really "forbidding": they provide seafood and coconuts (at least).

Also the GIS simulation makes the coastal route almost unavoidable between Iran and Pakistan and between Pakistan and India.

the incredibly productive mangrove forest, an idyllic environment which, for some obscure reason, humans have since largely abandoned.

Sorry but people still fish over there.

And, interestingly and incredibly, no humans remained behind anywhere along this route between Africa and India.

Who says that? Remember L6, which seems more Yemeni than Ethiopian in fact. There are also some rare M lineages in Arabia, though they can be backmigration products.

Maju said...

These humans of the Indus mangroves next again rapidly adapted to a new environment and spread through Pakistan/India some time before Toba erupted, remaining restricted to that subcontinent for at least the next 20-30,000 years.

No. I have no problem with them adapting to "new environments" as long as they are tropical enough but I don't think they remained restricted to South Asia for long. As soon as the expansion began, they were knocking at the gates of SE Asia, quite obviously.

But around 40-50,000 years ago they suddenly expanded further again, but in no more than just two groups, one moving east and the other west, each containing a wide variety of haplogroups.

No. I think that the expansion to the East is older, maybe not much older or maybe much older. It belongs to the M expansion episode, not the later R expansion one, which can be the result even of some backflow from the East.

The other group was able to move east through the highly desirable mangrove swamps of what is now Bangladesh (Again subsequently abandoned until humans were able to more recently clear the mangroves and farm the region).

How do you know they were abandoned?

From the mangroves of Bangladeash humans were able to next reach Australia/New Guinea and Japan, and most points in between (including the Andamans).

Yes. Not just the mangroves of BD but also those of Burma etc. And not just the mangroves but also the hills and valleys.

Areas like the Ganges Delta (maybe an estuary in the past anyhow - now under the sea) and the Irrawaddy and the Mekong and the other rivers were surely important centers for early human expansion. Most likely they went up and down the rivers and also, as you say, along the coast (and through the hills and whatever was not too cold).

The modern haplogroup distribution is simply the result of founder effects established during these two rapid expansions out of India.

Roughly yes. There was a secondary expansion center in SE Asia anyhow, as shown by the 12-point star of N (much smaller than the 40 point star of M, and its many secondary stars).

Am I correct? Is that how you see it? -

Rather not. I am not sure of many things but I'm sure that exploitation of coastal and riverine routes along tropical Asia was central to the process.

But that divergence may be only a little more than 50,000 years old.

How do you know?

Maju said...

Did you read about the Crete finding anyhow? Looks like either H. erectus boated a lot or H. sapiens did very early on.

terryt said...

"What I know is that D and C look like minor localized founder effects with a spread center in SE Asia"

So you choose 'minor localized founder effects' for absence of C or D through much of Eurasia yet, for the absence of C, F or CF in Africa, you choose 'drifted out by the spread of E'. Surely it's just as likely that C and D have been 'drifted out' by the expansion of F-derived haplogroups.

"Sure SE Asia is north of Australia but quite south of Japan".

And, especially at times of lowered sea level, connected all the way by a series of closely spaced strings of islands.

"because further inland it's even much worse"

Depends on how far inland you go. Historically most immigrants have entered India from the northwest. My guess is that this entry point goes back a long way, probably even to H. erectus times.

"Areas like the Ganges Delta (maybe an estuary in the past anyhow - now under the sea)"

It would still have been dense mangrove swamp. The ecological zone would simply shift.

"How do you know?"

Many people claim that Y-hap A first appeared just 60,000 years ago. If that is so then Y-hap C itself cannot be older. C is still more recent than whatever date you care to postulate for Y-hap A. I'll grant that the diversification of C may go back 100,000 years if your comment, 'Or 100,000 maybe. I really can't say at this stage of research' is relevant. But that makes a C y-hap connection in the direction Japan to Australia even more likely.

Maju said...

Surely it's just as likely that C and D have been 'drifted out' by the expansion of F-derived haplogroups.

Fair enough.

Whatever the case the original proto-Eurasian population (still in Africa) had both DE and CF most likely (maybe in the form of CF'DE. Unless you want FC to have been wandering in Asia for longer (but D has been argued to be the oldest East Asian clade).

IMO the survival of C and D (Eurasian variant of DE) in East Asia (as well as of mtDNA N probably) responds to the logic of the spread in SE Asia, with probably many isolated populations since the beginning (unlike in South Asia where isolation was then the exception, not the rule).

Depends on how far inland you go. Historically most immigrants have entered India from the northwest...

Only after the domestication of horse and camel. Neolithic spread via Balochistan.

It would still have been dense mangrove swamp. The ecological zone would simply shift.

Possibly (but notice that we are talking of the Ice Age anyhow). Whatever the case the landscape was different with much larger areas in the Bengal Sea available for human exploitation and also with a drier Bengal (as it is now).

Many people claim that Y-hap A first appeared just 60,000 years ago.

That's a ridiculous claim. Even the more common 100,000 BP is probably too low. Y-DNA A probably dates from the same time as mtDNA L1.

But that makes a C y-hap connection in the direction Japan to Australia even more likely.

Meh. Both C and O might well have spread in East Eurasia along the coast. In fact I would think that all oriental lineages did, more or less.

But these processes of spread were anyhow much more complex necesarily that the simplified vision of just a few arrows on a map. After all, if we are dealing with, say, 20,000 years, then that means c. 7000 generations, each of which surely moved something in one or another direction or even in several different directions. Even the best estimated arrow on a map will only capture a tendency and never the whole complexity.

terryt said...

"But these processes of spread were anyhow much more complex necesarily that the simplified vision of just a few arrows on a map".

We're certainly in agreement there. Yet earlier you said, 'Both C and O might well have spread in East Eurasia along the coast'. Perhaps you meant 'at different times'. I'd then definitely agree.

"but notice that we are talking of the Ice Age anyhow".

Not if we're talking pre-Toba. And you mention, 'Even the more common 100,000 BP is probably too low'.

"Only after the domestication of horse and camel. Neolithic spread via Balochistan".

By one and a half million years ago Australopithecus/H. habilis/H. erectus (a tropical species surely) was able to move as far north as the Caucasus foothills (40 degrees north). I'll grant the later tropical species, H. sapiens, may not have been able to reach that particular region because of competition with Neanderthals. But we have no idea how far H. sapiens had moved north at the period their fossils first appear in the Levant (before the Ice Age ushered in by Toba's eruption). But if tropical H. erectus could survive so far north surely tropical H. sapiens could too.

Anatolia is really just the western extension of the Iranian Plateau ecological region. I'm sure we can presume that H. erectus was spread across the whole region, even if only along the lower slopes of south-facing mountain ranges. Certainly as far north as the southern shore of the Caspian sea.

Homo erectus also appeared at an early date in Northern China, as far north as 40 dgrees (at Zhoukoudian). If you're postulating an emergence from Africa before the 70Kya Ice Age there's no reason at all why H. sapiens could not also have rapidly reached Northern China, especially as it seems that savanah grassland has always been the Homo genus' first choice of habitat. In fact movement onto the savanah is often postulated as the reason for our upright posture in the first place. And the Bushmen of South Africa are usually held up as a great example presenting the lifestyle of our earliest ancestors.

Expansion through this ecological zone before adapting to any other environment, such as mangrove swamp or any other coastal environment, is the most likely scenario. Certainly Occam's razor would suggest as much.

"Y-DNA A probably dates from the same time as mtDNA L1".

I wouldn't be so sure. It's certainly not necessarily so.

Maju said...

Yet earlier you said, 'Both C and O might well have spread in East Eurasia along the coast'. Perhaps you meant 'at different times'. I'd then definitely agree.

Different time-frames is a reasonable possibility, with O spreading after C maybe. But it's not strictly necessary.

Not if we're talking pre-Toba. And you mention, 'Even the more common 100,000 BP is probably too low'.

For Y-DNA Adam!

The last Ice Age (or glacial period within the Quaternary Ice Age) began circa that date of 100,000 BP. Definitively after the Abbassia Pluvial it was all Ice Age with much lower sea levels everywhere.

By one and a half million years ago Australopithecus/H. habilis/H. erectus (a tropical species surely) was able to move as far north as the Caucasus foothills (40 degrees north).

And further north, as they lived in Europe too (I live North of 40 degrees and this is rather south in Europe). But Siberia certainly looks a lot more challenging. That's why all Siberia nowadays is still a semi-desert in demographic terms (i.e. almost nobody lives there, even with modern technology).

But we have no idea how far H. sapiens had moved north at the period their fossils first appear in the Levant (before the Ice Age ushered in by Toba's eruption).

We have no evidence of them existing further north, unless you want to mention the Japan tools, whose authorship we don't know at the moment. All other suspicious remnants are in the south: North Africa, India, south China...

But if tropical H. erectus could survive so far north surely tropical H. sapiens could too.

H. erectus is a catchall term for almost 2 million years of Homo spp. They had x10 time to adapt biologically or culturally or both. And anyhow they never reached much farther north than the rather mild climate of the Caucasus. Sochi is where the Russian elite goes to the beach, right?

Homo erectus also appeared at an early date in Northern China, as far north as 40 dgrees (at Zhoukoudian).

Seems like c. 40 degrees was their limit, right?

If you're postulating an emergence from Africa before the 70Kya Ice Age...

I'm not postulating either. I keep an open mind on the issue.

there's no reason at all why H. sapiens could not also have rapidly reached Northern China.

There is reason: genetic patterns are from south to north. Please! All are (pigmentation, Y-DNA, mtDNA, even autosomal). There is no single genetic pattern that links NE Asia with Europe skipping tropical Asia (except some very derived lineages that belong to late expansions of specialized groups).

Expansion through this ecological zone before adapting to any other environment, such as mangrove swamp or any other coastal environment, is the most likely scenario.

You're stubborn like a mule! It's like a hypnotizer saying "repeat with me: tropical savanna and arctic steppe are the same super-cool (erm... warm, erm... whatever) thing, mangroves are dangerous, people could no boat before they got the magic gift of navigation from Tangaroa in the sacred waters of Mindanao and Borneo. Repeat with me..."

Well, I happen to think that coasts and rivers are the most productive environments by far and that savanna is warm and that boats or rafts were used even by erectus peoples and that the waters of Indonesia are quite dangerous for unexperienced kids with canoes, unlike the Red Sea or the Mediterranean or the African Great Lakes or the many broad rivers that exist between the Congo and the Yangtze.

Certainly Occam's razor would suggest as much.

Certainly you're gonna make Occam get out of his tomb and proceed to operate your brain you with his razor.

"Y-DNA A probably dates from the same time as mtDNA L1".

I wouldn't be so sure. It's certainly not necessarily so
.

Now it's me who appeals to Occam. If Bushmen are mtDNA L0 and L1 and Y-DNA A... then... razor!

terryt said...

"If Bushmen are mtDNA L0 and L1 and Y-DNA A... then... razor!"

There's absolutely no reason at all that mtDNA L0 and Y-DNA A need have originated at anything like the same time. If you can't understand that then you desperately need to take a course in genetics. I accept that haplogroup dating is very imprecise, but virtually all studies suggest that mtDNA L0 is much older than Y-DNA A.

"unless you want to mention the Japan tools, whose authorship we don't know at the moment".

Little green men from space?

"Seems like c. 40 degrees was their limit, right?"

Where do they have to go very far north of 40 degrees? The links I've just provided at the Crete post show that climate has actually fluctuated greatly, even during ice ages. How long would it take to move east through the region?

"boats or rafts were used even by erectus peoples"

Can you find anyone else who would accept that hypothesis?

"I keep an open mind on the issue".

What?

Maju said...

There's absolutely no reason at all that mtDNA L0 and Y-DNA A need have originated at anything like the same time.

I meant L1.

There is no phylogenetic need (naturally: the two trees are different things) but there is common sense need. Bushmen don't have L2 or whatever else that could account for a "third wave". Y-DNA should therefore be about as old as mtDNA L1.

It's Occam's Razor at its best.

"boats or rafts were used even by erectus peoples"

Can you find anyone else who would accept that hypothesis?
-

I presume a lot do. But anyhow it's not my problem because I don't need public acclamation to think on my own: there is sufficient evidence in favor of boat usage at very ancient times. There is absolutely no evidence against it, just what in colloquial Spanish would be called "pajas mentales" ("mental masturbations").

terryt said...

"the waters of Indonesia are quite dangerous for unexperienced kids with canoes".

I'd bet, then, that by examining the directions of current flow in the Wallacean seas it would be possible for you to come up with the most likely first route across it. That would be the logical place to start looking for evidence. The first route is very unlikely to have been via Java and Flores. H. erectus/soloensis survived on Java until about 30Kya and Hobbits on Flores until 10-12Kya.

"I meant L1".

Makes no difference. My comment still holds.

"Y-DNA should therefore be about as old as mtDNA L1".

Not so at all. Both arose from some previous ancestor and it seems pretty well accepted that basal mtDNA is older than basal Y-DNA. Y-hap A may not have appeared until just before (or even after) mtDNA L3. And Y-hap CF need not have emerged from Africa at the same time as M and N (who also need not have emerged together).

"Bushmen don't have L2 or whatever else that could account for a 'third wave'".

I agree that both mtDNA and Y-DNA surviving haplogroups appear to have originated in southern Africa, but it doesn't follow that they necessarily arose at the same time. And we don't need to count 'waves'. Population movement was probably reasonably common.

"but there is common sense need".

Only for you, with your very limited perspective.

"I presume a lot do".

You 'presume'? Who?

"there is sufficient evidence in favor of boat usage at very ancient times".

No there's not. Only in your pajas mentales.

Maju said...

I'd bet, then, that by examining the directions of current flow in the Wallacean seas it would be possible for you to come up with the most likely first route across it.

I don't have enough oceanographic and specially paleo-oceanographic data to do that.

"I meant L1".

Makes no difference. My comment still holds
.

To me it makes all difference. mt-L1 and y-A should be similarly old. Otherwise you'd need to explain a male-only migration and gender-only genocide in the MSA. I don't see Bushmen nor other foragers doing that kind of thing, sincerely.

... it seems pretty well accepted that basal mtDNA is older than basal Y-DNA.

Molecular clock conjecture. It contradicts common sense and Occam's razor. I just can't take that at face value.

"there is sufficient evidence in favor of boat usage at very ancient times".

No there's not. Only in your pajas mentales
.

Not counting the issue of river crossings and Bosphorus crossing:

- Iberia: 900,000 BP
- Flores: unknown date but very old
- Crete: 130,000 BP

And people anyhow needed to cross rivers and lakes and swamps...

The evidence is overwhelming.

Maju said...

Who?-

Not only the authors of this study seem inclined to believe that, Julien Riel-Salvatore just replied to my question at his blog that he also suspects the same thing. There must be many others, otherwise the coastal migration hypothesis would not be so popular among academic circles.

terryt said...

"I don't see Bushmen nor other foragers doing that kind of thing, sincerely".

Ah. The Bushmen, a people noted for their extensive use of coastal resources and their advanced boating technology.

"mt-L1 and y-A should be similarly old. Otherwise you'd need to explain a male-only migration and gender-only genocide in the MSA".

Even amoung the Bushmen we find Y-hap is E. So we have 'male-only migration and gender-only genocide' with its arrival? Perhaps, to some degree. But surely it's more likely that A and B have been 'drifted out', as you term it. So pre-A could have been drifted out of populations containing L1.

"otherwise the coastal migration hypothesis would not be so popular among academic circles".

I can't begin to imagine why that would be so. Let's look at the supposedly close genetic connection between India and Australia, starting with Y-chromosomes.

The presence of Y-hap C in both regions doesn't help us. You've already pointed out that just because Japan has C1 and Australia has C4 doesn't mean at all there's any ancient connection. So the fact that India has C5 is similarly no indication of ancient connection.

We're on firmer ground with F-derived Y-haps. They are the most common Y-haps in India but they are certainly not so in Australia, and could well have arrived some time after its original colonisation. And surely the major haplogroups would have had the least chance of being drifted out during any migration from India.

We observe an even greater discrepancy between India and Australia when we consider mtDNA. India is dominantly M-derived (even when we include N-derived R), and Australia is almost exclusively N-derived. How can we explain that? Again surely it's much more likely that minor haplogroups would be drifted out rather than major ones. Why the discrepancy?

At some stage, somewhere, you commented that it looks as though N spread from the margins of an out of India migration containing mostly M. But the pattern makes much more sense if we are prepared to consider the possibility that N is the earlier migration, and M's expansion tended to drift out N haplogroups in regions it expanded through. But several N-derived haplogroups (notably R and its derivatives, but also X, A, N1/N6, N2/W and Y/N9) have since themselves expanded independently from the various regions to which they had been confined by M's expansion.

Ibra said...

Maju, the mutation rate decays over time rather than stay constant. What is your take?

Maju said...

Maju, the mutation rate decays over time rather than stay constant.

Over time backwards, you mean? That would make sense considering the effects of drift (and selective quasi-drift). Anyhow all is too sensible to population sizes and other ill-known variables.

Low population sizes would kill (by mere drift) nearly all novel mutations. Only few would make it and become fixated.

On the other hand, larger population sizes would allow many more mutations to happen and survive but not to become fixated.

It's damn tricky without knowing the population sizes involved.

What is your take?.

No take. I just distrust the method. It's not and can hardly be a C14 of genetics, just a wannabe. I think it can only be, in the best case, an approximation that should be always contrasted with archaeological data. And knowing which is "the best case" is most difficult only on the merits of the MC method alone.

Archaeology only can provide (where available) a trustful dates and other crucial data about prehistory. Where not available, it's much of a guess game.

For example, in Europe we know that there was a large demic expansion after the LGM and that the people involved had modern morphotypes (in the Med-Nord mesocephalic Caucasoid range). Instead we know that Neolithic spread through a double front (plus several other areas) and that in the Mediterranean at least caused no major population replacement, though must have left some genetic influence too.

So I radically distrust Neolithic replacement proposals, which seem to me extremely biased and ignorant of the almost necessary archaeological reference.

But in other areas archaeology is less conclusive. But maybe we can use Europe to synchronize the molecular clock with reality?

terryt said...

"Low population sizes would kill (by mere drift) nearly all novel mutations. Only few would make it and become fixated".

Not necessarily the novel ones. Occasionally a novel one would take over and drift out the basal one, especially in small populations or those fluctuating in size. This is what makes the molecular clock so unreliable, even assuming mutation rates to be constant (which, in itself, is doubtful).

"But maybe we can use Europe to synchronize the molecular clock with reality?"

Possbly. That's what I was hoping with the Basque/Irish separation, but it seems too recent to be of any value.

Maju said...

Sure, Terry, occasionally a new one would take over. But in general the novel mutations are at serious disadvantage at the early stages (1 vs. most) in the roulette of life, so we can perfectly assume that for very lengthy periods of time effective mutations simply would not happen (drifted out).

This is probably particularly true for fixed loci such as STRs and less true along the whole length of a chromosome such as Y or the mitochondrial DNA ring.

And, if I'm correct in my last observation, STRs are not a good reference to measure with the molecular clock. We need whole Y chromosomes or at least large normalized sections of the Y-DNA.

For example, let's take R1b1b2. We see that through a single haplotype stage (modal), many SNPs accumulated: all those between R1b1b2a1 and R1b1b2a1a (ok, random sample but looks like anyhow). This probably means that, at that point, there was a low population size and the expansion only happened later on.

So probably measuring age with mere STRs is misleading. However the longer the chain, the better, I guess. But the real thing would be to compare whole Y chromosomes or at least large representative fractions of them.

That's what I was hoping with the Basque/Irish separation, but it seems too recent to be of any value.

Should not be too recent. Probably late UP. You can also use larger sets like R1b, R1, R, P, each one includes a larger population for whom we may estimate a coalescent age based on archaeology. For instance my age for the P node is c.50-40 kya. We have a whole major lineage branching out since that date to probably c. 15,000 years ago. That's an archaeologically-supported timeframe. There can be others, of course.

Basques are anyhow not necesarily the best representative of Franco-Cantabrian region UP peoples anyhow. Other groups such as Gascons and Occitans in general should be also a reference. That's one of the reasons I always complain that France is under-researched.

Maju said...

Extending my previous comment on some minor details:

Probably late UP...

Well, either late UP or Epipaleolithic, that means 15-10,000 years ago, rather than just 15 Ky. After all Ireland was not colonized before the Epipaleolithic and we don't know of any possible continental origin for its "national" lineage. But in that timeframe anyhow.

Ibra said...

“Over time backwards, you mean? That would make sense considering the effects of drift (and selective quasi-drift). Anyhow all is too sensible to population sizes and other ill-known variables.”

It starts off at the pedigree rate (u) and then decays to a fraction of that rate. As a specific example, it starts out at (u), decays and then levels of at (3/4)u the further back in time you go. Check pp.7, figure 3 of Loogväli et al. The original assumption of geneticist is that the cure must be flat and straight, hence the oversimplified formula variance = 0.75*u*time. The curve is an L shape decay curve therefore there is room for an improved mathematical treatment.

Maju said...

That's what Henn says, right? I don't see that Loogväli proposes any clear method but Henn does appear to show an archaeologically-backed curve in which the pedigree rate would apply for 5Kya and later and the evolutionary rate for 15 Kya and before. However the intermediate section is ill defined: a mere blank area.

I really don't know. I can't have a take when the very premises of the MC seem so feeble and controversial. I prefer to see things from a non-MC perspective and use MC estimates only for what they really are: erudite guesses.

terryt said...

"After all Ireland was not colonized before the Epipaleolithic and we don't know of any possible continental origin for its 'national' lineage".

That's what I was getting at in comparing Basque/Irish P312 Y-haps. Surely the L21 mutation can't be older than 10,000 years. The other mutations within P312 may be of much the same time frame, some older some younger but not by a huge amount.

"Other groups such as Gascons and Occitans in general should be also a reference".

I think their R1b1b2 Y-haps are also P312 though. The U106 mutation does make it into France (so more work there would be illuminating) but U106 seems to be basically a German/Baltic haplogroup.

Maju said...

There may be other important subhaplogroups. Most R1b in SW Europe is surely R1b1b2a1 but does not fall in any known subhaplogroup. There are several known subhaplogroups but include only small apportions of all R1b.

There's too much "asterisk" yet around to be able to tell too much with too much confidence.

Maju said...

If one thing we can take from Balaresque's paper is that R1b1b2a1 seems to branch into 16 subclades. Each of them could be (should be) a distinct haplogroup and many look like having a SW origin (important Iberian share of the cake - we can't know about France without looking at the raw data - in at least 8 of them).

There's still a lot of research to be done before we get things straight in this issue of R1b. But at least I'm confident now that R1b1b2a1 (most of R1b and certainly most of R1b1b2) has a West or Central European origin.

terryt said...

"But at least I'm confident now that R1b1b2a1 (most of R1b and certainly most of R1b1b2) has a West or Central European origin".

That certainly seems to be the case for R1b1b2a1 as I see it. I'm less sure about R1b as a whole.

"R1b1b2a1 seems to branch into 16 subclades. Each of them could be (should be) a distinct haplogroup"

It seems most of those 16 clades group into two clumps though, U106 and P312. According to the reliable source, Wikipedia, the to groups tend to be distributed somewhat separately.

Maju said...

According to the reliable source, Wikipedia...

Wikipedia is as reliable as anybody. Always check the sources and if these don't exist or look doubtful, look for a second back-up source. Whatever the case, don't damn call Wikipedia "reliable" by default.

AFAIK in this case it's more or less correct. But could be not.

The case is not with the KNOWN structure but with the 90% of UNKNOWN structure in the SW. Seems that in the North the KNOWN haplogroups already span most of R1b1b2a1 but that's clearly not the case in the South.

Until we clarify that we will have too many doubts.