May 20, 2011

Major upheaval of human Y-DNA phylogeny: we are all 'A' now

Fascinating: reality never stops surprising us. All the basal phylogeny of human Y-DNA has been revised quite radically.


Now super-haplogroup BT, Y(xA) or (my personal favored name) B'CDEF is just a branch, a sublineage of A. And not just of A but of a fraction of a fraction of it:

Fig. 1
To the left we have the new basal phylogeny of the human Y-DNA. Please ignore the "time" axis. I'll get to that later.

We can well ignore the proposed nomenclature and begin talking of A as the pan-human lineage or "Y-DNA Adam". This primeval lineage split then into A1b (found at 8.3% among Bakola Pygmies and 1.5% among Mozabites) and A1a-T (or  Y(xA1b) or A1a'2'B'CDEF, using mtDNA's "superglue" nomenclature's fix-it-all method), which includes all the rest of the World's population. 

Don't worry too much about the nomenclature because it will obviously cause an upheaval in the naming conventions of at least A. All these names are surely just provisional.

Anyhow, this second lineage is yet split between A1a and A2'3'B'CDEF (A2-T in the graph). A1a is found mostly in Niger: among the Fulbe (14.9%) and their Tuareg neighbors (4.5%), as well as among Middle Atlas Berbers of NE Morocco (2.9%).  

Importantly Sudan and other large areas of Africa SE Africa, much of Middle Africa, were not sampled. But I'd say that this distribution is suggestive of an origin near Chad Lake in relation with the expansion of mtDNA L1. But I'd wait until we have results from Sudan because Sudan, notably the South, hosts huge Y-DNA diversity and a lot of Y-DNA A, so it cannot be ignored so easily. 

Using Wikipedia as quick reference, we can see that Y-DNA A1a has also been reported among several peoples of Guinea-Bissau (2.8-5.1%), notably the Mankanha speakers (7.8%). Also 5% of Mandinka from Senegal and Gambia, 2% of Dogon from Mali, 3% of Moroccan Berbers and 2% of unspecified Malians. Basically we can say that A1a is somewhat common (always at low frequencies) through West Africa. 

Frequency of Y-DNA A per Chiaroni 2009
However no further data on the crucially basal A1b lineage is found in this article at least. Anyone?

Besides, the next division is between A2, A3 and the remainder: B'CDEF (or Y(xA) or B-T). A2 is exclusively a Khoisan lineage, while A3 is split between Khoisans and the peoples of the Upper Nile (Sudan, Ethiopia...), having greater basal diversity in this last region (A3a and A3b2 are both Sudanese/Ethiopian, while only A3b1 is a Khoisan lineage).

In any case, the pattern found now in Y-DNA seems to suggest a flow from West or Central Africa to East Africa and then to Southern Africa (Khoisan peoples). This is somewhat contradictory with the pattern revealed by mtDNA (suggesting an origin in East Africa around where the oldest fossil H. sapiens are known to have existed, by the Omo river) or the pattern suggested by some autosomal diversity measures performed recently that proposed Southern or Central-SW Africa instead.

Typically they forget to (or could not) take samples in crucial areas like Angola (other than Khoisans), Mozambique, Tanzania (not even the Haza and Sandawe) or Sudan:

Fig. S1 (see: supp. materials).  
Red: A1b, green: A1a, black asterisks locations of A1a from other papers.

The technical differences between the old phylogeny and the new one are explained in detail and best perceived in fig. 2 (below). Besides of finding a large list of new SNPs, Cruciani et al. suggest that M91 is an unstable (and hence unreliable) location, while P108 and P97 are stable but were interpreted wrongly when first described, being the polymorphisms the ancestral ones, i.e. those identical to what is found among Chimpanzees. 

Fig. 2


Time-line absurdities

The authors propose a time-line for the human Y-DNA that makes no sense. Notably CDEF (CT) is proposed to have only 39 Ka, being more recent even that Aurignacian and several findings of Eurasian remains of H. sapiens (not even considering Skhul and Qahfez). It is also contradictory with so many proposals of Y-DNA timelines that suggest a CDEF age of c. 70 or 80 Ka. (Karafet 2008 for example), which I still consider a bit too recent - mind you. 

At the moment there two possible archaeologically consistent scenarios for the Out of Africa migration, one would have happened c. 90 Ka ago, reaching South Asia by c. 80 Ka (Petraglia 2010). The other one, proposed by Armitage this year (discussed here, see also here), would have the coastal migration by South Arabia happening c. 125 Ka ago and could have reached South Asia soon after. There could even have been two successive migrations.

As Y-DNA CDEF is central to the Out of Africa migration, it must have coalesced before this one happened. Unless one would argue for a back-migration of DE into Africa, what I find hard to sustain. Even if you'd do that, CDEF would have need to be consolidated c. 80 Ka ago at the latest.

That is double than suggested in this paper. It could be triple or even more. That would make "Y-DNA Adam" (everything else equal) at least as old as 285 Ka, surely more.

Of course, I am not believing a word on Y-DNA age estimates, because the hunches are so wildly different and so poorly argued (not to mention that no scientific proof was ever provided supporting such statistical methods) that it's a total waste of time.

The phylogeny however stands and is an invaluable piece of information.


Important update (May 27): Other possible populations with A1b

Argiedude believes that he had identified A1b lineages in a number of populations (based on other studies and using mostly STR haplotype sequences). He included this spreadsheet (should be available for a year) where the likely A1b individuals were identified by him as "A4". See the commentaries for further details.

The populations with possible A1b are therefore expanded from just two (Bakola Pygmies and Mozabites) to several, with a peak of frequency in Southern Ghana. Also in Gabon, SE Nigeria and Cameroon, and as isolated individuals in Zambia, Ivory Coast, Burkina Faso  (and then, of course, across the Atlantic in America).


Update (May 2 2012):

Marnie reports at her blog that A1b (the earliest splitting-branch) is now being renamed A0 and that it has been detected in an African-American man previously matched to modern Cameroonians from near Bouea.

Also the Family Tree Y-DNA A project has detected two branches of A0 (former A1b), although one is still a private lineage (too rare to be accepted as a distinct haplogroup).

128 comments:

  1. It is not that I like easy triumphalism (this was already hidden in the data), but this result matches exactly my prediction (except maybe time-line which I agree seems odd).

    Now the hard nut to crack is the CT haplogroups biogeography, how and when they did disperse.

    The hypothesis of an alternative dispersion route West asia-->East asia-->SEA-->Oceania-->SA-->CA-->Europe/CA-->America, in the opposite direction of the "mainstream southern route OOA", that I saw also hidden in the data when I studied this matter in deep, is still alive (I have to update my mental database with the new findings since last year, but I do not remember having seeing anything that falsifies it).

    See you, Maju, as soon as research advances eventually confirm this hypothesis.

    Aupa Kortatu !

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  2. Where was your "prediction" written down? I do not remember that "prediction"... but maybe is just my bad memory.

    "Now the hard nut to crack is the CT haplogroups biogeography"...

    What about this? I think I have that part pretty much "tamed", so to say and fitting with mtDNA patterns almost 100%.

    Of course there may always be a new "upheaval" and we need to rethink it all, but MNOPS was handy indeed.

    ..."SEA-->Oceania-->SA-->CA-->Europe/CA-->America"...

    Something like that but skip Oceania: those who crossed Wallace Line surely remained there.

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  3. "The technical differences between the old phylogeny and the new one are explained in detail and best perceived in fig. 2 (below)".

    Thanks Maju. Brilliant. However, like Carpetanuiq, I agree it is not entirely unexpected.

    "Something like that but skip Oceania: those who crossed Wallace Line surely remained there".

    I agree. However I'd place the back-migration of Y-haps P and O, and mtDNA R to somewhere near Wallace's Line.

    "Notably CDEF (CT) is proposed to have only 39 Ka, being more recent even that Aurignacian and several findings of Eurasian remains of H. sapiens"

    I agree that seems problematic. But note that the B/CT split is about 75,000 years ago. So the 7 mutations at the base of CT could have happened outside Africa. A situation I have long considered a possibility. It just means that E or DE have moved back into Africa. Where does DE fit in the diagram?

    "a CDEF age of c. 70 or 80 Ka. (Karafet 2008 for example), which I still consider a bit too recent - mind you".

    That fits the B/CT split very well though.

    "the pattern found now in Y-DNA seems to suggest a flow from West or Central Africa to East Africa and then to Southern Africa (Khoisan peoples). This is somewhat contradictory with the pattern revealed by mtDNA"

    But I keep telling you that there is no reason why mtDNA should correlate closely with Y-hap. In the pacific we see haplogroup swapping. So why not elsewhere?

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  4. "I'd place the back-migration of Y-haps P and O, and mtDNA R to somewhere near Wallace's Line".

    Do you mean MNOPS(xM,S)?

    IDK, Sundaland is indeed a favorite spot for the coalescence of MNOPS as such but Indochina would do (specially if M and S happen to be "brother" haplogroups, what I'm almost sure will be found eventually to be the case).

    But notice that this, in any case, would place the origin of NO, i.e. MNOPS after detaching from M and S (heading to Melanesia) and P (heading to Bengal and further West) in SE Asia. Which is what I have been arguing for all the time.

    But never mind... it'd be an off-topic matter. Just warning you about what your own thread may bring you to.

    "So the 7 mutations at the base of CT could have happened outside Africa".

    We still need all Australian and Melanesian haplogroups ready between 60 and 50 Ka., all European lineages ready by 48 or 40 Ka...

    Not to mention the much older colonized areas of South and East Asia.

    "Where does DE fit in the diagram?"

    After some thinking, I understand it's part of CT (= from C to T in alphabetical order), aka CF (current ISOGG nomenclature), aka CDEF or CF'DE (my favorites), aka Y(xA,B).

    "It just means that E or DE have moved back into Africa".

    I do not swallow that.

    "That fits the B/CT split very well though"

    That is also a problem because the B/CDEF split should be at least somewhat older than the OoA. Afer all most Africans who remained are CDEF (DE).

    In order to think otherwise, you'd have to get DE back-migrating into Africa... but with no women!!! In fact with Africa retaining huge female lineage diversity, not just in a small region but all across the continent.

    It's so weird that it is not acceptable.

    "I keep telling you that there is no reason why mtDNA should correlate closely with Y-hap".

    I think they should in most cases at least. And in fact I have been able to get them (before this revision at least) to match each other to some extent. What once was an impossible puzzle has become a reasonably easy one for me now.

    I have yet to ponder in detail how they can correlate after this revision but I already noticed a correlation of the oldest basal branchings with mtDNA L1, which is quite interesting.

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  5. "Do you mean MNOPS(xM,S)?"

    Yes.

    "We still need all Australian and Melanesian haplogroups ready between 60 and 50 Ka."

    Yes. That is a huge problem for the datring. Unless ... C and K repalced earlier haplogroups in the region, which I think is unlikely.

    "all European lineages ready by 48 or 40 Ka..."

    I don't see that as such a huge problem. Perhaps R-derived haplogroups were the first modern haplogroups into Europe. Previous ones died out. But again that seems unlikely.

    "That is also a problem because the B/CDEF split should be at least somewhat older than the OoA".

    Not necessarily so. Perhaps mtDNA M and N moved out of Africa with Y-hap CT. That fits your old diagram of African mtDNAs. L3 (including mtDNAs M and N) expanded with Y-hap BT at the 23 mutation mtDNA level, perhaps 75,000 years ago. If that is the case then earlier mtDNA L expansions are associated with the four previous Y-hap A expansions: A1b, A1a, A2 and A3.

    "And in fact I have been able to get them (before this revision at least) to match each other to some extent. What once was an impossible puzzle has become a reasonably easy one for me now".

    I'll even help you on the way:

    "I have yet to ponder in detail how they can correlate after this revision but I already noticed a correlation of the oldest basal branchings with mtDNA L1, which is quite interesting".

    Specifically the L1b, L1c and L2''6 separations at 9 mutations would be my guess. As you say in your original post:

    "A2 is exclusively a Khoisan lineage"

    Presumably associated with the original L0/L1''6 split in some way.

    "A3 is split between Khoisans and the peoples of the Upper Nile (Sudan, Ethiopia...), having greater basal diversity in this last region (A3a and A3b2 are both Sudanese/Ethiopian, while only A3b1 is a Khoisan lineage)".

    Presumably associated with mtDNAs L5, L2, L6 and L3'4 around the 13-16 mutation level. Then L3 moved around and out of Africa with Y-hap BT.

    "In order to think otherwise, you'd have to get DE back-migrating into Africa... but with no women!!!"

    Surely not all African women would have left with Y-hap CT. I'd guess there were plenty of women still there. You even suggest that to be the case:

    "with Africa retaining huge female lineage diversity, not just in a small region but all across the continent".

    ReplyDelete
  6. "That is a huge problem for the datring. Unless ..."

    Unless we ignore the tentative, speculative and unscientific dating for good.

    You are trying to place a non-zero value to the weight of TRMCA as evidence, actually a 10/10 somehow, miraculously. I totally discard it from the beginning.

    I can only accept date estimates that are based on serious data, like archaeological checks, realistic Homo-Pan divergence ages, etc. Your usual TRMCA are more like the jokes we made about economics in the faculty:

    There's a physicist, an engineer and an economist and they are in the middle of nowhere with a can of beans. The physicist proposes to open the beans applying certain funny laws of physics, the engineer does something of the like too and the economist then approaches the problem as taught in university: "let's suppose we have a can opener"...

    Similarly, the molecular clock statistician makes a lot of assumptions, suppositions and wild speculations and then reaches to a random (or pre-fabricated) conclusion that is absolutely trivial, except for the confusion it generates.

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  7. As for the A lineages, the problem now is precisely that A1b and A1a diverge before A2 and A3, while L0 diverges before L1 does.

    That's something that needs some meditation and I do not think that your vague discursive zig-zags point to anything of use: do they?

    As for DE back-migrating to Africa, there are two problems:

    1. Sure that there remained women in Africa but also men and that I do not see in the data.

    2. The diversity of DE is probably higher in Africa than in Eurasia and certainly than in West Eurasia, where the backmigration would have begun presumably.

    There's no particular indication of any backmigration into Africa south of the Sahara either, neither archaeological nor genetic.

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  8. "That is double than suggested in this paper. It could be triple or even more. That would make "Y-DNA Adam" (everything else equal) at least as old as 285 Ka, surely more."

    Thanks for reminding me about that, Maju. That's a really important point. A time of ~300,000 - 400,000 years is exactly the time when Neanderthals started to become isolated and gene flow between Europe/West Asia and Africa became severely limited, and also agrees with the recently published autosomal DNA time of last "point of contact."

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  9. In truth, we can't say that either because, in truth we do not know if the "age estimates" keep any proportion (what happened to different population sizes, etc.?)

    And anyhow I do not agree with placing the Sapiens-Neanderthal divergence so late in time at all. IMO it's from 1 million years or more.

    H. sapiens is NOT H. heidelbergensis but probably H. rhodesiensis, which may have began its divergence in Southern Africa, from H. ergaster - mind you. See here, among other entries.

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  10. AFAIK, gene flow between Europe and Africa has always been limited, even in recent times.

    If you follow the maps link: you do not see any appearance of contact between H. heidelbergensis and H. rhodesiensis.

    This is coincident with the latest (pre-OoA) archaeologically certain flow being with Acheulean, c. 900,000 years ago.

    That's, I understand the real divergence between our two species.

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  11. Maju,

    There are always two dates: one signifies when groups or sub-species became somewhat separated, the other is when they became virtually isolated. I agree with you that separation started early, likely at the beginning of heidelbergensis or just before. However, initially the Central European climate was a very mild, humid, sub-tropical one, which would have made both geographic gene exchange as well as compatibility easy. It is only much later that severe climate both separated the areas with cold, dry wasteland and drove evolution in different directions.

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  12. I am talking of c. 1 Ma for isolation: then is when we see the first transitional types in Europe (H. antecessor) and the first Acheulean out of Africa.

    And then is the good date for all corrections I need to apply with the Pan-Homo divergence in mind (often 50-100% more) for your usual TRMCA hunches to make any sense.

    I imagine that with the Sahara and then the Mediterranean in between isolation and beginning of serious divergence were about the same process. Of course, there can always have been some minor introgression after that but it's quite irrelevant.

    I do not think climate is that important in this process of divergence as totally different geographies, separated by seas and deserts. We are talking for example of many hundred of thousands of years of divergent coalescence in SW Europe and Southern Africa... only for the H. rhodesiensis and H. heidelbergensis to be perceived as such.

    After that both species begin expanding and eventually reach each other at the evolutionary level of Neanderthal-Sapiens - or similar (meanwhile there were many H. ergaster in between). but that is already at the OoA stage, some 100 Ka ago (grosso modo).

    All the rest is wild speculation and nefarious influences by that aged and stubborn Louisianan paleoanthropologist whose name can't recall right now.

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  13. "But notice that this, in any case, would place the origin of NO, i.e. MNOPS after detaching from M and S (heading to Melanesia) and P (heading to Bengal and further West) in SE Asia. Which is what I have been arguing for all the time".

    'Which is what I have been arguing for all the time'? You certainly have a very selective short-term memory. I remember the abusive comments you made when I first suggested that some K-derived Y-haps had moved back west from near Wallacea. The same reaction when I had the audacity to suggest the same for mtDNA R. You were absolutely certain in those days that virtually everything had moved from India in a series of unidirectional movements. And you still seem reluctant to accept anything other than unidirectional movenments, as demonstrated by your recent outburst concerning a back-movement by Y-hap M2a in the Pacific.

    I am certain that our whole evolution has been driven by movement back and forward of various human groups. And the scattered and sparse distribution of Y-hap A1b argues that it has been replaced through much of its original distribution by the back-migration of another haplogroup. I wonder what on earth that other haplogroup could be?

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  14. "I remember the abusive comments you made when I first suggested that some K-derived Y-haps had moved back west from near Wallacea".

    You do have a selective memory, I believe. Please quote or retrieve your accusations.

    I think that I explained to you that I had already considered that option (back-migration from Melanesia) myself but that I had discarded it for reasons of parsimony. That I suspected that most or all of that K in Melanesia was part of a single haplogroup (now known to be MNOPS).

    There could well be even less basal diversity in that part of the world that is apparent now but it's not a too researched area, so it may take many years before we know.

    "I am certain that our whole evolution has been driven by movement back and forward of various human groups".

    Well, I am certain that you are mostly wrong in your certainty. Mind you.

    "And the scattered and sparse distribution of Y-hap A1b argues that it has been replaced through much of its original distribution by the back-migration of another haplogroup".

    It does not need to be "migration", drift alone does that. We are talking of most of humankind's history: hundreds of thousands of years! A brutal time span... and it is still there!

    That's the amazing thing: how a lineage that should have been erased once and again if we are to hear to the population replacement mongers like you and so many others, is still there at very small levels, surviving migrations and even drift! An not in one population but at least two, two very different ones!

    People (and their lineages) seem to persist way more than you, Dienekes and others like to believe.

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  15. "You do have a selective memory, I believe. Please quote or retrieve your accusations".

    Your comments were made in response to this essay:

    http://humanevolutionontrial.blogspot.com/2009/06/human-evolution-on-trial-mitochondrial.html

    Your comments were deleted when Tim reposted the collection of essays.

    "It does not need to be 'migration', drift alone does that".

    Not an adequate explanation in This case. 'Drift' would hardly occur in a population with just one haplogroup, A1b in this case.

    "how a lineage that should have been erased once and again if we are to hear to the population replacement mongers like you and so many others"

    I have never claimed 'population replacement'. On the other hand I'm sure we can talk about 'population enhancement'.

    "People (and their lineages) seem to persist way more than you, Dienekes and others like to believe".

    They 'persist' but often at a reduced proportion.

    "Well, I am certain that you are mostly wrong in your certainty. Mind you".

    So how would you explain our evolution? A sweries of expansions of groups in which every single member has simultaneously undergone the same mutations?

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  16. Then you do have at least a long-lasting memory. Because that was many years ago.

    "'Drift' would hardly occur in a population with just one haplogroup, A1b in this case".

    Who said it was that way? You are the one associating single haplogroups with single populations, not me. I do not see that Western Pygmies have a single haplogroup: in fact they are dominated by lineages of the B clade, if my memory is correct.

    As mtDNA is usually more informative (and mtDNA suggests a Westward flow), I'd assume that the population first migrating Westward retained a Y-DNA diversity then lost in the East. But whatever, it's not like we're going to solve the problems of the world by clarifying this matter.

    "we can talk about 'population enhancement'".

    Uh?

    "They 'persist' but often at a reduced proportion".

    If they can persist from such deep levels in Africa, I see no reason why they should not persist in Eurasia, where they are bound to be of much more recent age in all cases.

    "So how would you explain our evolution?"

    IDK: but as we are a different species from all other known Homo ones, I presume that isolation and "luck" played a huge role.

    At least isolation at the level of Africa South of the Sahara, maybe (even if less intensely so?) at a regional level within Africa itself. Hard to tell but very possible.

    For me anyhow the people at Omo 190 Ka ago are already fully evolved modern Homo sapiens. So there is where maybe all began for us.

    "A sweries of expansions of groups in which every single member has simultaneously undergone the same mutations?"

    What?! If a population is small enough for a long enough time: all will have almost the same alleles because of inbreeding. It's inbreeding what creates new species but in huge swathes of time only.

    Admixture does not reinforce the formation of new species but actually dilutes and counters that process. Admixture is the anti-speciation process.

    If H. sapiens would have remained isolated in diverse populations for a million years or so, then each "race" would have coalesced into a new species eventually, just as Neanderthals did. But as the opposite is happening, H. sapiens will remain a single global species until extinction arrives (when and how: that's another debate).

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  17. "However no further data on the crucially basal A1b lineage is found in this article at least. Anyone?"

    It happens I totally identified this clade back in January, when I was looking in depth into y-dna A and B, precisely to uncover stuff like this. I wrote about this new clade in rootsweb:

    http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2011-01/1294013598

    But the file included there, with a map of the distribution of A1b, has run out of time in that site, so here it is again, reuploaded:

    A y-dna (2010 update).xls

    There's a map in this file showing A1b's distribution. The clade is called A4, since at the time I didn't know anything about its SNPs.

    I have more to say, but for now, I'm just hoping this lengthy post will make it through. I still haven't read everything you wrote, nor the comments.

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  18. A1b is not particularly associated with Pygmies. Here's a frequency table I constructed the other day.

    Frequency of A1b:

    5/242 2,0% Ghana, south
    4/1184 0,3% Nigeria, southeast
    1/266 0,4% Cameroon, southwest
    6/795 0,8% Gabon
    2/330 0,6% Baka Pygmies (Gabon, Cameroon, C.A.R.)

    N/A 0,5%? African Americans (USA, Brazil, etc.) [European y-dna excluded]
    2/1450 0,1% African Americans (USA only) [European y-dna excluded]


    Also, A1b couldn't be present in Bantus because of absorption via Pygmies, because in such case Bantus would have had to absorb 50 B2b lineages for every single A1b lineage they received from the Pygmies, but in fact, Bantus in west and central Africa have about 0,3% to 0,5% of either A1b and B2b.

    By the way, I would presume that before rearraning the entire naming system, they would invent a name such as pre-A, right?

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  19. How is it that you did not know about its SNP? I mean, you should have identified it as A1, right? Because P108 stands, only that the direction of the phylogeny is reversed.

    "Also, A1b couldn't be present in Bantus because of absorption via Pygmies, because in such case Bantus would have had to absorb 50 B2b lineages for every single A1b lineage they received from the Pygmies"...

    That's correct.

    It is very interesting anyhow. I would just make sure that you identified the clade correctly: how did you do that?

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  20. With A1b being, frankly, more associated with West African Bantus than with anyone else, plus the new hierarchy now establishing A1 as more basal than A2 and A3, and A1 is also unquestionably West African Bantu, well, how about that? The oldest clades of y-dna are found in West African Bantus, not the Khoisan, Pygmies, or East Africans.

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  21. There are not "West African Bantus", they'd be Niger-Congo (of which Bantu is a branch).

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  22. Maju, I identified the clade based on haplotypes, many of the samples weren't SNP-tested. From the few that were, I could tell that the clade was A+, A1-, and A3-. I wasn't sure about A2, but the haplotype modals were so bizarre that I thought for sure it must be a whole new clade of A, that's why I called it A4 in the xls file.

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  23. Errata:

    plus the new hierarchy now establishing A1 as more basal

    I meant to say A1a, not A1. My point was that A1b and A1a are [b]both[/b] associated with West African "Bantus" (Niger-Congo, as Maju clarified above), so this is pretty interesting, in light of the constant talk of the Khoisan and East Africans, and even Pygmies being a sort of cradle of mankind with the most basal lineages (which may well still be the case for mtdna, sure, but not in the y-dna, anymore!).

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  24. Regarding how I idnetified the clade, I forgot to add that last April, just 3 months after I wrote about "A4", a huge new study came out by Batini in which he tested hundreds of A and B samples, the most complete study of y-dna A and B yet. 2 of these samples were SNP-tested as A1b, and effectively, they belonged to the clade I identified in January, specifically to A4c. Bringing up another point about A1b ot being particularly associated with Pygmies. A1b can be clearly divided into 3 subclusters, and Pygmies, despite 330 samples, belong to just 1, as I noted above, but West African "Bantus" belong to all 3.

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  25. "You are the one associating single haplogroups with single populations, not me"

    But A1b is the oldest African clade, so what happened to A1b before any other mutation appeared? Presumably A1b made up the whole population unless it replaced some older clade. But, of course, you don't accept that clades can be 'drifted out' through the arrival of newer clades.

    "I'd assume that the population first migrating Westward retained a Y-DNA diversity then lost in the East".

    How can you say it was 'lost in the East' when you've just complained, 'how a lineage that should have been erased once and again if we are to hear to the population replacement mongers like you and so many others'. Are you arguing 'population replacement' in this case simply because once more it suits your belief?

    "As mtDNA is usually more informative (and mtDNA suggests a Westward flow)"

    Surely once you accept haplogroup replacement there is no need at all to see the basal Y-hap as coinciding with basal mtDNA. So it becomes quite possible to have a westward-moving mtDNA followed by an eastward-moving y-hap.

    "I presume that isolation and 'luck' played a huge role".

    Really?

    "For me anyhow the people at Omo 190 Ka ago are already fully evolved modern Homo sapiens. So there is where maybe all began for us"

    But they must have sprung from somewhere. It's surely unlikely they sprand from a population that had been isolated in Omo since H. erectus first evolved. You're even aware of the difficulty with such a belief because you wrote:

    "If a population is small enough for a long enough time: all will have almost the same alleles because of inbreeding".

    So it cannot be as simple as:

    "It's inbreeding what creates new species but in huge swathes of time only".

    New genes have to be introduced periodically, at which time selection acts on any new combinations available.

    "Admixture is the anti-speciation process".

    It is a necessary part of speciation.

    "If H. sapiens would have remained isolated in diverse populations for a million years or so, then each 'race' would have coalesced into a new species eventually"

    Obviously it hasn't remained isolated long enough to have become separate species. And it is most unlikely that any species since H. erectus has done so either. The regional variations of ancient human species presumably has much the same cause as the regional variation we see today. It's just that today:

    "the opposite is happening, H. sapiens will remain a single global species until extinction arrives"

    "A1b couldn't be present in Bantus because of absorption via Pygmies"

    Yes. It is much more likely that A1b entered Pygmies from West Africans rather than the other way round.

    ReplyDelete
  26. "(which may well still be the case for mtdna, sure, but not in the y-dna, anymore!)".

    I don't think you'll get Maju to agree with that. He is very much opposed to the idea of independence of mtDNA and Y-hap.

    ReplyDelete
  27. I'll see to upload the file as appendix to this entry with due warnings and explanations.

    "A1b can be clearly divided into 3 subclusters, and Pygmies, despite 330 samples, belong to just 1, as I noted above, but West African "Bantus" belong to all 3".

    Alright. That would make sense.

    I must insist into not calling West African "Bantus", because that's like calling Arab to Hebrews, Semitic to Cushitic and Berber peoples, Latin to Germanics, etc.

    While the Bantu subfamily of languages has a relatively recent origin (a few thousand years - comparable to Germanic or Romance languages maybe), Niger-Congo hosts A LOT more diversity, including families that may not be Niger-Congo at all in the end, as it's the case of the Mande and Ubangi linguistic families. In any case, they are not "Bantu", just like Greeks are not Latin nor Slavic.

    There are no Bantu languages West (nor North) of Southern Cameroon and there are not even Bantoid languages West of Eastern Nigeria.

    ReplyDelete
  28. "But A1b is the oldest African clade"...

    That's a fundamental misunderstanding: A1b and Y(xA1b) are exactly as old. A1b is only the oldest divergent (or minority) branch. But in any fork, both branches stem from the same point of divergence.

    Furthermore, this is not truly valid because the Y chromosome is never so completely explored, but just count the known mutations to A1b and A1a-T. The branch leading to A1b appears to be more than four times longer than the one leading A1a-T.

    This is not conclusive in any way but it's easy to think that A1a-T is in fact quite older than A1b (as we know it, not pre-A1b).

    I'd suggest to consider the alternative chronology of:

    1. A1a-T
    2. A2-T
    3. BT
    4. CT

    The others can't be measured because they do not include internal forks but they look all more recent than CT on first sight. It may be misleading but it is a possible interpretation that we should not discard. Seriously.

    Similarly, in the much more clear case of mtDNA, L1"6 is quite clearly older than L0, regardless than L0 is the first divergent lineage, much as A1b is in Y-DNA.

    "How can you say it was 'lost in the East' when you've just complained, 'how a lineage that should have been erased once and again if we are to hear to the population replacement mongers like you and so many others'".

    Please, drift! We are talking of the very beginnings of Humankind as we know it: population densities were surely very low and drift had a lot of time to act.

    "Are you arguing 'population replacement'"...?

    I am NOT arguing "population replacement".

    "... it becomes quite possible to have a westward-moving mtDNA followed by an eastward-moving y-hap".

    It does not make sense to me at all. First I cannot easily conceive female- only (or actually even male-only) migrant groups. But specially, I can hardly conceive "two Humankinds" at the beginning of all.

    It is much simpler when you realize that the first diverging branch is not "the oldest lineage". Often (but not necessarily) the larger lineage is the oldest one. That can be tested in the case of mtDNA with great accuracy: L1"6 is clearly older than L0, for example. However M is not older than the African L3 subclades most likely (it's not a rule, just a possibility that often happens).

    It looks like an interesting playground for puzzle-solving Me. I'll surely post on that eventually, when I have dedicated the matter enough time.

    "It's surely unlikely they sprand from a population that had been isolated in Omo since H. erectus first evolved".

    In Omo only not, but in a relatively limited East African area maybe yes.

    "You're even aware of the difficulty with such a belief because you wrote:

    "If a population is small enough for a long enough time: all will have almost the same alleles because of inbreeding"".

    And that is what we find in Homo sapiens, yes or yes? To me at least it looks as a rather homogeneous initial population that diverged (how many times have we read the word "bottleneck" regarding human initial history?). We cannot of course ignore the possibility that it interacted with other African "archaic Homo" but we know nothing about it at this point.

    I'll leave that open (because "la vida te da sorpresas") but for me it all begins at Omo (very roughly) with a high probability.

    ...

    ReplyDelete
  29. ...

    "New genes have to be introduced periodically"...

    Not necessarily, they do not have to. A relatively small population can have enough diversity. Unless you systematically breed with your cousins, generation after generation, inbreeding depression does not happen. A population of a few thousands should be perfectly viable on its own.

    Also H. sapiens has some unique traits that are difficult to explain if the proto-species systematically outbred. For example, admixture with other H. rhodesiensis/ergaster would have tended to reduce cranial capacity (quite obviously), so it was surely selected against (up to a point, I imagine). But most likely, from a given moment on, there was a whole region that only us inhabited, so outbreeding was not possible anymore but at the edges. That region was first a large chunk of East Africa and then all Africa south of the Sahara (and eventually the whole planet).

    Much is very speculative I reckon, but you are pushing me to speculate.

    "[Admixture] is a necessary part of speciation".

    No. I do not see it that way: reproductive isolation is what creates new species. New species aren't but forks of the old ones.

    Some admixture (introgression) may be unavoidable because the process of isolation is typically imperfect but that is not central to the process. At "best" accessory, at "worst" counter-productive (stops the process of speciation, of forking, reinstating the single original species).
    "It is much more likely that A1b entered Pygmies from West Africans rather than the other way round".

    Neither. Both retain some of the ancestral diversity and both derive to some extent from the same fork in early human history, as is apparent by the presence in both groups of Y-DNA B, mtDNA L1, etc. Just that while West Africans seem to have incorporated other lineages (second wave?), Pygmies did not (remained isolated).

    "He is very much opposed to the idea of independence of mtDNA and Y-hap".

    I am opposed to the idea of wandering amazon and male-only tribes, indeed. But there are even better reasons, with enough care and intelligence, both tend to converge from that apparent divergence and that is quite satisfying for those like me who expect men and women normally migrating together - even if also intermarrying with other groups, what makes the lineages' pairings change along time in a manner that can be confusing.

    ReplyDelete
  30. Argiedude: I'm thinking you may want to write the authors of this or the other paper with your finding. It looks important enough and you may at least get some credit for the discovery.

    ReplyDelete
  31. Argiedude: I'm thinking you may want to write the authors of this

    That's a thought. I think I will.

    or the other paper with your finding.

    The Batini study? I wish I could've been able to give them a few personal opinions before they started the tests. The most interesting thing I found of y-dna B is the existence of a cluster with a very distinctive haplotype, namely the presence of 392=13, almost unheard of outside of y-dna P (Q, R1a, R1b, etc.). And this cluster is located geographically almost on the northern half of the Sahara, including Morocco and Egypt. But incredibly, despite finding 2 dozen samples, not one of them had tested any downstream SNPs, just B. when the Batini study came out, I thought for sure the mystery would be settled, but they found just a single sample from this cluster... and they didn't test it (for downstream SNPs)!

    ReplyDelete
  32. "This is not conclusive in any way but it's easy to think that A1a-T is in fact quite older than A1b (as we know it, not pre-A1b)".

    A very good explanation.

    "First I cannot easily conceive female- only (or actually even male-only) migrant groups".

    No need to conceive of female- only migrant groups at all. But male-only migrant groups are by no means impossible. In fact at the margin of an expanding population we would expect the males to move beyond the originally correlated females.

    "I can hardly conceive 'two Humankinds' at the beginning of all".

    We seem to have at least three: African, Denisovan and Neanderthal.

    "L1"6 is clearly older than L0, for example".

    We have no way of knowing if it was 'older'. L0's expansion is more recent however.

    "However M is not older than the African L3 subclades most likely (it's not a rule, just a possibility that often happens)".

    And CT is not older than any Bs. In fact I would not be surprised if it's eventually shown that CT is just one B haplogroup, in the same way that mtDNAs M and N are just two L3 haplogroups. And in the same way that Y-hap E1b1b1b is no older than other E1b1b1s.

    ReplyDelete
  33. "And that is what we find in Homo sapiens, yes or yes?"

    Almost certainly no.

    "To me at least it looks as a rather homogeneous initial population that diverged"

    But if that population had been confined 'in a relatively limited East African area' for any length of time it would have become too inbred to have been robust enough to have expanded. I'll concede the 'initial population' may have only recently become isolated within a relatively limited area. But before than it would have been receiving genes from a number of sources.

    "Not necessarily, they do not have to. A relatively small population can have enough diversity".

    Only if it has just recently become 'relatively small'. I know that you are fully aware that single 'genes' do not act on their own. It is combinations of genes that are responsible for any character. One main product of hybridisation is that it gives rise to new combinations of genes. It may be mainly this fact that leads to hybrid vigour.

    "Unless you systematically breed with your cousins, generation after generation, inbreeding depression does not happen".

    Any population of any limited size will undergo inbreeding depression. In fact my old textbook claims that any population not infinitely large will undergo inbreeding, i.e. all species. In fact that's why individual species look much the same as each other.

    "Also H. sapiens has some unique traits that are difficult to explain if the proto-species systematically outbred. For example, admixture with other H. rhodesiensis/ergaster would have tended to reduce cranial capacity (quite obviously), so it was surely selected against (up to a point, I imagine)".

    Selection would eliminate any hybrids with reduced cranial capacity even after a hybridisation event. But such an event is quite possibly responsible for introducing other advantageous qualities to the admixed population. Hybrid vigour if nothing else.

    "No. I do not see it that way: reproductive isolation is what creates new species. New species aren't but forks of the old ones".

    That is very much 19th century, 'survival of the fittest', ideology. The idea was that some vastly superior population (in Victorian times obviously Europeans, especially European men) gave rise to new, superior species. In contrast, you have even blogged that evolution is no simple process.

    ReplyDelete
  34. "Then you do have at least a long-lasting memory. Because that was many years ago".

    But surely you remember when you finally had to admit that mtDNA R had also started out from SE Asia, after a long period of abusive, arrogant and wildly speculative denial of the possibility. On that occasion too you suggested I'd made a 'lucky guess'. So just have another read of the comment you made elsewhere:

    "My ignorance is parsimonious and conservative however, while yours is arrogant and wildly speculative. I'm likely to be right".

    ReplyDelete
  35. "Almost certainly no".

    Aren't we a single species? Aren't we very much homogeneous? Yes we are, indeed. That's because almost all of our genes are the same.

    And that's why I gain almost as much with the survival of a random Bushman than with that of my niece: their genomes are almost the same and almost the same as mine as well.

    "... it would have become too inbred to have been robust enough to have expanded".

    Mere breeder's theory. What happened to that finding that marrying your fourth cousin was somehow "ideal"? What happened to outbreeding depression?

    Also there may have been punctual introgressions of key genes while the rest remained "inbred". That is very typical in wild species - that's what the original meaning of the term "introgression" is in fact: species remain neatly apart but they exchange some key highly adaptive genes via short-lived, small, hybrid populations.

    "Only if it has just recently become 'relatively small'".

    Uh? I think the Onge look a very healthy people. They have been isolated for many many millennia.

    They are surely more extreme than the original "Humankind" (which was no doubt larger and more extended, as even a tiny fraction of Africa is a lot larger than the Onge island) but they clearly show that a tiny isolated population can be perfectly healthy (assumed no bacterial shock or genocide from cousins).

    "Selection would eliminate any hybrids with reduced cranial capacity even after a hybridisation event"?

    Why?

    Selection is something highly imperfect: whatever that doesn't kill you, is more or less viable. A smaller head is clearly viable, specially in cooperative species like ours, it even seems that brains have decreased somewhat since farming began.

    Obviously people with mediocre intelligences are highly fit while some geniuses are probably not so good for survival. Intelligence alone does not give you the edge.

    In fact selecting for a single trait such as a big brain is the same as inbreeding for such group of alleles, as all the "hybrid vigor" from smaller brain type genes is blocked. Each time that speciation selects one gene or set of genes it creates a genetic zone of "extreme inbreeding", where only one kind of allele exists.

    But it works.

    "That is very much 19th century, 'survival of the fittest', ideology".

    Not at all. It is the survival (as distinct species) of the different and isolated and (as ample but single species) of the indistinct and interbreeding. Humans were once the first category (speciation) but are now the latter (anti-speciation trend).

    "... you finally had to admit that mtDNA R had also started out from SE Asia, after a long period of abusive, arrogant and wildly speculative denial of the possibility".

    It all depends on what the evidence says. Once said A and then new evidence appeared and said B.

    I am scientific and flexible enough as to have said A when the evidence said A and B when the evidence said B. But you are stubborn enough as to have said B without any reason when the evidence clearly said A, and then, when it changed (expanded) and said B, you rubbed and still rub it once and again on my face with that "I told you" crap, not even realizing that it is precisely that "I told you" what makes you to be wrong because you followed your own unfounded opinion instead of the objective data.

    You were lucky enough to have reality side with your unfounded opinion but there's also that story about a donkey who accidentally played a flute, you probably know it, right?

    ReplyDelete
  36. Maju, was the article open access? Cause it isn't anymore, not even the supplements.

    Also, thanks for the clarifying comments regarding P97 and P108 (about them being originally misread). When the Batini study came out, the first thing I did was search for samples belonging to the "A4" cluster I observed before, expecting it to be a whole new lineage, and was disappointed when I saw it labeled as A1b. So it turns out it was a mistake and it really was a whole new lineage, hell of a whole new lineage, in fact.

    ReplyDelete
  37. I could access it freely then, now I get a message of "technical difficulties". I could not see anywhere it being "open access" (hence the unusual "freely accessible" tag) and I do not think I downloaded the paper (so I can't share a copy).

    It may have been a pre-pub free access period? Maybe. At the moment I thought it was too short (letter format) for to be closed. Anyhow AJHG (and PNAS) papers are accessible after 6 months of publication.

    As for the mutations, indeed: only one mutation (M91) was revised as unreliable. The other two were found to have been interpreted wrongly in the construction of the phylogeny, to be the Chimpanzee variant in A and A1 respectively.

    Then they also find new mutations defining A1a-T and A2-T.

    ReplyDelete
  38. "Where was your "prediction" written down?"

    In your blog (and maybe also in Dieneke´s). I´m quiet new in commenting in these biogeography issues and not very prolific so I´m sure you can find it. May I suggest you to use google ?

    ""Now the hard nut to crack is the CT haplogroups biogeography"...

    What about this?"

    Not that I have read the whole discussion thread in deep (137 comments !), but I think that TerryT does a good job demolishing the purported evidences you bring up to this discussion thread in order to show the validity of the southern route.

    By the way I´ve seen that Terry was claiming a northern route hypothesis before me, and I want to aknowledge it here, if I may. I wonder if he still sticks to this hypothesis or not.

    ReplyDelete
  39. So they first found M91, and being an STR-like unreliable marker, they happened to get it wrong. Then they found the reliable marker P97, but interpreted it according to its alignment with M91, which was wrong, so they interpreted P97 also in an erroneous manner.

    ReplyDelete
  40. "May I suggest you to use google ?"

    I doubt Google will find it: comments do not show up in their searches I believe. It's you who makes the claim anyhow, so it's your job to document such claims, not mine.

    "... I think that TerryT does a good job demolishing the purported evidences you bring up to this discussion thread in order to show the validity of the southern route".

    I do not think so but whatever rocks your boat - for every light there must be a shadow, I guess.

    I understand that the Southern Route is absolutely clear in the patterns of both mtDNA and Y-DNA and Terry is just being obsessive-compulsive about a fetish conjecture for which he has no evidence whatsoever.

    However, as it's a matter of belief, it seems... there's a point beyond which we can't debate anymore: I demonstrate once and again the Southern Route but for some the Northern Route is a matter of faith, as it is not of fact at all.

    "I´ve seen that Terry was claiming a northern route hypothesis before me"...

    There will be more people for sure, the northern route has been hanging around for long but never had any good logic behind: why would people adventure first to Siberia when they could stay in the Tropics? It's just weird! They began heading to Siberia when there was no more room in the Tropics, it seems very clear to me from mtDNA.

    ReplyDelete
  41. "Aren't we a single species? Aren't we very much homogeneous? Yes we are, indeed. That's because almost all of our genes are the same".

    And the vast majority of those genes are exactly the same as most of our predecessors.

    "Mere breeder's theory".

    Not so. Breeders practice.

    "What happened to that finding that marrying your fourth cousin was somehow 'ideal'?"

    Called 'line breeding' when done with domestic animals.

    "Uh? I think the Onge look a very healthy people. They have been isolated for many many millennia".

    And could you tell us where exactly have they expanded to?

    "Why?"

    Because that is what you claimed to be so:

    "admixture with other H. rhodesiensis/ergaster would have tended to reduce cranial capacity (quite obviously), so it was surely selected against"

    "Not at all. It is the survival (as distinct species) of the different and isolated and (as ample but single species) of the indistinct and interbreeding".

    Again that's a 19th century belief in the immutability of species.

    "But you are stubborn enough as to have said B without any reason when the evidence clearly said A".

    The evidence did not clearly say A. You simply refused to consider that it might say anything else. I agree that new evidence proved B, but the evidence was sufficient to prove B long before the decisive evidence was discovered. It's just that you could only see A because refused to consider any other possibility.

    "you rubbed and still rub it once and again on my face with that 'I told you' crap"

    Because you have learned nothing since then, as shown by:

    "You were lucky enough to have reality side with your unfounded opinion"

    As I pointed out above it was not an 'unfounded opinion'. You were simply too arrogant to see what the evidence actually showed. You were blinded by your belief.

    "that story about a donkey who accidentally played a flute, you probably know it, right?"

    No, I don't, but presumably it's totally irrelevant.

    "I understand that the Southern Route is absolutely clear in the patterns of both mtDNA and Y-DNA and Terry is just being obsessive-compulsive about a fetish conjecture for which he has no evidence whatsoever".

    There you go again. You cannot see the evidence because you refuse to see it. Time for me to provide a proverb: There are none so blind as those who refuse to see.

    "By the way I´ve seen that Terry was claiming a northern route hypothesis before me, and I want to aknowledge it here, if I may. I wonder if he still sticks to this hypothesis or not".

    Thank you. I have never doubted that Y-hap F and mtDNA M moved east via the 'southern route', but I still claim a northern route for Y-hap C and mtDNA N. But Maju's belief prevents him from seeing the evidence for it. So, like mtDNA R and Y-hap MNOPS, we will just have to wait until the evidence becomes blindingly obvious.

    ReplyDelete
  42. I thought it was a more universal story but it seems it's a Spanish one, written by a Basque (Tomás de Iriarte). It's a poem but also moralist fable and it's in all school curricula over here.

    A boy forgets a flute and the donkey smells it, accidentally producing some sounds by mere breathing. The donkey then begins: "How good I am at playing the flute. Donkey music is not that bad".

    You know.

    ReplyDelete
  43. In other words: Reality (defined by the facts we know) is the score to play. If you can only play do (C), you will always be wrong except when is time to play do.

    Occasionally Reality, the score, and your insistent monotonous sound will be in agreement but that is a mere fluke. Yet you, like Iriarte's donkey, pride on the fluke and claim merit that you totally lack for that.

    I thought you were smarter and I think that on occasion you do show hints of such intelligence but then you just overdo yourself again. Often it is smarter to shut up and meditate.

    And it is certainly not valid in any case to claim "merit" for a fluke and try to use that self-attributed "merit" to make yourself the infallible measure of all things prehistoric and genetic.

    That way you only make a fool of yourself. And it's sad. And it pains me to be forced to clarify this issue in such blunt terms. Yet I cannot leave it standing either.

    ReplyDelete
  44. @Maju:

    "why would people adventure first to Siberia when they could stay in the Tropics?"

    Who said Siberia ? It could be Siberia, steppe or silk road route. It depends on the climate at these times. The minimum energy principle suggests that the rule is as follows: once in Levant, when possible, expand over the most similar ecosystem. I do not buy the "scatter in all directions rule" unless all directions are symmetric. That´s not the case in Eurasia: tundra, taiga, steppes, deciduous forest and deserts. The colder the climate, the northern this latitudinal pattern and viceversa.

    ¿ O es que la flauta solo suena dónde hay madera, por ejemplo en Siberia ?

    @TerryT:

    We differ. I do not see any reason why C (the haplogroup, not the note) should had followed northern and F southern. Think about a C small population (the low mutation rate) through the northern route, then still small accross the coast with scattering through Oceania, until they reach India where the population explodes, higher mutation rates and therefore new haplogroups. That still makes compatible a northern route with F and derived Haplos originating in India. Is there some data I ignore that makes this scenario impossible ?

    ReplyDelete
  45. Must be Siberia (Altai). The Silk Road as historically famed goes further south but needs camels. (Steppe is an ambiguous term). Altai is the only known crossroads between West and East Eurasia north of the Himalayas.

    "... once in Levant, when possible, expand over the most similar ecosystem".

    The origin is East Africa, and the most similar ecosystem then was India (then largely savanna too). We do not even know with any certainty if the went to India through Levant, even if an expansion to (but not necessarily through) Palestine is part of the process.

    "I do not buy the "scatter in all directions rule" unless all directions are symmetric".

    I can agree with this: the most appropriate direction is therefore following the tropical ecosystem. Notice that South Asia (and also SE Asia to some extent at least) holds many commonalities with African ecosystems, first of all their tropical nature. In South Asia there are even lions and elephants, just like in Africa!

    ReplyDelete
  46. "Yet you, like Iriarte's donkey, pride on the fluke and claim merit that you totally lack for that".

    If that's what you believe, then so be it. I'm getting sick of pointing out how blind you are.

    "And it is certainly not valid in any case to claim 'merit' for a fluke"

    Maju, it was no 'fluke'. And are you claiming I managed a fluke twice? And I notice you've gone very quiet concerning Y-hap E1b1b. Another fluke on my part? Those flukes are becoming regular.

    "the most appropriate direction is therefore following the tropical ecosystem".

    Unlikely to be 'tropical' if, by that, you mean jungle. I'd agree with 'savannah' including scattered clumps of trees.

    "It depends on the climate at these times".

    Exactly.

    "We do not even know with any certainty if the went to India through Levant, even if an expansion to (but not necessarily through) Palestine is part of the process".

    But you did blog a recent paper regarding a moister period in the Arabian Peninsular. Such a moister period would surely make parts of the Iranian Plateau more habitable too.

    "In South Asia there are even lions and elephants, just like in Africa!"

    And until recently lions and elephants were widesprad through Asia and even in Europe.

    "Think about a C small population (the low mutation rate) through the northern route, then still small accross the coast with scattering through Oceania, until they reach India where the population explodes"

    I don't think you could make a case that Y-hap C has ever exploded in India. And C certainly reached Oceania only in the last few thousand years. However it has presumably been present in Australia and around Wallacea for 50,000 years or so.

    "That still makes compatible a northern route with F and derived Haplos originating in India. Is there some data I ignore that makes this scenario impossible ?"

    I suppose it is possible that F followed a 'northern route', but unlikely. We have basal F haplogroups such as G and IJ
    in Southwest Asia. To me it seems likely that they survive there from F's original movement through the region.

    ReplyDelete
  47. Oh. And back to an earlier comment:

    "Uh? I think the Onge look a very healthy people. They have been isolated for many many millennia".

    Like most people around the planet their haplogroups show they were originally a mixed people. Their mtDNA is basically Indian in origin (M) and their Y-hap is East Asian (D). The same holds true for most other surviving populations in regions marginal to human geographic expansion. Indigenous Americans y-haps are Central Asian (Q) and their mtDNA is East Asian (A,B, C and D). Polynesian Y-haps are mainly South Wallacean (C2) and mtDNA Southeast or East Asian (B). In fact modern haplogroup distribution shows most populations are a mix of populations. They have haplogroups with origins in several different regions. In other words a mix of populations who have undergone a period of 'reproductive isolation'.

    ReplyDelete
  48. "it was no 'fluke'".

    Then how did you "know"? You make so many claims with mere stubbornness and no evidence! This was one of them: the evidence pointed elsewhere (South Asia) but you insisted... until the evidence changed like a roulette and pointed to where you were playing.

    And you dare to claim "merit" for that?!

    "And are you claiming I managed a fluke twice?"

    I am not but that would be perfectly possible: you make a zillion claims, some must be right at some point, of course.

    The issue is not whether you get it right a posteriori by mere chance or divine revelation, I do not care if you are a visionary but whether you can get right according to the available evidence at any given moment, if you can be scientific. And that you don't seem able to.

    You lacked the evidence and yet you claimed that anyhow: you were wrong (according to available evidence back then) and that is what matters.

    Evidence, material info, rational expositions, logical conclusions! That is what we need not divine inspiration... or flukes.

    ReplyDelete
  49. "Unlikely to be 'tropical' if, by that, you mean jungle".

    I do not mean jungle, or not only that: I mean hot and without winters: the perpetual summer of the tropics that allows us to go naked all year round, the reason of our hairless and sweaty evolution.

    "Such a moister period would surely make parts of the Iranian Plateau more habitable too".

    I do not know and does it matter at all anyhow? Hypothesis is not evidence. Where are the likely H. sapiens tools? Bones? In India, in Arabia... but not in Altai until much later.

    "Like most people around the planet their haplogroups show [that the Onge] were originally a mixed people".

    Not true but it doesn't matter because they'd be just themselves in isolation for maybe 60 thousand years!!! The example stands no matter what. And there are a zillion of small island populations in other species that are perfectly healthy, totally dismissing the "inbreeding" theory.

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  50. @Maju:

    "Must be Siberia (Altai).etc..."

    Is it correct to extrapolate the situation of these areas during the last 2000 years to the last, let´s say, 60.000 years ? Do we have already complete and accurate paleoclimate data in these euroasiatic areas ? I doubt it.
    Same regarding the archeology and paleoanthropology of these areas.

    "The origin is East Africa, and the most similar ecosystem then was India (then largely savanna too)etc...." and "the most appropriate direction is therefore following the tropical ecosystem".

    The origin in East Africa hypothesis has been shattered by last findings. North africa is as well possible. Similar ecosystems in Africa and India is not enough: you still have to proove continuity (or at least not big discontinuity) of ecosystem from Africa to India, or could our ancestors fly ?

    @Terryt:

    "However it has presumably been present in Australia and around Wallacea for 50,000 years or so".

    This is a key data.

    "We have basal F haplogroups such as G and IJ in Southwest Asia"

    What do you mean by southwest asia ? could you please be more specific, i.e. quote countries. Are you referring to Anatolia and Levant and are you implying that F was present there before going into India letting populations that derived into G and IJ ?

    Again old presence of IJ and G in theses areas is perfectly compatible with my hypothesis. After havong crossed the northern route, SEA, Australia (this is what I referred to whan speaing about Oceania) and reaching India, some went to central asia splitting there in several branches: GIJ, MNOPS....

    @both: easy guys, let´s keep this interesting discussion within scientific parameters: hypothesis, evidences and arguments.

    ReplyDelete
  51. I am basing my claims about Altai on the available archaeological data, and also paleoclimatic one. There was only one narrow corridor all the time in the Ice Ages and that one went through Altai (West end) and Mongolia (East end). North of it: cold and huge lakes, south of it the desert, then the impossible Tibetan highlands and then the Himalayas.

    Altai has a long archaeological record, first associated with Neanderthals and Mousterian and then (since c. 40 Ka ago) to H. sapiens and related tecno-cultures of Western affinities: Altai "Aurignacian", Gravettian, etc.

    So I am extrapolating nothing, mind you. I have looked at the matter with some careful attention in the past before making up my mind.

    "The origin in East Africa hypothesis has been shattered by last findings".

    Uh? Tropical Africa in general if you wish.

    It is true that the South Asian MSA is most similar to South African and not East African one. But, unless they took an airplane, they must have gone via East Africa anyhow, just that we have no direct evidence of that (under water?)

    "North africa is as well possible".

    No. I do not think so. Not at all.

    "you still have to proove continuity (or at least not big discontinuity) of ecosystem from Africa to India, or could our ancestors fly ?"

    I have to prove nothing because this is not meant as "evidence" - just countering your discourse. It was you who began talking about climate, totally ignoring key issues such as temperature (until advanced clothing was designed and manufactured) and solar radiation (for vit. D until white skin evolved).

    I'm just pointing out that, based on climatic conditions, the logical thing is to stay as close to the Tropical Belt as possible. Because of temperature (we do not have body hair) and insolation (vit. D production). Believe it or not, our evolution as species is tightly adapted to the tropics and moving out of them, specially as far away as Altai, is a major challenge.

    ReplyDelete
  52. "Then how did you 'know'?"

    The situation for both Y-hap MNOPS (or K as I called it at the time) and mtDNA R relied on much the same evidence. Apart perhaps from the Himalayas, Wallace's Line has been the most difficult barrier to human expansion since H. erectus first reached SE Asia, although some did make it to Flores. However descendants of both the above haplogroups did manage to cross the line during the Upper Paleolithic, so presumably their ancestors were close by. That placed Y-hap K and mtDNA R in the region. Such a placement actually fitted all the available evidence, whereas placing the two haplogroups' origin in India didn't really fit. In the case of MNOPS we have NO to the north of SE Asia and P to the west. In the case of mtDNA R we also have the apparent lack of any ancestral N haplogroups in India, unless we regard R itself as such an ancestor. This latter is what you insisted on, refusing to consider any other possibility.

    "the evidence pointed elsewhere (South Asia) but you insisted..."

    It was you who 'insisted' on South Asia, for which there was really no evidence.

    "until the evidence changed like a roulette and pointed to where you were playing"

    Obviously I had been able to see the pointer before 'the evidence changed like a roulette'. In fact I deny that the evidence actually 'changed'. It just became more definite.

    "you make a zillion claims, some must be right at some point, of course".

    I admit that some claims are yet to be proved with such clarity, but I'm sure they will be.

    "whether you can get right according to the available evidence at any given moment, if you can be scientific. And that you don't seem able to".

    As I pointed out above the available evidence did actually support my claim. It was just that you were so convinced your theory was correct that you refused to consider any other possibility.

    "Evidence, material info, rational expositions, logical conclusions!"

    And that's exactly what I provided, but you were deliberately blind.

    "Not true but it doesn't matter because they'd be just themselves in isolation for maybe 60 thousand years!!!"

    What? Again you are being deliberately blind. There is no evidence for people on the Andamans until about 12,000 years ago. Of course they could have been there before that, but there is no evidence.

    "there are a zillion of small island populations in other species that are perfectly healthy, totally dismissing the 'inbreeding' theory".

    Most have only been on such islands for just a few thousand years.

    "I do not mean jungle, or not only that: I mean hot and without winters: the perpetual summer of the tropics that allows us to go naked all year round, the reason of our hairless and sweaty evolution".

    We have no idea when our 'hairless and sweaty evolution' occurred. Neanderthals, for example, could well have been hairless.

    ReplyDelete
  53. "Where are the likely H. sapiens tools? Bones? In India, in Arabia... but not in Altai until much later".

    That conflicts with this statement:

    "Altai has a long archaeological record, first associated with Neanderthals and Mousterian and then (since c. 40 Ka ago) to H. sapiens and related tecno-cultures of Western affinities: Altai 'Aurignacian', Gravettian, etc".

    So humans of some sort have been there a long time. And we have no way yet of knowing which of these humans represent the first 'modern' humans.

    "There was only one narrow corridor all the time in the Ice Ages and that one went through Altai (West end) and Mongolia (East end). North of it: cold and huge lakes, south of it the desert, then the impossible Tibetan highlands and then the Himalayas".
    So? Doesn't that fit the suggestion?

    "What do you mean by southwest asia ? could you please be more specific"

    G in or near the Caucasus, I in Eastern Europe, J through much of the Arabian Peninsular.

    "Are you referring to Anatolia and Levant and are you implying that F was present there before going into India letting populations that derived into G and IJ ?"

    Yes.

    "reaching India, some went to central asia splitting there in several branches: GIJ, MNOPS...."

    One thing Maju and I agree with each other on is that MNOPS is Southeast Asian.

    "@both: easy guys, let´s keep this interesting discussion within scientific parameters: hypothesis, evidences and arguments"

    Sorry. But Maju's attitude has annoyed me for a long time. Several times he has argued that I have come up with some 'crazy idea' and he refuses to consider it. Next thing the 'crazy idea' is proven and he claims i made a 'lucky fluke'. Who is the crazy one?

    ReplyDelete
  54. "The situation for (...) mtDNA R relied on much the same evidence".

    Nope. The evidence changed a lot for mtDNA R: first (for many years) most basal diversity was in South Asia and then, this year, it was in SE Asia. But you were arguing for the second solution with the first data set, what is wrong.

    "However descendants of both the above haplogroups did manage to cross the line during the Upper Paleolithic, so presumably their ancestors were close by".

    That logic could "support" even L2"6 to have coalesced in Sumatra. It's so sloppy and non-systematic that I really hate it. Instead of approximating the origin based on what is INSIDE the haplogroup or DOWNSTREAM of the node, you mix up and down, inside and outside with no method.

    My method is to estimate a centroid based on location of descendant haplogroups. That's the basic of my method and needs not to know the ascendant ones. Actually you cannot know the centroid location of upstream nodes until you determine the centroids for downstream ones. Because today we have only downstream data.

    After doing that for all haplogroups in a given set, I may agree to compensate towards the shared origin of the larger haplogroup (makes sense, I understand) but it's not the basic method: it is a correction, a refinement.

    In the case of R, with most subhaplogroups in South Asia and the rest almost equally split west and east of it (old data), the SA origin was natural conclusion. Yet you opposed it without any grounds.

    Then the flute made some sound...

    "There is no evidence for people on the Andamans until about 12,000 years ago".

    Their genetics is evidence of much older presence IMO.

    "Neanderthals, for example, could well have been hairless".

    It's possible but that's somebody else's problem (Neanderthals' problem), not ours. In any case they had solved some sort of adaption to cold weather quite obviously, at least to mildly cold weather. And we had not, not yet.

    ReplyDelete
  55. Since 125 and/or 90 Ka in Arabia, since 120 and/or 80 Ka in South Asia are not comparable with since c. 40 Ka in Altai.

    All are "long ago" but the former "long ago" is twice or thrice the latter. I believe that you can perfectly understand that and I fear that you only choose to ignore this difference in order to either:

    1. Annoy me.

    2. Make a pretense of defense of something indefensible... again. I really hate discursive cheaters, so you'd better not because it really annoys me.

    "And we have no way yet of knowing which of these humans represent the first 'modern' humans".

    Annoying repetitive nonsense (again). We have discussed this before and it is 100% clear that there was first a NeanderthalWithMousterian period and then a SapiensWithMode4 one.

    You just like to confuse everything so we cannot reach to any logic destination (unless that one is where you have decided in advance).

    Go debate with someone else and come back when you are able to have a logical respectful debate.

    ReplyDelete
  56. @Maju,

    Ok for the Altai corridor. It makes sense. The stubborness regarding tropical preferences of our prehistoric ancestors doesn´t.

    @Terryt:

    "One thing Maju and I agree with each other on is that MNOPS is Southeast Asian".

    Could you please summarize your position regarding the scattering of C-T across Eurasia ?

    Here is my position, very simplified and schematic of course. I´m not sure about the timing. I´m confused about yours. Sign / should be interpreted as parallel threads.

    West Asia / Levant (CDE)-->Levant (E) / EA (CD)--> E was a coastal group; expansion of E through mediterranean and red sea / assuming Maju thesis that the only possible corridor was Altai CD arrives to Amur river, Manchuria coast and and disperse south through the coast of China, then to te south SEA and India. Small group, low mutation rate. Some might have gone up through some rivers. This explains presence of D in Tibet and Andaman and C in Australia are renmants of this first scattering through EA. An offshoot of this group arrives to SA, where there were not previous AMH. There, haplogroup F arises. An offshoot of this F group goes to central Asia (through Hindu Kush) and there split into GIJ which goes west and K or MNOPS goes east to Xingjiang / Qinhai. From there this MNOPS haplogroup disperses across EA following river vectors to the east and the to the north (Yellow, Yangtze, Mekong, Salween. See this map: http://www.japanfocus.org/-Brahma-Chellaney/2458). GIJ is around the Caucasus and spread to Europe during Neolithic times.

    If this scenario is correct, there must have been some time in the past where haplogroup E was predominant or even unique in all WA and Europe until the other GIJ first and R later arrived. Ancient prehistoric DNA will confirm or falsifie this.

    ReplyDelete
  57. BTW have you seen these videos ?

    http://www.youtube.com/view_play_list?feature=iv&p=063C7039872C3DE0&annotation_id=annotation_563308

    HT to RZB !

    They are related with the stuff under discussion in this thread. It is from first semester 2009 but looks like if it was from the 80´s of past century. Everything has changed since then.

    I had to refrain myself several times and do not throw my laptop through the window: each time I saw the map with the arrows showing the OOA southern route...

    In some chapter I can not remember now there is even a flute which seems to play an important role. Donkeys appear also, but doeas not play any important role...

    It was interesting to see it anyway !

    ReplyDelete
  58. "The stubborness regarding tropical preferences of our prehistoric ancestors doesn´t [make sense]".

    I ask you the same as to Terry and anyone: that if you're going to defend the unlikely "northern corridor" hypothesis, you provide some evidence (or else keep a more humble attitude).

    There are strong reasons for a "tropical preference" as outlined above but there is also a host of archaeological and genetic evidence, which is much more important.

    ReplyDelete
  59. "The evidence changed a lot for mtDNA R: first (for many years) most basal diversity was in South Asia and then, this year, it was in SE Asia".

    The 'evidence' didn't change, merely the interpretation. B was always diverse in SE Asia. P was always in Melanesia/Australia/New Guinea, F was always in SE Asia and so on.

    "That logic could 'support' even L2"6 to have coalesced in Sumatra".

    How so?

    "My method is to estimate a centroid based on location of descendant haplogroups".

    And it has been shown that method doesn't work. You've had to periodically alter your conclusions. A far better method is to look at the distribution of closely related haplogroups, then look at the distribution of their ancestor. That method has worked every time for me.

    "In the case of R, with most subhaplogroups in South Asia and the rest almost equally split west and east of it (old data), the SA origin was natural conclusion. Yet you opposed it without any grounds".

    I had very definite reasons to oppose it. Of course the reasons are actually very complicated, and if you really wish to understand them you will have to read the whole series of essays, starting with this one:

    http://humanevolutionontrial.blogspot.com/2009/06/human-evolution-on-trial-finding-your.html

    The evidence I used is based on a study of the origin of Polynesians though, so you may get away with starting here:

    http://humanevolutionontrial.blogspot.com/2009/06/human-evolution-on-trial-change.html

    "Then the flute made some sound..."

    And, in your case, very much the wrong sound.

    "Their genetics is evidence of much older presence IMO".

    In your opinion? On what grounds? Related Y-haps are spread from Japan, through Tibet and down sporadically into SE Asia. There is no reason to believe that Andaman D is particularly ancient. And one mtDNA is shared with India so is presumably not ancient.

    'In any case they had solved some sort of adaption to cold weather quite obviously, at least to mildly cold weather. And we had not, not yet".

    No. But 'we' were quite capable of borrowing that adaptation when we made contact with them.

    "Since 125 and/or 90 Ka in Arabia, since 120 and/or 80 Ka in South Asia are not comparable with since c. 40 Ka in Altai".

    I'm sure I've read somewhere that 'humans' have been in the Altai region since 160ka.

    "I fear that you only choose to ignore this difference in order to:"

    Make the evidence fit your pre-existing belief.

    "Annoying repetitive nonsense (again). We have discussed this before and it is 100% clear that there was first a NeanderthalWithMousterian period and then a SapiensWithMode4 one".

    And I have consistently tried to point out that Mode 4 industry in no way defines the earliest sapiens presence. Australian Aborigines did not have mode 4 industry when Europeans arrived there. So presumably the Mousterian/Mode4 transition does not coincide with the Neanderthal/sapiens transition. The absence of Mode 4 in no way means the absence of sapiens.

    "You just like to confuse everything so we cannot reach to any logic destination (unless that one is where you have decided in advance)".

    The evidence overwhelmingly shows that it is you who is doing that. The destination 'you have decided in advance' consistently prevents you from seeing the evidence for what it really shows.

    ReplyDelete
  60. "Could you please summarize your position regarding the scattering of C-T across Eurasia ?"

    Here goes:

    Mitochondrial DNA haplogroups M and N emerged from Africa, although probably in the form of pre-M and pre-N. Because Y-haps are replaced more easily than mtDNA I find it most unlikely that three Y-haps accompanied the two mtDNAs. More likely one Y-hap: CT. The population became spread from North Africa (L3 and Y-hap B) and through parts of SW Asia (M, N and Y-hap CT). Within that region Y-hap CT first formed into DE and CF, then further split into C, D, E and F. These haplogroups each coalesced in the geographic margins of that distribution, or were pushed there with the development of arid conditions: E into Africa, F into the southeast and C and D somewhere in the northeast.

    "assuming Maju thesis that the only possible corridor was Altai CD arrives to Amur river, Manchuria coast and and disperse south through the coast of China, then to te south SEA and India".

    That is what I beleve the evidence shows. However in East Asia C and D separated; D moving south via an inland route while C moved down the coast. That's why we have D in Japan, Tibet and Burma/Andaman, and C5 in Northwest India/Pakistan/Nepal, C3 in Mongolia, C1 in Japan, some sort of C* (perhaps Maju would call this C7) around the South China Sea, C2 in Southern Wallacea and C4 in Australia.

    "An offshoot of this group arrives to SA, where there were not previous AMH. There, haplogroup F arises".

    I'm resonably certain that the evidence supports an entry of F into India from the northwest.

    "An offshoot of this F group goes to central Asia (through Hindu Kush) and there split into GIJ which goes west"

    My guess would be that G and IJ were left behind in SW Asia where F itself became drifted out because of a low remnant population.

    "and K or MNOPS goes east to Xingjiang / Qinhai".

    I'd say F-derived K spread from India east into SE Asia, where MNOPS formed.

    "If this scenario is correct, there must have been some time in the past where haplogroup E was predominant or even unique in all WA and Europe until the other GIJ first and R later arrived".

    I'd place E's re-entry to Africa (if it ever actually left it) reasonably early in the piece. But I agree that G and IJ were possibly unique in SW Asia (but not yet in Europe) until Y-hap R arrived. They are likely the oldest SW Asian haplogroups.

    ReplyDelete
  61. You know what I tell you: that after due review of the data as compiled in Wikipedia right now, R must be South Asian (again).

    West and South Asian basal sub-lineages: 10 (of which 6.5 are SA and 3.5 WEA). They are: R1, R2'JT, R3, R5, R6'7, R8, R30, R31 and U.

    East Asian and Oceanian basal sub-lineages: 7, of which 4 are East and SE Asian and 3 are from Near Oceania. They are: R9 (incl. F), R11'B, R12'21, R14, R22, R23 and P.

    So not just this side of Movius Line has the largest basal diversity but South Asia has the largest one of all four regions. It's pretty clear, I think.

    However the center of this scatter may well have been at or near Bengal (Orissa?)

    ReplyDelete
  62. "And it has been shown that method doesn't work. You've had to periodically alter your conclusions".

    Because the known structure (of course not the real structure) of the lineage has changed. If the data changes I must change my conclusions (unless the change is irrelevant).

    Being stubborn is NOT a virtue.

    "I had very definite reasons to oppose it. Of course the reasons are actually very complicated, and if you really wish to understand them you will have to read the whole series of essays"...

    Hahaha! Good try. The reasons are never that complicated and if you cannot explain them or you want me (or others) to re-read your boring old essays, which deal with a huge variety of matters (of which the OoA must occupy a line or two) and are written in pseudo-lawyering style for people who believe in the Bible, and which I read back in the day anyhow... you're done.

    Try writing a new short and simple article, with explanatory maps and graphics, on the matter of our concern. Then I will read it. But I do not need to bother about the sex of angels, so to say, in order to find a hidden annotation (if it exists at all) that informs me of something you believe but is probably wrong.

    "... based on a study of the origin of Polynesians"...

    Irrelevant. Polynesians! C'mon! Polynesians are not even old...

    ReplyDelete
  63. Andaman:

    "And one mtDNA is shared with India so is presumably not ancient".

    The other is basally descended from M.

    Anyhow, my understanding that Y-DNA D is old and originated in SE Asia has been documented by me in several occasions and I am sure that, unless you are even more chaotic than I believe, you must have it bookmarked. Amuse me and tell us which is that one paper (I'm not bothering because I really really hate this kind of repetitive circular pointless discussion).

    "I'm sure I've read somewhere that 'humans' have been in the Altai region since 160ka".

    Homo sapiens.

    "And I have consistently tried to point out that Mode 4 industry in no way defines the earliest sapiens presence".

    And I have repeatedly told you that we have the following sequence:

    1. Neanderthal with Mousterian
    2. Mousterian without skeletal remains
    3. "Aurignacian" without skeletal remains
    4. "Aurignacian" with H. sapiens

    Even a child can see how Aurignacian seems to fit with H. sapiens and Mousterian with H. neanderthalensis.

    Irrational stubbornness is NOT a virtue.

    "Australian Aborigines did not have mode 4 industry when Europeans arrived there".

    Logically. They belong to the Eastern Eurasian tradition. It is not relevant for Altai or otherwise in West Eurasia.

    Even a child can understand that.

    And there were never Neanderthals nor Mousterian in Australia anyhow.

    ReplyDelete
  64. By the way, you two: there is not such thing as Y-DNA CD. There is DE and CF. C and D are not directly related even if both may have spread in roughly the same pulse from SE Asia.

    There is strong evidence for each of them originating in SE Asia in any case, not Altai or Amur or whatever "frozen Negrito" fantasies you have.

    ReplyDelete
  65. @Maju, sorry if you find my answer arrogant. I´m still not convinced by your tropicality arguments.

    @TerryT: Thanks for clarifying your position. I have not clear yet the biogeography of F you propose.

    You say first: "F into the southeast", then "I'm resonably certain that the evidence supports an entry of F into India from the northwest" and finally "I'd say F-derived K spread from India east into SE Asia, where MNOPS formed".

    So according to you while C and D (I accept maju criticism) went east through the north, E went west (Africa, Mediterranean Europe), F went somewhere to South Central ASia. I suppose you mean Iran, Afganistán or Pakistan and from there spread to India and then SEA. Correct ? If yes, that´s another possibility different from the one I propose. I have to think about it.

    @Both. Clearly there is still not enough data or evidence as to decide which is the correct route: southern, my version of northern or TerryT version. I still stick to my version, but now I´m more willing to accept the short timing for CT Haplogroups, and according to this I make here the following prediction: if ever a preneolithic Y-haplogroup is found in Europe, I bet it will be an E. That is from Auragnician to first Neolithic introgressions from West Asia, everything in Europe was done by E peoples.

    ReplyDelete
  66. "I´m still not convinced by your tropicality arguments".

    We do not have to agree. I just say that you should explore the fine detail of haplogroups, notably mtDNA, before you can have a founded opinion. Add to that some archaeology, which, as of late, is producing results highly supportive of the tropical OoA route.

    "That is from Auragnician to first Neolithic introgressions from West Asia, everything in Europe was done by E peoples".

    No. Actually it was F subclades, probably I and R1b (mostly). There's almost no E in Europe and all of it can be explained on Neolithic (or other but always secondary) grounds.

    ReplyDelete
  67. "Being stubborn is NOT a virtue".

    I'm surprised you haven't realised that yet.

    "You know what I tell you: that after due review of the data as compiled in Wikipedia right now, R must be South Asian (again)".

    This is what the link starts with:

    "As of June 2009"

    Are you claiming that it is compiled 'right now'?

    "The reasons are never that complicated and if you cannot explain them or you want me (or others) to re-read your boring old essays, which deal with a huge variety of matters"

    A basic aspect of those essays is that what we already believe often prevents us from interpreting the evidence correctly. I called the phenomenon the 'Chinese drover's dog syndrome' after my father's mistake. You, along with many others, have long been led astray by the 'Great Rapid Southern Coastal Migration Theory'. The theory itself was invented to explain an apparent anomaly: how could modern humans have left Africa 40-45,000 years ago and reached Australia 50,000 years ago? But that anomaly was a product of several wrong assumptions in the first place. The link you provided goes on:

    "South Asia lies on the way of earliest dispersals from Africa and is therefore a valuable well of knowledge on early human migration.[4] The analysis of the indigenous haplogroup R lineages in India points to a common first spread of the root haplotypes of M, N, and R along the southern route some 60–70 kya".

    So the authors of the link are suffering from Chinese drover's dog syndrome. And another example of the syndrome from you:

    "So not just this side of Movius Line has the largest basal diversity but South Asia has the largest one of all four regions. It's pretty clear, I think".

    The 'basal diversity' has nothing to do with it. The Southeast Asian haplogroups R11'B6 and B4'5 are really a single haplogroup that expanded immediately along with the rest of R. Their origin cannot be India. The diversity in South and SW Asia presumably developed as the haplogroup expanded into a previously unoccupied habitat.

    "Because the known structure (of course not the real structure) of the lineage has changed. If the data changes I must change my conclusions (unless the change is irrelevant)".

    But your conclusions haven't changed just the once. The fact you've had to change so often shows that your method is inadequate. Your pre-existing belief in the 'Great Rapid Southern Coastal Migration Theory' led to you placing all mtDNA(xL) and all Y-hap(xCDE) into India. At least you have now shifted mtDNA R and Y-hap MNOPS into SE Asia (although you may be having second thoughts regarding R). And you have also placed Y-haps O1, O2 and O3 in South China rather than in SE Asia. In both cases I doubt that you have shifted them far enough from India, but that is not important. But the interpretation of haplogroup expansion that your belief in the 'Great Rapid Southern Coastal Migration Theory' required led to you placing Y-hap E1b1b1 into Northeast Africa in the Paleolithic, rather than in the early Holocene.

    ReplyDelete
  68. "Anyhow, my understanding that Y-DNA D is old and originated in SE Asia has been documented by me in several occasions and I am sure that, unless you are even more chaotic than I believe, you must have it bookmarked. Amuse me and tell us which is that one paper"

    This is what Wiki says:

    http://en.wikipedia.org/wiki/Haplogroup_D_(Y-DNA)

    "The Haplogroup D Y-chromosomes that are found among populations of the Japanese Archipelago [D2] are particularly distinctive, bearing a complex of at least five individual mutations along an internal branch of the Haplogroup D phylogeny, thus distinguishing them clearly from the Haplogroup D chromosomes that are found among the Tibetans and Andaman Islanders"

    So the haplogroup basically split in two. And:

    "Haplogroup D1 among the Tibetans (as well as among the mainland East Asian populations that display very low frequencies of Haplogroup D Y-chromosomes), Haplogroup D2 among the various populations of the Japanese Archipelago, Haplogroup D3 among the inhabitants of Tibet, Tajikistan and other parts of mountainous southern Central Asia, and paragroup D* (probably another monophyletic branch of Haplogroup D) among the Andaman Islanders. Another type (or types) of paragroup D* is found at a very low frequency among the Turkic and Mongolic populations of Central Asia".

    So there you have it. If you're going to claim diversity = origin then Tibet looks the most likely. Three haplogroups there (D1, D3 and D*), and just a single one in each other region.

    "Even a child can see how Aurignacian seems to fit with H. sapiens and Mousterian with H. neanderthalensis".

    So when did Aurignacian reach Australia?

    "There is strong evidence for each of them originating in SE Asia in any case"

    No there isn't.

    "Irrelevant. Polynesians! C'mon! Polynesians are not even old..."

    And that is exactly why they can tell us so much.

    "F went somewhere to South Central ASia. I suppose you mean Iran, Afganistán or Pakistan and from there spread to India and then SEA. Correct ?"

    That is what the evidence suggests to me.

    "No. Actually it was F subclades, probably I and R1b (mostly). There's almost no E in Europe and all of it can be explained on Neolithic (or other but always secondary) grounds".

    Another thing Maju and I agree on.

    ReplyDelete
  69. "This is what the link starts with:

    "As of June 2009""...

    Decontextualizing everything again? It's not that section (Origin) but the next one (Distribution) what matters - at least for me.

    Either you bother paying attention to what I say and I mean or I will have to stop replying to you altogether (what doesn't mean I agree, as you have insultingly claimed elsewhere).

    "The theory itself was invented to explain an apparent anomaly: how could modern humans have left Africa 40-45,000 years ago and reached Australia 50,000 years ago?"

    That is NOT the why behind the coastal migration hypothesis: it is to explain that many closely related haplogroups (specially mtDNA) are found between Sahul and West/South Asia (Metspalu 2005).

    Anyhow if it had not been formulated before it was because of an obvious "Nordicist" bias. Once formulated the Tropical route is only natural, regardless of whether it is coastal, riverine or whatever.

    "The 'basal diversity' has nothing to do with it".

    Humor me: I am 100% persuaded that it's all about basal diversity: about how the branches that hang from each node are scattered through the geography.

    "The Southeast Asian haplogroups R11'B6 and B4'5 (...) Their origin cannot be India".

    Nobody says that. These SUBlineages are from SE Asia... but R as a whole is from further West. Or so it seems.

    Btw, R11'B cannot weight more than, say, R5 or U, can it?

    "The fact you've had to change so often shows that your method is inadequate".

    No. And actually I am now wondering how was I mislead into believing I had to change my conclusions, which are not mine anyhow. I adopted them from someone else, who in turn took them from a classical paper, the first one to show that most basal sublineages of R were located in South Asia and nowhere else.

    This paper was no other than Palanichamy 2004 and specially Fig. 2. The details of that figure have varied along the years but mostly R has remained most basally diverse in South Asia.

    But IF the details change, I would need to change my opinion. My opinion is not set on stone nor divine inspiration: it is set on knowledge... and knowledge changes. Only religious people do not change their mind when confronted with contradictory facts.

    "So the haplogroup [Y-DNA D] basically split in two"...

    NO. See Hong Shi 2008.

    "So when did Aurignacian reach Australia?"

    Since when did we start talking about Australia. Altai (or otherwise West Eurasia) is not Australia.

    Bouncing inconsistently from here to there only makes you more annoying, not more reasonable.

    "Another thing Maju and I agree on".

    What I'm beginning to find rather embarrassing, to be sincere.

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  70. @Maju:

    I know the recent archeologic results you are talking about. By far no conclusive. However I agree that I have to improve my knowledge of mt-dna. This wasn´t a problem when I studied the whole matter one year ago and AFAIK there is nothing new in since then. As said the whole matter about Ooa route is wide open and only new results will decide.

    @Terryt: thanks for confirming I was interpreting correctly your words.

    @Both: Regarding E, from this wikipedia link:

    http://en.wikipedia.org/wiki/E1b1b1a

    "Trombetta et al. (2011) proposed that the earlier E-V68 population may have migrated by sea directly from Africa to southwestern Europe, because they observed cases of E-V68* (without the M78 mutation) only in Sardinia, and not in the Middle Eastern samples".
    Sardinia !

    "E-M78 is widely distributed in North and East Africa, West Asia "up to Southern Asia", and all of Europe." All Europe ??

    "The E-V12* paragroup is also observed in Europe (e.g. amongst French Basques) and Eastern Anatolia (e.g. Erzurum Turks).[1]"
    (As you know E-V12 is an E-M78 subclade). In French Basques ??

    E-V13 could be, as you say a more recent expansion, but what about E-M68* and E-V12 ? IMO these could be interpreted as tips of a paleolithic european E-ceberg.

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  71. I just have a ciuple of days ago a conversation with a Spanish prehistorian and (while we agree in most) he opened my eyes re. the theory I had about E1b1b1b1 having spread in the Solutrean in West Iberia. I have to re-check but it seems I got the archaeological origin of my theory, the part affecting Asturias, wrong.

    So maybe in Iberia E1b1b1b1 is Neolithic after all. There's growing evidence for Cardial/Epicardial "bouncing" in NW Africa at the time.

    But the source is in NW Africa for sure and this clade has no other possible origin. I do not think it can be considered "Neolithic" in that region because it would imply a brutal founder effect and a distinct origin, where the signals of the origin would have been erased.

    The only thing that changes therefore is that E1b1b1b1 would have crossed the strait only with Neolithic, possibly within the Cardial culture.

    Anyhow, smaller clades represented by 1 or a few erratics can hardly justify any theory. First sample Africa properly, then we talk.

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  72. "As said the whole matter about Ooa route is wide open and only new results will decide".

    Not for Maju though.

    "Sardinia !"

    Exactly. Supports the idea that it 'migrated by sea directly from Africa to southwestern Europe'. But doesn't solve the problem of where in Africa.

    "So maybe in Iberia E1b1b1b1 is Neolithic after all".

    My guess is slightly pre-Neolithic. Late Holocene.

    "But the source is in NW Africa for sure and this clade has no other possible origin".

    Again my guess is that it arrived in NW Africa around the same time as it arrived in Sardinia and in Iberia. I see no evidence to the contrary.

    "It's not that section (Origin) but the next one (Distribution) what matters - at least for me".

    The distribution map is presumably based on the 2009 data. Certainly the distribution is exactly as I've understood it.

    "it is to explain that many closely related haplogroups (specially mtDNA) are found between Sahul and West/South Asia (Metspalu 2005)".

    That has nothing to do with any 'coastal' or 'rapid' migration from Africa. Merely a secondary expansion from India with which I have no argument.

    "Once formulated the Tropical route is only natural, regardless of whether it is coastal, riverine or whatever".

    I cannot understand how you can be so certain of that. And I presume Carpetanuiq cannot understand it either.

    "Humor me: I am 100% persuaded that it's all about basal diversity: about how the branches that hang from each node are scattered through the geography".

    There you go again. Altering your perspective depending on what you already believe to be the case. You were prepared to completely ignore 'how the branches that hang from each node are scattered through the geography' in the case of E1b1b1, yet now you're claiming such branches show origin.

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  73. And you suffer the same problem with regard to Y-hap D in response to my comment, 'So the haplogroup [Y-DNA D] basically split in two':

    "NO. See Hong Shi 2008".

    From the paper:

    "and a deep divergence was observed between northern and southern populations".

    That is exactly what Wiki claimed. And:

    "Our data also disapproves the notion of Indian origin since no D-M174 was detected in the 996 individuals across India".

    So there goes the southern migration of D. And the authors contradict themselves:

    "The hypothesis of northern origin of D-M174 is not supported by our data because D-M174 is rare in Central Asian populations (Table 1) and the few Central Asian D-M174s are all located at the peripheral positions of the Y-STR network (Figure 3)".

    But in the conclusion:

    "The current fragmented distribution of D-M174 is likely due to the combination of later Neolithic population expansion and the last glacial".

    This surely could account for 'the peripheral positions' and scattered distribution. And they're honest enough to admit:

    "In surprise, we observed two DE* in the Tibetan samples, which was previously only observed in Africa (Nigerians), but not in other world populations".

    Hmmm.

    "the Andaman Islanders posses most of the major East Asian specific Y chromosome lineages including D-M174, O3-M122 and O2-M95, a strong indication of a relic Paleolithic population [28]".

    You know what I think of O3 and O2 being Paleolithic in SE Asia.

    "In summary, we demonstrated an ancient Paleolithic population migration in East Asia, predating the previously suggested northward population movement".

    Northward?

    "Since when did we start talking about Australia. Altai (or otherwise West Eurasia) is not Australia".

    That is basic to our discussion. We know that 'Denisovan genes' are found in New Guinea and Carpetanuiq and I are arguing a northern route. Connections between Altai and Australia are very much a consideration. and you are claiming that the Aurignacian is a defining marker for H. sapiens. So, I ask again:

    "when did Aurignacian reach Australia?"

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  74. It's like talking to a wall. I have better things to do and I bet that you do too.

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  75. Yes I do. But I'll just make one more comment. You have accused both Dienekes and me of obliterating haplogroups to fit a theory, but I must point out that you are more than happy to obliterate any trace of mtDNA N's route through India. You claim it may have been a minor haplogroup that got 'drifted out' in India, yet was able to expand considerably once it had move east beyond India. This ignores the fact that M, so prodigeous in India, was somehow able to make way for N in the east. This belief doesn't make sense.

    You next postulate yet another major obliteration of mtDNA N during its movement back west through India, yet granting mtDNA R the ability to expand greatly in that subcontinent. Again N was able to magically expand once it had emerged from India, this time in the west. None of this makes sense, but I'll leave you to persist in your rather strange beliefs. And you can go on making up interpretations of the evidence to fit those strange beliefs.

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  76. "You claim it may have been a minor haplogroup that got 'drifted out' in India, yet was able to expand considerably once it had move east beyond India. This ignores the fact that M, so prodigeous in India, was somehow able to make way for N in the east. This belief doesn't make sense".

    Well, that's what the data says (more or less: I don't like your words of "making way for").

    I don't care if it "makes sense" to you or not: that's what I see when the phylogeny is projected onto a map. You get the same results and is equally "impossible" for both routes.

    But it makes all sense as:

    1. Expansion of M in SA
    2. Expansion of M subclades in SA and EA
    3. Expansion of N is EA
    4. Expansion of R and some other N subclades (N1'5, N2, X) in SA and WA

    Each step may be of 5 Ka or so (maybe half, maybe double). In order to go that fast forth and back, you need a relatively empty Asia, even after the first expansion, and you may benefit of boating as well.

    "granting mtDNA R the ability to expand greatly in that subcontinent".

    R expanded but not that much in SA: most of its expansion (by numbers, not basal diversity) happened in West Eurasia (frontier) and East Asia (expansion of Y-DNA NO maybe).

    "Again N was able to magically expand once it had emerged from India"...

    That must not be understood as N but as three different lineages (four with R): N1'5, N2 and X. All have a basal branch (1/2) concentrated in South Asia.

    So you should only say X: X is the only mystery Western basal sublineage of N because it only shows expansion signals once in the Levant. It probably traveled all that journey as private lineage anyhow.

    But we have discussed ALL THIS a zillion times. I am patient and I can repeat myself once, twice... but my patience has a limit. You should already have understood my stand not as something "hostile" that you must fight against but as something that makes enough sense, that is a good theory.

    You reject it? Your problem. But don't make me repeat my explanation once and again: save a copy and read it when in doubt.

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  77. Hmm...none of you has adressed to my point: should I supose that you both agree that E is the real paleolothic Y-Haoplogroup in Europe until Neolithic Y-haplogroups made its introgression (I´m referring to G,I,J and R´s) ?.

    Just to clarify, Maju, when I say E, I´m not refering to E1b1b1b1 (= E-M81). This one seems to be too young to explain Auragnician by any timing. Even E-M68 seems to be too young, assuming its current timing (18.000 yBP according to Cruciani et all 2007) is correct.
    And the same applies to E-M215: 22.000 yBP according again to Cruciani et all 2004.

    I expect a re-timing and/or re-structuring of this E Y-haplogroup in near future, since IMO there is no doubt by now that E was the only player in Eurotown until Neolithic. In other words, during LGM there was a great divide, E in the west side of Eurasia, C and derived in the east/south east. After LGM everything changed.

    (to be continued in next)

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  78. Now, coming back to F derived Y-haplogroups, assuming my hypothesis is correct, I want to guess here a possible route.

    Let´s assume F originated somewhere in the Indo Valley.
    From there to north asia there are two possible routes:

    First route: West of Pessawar, through the Kyber, then to Turkmenistan / East Iran. From there to Caucasus it´s peanuts. This is the likely route for G first and IJ later.

    Second route: north of Pessawar to upper Indo Valley. This is the route followed by K. From Indo Upper Valley you can link with Brahmaputra upper river and also with Xingjiang. I ignore how hard it might be to go from Upper Indo to Upper Brahmaputra. But from Upper Indo to Xinjiang it doesn´t seem so hard (I´ve been in the other side, sleeping somwhere in Yarkand valley and on the foots of Muztagata and although high, mountains don´t seem so inaccessible there. Maybe not peanuts though...

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  79. "... should I supose that you both agree that E is the real paleolothic Y-Haoplogroup in Europe until Neolithic Y-haplogroups made its introgression (I´m referring to G,I,J and R´s) ?"

    I think I replied to that before. IMO the Paleolithic haplogroups of Europe are R1b and I, maybe R1a in East Europe as well.

    I do not think that there was any E in Europe before the Holocene, unless it was in small frequencies and restricted to Iberia (i.e. Solutrean Age arrival in the context of the Oranian genesis). E is an African lineage and the colonization of Europe came from West Asia and ultimately from South Asia. Hence we should expect the Y-DNA lineages to be F (not E, C, D, B nor A).

    What within F? It's clear that R1b and I look like very old and well established in Europe. The rest not so much (but prove me wrong).

    Even though I have doubts re. R1a it may have arrived to East Europe in the Neolithic: more archaeological research in Samara Valley is needed to determine if the PIE peoples of that area were derived from Paleolithic East Europeans, like Dniepr-Don or from new arrivals via Central Asia. Sadly no research has ever been done under the Samara culture levels, which are already from the 5th millennium.

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  80. "that's what I see when the phylogeny is projected onto a map".

    Thank you. That's what you see. It could be wrong.

    "I don't like your words of 'making way for'"

    Surely that is a necessary precondition for N to be able to expand in the region.

    "R expanded but not that much in SA"

    That contradicts what you said the other day:

    "So not just this side of Movius Line has the largest basal diversity but South Asia has the largest one of all four regions".

    Sounds like a pretty major expansion in South Asia.

    "All have a basal branch (1/2) concentrated in South Asia".

    It's difficult to claim that without resorting to special pleading.

    "save a copy and read it when in doubt".

    I have saved it, and consider it often. But it still doesn't make sense.

    "should I supose that you both agree that E is the real paleolothic Y-Haoplogroup in Europe until Neolithic Y-haplogroups made its introgression (I´m referring to G,I,J and R´s) ?".

    No. I don't think either of us agree with that.

    "IMO the Paleolithic haplogroups of Europe are R1b and I, maybe R1a in East Europe as well".

    I'm inclined to agree with that.

    "R1a it may have arrived to East Europe in the Neolithic: more archaeological research in Samara Valley is needed to determine if the PIE peoples of that area were derived from Paleolithic East Europeans"

    I'm aslo inclined to agree that R1a is Indo-European but possibly not originating in East Europe specifically.

    "Let´s assume F originated somewhere in the Indo Valley".

    To me it seems that because it ultimately came from Africa it presumably first coalesced somewhere near Africa. That means the following is likely to be the reverse of what actually happened:

    "From there to Caucasus it´s peanuts. This is the likely route for G first and IJ later".

    F moved into India from the northwest, accompanied by members of its descendant haplogroup K. Some of these made it all the way to SE Asia where M and S crossed Walalce's Line, NO moved north and P moved back west through India and out into Central Asia. Probably via the Upper Indus. To me that seems to best fit all the haplogroup evidence.

    "I´ve been in the other side, sleeping somwhere in Yarkand valley and on the foots of Muztagata and although high, mountains don´t seem so inaccessible there. Maybe not peanuts though..."

    I think F's route from the Upper Indus to the Middle Brahmaputra most likely followed the foothills of the Himalayas, basically the Siwalik hills.

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  81. I'm not going to discuss one-liners. It's crazy.

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  82. Ok. Thanks both for clarifying your position regarding paleolithic Y-chromosomes. We clearly disagree.

    @Maju: "It's clear that R1b and I look like very old and well established in Europe"

    Neither Y-DNA trees (all share the well-known timing problem) nor timing ancient DNA studies done so far (you can see Dienekes or JeanM compilations, which I suppose are comprehensive) decide this issue, so we must wait for new results. On the contrary most people tend to think now about a neolithic entrance of I and R.

    @Terryt, I agree that your description of F Haplogroup biogeographic history, which is not fully clarified, is one of the possible scenarios.

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  83. Sorry, in stead off "which is not fully clarified" I meant "which is now fully clarified"

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  84. There's almost no aDNA of the Y-chromosome kind and would it show up as R1b, I'm sure they'd yell "contamination".

    What "most people think" is not my problem, if I would base my opinions on what "most people think" I would not exist as I do and we would not be having this conversation.

    What I care is about where is the basal diversity for each clade and, in the case of I, it seems to be in Eastern Europe (and I is almost non-existent outside the subcontinent), so I is clearly a European lineage.

    As for R1b, it is clearly a West Asian lineage by the same measure. But when we reach the level R1b1b2a1 (old nomenclature), then it is a European clade.

    If you think that the differences under this node have arisen in the last few thousand years, you should be outlining HOW that may have happened, how there is a whole lineage centered in SW Europe, etc.

    I have thought about that in depth (here, here or here for instance) and you can only think of what "most people" (like Dienekes or Jean, with all the prejudices they insert in such considerations) think.

    Think on your own. Otherwise it's useless.

    "... we must wait for new results".

    We must always wait for further data but that does not mean that we do not use what we have to think about it.

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  85. "I´ve been in the other side, sleeping somwhere in Yarkand valley and on the foots of Muztagata and although high, mountains don´t seem so inaccessible there. Maybe not peanuts though..."

    Interesting. It certainly wouold take only a summer to move through the mountains. I thought at one stage that C may have moved by that route, but any route through that region would involve Kashmir. And Kashmir haplogroups are mainly R1(b?) and J(2?).

    "if I would base my opinions on what 'most people think' I would not exist as I do and we would not be having this conversation".

    And that is exactly why I spend time at your blog. Very thought provoking discussion.

    "but that does not mean that we do not use what we have to think about it".

    I distinctly remember you claiming I couldn't do just that.

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  86. @Maju:

    1. I agree that "most people" (here I include both amateur bloggers and commenters but also academic experts) conclusions based on all avalaible updated data can be wrong. As you know I think it is the case regarding the OOA route. But regarding Y-haplogroups in Europe the evidence is starting to be so overwhelming that we are only lacking a "puntilla", which will be some pre-neolithic Y-dna.

    2. "We must always wait for further data but that does not mean that we do not use what we have to think about it"

    When there are not enough data to reach definite conclusions, I prefer the middle honest way and conclude: we don´t know yet.

    In biogeographic studies there are several kinds of fallacious reasoning. Two instances:
    --If a haplogroup is more frequent in a regional area today, then it originated there.
    --if a haplogroup is more diverse in a regional area today, then it originated there.
    I can think of many real situations and likely theoretical scenarios where these arguments fails. Despite of this many of the amateur conclusions I read in this field (including yours) are based on this fallacious reasoning. It is not that I dislike especulation, science needs it...but let´s label speculation as speculation and science as science. At present Paleolithic presence of I and R Y-haplogroups is just speculation.

    @Terry:

    "Interesting. It certainly wouold take only a summer to move through the mountains. I thought at one stage that C may have moved by that route, but any route through that region would involve Kashmir. And Kashmir haplogroups are mainly R1(b?) and J(2?)."

    People thinks "more than 7000 meters high, that must be an impossible barrier, wiht permanent f snow" etc...I was there in summer, August, all green around, not really cold and most of the peaks looked like doable. We (my chinese guide and someone from Israel we met on the foots of the Muztagata), slept in the house of a Kirguiz (with or next his several spouses) and he told me that to cross from there to Tadjikistan or Pakistan valleys, where he also had summer pastures was not hard. Possibly a matter of days (once you know the correct route fo course). I can not resist to comment an anthropological anecdote. Half jokingly I told the Kirguiz that he should marry one of his daughters to my chinese guide. "No, he is a Han" he answered. And that was not so far away.

    To be coherent with my methodological comment to Maju above, the Kashnir haplogroups might be remnants of this first human trekkings, but also could be of more recent (post-neolithic) origin. We don´t know.

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  87. "In biogeographic studies there are several kinds of fallacious reasoning. Two instances:
    --If a haplogroup is more frequent in a regional area today, then it originated there.
    --if a haplogroup is more diverse in a regional area today, then it originated there".

    The first one is fallacious but the second is not. It may need qualification in some cases but it is correct in principle, and normally also in the end.

    Highest diversity (but not frequency) indicates approximate origin unless otherwise proven (I know no example so far) or the data is extremely faulty (oversampling here, undersampling there, etc.)

    I also understand that it is impossible for Paleolithic DNA lineages to have vanished in such absolute terms even if there was demic replacement in Neolithic.

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  88. "the Kashnir haplogroups might be remnants of this first human trekkings, but also could be of more recent (post-neolithic) origin. We don´t know".

    My conclusion, once I had been told the haplogroups (by Ebizur I think), was that they were more recent. Possibly pre-Neolithic but certainly not ancient Upper Paleolithic.

    "Highest diversity (but not frequency) indicates approximate origin unless otherwise proven (I know no example so far)".

    But E1b1b1- M35's highest diversity is in the Horn of Africa, Ethiopia and the Upper Nile. Yet you insisted that did not mean E1b1b1-derived haplogroups had originated somewhere within that region. How about some consistency?

    "I also understand that it is impossible for Paleolithic DNA lineages to have vanished in such absolute terms"

    But hang on. Isn't that exactly what you are claiming happened to mtDNA N in India? Basically twice?

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  89. I'm being extremely consistent Terry and I'm tire that you do not want to understand what I say.

    "E1b1b1- M35's highest diversity is in the Horn of Africa, Ethiopia and the Upper Nile. Yet you insisted that did not mean E1b1b1-derived haplogroups had originated somewhere within that region".

    Because that is the region of origin of E1b1b1 and NOT necessarily of its "son" sublineages.

    It should be plainly clear, just like my mother was born in Treviso but I was born in Bilbao: I am not my mum, so wherever she was born is not informative about my own birth place.

    If I were with you in person, I'll insist on this until you acknowledge looking to me into the eyes that you understand the difference - and would you not, I would not speak to you again. Because you have me quite tired with your intentional "misunderstandings" of what I say and what I mean.

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  90. "Isn't that exactly what you are claiming happened to mtDNA N in India?"

    NO!!!

    So you think that a "drift out" of private lineage L3(pre-N) (I understand), numbering what I can count with one hand probably, is comparable to the extermination of ALL the lineages of tens of thousands that lived in Europe at the arrival of farming and who readily became farmers in so many cases?

    Well, you love to compare speed with bacon (that's how it's said in Spanish "apples and oranges") and I hate the hypocrisy you display so annoyingly all the time with that attitude.

    It's possible (very likely) that in all the UP, specially in the LGM, many founder lineages were lost in Europe (and other places). That's part of drift. But we are talking here of what was left after the Magdalenian explosion and the adoption of farming by Epimagdalenian and Epigravettian peoples. That I do not accept that could have been completely erased, in fact I think it thrived instead.

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  91. "you have me quite tired with your intentional 'misunderstandings' of what I say and what I mean".

    It is not intentional misunderstandings. I am merely asking for some consistency in how you go about interpreting the evidence. At present the only consistency you display is that you alter you interpretation depending on the answer you wish to come up with. In other words you form your conclusion and then interpret the evidence appropriately.

    "Because that is the region of origin of E1b1b1 and NOT necessarily of its 'son' sublineages".

    You accept that E1b1b1 originated in the Horn of Africa, Ethiopia and the Upper Nile. So surely you accept that either it or its 'son' E1b1b1b-V257 must have left from that region. My guess is that the population that left included both haplogroups, although E1b1b1b may have formed somewhere along the route, and then finished up scattered around the Western Mediterranean. To me no other interpretation is possible. Of course it is quite possible there is some other explanation but so far you have offered none. You've merely claimed that E1b1b1b-V257 somehow miraculously arrived in Northwest Africa some time during the Upper Paleolithic (by aeroplane?) and much later managed to reach Iberia and Sardinia. You claim this to be fact without offering the slightest evidence, or even explaining how it could possibly have happened that way.

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  92. "It's possible (very likely) that in all the UP, specially in the LGM, many founder lineages were lost in Europe (and other places)".

    I agree. But it is most unlikely that, once lost, they would miraculously reappear some huge distance away thousands of years later.

    "But we are talking here of what was left after the Magdalenian explosion and the adoption of farming by Epimagdalenian and Epigravettian peoples".

    If anything such miracles are more likely to have happened later in human prehistory than during the Paleolithic.

    "So you think that a 'drift out' of private lineage L3(pre-N) (I understand), numbering what I can count with one hand probably, is comparable to the extermination of ALL the lineages of tens of thousands that lived in Europe at the arrival of farming and who readily became farmers in so many cases?"

    I'm saying that a subsequent expansion of either is equally unlikely to have occurred.

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  93. "It is not intentional misunderstandings".

    It is misunderstanding because you are constantly claiming I say what I do not say. Even you dare to go around saying "Maju and I agree" in something I do not agree at all.

    You see the world with very peculiar glasses. And I think they are intentional - or alternatively you are plainly dumb and have the intelligence of a Paranthropus. Because an intelligent person cannot insist so much in the same "errors" unless on purpose.

    So I have the choice to consider you outrageously dumb or evil and mischievous. Whichever the case, I'm tired: my patience has limits.

    "At present the only consistency you display is that you alter you interpretation depending on the answer you wish to come up with".

    NO! You mix totally different categories happily in order to make me look like saying "elephants are small" when I was saying "mice are small". So you say "what's the difference: they are all mammals?!" and I say: "you are either very dumb or very evil and, whatever is the case, I'm tired of that".

    Really fucking tired, you can believe me.

    "You accept that E1b1b1 originated in the Horn of Africa, Ethiopia and the Upper Nile. So surely you accept that either it or its 'son' E1b1b1b-V257 must have left from that region".

    NO. The same that my mother's birthplace is not my birthplace. She moved here and bore me here.

    Similarly E1b1b1 spread around before coalescing into "son" lineages.

    Got it? Can you understand something as simple? Do I have to write it in capital letters, give you a private tuition on the difference between a parent and a child?

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  94. "The first one is fallacious but the second is not. It may need qualification in some cases but it is correct in principle, and normally also in the end".

    I agree that the second situation (more variety) is a more robust signal of origin, but not a definite one. I can imagine many theoretical cases where the reasoning fails, and therefore is fallacius. Think for instance about haplogroup O. If my hypothesis is correct it originated and differentiated in central asia (let´s say Xinjiang). Then different subclades dispersed through different river routes, to east and south asia. Finally through migrations many ended in the south (let´s say around HK).
    Now, if we test people from China
    we will conclude a false place of origine.

    Of course this is an hypotethical (theoretical case). And something similar might have happened with Haplogroup E, which you are discussing with TerryT.

    AFAIK there is not, up to now, a definite correct way to infer the origin from present tests or data, just likely guesses. On the other hand ancient DNA will be more definite.

    "I also understand that it is impossible for Paleolithic DNA lineages to have vanished in such absolute terms even if there was demic replacement in Neolithic"

    Again not impossible. We have a recent case of massive replacement for one reason or the other, the Americas. Let´s wait 1000 years more and see. Of course I mean Y or mtDNA.

    To conclude: no absolute general method, just carefull study of each case including as much data from different sources as possible (bones, tools, genes, languages etc...) and a coherent full picture.

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  95. "I can imagine many theoretical cases where the reasoning fails, and therefore is fallacious".

    I can only imagine two cases:

    (1) the origin region has been totally (or almost totally) deprived of its original population - I doubt this has happened anywhere before the 18th century.

    It might have happened in very peculiar low density regions but only re. Y-DNA, not re. mtDNA in any case, which acts as control. These very low density regions are by this reason extremely unlikely to be at the origin of anything, being just marginal sites of settlement for the populations of denser areas.

    We should consider the possible exceptional cases one by one, not assuming this exceptional situation as any sort of "normal thing" in any case.

    (2) The region has received genetic flow from several related populations (suggested but never really studied AFAIK for colonial populations like USA, Brazil, etc.) Careful discernment of the phylogenetic structure should expose this mirage because... even if Brazil has got, say, R1b from sources other than Portugal, we should not expect ALL Portuguese R1b lineages to be present, because the origin of the immigrants was for sure irregular and they caused micro founder effects once in America. We should be able to discern that, even if it is not easy.

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  96. "Think for instance about haplogroup O. If my hypothesis is correct it originated and differentiated in central asia (let´s say Xinjiang)".

    Nah. Uyghuristan was a desert before the Holocene and was first colonized, it seems, by West Eurasian clades like R1b, R1a, etc.

    If O would have originated in Central Asia, Altai or Siberian populations would retain some high diversity residue, as happens with Q.

    In any case, you cannot prove a hypothesis on another hypothesis because that would leave us to total uncertainty and capriciousness of thought instead of reason and scientific methodology.

    "AFAIK there is not, up to now, a definite correct way to infer the origin from present tests or data, just likely guesses".

    Of course only a time machine would solve our problems (in theory because we could contaminate the past with our DNA - the horror!) But, while no time machine nor divine omniscience is available, the best method is that of diversity and I'd dare add that phylogenetically discerned basal diversity is much more informative than mere statistical count of number of haplotypes.

    Of course aDNA can give us some extra clues but it has its own problems, one of them being that samples are always necessarily small and non-random (specific sites with specific non-shuffled populations). Another problem is accuracy of testing and seriousness of researchers (can you believe that there is still people wasting precious ancient bone matter in HVS-I tests?!)

    ...

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  97. ...

    "We have a recent case of massive replacement for one reason or the other, the Americas".

    This is a very bad example because it really implies industrialization. Massive demic colonization really did not catch (with some localized exceptions) until the 18th century and specially the 19th century, when most of the disgraceful "whitening" of America (North and South) happened. Without organized genocidal racist policies, railroad, long distance ships and the kind of uprooting caused by the industrial revolution and related process (enclosures, etc.), all that would have never happened, at least not in any comparable scale.

    What we have in these processes are the most technologically advanced fraction of Humankind (industrial) against the most technologically backwards sectors (Paleolithic or initial Neolithic). It's like claiming that Jews were in fact exterminated in the first historical pogrom ever because Hitler almost did that in the 20th century with industrial methods and German discipline. Even the quite exhaustive Roman genocide cannot be compared: crucifixion does not stand side by side with Auschwitz, just like a legionnaire and the Hiroshima bomb cannot be compared either.

    We have to understand that, even if the motivations (racism, xenophobia, war "logic") may have been similar at various times, the effectiveness potential was not at all. If North America would have been colonized in the Middle Ages, the Cherokee would still live in their ancestral homeland and the European colonization of America would have been extremely patchy and full of admixture processes. And that's the Middle Ages: advanced Iron Age! Go figure with the primitive farming styled by the first Neolithic peoples, not so different at first from hunter-gatherers in fact.

    In fact you can wonder if the Cherokee (Neolithic farmers) replaced the Sioux or other hunter-gatherer peoples. And in general the answer is negative. And from the linguistic diversity of North America we can infer that not much of such replacement had happened in the continent and that instead many peoples had incorporated the technology of agriculture.

    This does not exclude specific invasions, local massacres, concrete expulsions from lands (the Iroquois expelled at least one tribe but not before offering them to adhere to their powerful confederation as full member) and assimilations. But what we see in pre-colonial North America is that diverse peoples with somewhat diverse levels of technology lived side by side and not any single wave of replacement existed.

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  98. @Maju,

    1. I was not trying to prove my hypothesis. Pls, just try to think abstractly (theoretically) for a moment.

    Forget for a moment our planet earth and the think of a planet where there is the following situation: a high plateau, from the plateau different rivers go down following different distant long paths and then converge into the same area in its mouth. Except this difference in heigh within plateau and rivers mouth area, everything is symmetrical.

    History or process one: an haplogroup originates in the plateau, population disperses through the different river long paths, differentiate through the path and arrives at the mouth.
    A climate change happens (glaciation) so that all plateau population starves, but mouth survives. After another climate change, a small sample of the mouth population, a pair, goes up arrives at the plateau and reproduce. At this moment an earth biologist arrives and effect test in the mouth and in the plateau. According to your methodology or the diversity fallacy he will conclude incorrectly that basal haplogroup originated in the mouth. A symmetrical history or process using a flood in stead of glaciation. I can see many similar situations in the earth: tibetan plateau / south of china; west asia and east-central Africa, the wide area between both beeing the sahara and its several paths (not necessarily river in this case) traversing it.

    ¿ Where is the source and where is the sink in all this cases ?
    aDNA of course is not perfect but might add an important piece of information.

    2. Regarding massive replacement IMO agriculture first and metal age provided such huge technological asymmetry moments so that this process could have taken place.

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  99. On Planet Earth, all the history of H. sapiens in Eurasia happened in the Ice Age, as far as I can tell (except the last bit, naturally). Also on Planet Earth Central Asia was inhabited by Neanderthals and some (probable) hybrid with Erectuses that is known as "Denisovans". Also on Planet Earth, the specific region you mentioned was essentially uninhabitable until the Holocene.

    Alternative Universes are surely nice for fiction, what is nice as evasion or even philosophical speculation, but not for our purpose here, which is boringly scientific.

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  100. Regarding point two, I find that the contrast between Neolithic and Epipaleolithic would be at most comparable to the difference between Industrial Era and Iron Age, that is the technological difference between Europeans and Black Africans at the Berlin Conference. As far as I can tell Tropical Africa stays nearly 100% Black and looks like it will continue to be that way (while the technological and developmental gap has narrowed). However European languages have become dominant in much of Africa (first stage of linguistic replacement without population transfer).

    You cannot compare Industrial vs Hunter-gatherers with Early farmers vs Hunter-gatherers. There's just NO comparison to be made.

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  101. @Maju, I see you dislike to think in terms of abstract models (theory = fiction ???). If you prefer to be surprised continously by new results, that´s up to you...

    In any case positions are pretty clear (at least for Terryt and me, since by your last two comments I´m not sure you understood mine), and IMO the discussion is becoming too repetitive. I might come back in next surprise, hopefully soon !

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  102. "If you prefer to be surprised continously by new results"...

    I do. I do not pretend to have the answer to everything, much less in advance to the data.

    I do not dislike theoretical considerations but theory is built on reality and not the other way around. A "theory" built on nothing is, depending on intentions and literary quality, at best a good story at worst pseudoscience.

    So either you build your "theories" (wild conjectures as far as I can tell) on something, or you highly improve your literary style, or please spare us from them.

    "and IMO the discussion is becoming too repetitive".

    In this I can agree and I really appreciate someone who can notice this drift and step aside on time. Thank you.

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  103. "to cross from there to Tadjikistan or Pakistan valleys, where he also had summer pastures was not hard. Possibly a matter of days (once you know the correct route fo course)".

    finding the correct route would only be a matter of several Summers. The eventual sighting of a relatively lush valley with plenty of undisturbed game would scream out for any observer to make a return trip next Summer with some of his relatives. And, perhaps, their wives.


    "You see the world with very peculiar glasses".

    On the contrary, I think you do. I'll explain:

    "You cannot compare Industrial vs Hunter-gatherers with Early farmers vs Hunter-gatherers. There's just NO comparison to be made".

    I disagree. In spite of your unwillingness to do so I think it's time we considered what the Polynesians can tell us about human movement into uninhabited regions. Sure, the Polynesians possessed a near-Neolithic technology, but the many similarities to other expansions into new regions outweigh such a single difference.

    The fact that the expansion of various bird species into the Pacific follows much the same route as did the Polynesians tells us that such similarities go much deeper than just to other human expansions, ancient or otherwise. For both birds and humans we simply have a species or a population expanding into so far unexploited regions. But individuals don't just spread out all over the place, invading the new region like a tsunami. They move into, and exploit, the most desirable locations. In many cases these desirable locations are separated by considerable expanses of undesirable locations. In exceptionally desirable locations population numbers grow. But by the time the ecology collapses the advancing wave has found yet more desirable locations up ahead. But sometimes people are forced to move back.

    During this expansion process we have a series of bottlenecks with just a limited number of haplogroups or species moving through. And drift operates on populations that remain in one region for any length of time. So we finish up with a series of founder effects scattered along the route. But any haplogroups present at the beginning of the process as just a small proportion of the population has no chance of surviving for very long without setting up a staging population along the way. That is a problem for mtDNA N in India.

    For example we see no such haplogroup survival and subsequent expansion during the migration into the Pacific. Marginal Polynesia is mostly Y-hap C2a1 and mtDNA B4a1a1a. Although these particular haplogroups are not actually present in SE Asia there is not the slightest possibility that they had survived the whole voyage un-noticed and expanded at the last moment. They formed along the way. Their ancestral haplogroups are common in SE Asia. C2a is virtually absent in Northern Melanesia though. But the gap is more probably explained as being the result of later Melanesian haplogroup expansion rather than being a private lineage that passed through and expanded when it reached the wider Pacific. Not surprisingly haplogroups present as a minority in the Eastern Polynesians increase as a proportion as we move west into Melanesia/SE Asia. And, just like several bird species, some haplogroups that formed along the way have even moved back in the direction from which they came.

    I believe any theory concerning haplogroup expansion that fails to take this model into consideration should not be taken seriously.

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  104. "In this I can agree and I really appreciate someone who can notice this drift and step aside on time. Thank you"

    I agree, but you don't seem to be following you own advice: 'theory is built on reality and not the other way around'

    "Similarly E1b1b1 spread around before coalescing into 'son' lineages".

    Can't have. Many E1b1b1 lineages remain in the region of origin as well. So only some E1b1b1 lineages can have left. Even some E1b1b1a derived lineages are also spread along the Nile, so that haplogroup must have diversified before E1b1b1a expanded. It is also unlikely that the diversification of E1b1b1 is spread over tens of thousands of years.

    "Think for instance about haplogroup O. If my hypothesis is correct it originated and differentiated in central asia (let´s say Xinjiang). Then different subclades dispersed through different river routes, to east and south asia".

    I'd actually place its origin within China, probably in The Yangtze or Hwang Ho basins. But certainly not in SE Asia as the current popular idea has it.

    "On Planet Earth, all the history of H. sapiens in Eurasia happened in the Ice Age, as far as I can tell (except the last bit, naturally)"

    I'm coming to see that there was considerable haplogroup expansion at the end of the Ice Age. Presumably from relict populations formed during the advance of the ice. For example R1b1a2a1a1b1b-L21 cannot have coalesced in Ireland before the Holocene when people first arrived there.

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  105. "... but you don't seem to be following you own advice"...

    This is MY blog, Terry, not yours. And I am at least slightly concerned about casual readers getting the wrong impression. So I like to make "closing comments" sometimes, mind you.

    Still I have stepped aside from your extenuating circular debates, only to have you lying about that and claiming that you and I agreed on stuff I never agreed to.

    So you better start behaving if you don't want me to get out the whip (start censoring you out of utmost annoyance). Another manipulation about what I say and you are out.

    You are really abusing my hospitality.

    WARNING ISSUED

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  106. "So I like to make 'closing comments' sometimes, mind you".

    OK. Go ahead. I won't respond to your comments regarding the significance of my Polynesian evidence, other than just a simple comment you might make just claiming 'it is wrong'. You need to tell us why it is wrong.

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  107. "But any haplogroups present at the beginning of the process as just a small proportion of the population has no chance of surviving for very long without setting up a staging population along the way. That is a problem for mtDNA N in India".

    First, there was no mtDNA N before it coalesced as such: it was L3 (call it pre-N but never N).

    Second lineages can perfectly survive in "private" form (low numbers) and later vanish because of drift or even outright extinction (think Toba for example). The same "problem" you think N has, many other lineages do and that is best explained by rapid migration in low numbers.

    Your Polynesian non-example is pointless. I am sure that among Polynesians there are also "private" lineages, likely to go extinct but the could have flourished if experiencing a founder effect. You cannot see that at that level because the Phylogeny does not reach to such detail (because the Phylogeny only pays attention to what is already established and not to the tiny "private" lineages).

    But I'm not going to debate Polynesians just because you feel so (partly because the data is not complete and partly because you and I do not agree on where the various Polynesian lineages originated).

    "Can't have. Many E1b1b1 lineages remain in the region of origin as well. So only some E1b1b1 lineages can have left".

    You do not understand basic genetics. That is your big problem. The "many E1b1b1 lineages" that "remain" coalesced only AFTER that expansion. You confuse the seed with the tree.

    "It is also unlikely that the diversification of E1b1b1 is spread over tens of thousands of years".

    Why not?

    "For example R1b1a2a1a1b1b-L21 cannot have coalesced in Ireland before the Holocene when people first arrived there".

    It is not restricted to Ireland. It can well have coalesced in Occitania or Guyenne.

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  108. @Maju
    "in the case of I, it seems to be in Eastern Europe (and I is almost non-existent outside the subcontinent), so I is clearly a European lineage."

    @carpetanuiq
    "(F) First route: West of Pessawar, through the Kyber, then to Turkmenistan / East Iran. From there to Caucasus it´s peanuts. This is the likely route for G first and IJ later.

    Second route: north of Pessawar to upper Indo Valley. This is the route followed by K. From Indo Upper Valley you can link with Brahmaputra upper river and also with Xingjiang."

    I am interested in northern routes as well, since during brief mild and wet spells, much of the region would have had lush growth of grass with huge herds of animals to hunt, while the south was much more arid. The Pakistani/Afghan valleys seem logical, since passes would easily be found during summer when hunting for mountain goat and sheep, and none of them are particularly arduous (they are used on foot to date). However, I envision a first route to the east and north of the Caspian Sea, which would have let directly into the earliest known Russian sites, and would have avoided Neanderthal-dominated areas, at first. At any rate, people living in that region would have been able to learn all the essential skills and develop all the tools that the first northern and central Europeans evidently brought with them from the get-go. They don't seem to be coming from some lush tropical place. I would associate that with R1b.

    Perhaps "IJ" followed a much more southern route through Iran and Anatolia a little later, when Neanderthals were already in decline, or contributing to their demise, separating into "I" and "J" in that region, and R1a yet later perhaps via the east and north of the Black Sea. Something like that could explain the range, east-west ordering, and limit of penetration found today. Clearly, I/J was completely separated into a southwest/west Asian and European branch during the ice age. I don't think "I" was present then in NW Balkans, since it is almost absent in Italy. So I see it likely that it was part of the Moravian refugium, and perhaps any Rhine valley one - if there was one - also perhaps explaining the subgroup dichotomy, with R1a either also present in Moravia, or at least in the Ukraine. Today's distribution then got shaped via post-LGM expansion and the neolithic (NW Balkans, Ukraine, England, Scandinavia), and a bit from dark ages and medieval migrations (Iberia, British isles). I1 seems to correlate well with neolithic agricultural explosion in extreme northern Germany and Scandinavia; I2 may have spread via the Balkan, Saale/Elbe, and eastern portions of LBK.

    I think the Brahmaputra River route with northern Myanmar and adjacent China is a viable option to explain very early Siberian sites that then moved towards Beringia. Even during wet times, it is hard to imagine people crossed the Gobi desert - although that would have been the most direct route. At any rate, there was obviously a major split between western and eastern y-haplogroups (a little less so with mtDNA), and perhaps another split between extreme northeastern and southeastern groups.

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  109. I have no clear options for the routes followed Westward from Iran but let's not forget that the South used to be coastal (in Balochistan) and the Persian Gulf "Oasis", so it's a reasonable route as well (and then up Mesopotamia to Kurdistan, Anatolia and Syria - and the Caucasus as well, as it seems a fetish place for some reason).

    With this I'm not rejecting the Central Asian route, attested specially with the Altai connection but I wonder if this one is not most related to Y-DNA P (R and Q) instead than to IJ and G.

    Actually one can even wonder if (pre-) IJ and G (i.e. the F and IJK branches leading to them) ever left the Persian Gulf Oasis at all.

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  110. @Eurologist,

    I´m not sure you are aware of the issue we are discussing in the thread. To summarize the issue under discussion is OOA route. Some, as Maju, stick, somewhat fanatically to the traditional southern route; some as Terryt and I are more open to OOA northern routes. I admit my hypothesis is quite radical.

    It would be nice if Maju could make a post with 3 maps each one describing the 3 different hypothesis under discussion (thanks Maju in advance if you decide to do it; if you need clarification do not hesitate to ask; I hope TerryT agrees with this suggestion).

    I wonder what´s your position regarding OOA routes. By what you comment I can guess that you support a southern route with F derived groups originating in SA and scattering from there to the rest of Eurasia.

    My northern route is compatible with F arising in SA. I´m not sure about the timing, but now I tend to think that F derived haplogroups scattered (originated ?) from SA after LGM and arrived and scattered through Europe during neolithic.

    Consistent with this view is my prediction that all pre-neolithic Y-Haplogroups in Europe were E derived not F derived. So I might agree with the routes you suggest for R and IJ but not with the timing. Of course in order to test this we need preLGM aDNA and refugium LGM aDNA new research.

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  111. That is NOT the issue the entry is about Carpetanuiq: the entry is about Y-DNA in Africa, nothing to do with northern route or southern route. All that is off-topic.

    "It would be nice if Maju could make a post with 3 maps each one describing the 3 different hypothesis under discussion"...

    I have not the slightest interest. I do not think that the northern route hypothesis merits much attention (because it's a zone too cold and too full of other Homo species not ours) - and not sure which is the third hypothesis. If you are so interested, do your own work, seriously. Then post here and be sure that I'll be there to debate it, at least until I get bored.

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  112. "With this I'm not rejecting the Central Asian route, attested specially with the Altai connection but I wonder if this one is not most related to Y-DNA P (R and Q) instead than to IJ and G.

    Actually one can even wonder if (pre-) IJ and G (i.e. the F and IJK branches leading to them) ever left the Persian Gulf Oasis at all. "

    Yes, I am also thinking a southern or even coastal route for IJ, and you are right, IJ and G could even be descendants from F that remained in the area. However, then one must postulate that F split from CF pretty much right during the journey east and IJ also split of from IJK, then. Perhaps Pakistan is a better place for that to happen, since this seems to require some extended population growth, while at the same time C and F* made it through to India. (So, in other words, if these splits happened early in some expanding population right ooA it is weird that the more basal ones are the ones that made it through and became more dominant in the east).

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  113. You make a good point, Eurologist.

    I must say that I do not postulate anything specific but that we also have that case with at least DE (leading to D) and most probably with mtDNA L3 (leading to N) as well, so it's clearly not impossible that several lineages were wiped out (drifted out or otherwise suppressed) on route and yet expanded in destination. This we also see in other haplogroups at more downstream levels (X, D, M8, A, etc.) That is why the concept of rapid migration has been proposed although I'm more and more inclined to see it as a natural process by which minor lineages (elsewhere suffering extinction by mere drift) locally thrive.

    However it is also possible that G and then IJ back-migrated to the Persian Gulf Oasis from South Asia instead of staying put all the time. I do not think we can safely discern between one or the other situation. But I do think that at least some of the migration to West Asia from South Asia happened by the Gulf Oasis and not only the Central Asian route.

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  114. "But I'm not going to debate Polynesians just because you feel so"

    If you are unable to see their relevance yoy are going to be perpetually handicapped in any discussion on genetics.

    "I am sure that among Polynesians there are also 'private' lineages, likely to go extinct but the could have flourished if experiencing a founder effect".

    Any private lineages will be derived from those that survive nearby. There will be none who have survived the whole voyage from SE Asia. So the chances of them forming a founder effect on any distant island is nil.

    "First, there was no mtDNA N before it coalesced as such: it was L3 (call it pre-N but never N)".

    Obviously a small population confined to a small region.

    "Second lineages can perfectly survive in 'private' form (low numbers) and later vanish because of drift or even outright extinction (think Toba for example)".

    Exactly. The chances of any private lineage surviving the rigours of a major migration are virtually nil.

    "You do not understand basic genetics".

    I am reasonably sure that I have had far more experience with practical genetics than you are ever likely to have.

    "You confuse the seed with the tree".

    But you ignore the seed.

    "Why not?"

    The diversification of all subclades suggest they diversified within just a few thousand years. If the diversification had taken place over a longer period we would see internal connections within the E1b1b1 clades.

    "It is not restricted to Ireland. It can well have coalesced in Occitania or Guyenne".

    I understand that R1b1a2a1a1b1b-L21 is confined to Ireland and Scotland. Have you a reference for it being present in Occitania or Guyenne? I think it is a different R1b1a2a1a1b1 haplogroup.

    "I am interested in northern routes as well, since during brief mild and wet spells, much of the region would have had lush growth of grass with huge herds of animals to hunt, while the south was much more arid".

    Exactly.

    "I would associate that with R1b".

    I think R1b's expansion is long after any original OoA C and F expansion. R derives from MNOPS, which is almost certainly an SE Asian. On the other hand I think R1b is early into Europe.

    "Perhaps 'IJ' followed a much more southern route through Iran and Anatolia a little later"

    I think IJ was 'left behind' as F moved on.

    "I1 seems to correlate well with neolithic agricultural explosion in extreme northern Germany and Scandinavia; I2 may have spread via the Balkan, Saale/Elbe, and eastern portions of LBK".

    I'm very much inclined to see it that way also.

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  115. "Even during wet times, it is hard to imagine people crossed the Gobi desert"

    It's not necessary to involve the Gobi Desert. Grassland, and even forest, is present on the northern and southern fringes.

    "and the Caucasus as well, as it seems a fetish place for some reason"

    We know that H. erectus was able to thrive there, so it's reasonable to suppose that H. sapiens could too.

    "Actually one can even wonder if (pre-) IJ and G (i.e. the F and IJK branches leading to them) ever left the Persian Gulf Oasis at all".

    Yes. Now we're getting somewhere.

    "I´m not sure you are aware of the issue we are discussing in the thread".

    Actually the thread is about Y-hap A, but we've moved downstream.

    "However, then one must postulate that F split from CF pretty much right during the journey east and IJ also split of from IJK, then".

    A scenario that is quite possible, and one I have been advocating for some time.

    "Perhaps Pakistan is a better place for that to happen, since this seems to require some extended population growth"

    I'd certainly place TL in that region. Possibly C, although to me it seems obviouls that C did not move to SE Asia through India. And nor did mtDNA N.

    "if these splits happened early in some expanding population right ooA it is weird that the more basal ones are the ones that made it through and became more dominant in the east"

    Rapid movement? And replacement by a combination of increased aridity and subsequent haplogroup expansion.

    "However it is also possible that G and then IJ back-migrated to the Persian Gulf Oasis from South Asia instead of staying put all the time. I do not think we can safely discern between one or the other situation".

    True, but we should consider what is the most likely scenario with consideration of other expansions, both human and other species, that we know a great deal about.

    "But I do think that at least some of the migration to West Asia from South Asia happened by the Gulf Oasis and not only the Central Asian route".

    With 'Gulf Oasis' rather than 'coastal' I can completely agree. Certainly for Y-hap F and mtDNA M.

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  116. I think "rapid movement" and the hypothesis of G and IJ remaining behind contradict each other. For this hypothesis, you need F to split off, then G and IJK from that, and then IJ from IJK - that requires some population expansion and a bit of time. Typically, it is the latest groups, the derived ones, that end up at the fringe and found new populations after migration and expansion - not the basal ones which at that point are typically reduced to a very slim minority.

    That's why in this case I favor back-migration as the more straightforward explanation.

    An alternative is that there were two migrations (of this group) eastward: a quick one of C and F, with some F left behind in southwest Asia, and then a second one later from the IJK that meanwhile developed. But it happens that K is one of the most successful and most widespread groups - quite unlikely for a latecomer to India.

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  117. "The chances of any private lineage surviving the rigours of a major migration are virtually nil".

    What the heck? Their only long term opportunity is (almost, in Paleolithic conditions) actually to colonize a new area and establish themselves as founder lineages. "California or bust" more or less.

    I cannot follow the track of the rest of the discussion. If you want to discuss with me, please avoid one-liners and quotes that make no sense on their own (it's a headache). Also please focus on something because it's like 200 different debates at the same time.

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  118. "If you are so interested".

    Not that interested. I just thought that could made easier the discussion. In any case it is off-topic as you say !

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  119. "What the heck? Their only long term opportunity is (almost, in Paleolithic conditions) actually to colonize a new area and establish themselves as founder lineages".

    I am in complete agreement that at times private lineages have 'expanded'. But one thing private lineages do not do is 'travel' as private lineages. They develop in situ through drift and are a product of previous expansion. Thus they 'colonize a new area and establish themselves as founder lineages'. But they arrive as part of the expansion of their 'parent' haplogroup. Some time later, with the arrival of a new group and new technology or the opening of a new route, they can become a major part of some local population, before that population itself in turn expands.

    Y-hap C2 provides a perfect example. It had drifted to a private lineage in Southern Wallacea, as a remnant of C's earlier expansion, before being able to join the general merriment of the Austronesian trading network. It joined, and possible even led, the Austronesian expansion east into the Pacific. But it certainly didn't travel there as a private lineage. It had become a major part of the southeastern Austronesian-speaking population.

    The fact that all the minority lineages present in the outer Pacific do not simply increase as we move back west towards SE Asia is because of a follow-on expansion of New Guinea/Northern Melanesian haplogroups such as K3, M and S. But very few of these haplogroups survive as far as Central Polynesia.

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  120. "For this hypothesis, you need F to split off, then G and IJK from that, and then IJ from IJK - that requires some population expansion and a bit of time".

    OK. I'll concede that the 'rapid' bit occurred once the population had entered India.

    "Typically, it is the latest groups, the derived ones, that end up at the fringe and found new populations after migration and expansion - not the basal ones which at that point are typically reduced to a very slim minority".

    Agreed. But G and IJ are basically found at a fringe of the F-hap population. They quite probably lived at that fringe before any back-migration from SE Asia was capable of reaching the region G and IJ now inhabit.

    "An alternative is that there were two migrations (of this group) eastward: a quick one of C and F"

    I think you're making the mistake of automatically assuming that C's presence in Australia and SE Asia is a product of movement through India, and that it accompanied F on that voyage. Take C out of the equation and it is easy to see what probably happened with F's expansion.

    "But it happens that K is one of the most successful and most widespread groups - quite unlikely for a latecomer to India".

    Almost certainly entered India with F, where pre-TL was left behind in the northwest and drifted to being a private lineage there before being able to later expand as T and L. So, entering further into India, we have the haplogroups pre-KMNOPS, pre-F1, pre-F2and pre-F4 and pre-H. F3 is a bit of a mystery. But along the way pre-G and pre-IJ had been left behind and drifted to their present haplotypes. K2, K3, K4 and MNOPS reached SE Asia, where NO moved north through into China and P moved back west through India and out into Central Asia, leaving R2 behind in India. In Central Asia Q went east as far as America, R1a remained pretty much where it was, R1b went west into Europe and R1c went southwest into Africa.

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  121. "I cannot follow the track of the rest of the discussion".

    Because you choose not to (I'm giving you the benefit of the doubt, and believe it is not because you are stupid). And you haven't responded to this:

    "I understand that R1b1a2a1a1b1b-L21 is confined to Ireland and Scotland. Have you a reference for it being present in Occitania or Guyenne? I think it is a different R1b1a2a1a1b1 haplogroup".

    I've got too many 1b's in there and it should finish with a b4 but, for me, the mystery clades within R1b1a2a1a1b-P312 are R1b1a2a1a1b1-M65 and R1b1a2a1a1b6-L238. Where are they found? R1b1a2a1a1b2-M153 is centred on the Pyrennes, R1b1a2a1a1b3-S28 is centred on the high country of Central Europe, R1b1a2a1a1b4-L21 is piled up at the extreme western margin of Europe and R1b1a2a1a1b5-L176.2 is smack in the middle of the other three.

    Nine subclades of R1b1a2a1a1b4-L21 have been found and I have no information as to whether all are actually Scottish or Irish: 4a, 4b, 4c, 4d, 4e, 4f, 4g, ai and 4j. Does anyone have that information? R1b1a2a1a1b4b-M222 is definitley Irish and Scottish, perhaps the 10,000 year marker.

    "In any case it is off-topic as you say"

    OK. Back to Africa. A1b and A1a look like remnants of an ancient spread that has been overlaid by later expansions, although their current distribution is presumably a product of their participation in those expansions. It seems the ancient spread reached as far as South Africa. We have A2 in the Khoisan, A3 mostly Khoisan but reaching Kenya, and BT somewhere across the Central African Sahel. Perhaps right along it, although A1b and A1a look like likely candidates for the western half of it.

    B, in the form of B1, B2a, B2b and B2c, became dominant through the forested region south of the Sahel though. CT became dominant through the grassland region that stretched northeast out into the Levant and Arabia. And beyond.

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  122. "one thing private lineages do not do is 'travel' as private lineages".

    I think they do. In fact there is no other explanation for so many examples of scattered "child" lineages far away from the reconstructed homeland of their parents and far away from where their siblings live.

    Drift only wipes them a posteriori, not before. Because drift needs time.

    "Y-hap C2 provides a perfect example. It had drifted to a private lineage in Southern Wallacea, as a remnant of C's earlier expansion"...

    On the contrary: C2 is not at any time "private" in Wallace. AFAIK it is hegemonic, totally the opposite case. Its migration and arrival to Wallacea may have happened as private clade but in this particular case there's not even much need to appeal for such seed-like migration because C probably coalesced (split in several sublineages) in nearby SE Asia (so there's almost no journey to account for).

    But the transition between C2-root and the C2a1 Austronesian sublineage probably happened in form of a very thin thread, a private lineage or almost. How many people have been reported as having C2a(xC2a1)? I understand that very few. How many C2a1 out of Polynesia? Again very few. This is a living example of "seed-like" migration in fact, between the Wallacean C2 homeland and the first Polynesian colonies where C2a1 became established as dominant, by means of founder effect.

    If it were a dog it would have bitten you.

    "The fact that all the minority lineages present in the outer Pacific do not simply increase as we move back west towards SE Asia is because of a follow-on expansion of New Guinea/Northern Melanesian haplogroups such as K3, M and S".

    Not at all. It is a product of founder effect "distillation" by which a simplified product with (normally) the hegemonic lineage is delivered more and more purified by the end of the migration. But this is a very special case because Polynesian populations may have experienced founder effects but never experienced large expansions of their own because of lack of land to colonize.

    It's like an 'in vitro' (or 'in silico' as they say now) repeatedly aborted example of founder effects that can't get really to the point, as happened in Asia after the OoA. Also the routes are very "narrow" and unique, unlike what we see in the continent, where they criss-cross all the time. It's not such a good example except for very limited purposes.

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  123. "And you haven't responded to this"...

    Got really annoyed before reaching that far. I did not even read that. But anyhow, you said:

    "I understand that R1b1a2a1a1b1b-L21 is confined to Ireland and Scotland. Have you a reference for it being present in Occitania or Guyenne? I think it is a different R1b1a2a1a1b1 haplogroup".

    L21 (or M529) is shared between South France and the Atlantic Islands. In any case it is not restricted to "Ireland and Scotland" but it's common in all the islands. See here (notice that there's a typo in the maps and M529 is listed as M259).

    Right now the lineage is known as R1b1a2a1a1b4 (L21/M529/S145) but this is just because of the sudden change in the nomenclature induced by the undue influence of FTDNA private company.

    ...

    In regards to the African lineages, I'd say that the expansion of B and the two A1's looks much like the same thing or almost.

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  124. "I think they do. In fact there is no other explanation for so many examples of scattered 'child' lineages far away from the reconstructed homeland of their parents and far away from where their siblings live".

    And I'm sure they don't. Have you any examples of scattered 'child' lineages far away from the reconstructed homeland of their parents? Especially examples that cannot be explained as remnants of a 'parent' expansion.

    "Drift only wipes them a posteriori, not before. Because drift needs time".

    Yes. They drift to being a private lineage in the region they have arrived at. They don't arrive in that region as a minor haplogroup (or private lineage) within a wider haplogroup population.

    "Its migration and arrival to Wallacea may have happened as private clade"

    I doubt it. It is related to Australian C4 and SE Asian C*. So presumably it arrived in Walalcea in some numbers.

    "But the transition between C2-root and the C2a1 Austronesian sublineage probably happened in form of a very thin thread, a private lineage or almost".

    Obviously the mutation that lies at the base of C2a can only have happened in a single individual. So if you're going to call that a private lineage you have to say that all lineages are private when they first form.

    "How many people have been reported as having C2a(xC2a1)? I understand that very few".

    According to Ebizur (at this blog, I'm fairly sure) very common from the Admiraly Islands east. In Polynesia proper it becomes dominated by C2a1.

    "How many C2a1 out of Polynesia? Again very few".

    Wrong. It is the most common Y-hap in marginal Polynesia.

    "This is a living example of 'seed-like' migration in fact, between the Wallacean C2 homeland and the first Polynesian colonies where C2a1 became established as dominant, by means of founder effect".

    That's basically what happened. C2-M38 left from Southern Wallacea. Around the Admiraly islands the mutation C2a-M208 appeared. Just west of Fiji C2a1-P33 appeared, to become the major haplogroup beyond those islands. The variety of haplogroups decreases as we move east. So how many private lineages traveled along with C2 to appear later, and subsequently expand?

    "But this is a very special case because Polynesian populations may have experienced founder effects but never experienced large expansions of their own because of lack of land to colonize".

    'Lack of land to colonize'? For God's sake Maju, they were moving into unoccupied islands. The population expanded greatly. Yet still no private lineages survived. And it's hardly a 'very special case'. Most human migrations into unoccupied regions have almost certainly been much the same.

    "It is a product of founder effect 'distillation' by which a simplified product with (normally) the hegemonic lineage is delivered more and more purified by the end of the migration".

    So would you mind explaining exactly how a private lineage could survive such 'distillation'.

    "the routes are very "narrow" and unique, unlike what we see in the continent, where they criss-cross all the time".

    They criss-crossed after all regions had been occupied, but to claim some undefined difference between the Polynesian expansion and the first OoA expansion is to invoke special pleading. It si extremely unlikely that the first OoA spread all over the earth like some Noachian flood.

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  125. "L21 (or M529) is shared between South France and the Atlantic Islands. In any case it is not restricted to "Ireland and Scotland" but it's common in all the islands".

    I did correct myself and suggest that the derived haplogroup R1b1a2a1a1b4b-M222 is the Irish/Scottish (and nearby islands) haplogroup. So the subclades of R1b1a2a1a1b4-M529 are spread through Europe much as I suggested. That is regionally diverse. From your earlier y-Hap R thread:

    "Notice that the expansion of the South clade to the Atlantic islands does not invalidate its southern character and probably represents an Epipaleolithic-to-Neolithic spread".

    Yes. So what is the subclade that makes up around 90% of Irish men with Irish surnameson the west coast? That one can be no older than 10,000 years.

    I notice I misread your comment:

    "How many C2a1 out of Polynesia? Again very few".

    None in fact. The expansion into the Pacific is exactly how haplogroups spread from Africa. For example there is no F in Africa. As the haplogroup moved east it broke into regional clades, just as the Pacific haplogroups did. Only the F migration seems to have consisted of more than one F clade at every stage of its movement. From west to east: G, H, F*, F1, F4 and F3. And for much of the time F was accompanied by its descendant haplogroup Y-hap IT (or whatever you like to call it). Again from west to east: IJ, TL, K1, MNOPS, K3, K2, K4.

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  126. "In regards to the African lineages, I'd say that the expansion of B and the two A1's looks much like the same thing or almost".

    The expansion may be, but the A1s look much more specifically West African than do the others. So they probably coalesced in West Africa on the margin of the whole geographic distribution but were picked up during B's later expansion.

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  127. ^^Not even reading: most are quotations and very little new input, all of which is fragmentary. Improve your style, Terry, please, if you want me to even read it at all.

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  128. "most are quotations and very little new input"

    The quotations are yours, and I quote them because they are wrong.

    "Improve your style, Terry, please, if you want me to even read it at all".

    We both know it is not the 'style' that makes you reluctant to read my comments.

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