December 12, 2011

On the origin of mitochondrial macro-haplogroup N

The notion that the migration of Homo sapiens out of Africa had to pivot around West Asia has been deeply entrenched in our minds, partly because geographical common sense, partly because Eurocentrism, partly maybe because of the Judeo-Christian-Muslim religious background of most influential researchers historically... 

However in the last years this idea has been challenged by the coastal migration theory that proposes a migration mostly along the coasts of the Indian Ocean rather than through the interior of Asia. This theory was first outlined by population geneticists, who needed to explain the facts of haplogroup distribution in Eurasia, not at all more diverse towards the West, as we could expect from the classical models pivoting around the Fertile Crescent, but rather towards the East and very specially in South Asia. Later it has been also corroborated, with lesser shadings maybe, by archaeologists who have sought material support in Arabia and India and found it.

While the origin of mitochondrial macro-haplogroup M in South Asia is seldom contested, that of its "sister" N is seldom agreed upon. The reason is that it is distributed somewhat evenly through all Eurasia, Australasia and even America.

This map, from the Metspalu 2005 paper (open access), illustrates the issue and how even renowned geneticists doubted not long ago on where to place the urheimat of the haplogroup:



The phylogeny has anyhow been refined in these six and a half years and you may notice that Australasia is not even included in the map, although it does play an important role, being surely more important than West Eurasia. In any case the map is illustrative of this state of confusion. Confusion that I will try (once again and hopefully for good) to dispel in this article.


The facts of mtDNA N

Macro-haplogroup N has 15 acknowledged basal haplogroups scattered through all Eurasia and Aboriginal Australia. They have diverse numerical importance but what matters to me here is how many mutations (coding region transitions, to be more precise) they are downstream of the N node. Why? Because this is surely indicative of the timing of their respective expansions in relation with N as such. 

Looking at this measure we find the following classes of N sub-haplogroups:
  • Elder daughters: one coding region mutation downstream of N: N1'5, N9, N11, S and R. Notice that among these R holds a special place, not for any phylogenetic reason but because it has a scatter as wide as that of her mother N, suggestive of a very early coalescence and some sort of association between both expansions. 
  • Two mutations downstream of N: N10 and O.
  • Four mutations downstream of N: N2 (incl. W), A and X.
  • Extremely long stems, rare clades without any known node under N: N8, N13, N14, N21, N22.
This distinction is not very important but I have always present in any case, because it implies that the various classes of subhaplogroups expanded at different moments after the N node. Notably there is a "pause" at the place of the third mutation and then after the fourth. So we can well imagine the expansion of N as a double explosion, first the two first categories and then the third and maybe the fourth.

Representing each haplogroup as a dot, where they might have coalesced (often a hunch within the local region), the result is as follows:

1.- Estimated coalescence of basal subhaplogroups of N

The size of the dots represents only the "class", that is: how many mutational steps they are under N, the larger the closer they are and the earlier they must have coalesced (according to the laws of probability). The peculiar macro-haplogroup R (whose approx coalescence location was estimated in the past and I will not explain here) has been painted of a lighter blue and given a slightly larger size. 

I have also outlined the cloud of N expansion at mutational steps 1 and 2 (no difference), which are followed by an apparent pause at mutational step 3, as mentioned above. The cloud has been pushed northwards a bit in East Asia in order to avoid disputes on where exactly did N9 coalesce (it does not make much of a difference if you prefer Beijing over Shanghai for this clade's coalescence in the end).

Notice that this N cloud is almost identical as would be the M cloud (not shown but look here for a reference if you wish). Whether they were simultaneous or, as I think, N coalesced and expanded a bit after M did, their geography was the same: South Asia, East Asia and Australasia without distinctions. This T-shaped region (with the East on top) was the homeland of the first Eurasian (or more properly non-African) population of Homo sapiens (excepted those who remained in Arabia, which are another story).


The geographic origin of N

Alright, I have described the scatter of N subhaplogroups and the most likely sequence of the expansion but my main purpose here is to estimate the origin, the urheimat of N: where did the N matriarch, the ultimate matrilineal ancestor of all N people today, live?

I apply the statistical principle by which the derived basal haplogroups should tend to remain not too far away from the common origin. Being the most removed ones, exceptions and never the rule. It does makes sense, right?

Hence if we can estimate the centroid of the geometry described by the 15 haplogroups, we will have found the origin of N - or at least a raw estimate of it. There are several methods to estimate centroids but I chose to use the geometric one. In fact, for simplicity, I divided the subhaplogroups in three sets of five (so they all weight the same) and estimated their centroids by geometric decomposition. Then I estimated the centroid of the resulting triangle.

If I am correct the raw centroid of N is at the lower Mekong:

2.- Possible origins of mtDNA N (blue flowers): A - 'raw' geometric centroid, B - corrected against directionality.

I have argued on occasion that, in order to compensate for the directionality of the expansion, a correction can be applied to the geometric centroid or raw estimate of the origin. This correction should pull the origin towards the parent node, in this case L3 in East Africa (estimated here). How much? Maybe 1/4, maybe 1/3... this step, even if probably very reasonable, is a guess and not rocket science. Here I chose to use 1/4 and then look for the closest coast, which is that of Bengal - alternatively I can use a crooked line that follows the geography and get the same result (even less ambiguously Bengal again).

If I would have chosen a 1/3 value for the correction, it would fall in a more central part of India, if 1/5 in Burma surely. We can't be sure of where exactly that happened but we can be more than reasonably sure that it was between India and Cambodia. 

And nowhere else: not in West Asia, not in Altai... thanks for the suggestions but I have heard that before... many times... always without a single piece of evidence nor well-reasoned backing of any sort. 

The data says otherwise: around the Bay of Bengal or even further East maybe. 


Getting R into the picture

I have said before (and is obvious for anyone interested on population genetics) that mtDNA R is peculiar. While it is not different phylogenetically from other subclades of N which are separated by just one coding region mutation, its geographic distribution is very different, because R, like its mother N, is everywhere. 

In order to show it more clearly, I drew approximate origins of all basal R-subclades (in lighter blue). The size of the circles follows the same logic as do those of N above, representing only the distance from the mother node (R in this case, what means one step further downstream in relation with N), and hence a probable order of coalescence:

3.- Scatter of N (deep blue) and R (cyan) subhaplogroups. The flower indicates the possible common origin.

The scatter of R fits very curiously within that of N(xR). They do not overlap too much maybe and it looks on first sight like R could have pushed other N around to the margins of the common expansion cloud. However this does not seem to happen with M, so maybe another explanation is needed, like undifferentiated N and R traveling together, mostly under the leadership of the latter and causing different founder effects in different locations.

Whatever the case it is worth a good meditation, because it is possible that both haplogroups (mother N and daughter R) coalesced in rapid succession in a single region (Bengal probably). 

54 comments:

  1. The trouble with a centroid approach is that it overlooks what I think of as the "mixed sands of different colors" effect. Once you blend populations with both M and N in them for a signficiant length of time, you can never separate them without an mtDNA identifying device.

    Since Western Eurasia has large swaths of area that have N-R but not M, while everyplace else has M-N-R, the N-R population had to predate the admixture of the two groups. You could never get the absence of M in Western Eurasia that is observed from random chance. It takes just dozens of iterations in a plausibly sized population for the M-N-R proportions to reach fixation and for it to become impossible for any viable population to split off from an M-N-R without keeping elements of each grouping.

    This puts the origin of N-R far to the West of your estimate, realistically, Iran, Turkey or some Arabian refugia. Then N-R can migrated East and blend into M sometime before 45,000 years ago when all three land in Ausralia and New Guinea. Given the increasingly early dates for Out of Africa, there are tens of thousands of years in which this can happen. But, since N-R are always present together, the R branch from N has to arise sometime prior to the admixture of N-R into M.

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  2. That's one of the most original arguments I have read, admittedly, and it's new to me. I understand anyhow that:

    1) Basic small population genetic logic applies:

    Founder effects allow for mixing and de-mixing of lineages. If A and B come together in pop. AB and then emigration happens, the resulting population will be A or B but hardly A+B anymore.

    We are discussing after all small populations of Paleolithic size, organized in operative bands of 20-30 individuals who cooperated larger "ethnic" or "tribal" groups which could be of a few thousands at the most. The tendency is once and again to coalesce into a single haplogroup (random but usually the dominant one) by mere drift, even if that not happens completely all the time (maybe several lineages survive but never many).

    So by this reason mixed colors do separate (not the autosomal DNA, which is recombined and surely what defines the outward aspect, but indeed the haploid lineages).

    ...

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  3. ...

    2) Even if they shared the overall "T region" M and N may have remained in part as separate populations.

    It looks to me that the N (and R) explosion happened mostly after the M one, in the wake of the M demographic explosion. If so we'd have many M-dominated populations and, initially, only one N-dominated one.

    It also looks rather obvious that N+R migrated, maybe in small numbers, towards West Asia getting only one relevant M adhesion (M1). This I interpret as the reconstructed proto-Western population of, say, Afghanistan (dominated by R but with some N*, leading later to N1'5, N2 and X) not having much relation with the M populations that dominated South Asia at the moment (whether they were hostile or inhabited different regions or exploited different ecological niches I can't discern).

    "You could never get the absence of M in Western Eurasia that is observed from random chance".

    It is best explained as the M expansion belonging more specifically to a first wave, with clear Eastward direction, while the N expansion is more ambiguous and the R sub-phase (if distinct at all) is already in partial reverse mode (Westward direction to some extent). These are two related but rather successive phases (not simultaneous) of the demic expansion in Asia and surroundings.

    So it's not random. What is random (stochastic, i.e. there is casualty but we can't see it) is that in the midst of all that M boom a single other L3-derived clade not just survived but actually starred its own smaller boom leading to an ultimately comparable takeover of Eurasia and the rest. That's why I think that you are right to some extent about the two populations being separated to some extent - however not as you imagine, separated in geography (or not only that) but rather by either identity, culture or economy.

    Their separation was not too tight anyhow, because they obviously exchanged male companions once and again. This would lead to a lengthy exploration on the arguable correlation of mtDNA and Y-DNA and to the issue of whether the populations were patrilocal, matrilocal or ambilocal. I think that ambilocality is the most correct inference (except in some conditions, notably subarctic climate, where patrilocality and nuclear family dominate) but it does not matter too much because mtDNA is chosen because it is normally less volatile than Y-DNA, representing better the "soul" of the populations than the patrilineages.

    ...

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  4. ...

    3) In the end, you can't deny the facts of the haplogroup scatter: regardless of whether we take all basal subhaplogroups or just the "elder" ones, the centroid falls always in the same area (SE Asia for N), not being compatible with the notion of a West Asian coalescence at all.

    If N would have coalesced in West Asia, we'd find the derived haplogroups mostly around that area and not along the Pacific Ocean. That is specially true for those coalesced in the immediate period, i.e. hanging from the N node by a very short, single-mutation, stem.

    You must come with an explanation for this anomaly, for why the region you posit as origin does not fulfill any of the objective expectations for such area.

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  5. "If N would have coalesced in West Asia, we'd find the derived haplogroups mostly around that area and not along the Pacific Ocean."

    This doesn't follow. We have very good reason, which you illustrate, to think that that N and R were both present in the very same wave of expansion from their common source. (The presence of R with N everywhere combined by the presence of very basal R and N in other places and R being just one tick apart from N, suggests that the N-R migration happened after R developed, but not very long at all after). During a rapid expansion (continental under well under 5,000 years), every place within the expansion territory is going to look equally basal. Ends are just as likely to be points of origin as centers. You have to resort to other means to identifical where in the territory of equally basal lineages the wave started. To see an excess of derived hgs on one side or another, you need a slow, serial expansion. If the expansion happens in less than one mutational beat, you don't see that kind of excess.

    The existence of an N-R cluster in the West without M that is not found elsewhere, point of origin on the West. So do a few other observations:

    1. The West Eurasian Neanderthal DNA doesn't overlap much with East Eurasian Neanderthal DNA, the amount of admixture is very similar, but the specific genes don't overlap. This points again to separated West v. East communities with West communities not having Eastern roots. Otherwise, you'd expect West Eurasian Neanderthal DNA to be a subset of the Eastern set.

    2. The presence of Y-DNA C (and arguably D) which are likewise found in Asia but not Europe, likewise supports the idea of Y-DNA F macrohg with mtDNA N-R women, but not Y-DNA hg C/D in that community. Y-DNA F macrohg is found in essentially the same places as N.

    3. The absence of L3 in Eurasia suggests that the M and N mtDNA mutations happened within 5,000 years or so (perhpas +/- 5,000 years) of the sources of the surviving Out of Africans, and India was inhabited pre-Toba and Arabia from 102kya, and the Levant 100kya. If L3 had gotten all of the way to SE Asia before breaking into N, we'd see a trail of many L3 derivatives across the path from Arabia to SE Asia (as we do with M and N) but we don't. The L3 =>M and L3=N splits had to happen early. L6 in Arabia could be a sister to M and N in the early Eurasian community, but we see nothing like that in Iran or South Asia or points East or points North.

    4. There had to be at least one West to East expansion. Given point 3, that expansion had to be either M or N.

    5. The fact that several Y-DNA D populations coincide with similarly old mtDNA M, but not similarly old mtDNA N-R in the Andamans, Tibet, and Japan. So, by ca. 35,000 years ago, the M to N-R admixture was not complete even if it had taken place in some places. The Y-DNA D people probably followed the Y-DNA C people and hooked up with mtDNA M women that were not yet mixed with mtDNA N-R women. But, the absence of Y-DNA D people in Australia and New Guinea, their relative isolation for long periods of time from Y-DNA C/O people in Japan and the Andamans, and their rarity in SE Asia and the depth of the genetic cap between CF and D, suggests that they are a different wave, from C and from F.

    6. The Neanderthal-Denisovian autosomal best fit population model shows two Neanderthal admixed AMH population waves in SE Asia prior to 45,000 years ago. One admixes with Densiovians. The other admixes with them and then post-admixture goes to Australia-Papua New Guinea. This fits an M wave followed by and N-R wave.

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  6. "During a rapid expansion (continental under well under 5,000 years), every place within the expansion territory is going to look equally basal".

    No. Where the haplogroup coalesced most basal subhaplogroups should be found.

    Whatever the case "equally basal" does not mean that the alleged origin holds almost no basal sublineages and is most distant from nearly all basal sublineages, which is what you propose.

    Also we have the issue of Y-DNA MNOPS, which also looks very strongly as having reached SE Asia and then "bounced" westward as P (which also appears to have coalesced in or near Bengal). The only advantage of Y-DNA is that it never stops accumulating mutation, so a well studied clade as P is easy to track almost step by step. You will probably argue that it is unrelated and more recent and that it did that migration later on but there is no mtDNA that fits that pattern other than N, not even at tiny levels. It is indirect and arguable confirmation but IMO it is quite supportive as these two lineages are the only ones that match each other's behavior on the map.

    "Ends are just as likely to be points of origin as centers".

    It does not make any sense: if you drop a bunch of fleas they will spread in all directions, mostly remaining near where they were dropped and with just few going far away.

    Whatever the case, with your logic no reconstruction is possible at all. You are just denying that we can track the flows of prehistoric peoples by looking at the genetics. That population genetics are flat and uninformative.

    "If the expansion happens in less than one mutational beat, you don't see that kind of excess".

    You do see it because "the fleas", the people, tend to stay nearby. It's the odd bunch who emigrates, regardless on whether they are highly successful or fail miserably.

    Whatever the case, we should NEVER expect a strong lack of diversity in destination.

    And if you are ready to accept that all is non-informative, then you must accept that population genetics is not for you because for you it all looks the same, equally featureless and meaningless.

    I say that is nothing but denial.

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  7. "1. The West Eurasian Neanderthal DNA doesn't overlap much with East Eurasian Neanderthal DNA, the amount of admixture is very similar, but the specific genes don't overlap"...

    I don't think this is correct (source?) but, anyhow, it is autosomal genetics! In this aspect, we do know that West and East Eurasians differ in nearly all that matters genetically, even up to the point that West Eurasians tend to cluster with Africans at K=2 (depending on samples and such) because of minor recent (?) admixture.

    Overall West and East Eurasians share very little autosomally (specially if contrasted with third populations like Africans) and that you say only speaks (if correct) of that same process of separate and hence divergent genetic drift, west and east of Assam.

    This process of divergence necessarily happened only after the Eurasian expansion, which is what we are discussing here. So we are here at a moment before this genetic divergence and surely before or at most at the very beginnings of phenotype divergence as well.

    That's why the Eurasian expansion was probably quite fast and then a very long period of lack of genetic exchange took place.

    "Otherwise, you'd expect West Eurasian Neanderthal DNA to be a subset of the Eastern set".

    Not at all: the admixture with Neanderthals (or other Heidelbergensis!!!) took place before the Eurasian expansion or at the very beginnings of it (admixture with Hathnora hominins in South Asia?) Then the populations diverged, retaining more or less (not all populations retain exactly the same) and even different fractions of this Neanderthal (?) admixture.

    Whatever the case we do not know enough of this matter so, sincerely I'd wish you had not introduced it so happily and without any backing.

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  8. "2. The presence of Y-DNA C (and arguably D) which are likewise found in Asia but not Europe, likewise supports the idea of Y-DNA F macrohg with mtDNA N-R women, but not Y-DNA hg C/D in that community. Y-DNA F macrohg is found in essentially the same places as N".

    Not at all. F is clearly associated with mtDNA M in South Asia and to some extent at least also in East Asia. F is "da man", while C and D are local phenomena restricted mostly to East Eurasia (and even to particular regions in that area). C does seem related with mtDNA N in some locations, notably Australia but in NE Asia probably as well, while F in East Asia is almost only MNOPS and seems most tightly associated with mtDNA R.

    So IMO: mtDNA M expanded (basically) with F in South Asia and with C and D in East Asia but C is also found with N. MtDNA R is most tightly correlated with MNOPS and it is MNOPS (P) which probably "brought" N and R to West Asia, grabbing some other "boys" in the process somehow (IJ and G - LT also but this one is mostly related to mtDNA M1). Don't ask me about the real life details of how these other men lineages were integrated: it happened and it's all I know.

    "3. The absence of L3 in Eurasia"...

    That's fallacious: M and N are the L3 in Eurasia. Out of seven basal L3 sublineages, two are in Eurasia since the beginning (plus a couple of further derived ones but restricted to the Arabian region). L3 does exist in Eurasia and in diversity quite unexpected for an African lineage: not one but two basal lineages!!!

    ... "suggests that the M and N mtDNA mutations happened within 5,000 years or so (perhpas +/- 5,000 years) of the sources of the surviving Out of Africans".

    Not at all: M and N are way too detached from the L3 to make such a claim. Within 10 Ka for M and withnin 15 Ka for N at the very least (assuming 2.5 Ka per mutation, what adds up to less than 150 Ka for all the mtDNA tree, so it's quite "fast" actually).

    "If L3 had gotten all of the way to SE Asia before breaking into N, we'd see a trail of many L3 derivatives across the path from Arabia to SE Asia"...

    Wrong reasoning. For both M and and N there is a "pre-" or L3* stage, which has left no traces:

    L3 > pre-M(1) > pre-M(2) > M

    L3 > pre-N(1) > pre-N(2) > pre-N(3) > pre-N(4) > N

    Neither the pre-M nor the pre-N are known to exist anywhere. So these two lineages traveled as 'private' (tiny) lineages for quite a while (or where violently pruned by a bottleneck, not a generally accepted hypothesis). Or most likely, they strongly suffered the effects of drift in Arabia, where other lineages remained instead - of the L0, L4, L6 and L3 haplogroups) and were pruned there just by drift.

    This makes sense for M but still demands that N was either pruned or was a tiny (private) "infiltrator" in the M ranks. The latter makes some good sense, as we also find the same kind of "infiltrators" in Y-DNA: D and C (although C can be considered a branch of F or, more correctly, C'F). What looks is like these lineages had no or very limited opportunity for expansion in South Asia and had to take their opportunities in the "wild east" of Eastern Eurasia (incl. Sahul).

    Two of these "wild frontier" lineages managed to make an impact back home and specially in the newly opened western frontier: mtDNA N (specially R) and Y-DNA P (from MNOPS). Why? Beats me. Dogs maybe?

    ...

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  9. ...

    "4. There had to be at least one West to East expansion".

    Via Arabia, small numbers. Archaeology supports it more and more.

    "... that expansion had to be either M or N".

    Pre-M and pre-N actually (no booming expansion: just private silent migration). Both in fact, however M took advantage early upon the arrival to South Asia and N had to carve its own niche with greater difficulty in the eastern frontier.

    In the Y-DNA side we see the same with F taking all the advantage in South Asia, while D and C are almost restricted to Eastern Eurasia (incl. Sahul). What we do not see is D nor C "bouncing back" as mtDNA N/R did, this is privilege of MNOPS and specifically its P subclade (which incidentally also seems to have coalesced near Bengal).

    "The fact that several Y-DNA D populations coincide with similarly old mtDNA M, but not similarly old mtDNA N-R in the Andamans, Tibet, and Japan".

    I agree that D looks more closely associated with mtDNA M or, more precisely, with some specific M sublineages (most M is not related to Y-DNA D at all but to F and in some cases to C).

    "So, by ca. 35,000 years ago"...

    Molecular clock nonsense. Please avoid.

    "The Neanderthal-Denisovian autosomal best fit population model shows two Neanderthal admixed AMH population waves in SE Asia prior to 45,000 years ago".

    I can only wonder where you get these dazing "models" of archaic-AMH admixture applied to archaeo-demographics. Never heard of them.

    I can loosely agree with that but more like an AMH-Neanderthal admixed pop. in South Asia c. 80 Ka. ago and a subset that admixed with H. erectus in Sundaland some time after that (with only small apportions of this admixture making it to the mainland, mostly being retained by Australasian aboriginals and such).

    "One admixes with Densiovians".

    For me there is no "Denisovan" admixture but this is just a proxy for admixture with East Asian H. erectus in Sundaland. "Denisovans" are surely a Neanderthal-Erectus hybrid that only existed in Altai - however because we have no other references for the genome of the H. erectus we speak of "Denisovan admixture" but this should not be read as such but accept that it is just a proxy for non-Heidelbergensis archaic admixture.

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  10. "I don't think this is correct (source?)"

    Don't have time to respond to all of these issue (maybe I'll do a referenced blog post sometime). But, the source re specific Neanderthal genes admixed in the East v. the West is a post of John Hawks on the subject earlier this year with a nifty chart plotting out the number of times particular Neanderthal genes were found in Eastern and Western populations.

    In a single source population that reached fixation and then split, you the graph should be almost an even grid. Instead, there is a Eastern leg of genese found in the West but rarely or never in the East and visa versa, with a shared core of genes at high frequency in each either due to being pre-split or due to having selective advantage.

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  11. In June, he said: "The initial answer is that the 1-4% [of Neanderthal admixture] is largely different in everybody".

    Earlier in March, he mentioned his own research where he speculates about very subtle and not at all clear differences between populations in this aspect: nothing that you can turn into "the specific genes don't overlap" - actually they do overlap a lot (just look at the huge bars near pos. O,0, which include almost all analyzed genes). In any case he concludes that "we're looking at the effects of drift in small ancient populations after they mixed with Neandertals", a very different conclusion to that of yours and instead almost identical to what I was saying: drift since the divergence period.

    Or you may mean this other post, which is similar, although I imagine that the title may have misled you. It should carry the word "slightly" somewhere but it does not.

    Nothing that can support your claims in any case.

    "In a single source population that reached fixation and then split"...

    But it does not reach fixation at all: it tends towards fixation but seldom reaches it, specially not when the population is expanding and migrating all the time. Maybe a few lineages are pruned but most stay until separation, when new founder effects are created:

    A + B > AB > A + AB + B

    Merge and divergence coexist as above.

    While in Y-DNA we should be able to locate all nodes as the SNP-defined ones, in mtDNA, which evolves much more slowly, that does not happen necessarily (or even often if the process is very fast, as this one was).

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  12. "This puts the origin of N-R far to the West of your estimate, realistically, Iran, Turkey or some Arabian refugia".

    You will not get Maju to accept that. I have been trying for years.

    "Then N-R can migrated East and blend into M sometime before 45,000 years ago when all three land in Ausralia and New Guinea".

    It's not as simple as that. In spite of Maju consistently refering to 'Australasia' we have very different scenarios for three regions within that. Australia is largely N with very little M. New Guinea/Melanesia is largely M, the only N being R-derived. Wider Oceania becomes mainly B with some element of Melanesian M haplogroups. So something complicated was happening in SE Asia.

    "However in the last years this idea has been challenged by the coastal migration theory that proposes a migration mostly along the coasts of the Indian Ocean rather than through the interior of Asia".

    And now it in turn has been discredited.

    "archaeologists who have sought material support in Arabia and India and found it".

    That material in no way supports anything 'coastal'. Arabia was well-watered and the population spread through much of it.

    "it implies that the various classes of subhaplogroups expanded at different moments after the N node"

    Are you really claiming that N2, N13 and N14 traveled all the way from where they orginated to where they are now found in the form of already-formed clades long after other members of N had made the same trip? Unlikely.

    "The tendency is once and again to coalesce into a single haplogroup (random but usually the dominant one) by mere drift"

    Any non-dominant haplogroup would be drifted out during any such migration.

    "the larger the closer they are and the earlier they must have coalesced"

    Unless the conclusion doesn't fit your belief. Especially when you compare N with 'the peculiar macro-haplogroup R' or with M.

    "I have said before (and is obvious for anyone interested on population genetics) that mtDNA R is peculiar".

    Only because you have difficulty fitting it into your belief. Try looking at it in exactly the same way as you look at M and N.

    "The size of the circles follows the same logic as do those of N above, representing only the distance from the mother node (R in this case, what means one step further downstream in relation with N), and hence a probable order of coalescence"

    Ignoring the fact that haplogroups R11'B6 and B4'5 actually have a stem of nothing.

    "the possibility that both haplogroups (mother N and daughter R) coalesced in rapid succession in a single region"

    Very unlikely. You're forced to ignore N-derived haplogroups with a stem of one mutation that lie far from any likley R region of coalescence.

    "I think that you are right to some extent about the two populations being separated to some extent - however not as you imagine, separated in geography (or not only that) but rather by either identity, culture or economy".

    Separated by geography is a far more likely explanation. Any two populations in close geographic proximity exchange genes (and haplogroups) eventually. We have many examples.

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  13. "If N would have coalesced in West Asia, we'd find the derived haplogroups mostly around that area"

    Not necessarily so. We know that much of the region has suffered either extreme aridity or extreme cold since any OoA.

    "During a rapid expansion (continental under well under 5,000 years), every place within the expansion territory is going to look equally basal. Ends are just as likely to be points of origin as centers".

    Exactly. N wide spread, even of one mutation haplogroups, suggests an early spread to most of the regions where it is now found. R would have coalesced in one of those regions and then undergone its own expansion.

    "There had to be at least one West to East expansion. Given point 3, that expansion had to be either M or N".

    Quite. And surely we should be able to see evidence for it. Which we do if we're prepared to consider that several SW Asian haplogroups, both mt and Y, do not represent back migrations from further east.

    "Also we have the issue of Y-DNA MNOPS, which also looks very strongly as having reached SE Asia and then 'bounced' westward as P (which also appears to have coalesced in or near Bengal)".

    Agreed. And probably accompanied mt-DNA R, rather than both N and R. I tend to agree with this:

    "F is clearly associated with mtDNA M in South Asia and to some extent at least also in East Asia ... C does seem related with mtDNA N in some locations, notably Australia but in NE Asia probably as well, while F in East Asia is almost only MNOPS and seems most tightly associated with mtDNA R".

    Sums it up. C took N to Australia, but somehow they missed New Guinea. Actually makes sense. But N and C are unlikely to have moved east through India.

    "It does not make any sense: if you drop a bunch of fleas they will spread in all directions"

    Not if they are blocked from spreading in some directions.

    "M and N are way too detached from the L3 to make such a claim. Within 10 Ka for M and withnin 15 Ka for N at the very least"

    Presumably they got stuck for a time and underwent a period of drift before they were able to expand further away from Africa.

    "Neither the pre-M nor the pre-N are known to exist anywhere. So these two lineages traveled as 'private' (tiny) lineages for quite a while"

    Very unlikley to have traveled very far at all while that severe drift was occurring.

    "these lineages had no or very limited opportunity for expansion in South Asia"

    Surely they would not have survived any journey through that region.

    "In the Y-DNA side we see the same with F taking all the advantage in South Asia, while D and C are almost restricted to Eastern Eurasia (incl. Sahul)".

    Which suggests very strongly that D and C did not move through South Asia.

    ReplyDelete
  14. Your one-liner style of saying nothing, Terry, is a waste of my time. For example:

    "I have been trying for years" [To persuade Maju].

    With no arguments, no reason, no nothing...

    "And now it in turn [the coastal migration model] has been discredited".

    What?! When?! By whom?!

    Your continuous confusion of your desires with reality make me wonder... but mostly annoy me.

    "Are you really claiming that N2, N13 and N14 traveled all the way"... ?

    No, I am not claiming that.

    "... from where they orginated to where they are now found"...

    Where they "originated" and where they are "now found" should be the same place or region anyhow, mind you. I don't believe in vanishing "originary haplogroups".

    What I do is just to have a clear conceptualization of each mutational step meaning a quite lenghty span of time and therefore I know that long stems are uninformative for all their length: we normally know the ancestral node's location and the descendant's final place of coalescence (= expansion signature in the form of branching) but we can say nothing about what happened in between.

    For all that ignorance we can't help, you exploit like a religious predator throwing wild ideas on what might have happened or not in the blanks of our knowledge. That may be fine to write novels but not to make science.

    Each time I tell you that you have to draw a "dotted line" between the ancestral node's location to the descenant node's location you avoid the matter: simple geometry and simple logic bother you.

    Your whole logic can be described as follows:

    Argument A: ok, but... unlikely...

    Argument B: I don't think so.

    Argument C: that you say only because it "fits your purpose".

    And of the real matter we are debating: nothing or just a couple of stubborn unsupported ideas almost always lacking all explanation at all via one-liners.

    En fin.

    "Try looking at [R] in exactly the same way as you look at M and N".

    That's difficult: each of these three haplogroups are peculiar in their own way. So no idea of what you may be suggesting in fact because, as happens all the time, your "reasoning" ( or should I rather say "nagging"?) stops here.

    "You're forced to ignore N-derived haplogroups with a stem of one mutation that lie far from any likley R region of coalescence".

    I'm not "ignoring" absolutely anything.

    ...

    ReplyDelete
  15. ...

    "Any two populations in close geographic proximity exchange genes"...

    Do they? Or more exactly: do they in a manner that withstands drift: more inter-tribal sex than the rate of lineage extinction in each of the tribes? Even if there's some genetic exchange, this may have no obvious repercussions or may manifest itself in other ways (like swaps of Y-DNA-mtDNA pairings).

    "We know that much of the region has suffered either extreme aridity or extreme cold since any OoA".

    Do we know that? Presumably (to use one of your favorite words) they could have found refuges all through the region. It is definitely less arid than Arabia, where we do find some likely survivors. If they were in the Fertile Crescent, we would know it (unless hordes of "clockwork Neanderthals" hunted them to the last corner of the Zagros and Palestine and Caucasus and Uzbekistan and what not with a genocidal success that would be the envy of Hitler).

    "Presumably [pre-M and pre-N] got stuck for a time and underwent a period of drift before they were able to expand further away from Africa".

    Yes, that's what happened most probably but that contradicts your notion of haplogroups having to remain in destination without expanding until they suddenly do. According to your inconsistent ideas pre-M would have traveled to Sindh or Gujarat, where it stood idle for millennia while waiting for the correct timing to flourish, instead of exploiting the resources of the new niche, right?

    Well... wrong!

    "Very unlikley to have traveled very far at all while that severe drift was occurring".

    Why? Couldn't the few people carrying these lineages be traveling from beach to beach or oasis to oasis, slowly and gradually through Arabia and the Persian Gulf until they reached a place that was lush enough for them to prosper so dramatically that in some dozens of generations they were using most of Asia and beyond? Wouldn't reaching a providential destination like South Asia be th trigger of such dramatic expansion of numbers in such a short time as the genetic track tells us?

    "Surely [Western R and associated N] would not have survived any journey through [South Asia]".

    That's just a conjecture ("surely"): facts say otherwise.

    And actually contradicts what you said just above:

    "Agreed. And probably [MNOPS] accompanied mt-DNA R, rather than both N and R".

    R made it but N* could not? Would maybe a migration through Siberia with no "big sis" to take care of the smaller lineages be more likely in your opinion? And, if so, why the colonization of Altai (the pivotal region of Siberia) happens to be clearly originated in South and/or West Asia and not East Asia?

    Your ghostly populations that leave no trace of their existence may be convenient in your mind but I can't accept them.

    ReplyDelete
  16. "Your one-liner style of saying nothing, Terry, is a waste of my time".

    You can make such stupid comments that it becomes so tempting:

    "Do we know that? [much of the region has suffered either extreme aridity or extreme cold since any OoA]"

    Are you denying it?

    "It is definitely less arid than Arabia, where we do find some likely survivors".

    I agree that Y-DNAs G, IJ and F3, and mt-DNAs N1'5, N2 and X are likely survivors, but you have always denied that to be so.

    "With no arguments, no reason, no nothing..."

    Years of arguments and reason, which you have opposed because you are totally committed to some contradictory belief.

    "What?! When?! By whom?!"

    Maju, there is absolutely no evidence for any 'coastal migration'. Most, except for you, now accept that to be the case.

    "No, I am not claiming that [N2, N13 and N14 traveled all the way]"

    What are you claiming then? You wrote:

    "This distinction is not very important but I have always present in any case, because it implies that the various classes of subhaplogroups expanded at different moments after the N node".

    From that it certainly seems as though you believe that N1'5, N9, N11, S and R left SE Asia/India first. Then N10 and O followed along behind. Then N2, N22, A and X left SE Asia/India. Finally the haplogroups with long stems left that region: N13, N14, N21 and N8.

    "Where they 'originated' and where they are 'now found' should be the same place or region anyhow, mind you. I don't believe in vanishing 'originary haplogroups'".

    I don't believe in vanishing haplogroups either, but you apparently do. You have N and M vanishing along any possible route they took from Africa. And N vanishing from any route it may have taken back west through India.

    "What I do is just to have a clear conceptualization of each mutational step meaning a quite lenghty span of time"

    But your conclusions concerning haplogroups with a limited number of mutational steps is confused. You include or exclude control region mutations depending on which suits your purpose for a start. If you're prepared to include conntrol region mutations you finish up with an extra mutation at basal R. If you exclude them you finish up with not one but three basal haplogroups with a stem of zero (R 11'B6, R24 and B4'5). With a stem of just one more mutation we finish up with a further nine haplogroups(R11, B6, B5, B4f, B4c, B4b'd'e, B4g, B4h and B4a). Yet you are determined to ignore that when considering R's origin. Totally inconsistent.

    "and therefore I know that long stems are uninformative for all their length"

    They are 'uninformative' only because you choose to judge them so. Earlier you wrote, 'Where they originated and where they are now found should be the same place or region anyhow'. Surely that makes such haplogroups very informative.

    "For all that ignorance we can't help, you exploit like a religious predator throwing wild ideas on what might have happened or not in the blanks of our knowledge".

    Maju, it is you who are twisting the data 'like a religious predator' to fit some pre-existing belief. You are not prepared to examine the evidence objectively.

    "Each time I tell you that you have to draw a 'dotted line' between the ancestral node's location to the descenant node's location you avoid the matter"

    'Dotted lines' tell us nothing. Strings of descedant haplogroups are what we should look for.

    ReplyDelete
  17. "That's difficult: each of these three haplogroups are peculiar in their own way".

    Rubbish. They are only 'peculiar in their own way' because you are desperate to fit them to your belief. Because of that you are forced to look at each from a different perspective. If you were prepared to adopt a consistent perspective you would see the simplicity.

    "Do they? Or more exactly: do they in a manner that withstands drift: more inter-tribal sex than the rate of lineage extinction in each of the tribes?"

    Even Pygmies and Negritos share haplogroups with their neighbours, so you're clutching at straws here.

    "Yes, that's what happened most probably but that contradicts your notion of haplogroups having to remain in destination without expanding until they suddenly do".

    Don't be ridiculous. No it doesn't.

    "According to your inconsistent ideas pre-M would have traveled to Sindh or Gujarat, where it stood idle for millennia while waiting for the correct timing to flourish, instead of exploiting the resources of the new niche, right?"

    As you say, 'wrong'. Pre-M and pre-N obviously made it out of Africa, but not necessarily very far. N coalesced in one region within their distribution while M coalesced in another. Neither particularly far from Africa. On the other hand you have N moving a huge distance before expanding. Inpossible.

    "Wouldn't reaching a providential destination like South Asia be th trigger of such dramatic expansion of numbers in such a short time as the genetic track tells us?"

    Yes. That takes care of M, but it completely ignores N.

    "That's just a conjecture ('surely'): facts say otherwise".

    Only the 'facts' as you choose to interpret them. The facts certainly do not fit any substantial distance traveled by any minor haplogroup embedded within another. Can you provide any examples, or just conjecture?

    "R made it but N* could not?"

    Of course. R left plenty of track through South Asia. N did not leave any track. R presumably had some technological advantage over the pre-existing South Asian population. My guess is that was improved boating and hence exploitation of coast and river bank, but I know you are bitterly opposed to any such an idea.

    "why the colonization of Altai (the pivotal region of Siberia) happens to be clearly originated in South and/or West Asia and not East Asia?"

    Yes, by long-established West Asian haplogroups such as N1'5, N2 and X.

    ReplyDelete
  18. A couple more observation. Note the complete lack in your map of N hasplogroups in India. And I presume that haplogroup way to the northwest is A. I'm certain it should be nowhere near as far north as that. In fact it should be round Tibet somewhere. That would alter the pattern on your map considerably.

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  19. "Are you denying it?"

    I'm asking for evidence: there's been more or less continuous inhabitation in Palestine and it's not the most fertile of countries in the pivotal region, being too close to the deserts for any good. There are areas, for example in coastal Anatolia, that must have provided good habitats for humans of any species all the time. And Anatolia is just one example: the whole region was never a desert and even the discontinuity that was suspected in the Zagros in the LGM (for cold and not aridity) seems to have never existed after all.

    So yeah, I'm questioning it: the area looks perfectly inhabitable to me in all the climatic conditions of the past.

    "From that it certainly seems as though you believe that..."

    Nope. You are wrong about what I "believe".

    "You have N and M vanishing along any possible route they took from Africa".

    I am? It's not me but the implacable Lady Reality. I'm all the time defending the shortest possible route.

    Would I be happier with another reality? I don't think so: I don't try toto impose my ideas to reality but rather bend them to the inevitability of facts - at least in science (politics is different because we do make choices in present time that affect the future).

    "You include or exclude control region mutations"...

    I always exclude it.

    "If you're prepared to include conntrol region mutations"...

    I'm not: I realized long ago that HVS-I can't be used to infer any molecular clock of any sort. And if you'd read some of the literature, you'd have realized as well.

    It may be an arguable decision but it's one that I have been consistent with since long ago (not in my first attempt however).

    "If you exclude them you finish up with not one but three basal haplogroups with a stem of zero (R 11'B6, R24 and B4'5)".

    Stem of one! There are no "zero" stems for the purposes of my analysis, HVS defined ones are discarded and treated as separate haplogroups. My whole point is that there can be lineages "tied in bunches" in the past reality without showing any such mutation.

    However you are right in one detail (not making any difference as far as I can tell anyhow): I forgot of private lineage R24. I will correct the last map in order to include it as soon as I gather where is it found.

    "Earlier you wrote, 'Where they originated and where they are now found should be the same place or region anyhow'".

    But this is a terminology trap you fall into constantly: pre-N is not yet N: N does not originate at the L3 node but where the last of the five defining mutations leading to N happened first, i.e. where the first woman carrying the full N-root haplotype lived. All her ancestors are not yet N but L3* (or if you wish pre-N or L3n...).

    So when I say "haplogroup origin", I think in Bengal or Cambodia for N, while when you say "haplogroup origin", you think in Ethiopia (L3).

    Well, actually you probably do not for N but you do for other haplogroups; i.e. N9's "origin" for you is the origin of N (Bengal/Indochina) and not where N9 coalesced (China). But that is YOUR problem because I have often pointed to this confusing sloppiness of your language, which in the end confuses you more than me.

    So I am 100% consistent when I say that all relevant haplogroups should be found more or less where or around they originated. Maybe it is not true for a private lineage however because the "trickle-ness" of its survival really allows (potential, not necessary) for many "private" migrations, which we cannot infer from the data.

    ...

    ReplyDelete
  20. ...

    "it is you"...

    You more! Hahaha! :P (sarcasm intended)

    Are we playing blame games or are we trying to discern a scientific puzzle? If you play, try at least to support your accusations with evidence.

    "'Dotted lines' tell us nothing".

    You have to plot the results on the map: there's an origin (ancestor) A and a destination (descendant) B, once we infer where each one coalesced (by the centroid or corrected centroid method) we must draw the dotted line because that is the resulting vector of our research.

    "Strings of descedant haplogroups are what we should look for".

    Not at all. That hypothesis of yours confuses back-migration with trail. There was maybe once a bread-crumb trail but the birds of drift ate it.

    And I don't think you can demonstrate your hypothesis in any reasonable way: there are not more basally derived lineages in the purported West Asian origin, these are not obviously older and you still need to argue for an ultra-fast migration between West Asia and Australia via Siberia, without losing the "Afro" tan in the process and while retaining extreme diversity.

    Why don't we see pre-S anywhere? Because the migration was very fast. And it's a lot easier to explain a hyper-fast migration if we begin in SE Asia (or Bengal) than in Palestine. And if we go directly than if we make the migrants go all the way through Siberia.

    And then all other meaningful genetic signatures of expansion in East Asia are clearly defined as South-to-North (regardless of minor recent back-migration) also West Eurasians are autosomally much closer to South Asians (low N) than to East Asians or Australians (high N).

    ReplyDelete
  21. Hi, just curious, which program are you using for this study?

    ReplyDelete
  22. I mean: I did not use any program other than GIMP (image freeware) for the image as such, the centroid-finding process was done using a simple ruler and the geometric decomposition method. Maybe is that what you were asking about, Orang More?

    ReplyDelete
  23. Map 3 updated to include small lineage R24 (Philippines).

    ReplyDelete
  24. I missed this:

    "I presume that haplogroup way to the northwest is A. I'm certain it should be nowhere near as far north as that. In fact it should be round Tibet somewhere".

    Really? Per Wikipedia:

    "Its subgroup A1 is found in northern and central Asia, while its subgroup A2 is found in Siberia and is also one of five mtDNA haplogroups found in the indigenous peoples of the Americas"...

    You may want to argue a location somewhat more to the West but hardly "Tibet" (most of which was deserted in the Ice Age anyhow - in fact it's only barely habitable today). I don't think Mongolia is likely either because, unlike M8/CZ and D, A is not associated to the Westward migration of Y-DNA N, which probably went through Mongolia/Buriat Country.

    ReplyDelete
  25. "Are we playing blame games or are we trying to discern a scientific puzzle?"

    I'd hope we are trying to solve a scientific puzzle, but you seem to be determined to ignore any interpretation of the evidence that coincides with some sort of religious belief.

    "I'm asking for evidence: there's been more or less continuous inhabitation in Palestine and it's not the most fertile of countries in the pivotal region, being too close to the deserts for any good".

    Yes. And X fits there perfectly. the Druze evidently have both X1 and X2:

    http://en.wikipedia.org/wiki/Haplogroup_X_(mtDNA)

    Quote:

    "The greatest frequency of haplogroup X is observed in the Druze, a minority population in Israel, Jordan, Lebanon, and Syria, as much in X1 (16%) as in X2 (11%).[4] The Druze also have much diversity of X lineages".

    And the peer-reviewed paper:

    http://www.cell.com/AJHG/retrieve/pii/S0002929707619806

    Quote:

    "haplogroup X is subdivided into two major branches, here defined as X1 and X2. The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples".

    And:

    "The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East".

    "There are areas, for example in coastal Anatolia, that must have provided good habitats for humans of any species all the time".

    Perhaps they were not coastal dwellers. On the other hand it does seem possible that Y-DNA G and IJ may be from inland Anatolia. Perhaps either N1'5 or N2 as well.

    "So yeah, I'm questioning it: the area looks perfectly inhabitable to me in all the climatic conditions of the past"

    So it probably was. The same can't be said for much of Saudi arabia and the steppe though. However an outcrop of X and members of A may have survived in places. As with Y-DNA C3 and C5.

    ReplyDelete
  26. "It's not me but the implacable Lady Reality. I'm all the time defending the shortest possible route".

    And carefully denying data that contradicts your belief.

    "I don't try toto impose my ideas to reality"

    Rubbish. You do that all the time.

    "I always exclude it [control region mutations]".

    Except when considering R11'B6/R4'5. Where you obstinately include them.

    "politics is different because we do make choices in present time that affect the future".

    You've obviously missed your vocation. How's this for deliberately obscuring the issue:

    "I realized long ago that HVS-I can't be used to infer any molecular clock of any sort. And if you'd read some of the literature, you'd have realized as well".

    I'm far less convinced of any 'clock' than you are. I'm not even considering the clock, just phylogeny.

    "Stem of one! There are no 'zero' stems for the purposes of my analysis"

    What is the mutation in that 'Stem of one'? If you're going to be consistent and exclude control region mutations you have no mutation between basal R and R11'B6, R4'5 and R24. If you're determined to consider them as three separate haplogroups surely you have to incorporate than into your calculations as to R's origin.

    "I forgot of private lineage R24. I will correct the last map in order to include it as soon as I gather where is it found".

    The Philippines. So R11'B6/B4'5 probably originated round the shores of the South China Sea.

    "But this is a terminology trap you fall into constantly: pre-N is not yet N"

    But N almost certainly coalesced in the region where pre-N was found.

    "N does not originate at the L3 node but where the last of the five defining mutations leading to N happened first"

    And it is very unlikely to have traveled far without either becoming extinct or leaving a trail of descendants.

    ReplyDelete
  27. "Really? Per Wikipedia"

    Wiki is obviously not up to date with A. Phylotree gives four basic A haplogroups: A5, A8, A10 and a fourth which includes the downstream haplogroup A2. A1 seems to no longer exist.

    The fourth haplogroup (which includes A2) is broken into A11 (Tibetan Plateau, China), A3, A7 and A9 ( all simply given as 'Asia') and A4, which includes 'Ainu' A4a, 'North Asian' A4b, A4c and A4d, 'Asian' A3 and Beringia/American A2.

    Turning to the other three A haplogroups: From the references A5a is given as 'Northern Asia' while A5b and A5c are 'Hmong-Mien'. Presumably all SE Asian A is A5. A8 is referenced as 'Volga Tatar and Arctic Siberia'. A10 is 'Volga Tatar and Tibet'. And this peer-reviewed paper has some interesting comments regarding it:

    http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21350/abstract;jsessionid=1D23F41DC8197F21618CF2584BF1AE86.d03t02?systemMessage=Wiley+Online+Library+will+be+unavailable+17+Dec+from+10-13+GMT+for+IT+maintenance.

    Quote:

    "the analysis of one major pre-LGM sublineage A10 showed a strong signal of post-LGM population expansion (about 15,000 years ago) and greater diversity in the southern part of the Tibetan Plateau, indicating the southern plateau as a refuge place when climate dramatically changed during LGM".

    So we can actually narrow its origin down more specifically from 'A1 is found in northern and central Asia, while its subgroup A2 is found in Siberia'.

    ReplyDelete
  28. I sent a reply to your comment regarding A but it seems to have dissappeared.

    "Its subgroup A1 is found in northern and central Asia, while its subgroup A2 is found in Siberia and is also one of five mtDNA haplogroups found in the indigenous peoples of the Americas"...

    The nomenclature of A is a mess but Wiki is out of date. A1 has now disappeared and A2 is a downstream clade within A4. A2 is American/Beringian while the other A4 haplogroups include 'Ainu' A4a, 'East Asian' A6 and 'North Asian' A4b, A4c and A4d.

    But A4 as a whole is a downstream clade within just one of the four basal A haplogroups. Its closest relations include 'Asian' A3, A7 and A9 as well as Tibetan Plateau/Chinese A11.

    all that is just one of the four basal A haplogroups. The remaining three basal A haplogroups are

    1) A5 ('Northern Asia', but A5b and A5c are SE Asian, especially Hmong-Mien.

    2) A8, widespread fromm Volga Tatar, Ainu and Arctic Siberia.

    3) A10, Tibet and Volga Tatar.

    Regarding this last haplogroup this peer reviewed paper has an interesting comment:

    http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21350/abstract?systemMessage=Wiley+Online+Library+will+be+unavailable+17+Dec+from+10-13+GMT+for+IT+maintenance

    Quote:

    " the analysis of one major pre-LGM sublineage A10 showed a strong signal of post-LGM population expansion (about 15,000 years ago) and greater diversity in the southern part of the Tibetan Plateau, indicating the southern plateau as a refuge place when climate dramatically changed during LGM".

    From all that we can get a better idea of A's distribution than we can from a dated Wikipedia entry.

    ReplyDelete
  29. I can't believe you are using the Druze, a recently formed religious sect (1000 years according to their traditions: "In 1017, Hamza officially revealed the Druze faith and began to preach the Unitarian doctrine") as example of anything. It is true that X probably coalesced in West Asia but that the two lineages are found in modern Druzes has nothing to do with it (specially as a branch is original from Egypt, according to their own traditions, what may explain the X1). Besides, most Druzes live in Lebanon, not Palestine.

    Regardless: X did coalesce in West Asia with all likelihood (by "phylo-geometry") but that is not a signature of the OoA but a signature of the colonization of West Asia from further East, where N coalesced. This means that X (as well as the other West Eurasian lineages) is probably not older than 50 Ka, because we have no evidence of AMH colonization of this area before c. 48 Ka BP (besides of the Skhul/Qahfez exception, too old and too "African" to be N or M).

    You can't cherry-pick X. You MUST look at N as a whole if discussing the OoA. When you understand N, you will understand X as 1/15 of it (and nothing more).

    Otherwise it's like the proverbial blind man who grabs the trunk of the elephant and claims it is a snake... you must understand the whole elephant N, not just a small part.

    "On the other hand it does seem possible that Y-DNA G and IJ may be from inland Anatolia".

    No. G and IJ are F-derived, so they are back-migrations from South Asia. Again, you must consider the whole elephant, F in this case, and not cherry-pick its parts.

    "Except when considering R11'B6/[B]4'5. Where you obstinately include [the control region mutations]".

    I do not: I consider each haplogroup here as a separate entity. Why do you even insist, when it's so obviously false?

    "I'm not even considering the clock, just phylogeny".

    I'm not even sure what you are considering. Obviously N does not descend from X but the other way around, yet you insist in considering X the root of all N... somehow. Just because it fits with your preconception of West Asia coming first and not last.

    You may of course want to ignore all sense of mutational timing for this purpose because only that way X can coalesce before S or N9 or...

    But that's pseudoscience.

    You also choose to ignore the geographic scatter and concentration and appeal to unproven conjectures (=desertization) to argue your point. In fact it's the kind of argument that someone we know would use to defend the origin of humankind in America: we can't understand because all the evidence has been erased somehow... you know. XD

    "If you're going to be consistent and exclude control region mutations you have no mutation between basal R and R11'B6, R4'5 and R24".

    You are not that dumb that you don't understand that I consider for all statistical purposes these three haplogroups as different, are you? R11'B6 is defined by a transition at 12950, but B4'5 is defined by a a multiple transition at 8281-8289d, while R24 has a longer sequence.

    So R11'B6 and B4'5 are in the "one mutation" or "elder" category (under R) and are represented as such in map 3.

    You are being trollish with this issue, because it is clear and is not important at all (unless you can argue that the ignored HVS-I mutations have any importance, what I'm sure you can't).

    "But N almost certainly coalesced in the region where pre-N was found".

    There is no pre-N because we are not our ancestors, we can't know where pre-N was anymore. We can infer however where "finished" N coalesced with some certainty, using as reference its descendants (and for the correction also its ancestor L3). And that is what I do in this entry.

    ReplyDelete
  30. "I sent a reply to your comment regarding A but it seems to have dissappeared".

    Probably that horrible Google spam filter that makes just random deletions without any method (I'm flippant it has not yet been removed/modified - it's about a year of useless annoyance now).

    It is in my mail, so I'll reply now and will make it appear as soon as I finish.

    ...

    Regarding A, at most it would be pushed southwards a bit to the Beijing/Yellow River area, again nothing that fundamentally changes anything (move N9 a bit to the North, A a bit to the South, would that make you happy? No). Sadly the reference paper is PPV, so I can't consider the data you mention but it should not make any big difference in any case (splitting hairs is not going to save your doctrine).

    ReplyDelete
  31. Sorry for the following one-liners, but I can't resist.

    "I can't believe you are using the Druze, a recently formed religious sect (1000 years according to their traditions: 'In 1017, Hamza officially revealed the Druze faith and began to preach the Unitarian doctrine')"

    The women were immigrants to the region?

    "X did coalesce in West Asia with all likelihood (by 'phylo-geometry') but that is not a signature of the OoA but a signature of the colonization of West Asia from further East"

    How come you are so certain of that?

    "where N coalesced".

    Again that is simply your belief. The data actually fails to support such a belief if you're prepared to look carefully, as I pointed out elsewhere.

    "You can't cherry-pick X. You MUST look at N as a whole if discussing the OoA".

    And surely you can't cherry pick R and alter your interpretation to fit what you want to believe. We will not arrive at the truth unless were use the same criteria consistently. 'X' may well be 'not older than 50 Ka' but pre-X is almost certainly older, and probably survived as a small remnant of the OoA somewhere in SW Asia. There is not the slightest evidence that any of its ancestors were ever in South Asia.

    "yet you insist in considering X the root of all N... somehow".

    Nonsense. I consider N the root of all N haplogroups. But each of those haplogroups did not migrate singly from N's region of origin. N expanded than the descendant haplogroups coalesced somewhere within the region they are now individually found. To me no other explanation makes the slightest sense.

    "Just because it fits with your preconception of West Asia coming first and not last".

    West Asia must have come before Se Asia, unless they flew across India.

    "You may of course want to ignore all sense of mutational timing for this purpose because only that way X can coalesce before S or N9 or..."

    I have no problem with 'X' coalescing later than several other N haplogroups. What I have difficulty with is the idea that it coalesced later and then moved all the way from SE Asia.

    "You also choose to ignore the geographic scatter and concentration and appeal to unproven conjectures (=desertization) to argue your point".

    It is you who are ignoring 'the geographic scatter' and appealing to 'unproven [and very unlikely] conjectures ... to argue your point'. How come there are no basal N haplogroups anywhere in India, yet no shortage of R haplogroups? Your explanation just doesn't make any sense.

    "we can't understand because all the evidence has been erased somehow..."

    You certainly believe the evidence has been erased in India. So what's the difference between the two of you?

    "R11'B6 is defined by a transition at 12950, but B4'5 is defined by a a multiple transition at 8281-8289d, while R24 has a longer sequence".

    Thanks for clearing that up. However you now have 8 haplogroups in SE Asia and further east (from the east: P, R22, R24, R23, R14, R12'21, B4'5, R11'b6 and R9), 6 in India (R6, R8, R7, R5, R30, R31, with a further 2, U and R2'JT, shared with SW Asia) and 3 in SW Asia (R1, R3 and R0). Time to rethink your hypothesis?

    "Regarding A, at most it would be pushed southwards a bit to the Beijing/Yellow River area"

    No. It would be pushed southwest. The haplogroup containing all A haplogroups except A5, A8 and A10 (your A1 and A2) looks to be a rapid expansion into a virgin region, so did not originate in that region. Much the same applies to A5, again an expansion into a virgin region, this time East and SE Asia.

    ReplyDelete
  32. "Sadly the reference paper is PPV, so I can't consider the data you mention but it should not make any big difference in any case (splitting hairs is not going to save your doctrine)".

    The data on A8 and A10 is basically from these papers, linked from Phylotree:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427195/

    Although I don't see any reference to either A8 or A10 it is given as a reference for thise haplogroups in Phylotree. Quote:

    "This study further confirms that (1) Alaska seems to be the ancestral homeland of haplogroup A2 originating in situ approximately 16.0 thousand years ago (kya)"

    Tending to confirm its movement into virgin territory at that time.

    And:

    http://malyarchuk-bor.narod2.ru/MBE_10.pdf

    Quote:

    "It was found that mitochondrial gene pool of the Volga Tatars consists of two parts, but western Eurasian component prevails considerably (84% on average) over eastern Asian one (16%). Eastern Asian mtDNAs detected in Tatars belonged to a heterogeneous set of haplogroups (A, C, D, G, M7, M10, N9a, Y, and Z), although only haplogroups A and D were revealed simultaneously in both populations".

    The Volga is a long way from Northeast Asia.

    ReplyDelete
  33. "The women were immigrants to the region?"

    It'd seem so as Druze are extremely endogamous, not even normally mixing among themselves beyond the local community. I find the insistence on using Druze, and Palestine Druze in particular, rather disturbing and useless.

    "How come you are so certain of that?"

    Because I made my homework in phylo-geometry, unlike you.

    "And surely you can't cherry pick R"...

    I am not "cherry-picking" R: R cherry-picks itself: it is anomalous and everybody knows that.

    In any case, it is trivial, not affecting the calculations for the origin of N. R is treated in that context exactly like any other basal subclade, just like X or N14.

    ... "and [pre-X] probably survived as a small remnant of the OoA somewhere in SW Asia".

    Just because you wish so? Nope.

    Before pre-X there was N and N was then not in West Asia but SE Asia or Bengal. That's the only "pre-X" we know anything about between L3 and fully formed X, so that dynasty of women migrated East well into Asia, maybe to the very shores of the Pacific Ocean, and then they migrated back.

    How exactly? Abducting flying saucers if you wish but that's the basics: L3 > N > X and not L3 > X > N.

    There are enough mutations between each of the known nodes (5 and 4) to have no reasonable doubt in this case about any overlapping of any sort.

    "But each of those haplogroups did not migrate singly from N's region of origin".

    Yes they MUST. N was once a single woman and all those haplogroups are their matrilineal descendants: they MUST have migrated (through the generations) from where the N granny lived.

    I don't care if they first accumulated the mutations and then migrated or if they first migrated and then mutated (or if, most likely, mutated on the march): they migrated from N's urheimat NECESSARILY.

    "West Asia must have come before Se Asia, unless they flew across India".

    Arabia only but that belongs to an early pre-N stage surely. Same for India: more advanced pre-N stage but still private until arrival to wherever the haplogroup coalesced (Bengal? Narmada? Burma? Cambodia? - depending on the correction we choose, which is indeed arguable).

    What you are claiming (or actually what you would be claiming if you could at least acknowledge the coastal route) is that the directional correction should be extreme, more than 1/2 of the L3-N raw distance. It would still fall in Arabia, so you have to decree it impossible and force the line via Egypt and Palestine, etc.

    I don't think that a directionality correction of more than 1/3 (Narmada) is acceptable in any case, much less with such a long stem as N has (5 mutations), which allows for so many events and travels...

    ...

    ReplyDelete
  34. ...

    "What I have difficulty with is the idea that [X] coalesced later [than "sister" haplogroups] and then moved all the way from SE Asia".

    Make it coalesce after the migration or, most likely, along the migration. The latter is the simplest logical solution: c. 5500 km make it an average of some 1400 km per mutational step (or 2000-5000 est. years). 1400 km is like migrating from Madrid to Paris every many many centuries or going from London to Edinburgh and back. It's no such a big deal, right?

    "How come there are no basal N haplogroups anywhere in India"...

    There are: N1'5, N2 and R. All them are documented in abundance and diversity in Palanichamy 2004. Only X is lacking among the Western lineages (M1 is also part of an Indian-based higher-tier lineage). You can build all your conjecture on the exceptionality of X or you can accept that it is just an exception and not any rule.

    "You certainly believe the evidence has been erased in India".

    Don't change the context. Evidence has been "erased" in every single case where a long stem exists: every unbranched mutation is evidence that was lost (probably to drift).

    "However you now have 8 haplogroups in SE Asia and further east (from the east: P, R22, R24, R23, R14, R12'21, B4'5, R11'b6 and R9), 6 in India (R6, R8, R7, R5, R30, R31, with a further 2, U and R2'JT, shared with SW Asia)"...

    I count: R3, R5, R6, R7, R8, R30, R31, plus several shared with West Asia: R1, R2'JT and U, i.e. all the Western R-derived haplogroups except R0.

    You make a distinction between West and South Asia anyhow that is quite misleading in any case. Both regions share a lot of genetics (in opposition to East Asia and Australasia) and both regions pull in the same Western direction when considering the phylo-geometry of macro-haplogroups like R.

    Time for you to get a ruler and make some geometry maybe?

    Whatever the case it's intuitively clear: 9 sublineages east of Assam, 11 lineages west of it, so the barycenter should fall to the west, even if only slightly.

    But I can't care much on whether the exact geographic origin of N and R falls west or east of Assam, that is not that important. You just like to split hairs and make issues of things that are mostly irrelevant and won't change anything regarding the big picture. Do you prefer an N-R origin in Burma? It's ok with me, in the Narmada valley? Fine too. In Cambodia? Less likely I'd say but I can concede.

    But you will never get to Altai or Palestine that way. And there's where you want to go and will never arrive, no matter how many hairs you split nor how much you move the N-R centroid between India and Cambodia.

    ReplyDelete
  35. "Make it coalesce after the migration or, most likely, along the migration. The latter is the simplest logical solution"

    No it's not.

    "Don't change the context. Evidence has been 'erased' in every single case where a long stem exists: every unbranched mutation is evidence that was lost (probably to drift)".

    We seem to agree that a haplogroup will diversify rapidly when it enters a new environment or is able to exploit the old environment in a substantially new way. But the lost branches do not become lost while a haplogroup is migrating. If drift is that severe the haplogroup will become extinct.

    "Do you prefer an N-R origin in Burma? It's ok with me, in the Narmada valley? Fine too. In Cambodia? Less likely I'd say but I can concede".

    What we disagree on is whether any haplogroup able to participate in such an expansion had previously been able to move any distance at all from where a previous migration had dropped them off.

    "Because I made my homework in phylo-geometry, unlike you".

    As evidence in support of your own hypothesis you raise the examples of M, N and A. So let's examine this 'phylo-geometry'. To come to any sort of valid conclusion as to the normal state of affairs we need to look at all haplogrousp with tails of five or more mutations, not just at the above three:

    We have 9 M mt-DNAs in that situation: M10, M11, M41, M53, M15, M28, M76, M77 and M26. We can eliminate the the first four as having traveled anywhere outside the region that undifferentiated M had dropped them off in. All four are found in India, and we agree that the original M woman lived somewhere near the subcontinent. M15 and M28 are found in Australia and Melanesia respectively. because we have Q in New Guinea with one mutation from undifferentiated M, and M14 in australai with two we can be reasonably sure that undifferentiated M reached that region. The remaining M haplogroups with long tails are scattered between India and australia,: M76 and M77 in South China and M26 in Sumatra. So, no M haplogroups with long tails moved very far from where their undifferentiated M ancestor dropped them off.

    "I am not 'cherry-picking' R: R cherry-picks itself: it is anomalous and everybody knows that".

    It is only 'anomalous' for you. You cannot make it fit your belief. So what about R? We have seven approriate haplogroups with long tails: R1, R3, R7, R8, R14, R22 and R23. We can eliminate R1, R7 and R8. These haplogroups are found where you claim the original R woman appeared: India. Norhtwest of India we have just R3. As near as I can tell this haplogroup is found in Armenia. But it looks very much as though undifferentiated R managed to reach that region. The nearby R0 and R2'JT haplogroups are just one mutaion away from undifferentiated N. The remaining three R haplogroups with substantial tails are scattered from Indonesia to New Guinea. But again we have P, one mutation from undifferentiated R, in New Guinea, the Philippines and Australia. So no R haplogroups moved anywhere once their ancestor undifferentiated R dropped them off.

    ReplyDelete
  36. So, with M and R we have precisely no haplogroups that can be shown to have moved at all after their undifferentiated haplogroup ancestor dropped them off.

    "Yes they MUST. N was once a single woman and all those haplogroups are their matrilineal descendants: they MUST have migrated (through the generations) from where the N granny lived".

    But they migrated as undifferentiated N, not individual haplogroups S, N1'5, N14 etc.), no matter how incipiently formed. And we still have five N haplogroups to go: N8, N13, N14, N21 and A. The first is South China, where you claim the original N woman lived. So you'd agree that undifferentiated N was definitely present in the region.

    The next two are Australian. Undifferentiated N reached there because S diversified there just one mutation removed from undifferentiated N. N21 is from Sumatra. Can you seriously claim that undifferentiated N spread from South China to australia dropping no-one off along the way? and we can be sure that undifferentiated N reached SW Asia. We have N1'5 there, just one mutation from undifferentiated N. And N2, two mutations, and X, four mutations.

    "that dynasty of women migrated East well into Asia, maybe to the very shores of the Pacific Ocean, and then they migrated back".

    That is a most unlikely scenario. Surely there is absolutely no reason why X, along with N1'5 and N2, cannot each have been dropped off during undifferentiated N's expansion.

    That leaves just A. Isn't it a case of 'special pleading' to claim its presence needs a different explanatioj from that applicable to all the other haplogroups?

    ReplyDelete
  37. I have no idea why you are using M above: it has way too many haplogroups to consider as you do, listing just some (not too clear which is the criterion either). Also the rambling is totally impossible to understand...

    "So, no M haplogroups with long tails moved very far from where their undifferentiated M ancestor dropped them off".

    And there is where you arrive after all that esoteric rambling: to a pointless fictitious conclusion about long-stemmed haplogroups.

    So then we should conclude that wherever N coalesced (even you agree it was in Asia), it was so because L3 dropped it there, right?

    I can't follow your "logic". Write a book and leave me alone.

    ReplyDelete
  38. "But they migrated as undifferentiated N, not individual haplogroups S, N1'5, N14"...

    Not as finished haplogroups but maybe as intermediate stages (when more than one mutation exists in a stem). We cannot say anything about N14 for sure, other than it looks a direct matrilineal distinct descendant of "granny N". You insist in our ignorance meaning anything: it does not.

    ReplyDelete
  39. "Write a book and leave me alone".

    You have claimed to be interesated in studying our prehistory and I'm taking you at your word. I am trying to point out your faulty reasoning, but you are stunningly defensive.

    "Not as finished haplogroups but maybe as intermediate stages (when more than one mutation exists in a stem)".

    Ridiculous. S cannot have migrated as an intermediate stage. S is just one mutation from N. If S reached Australia as N it is almost a certainty that N13, N14 and O di so as well. You even have a post that claims as much:

    http://forwhattheywereweare.blogspot.com/2011/02/laotian-genetics-mtdna.html

    Quote:

    "the novel basal M haplogroups found in high diversity in the Laos sample and surrounding populations support the fast migration and in situ differentiation model"

    Do you really believe that an insitu model is applicable only to haplogroup M?

    "I have no idea why you are using M above: it has way too many haplogroups to consider as you do, listing just some (not too clear which is the criterion either)"

    You are being deliberately stupid here. At least I hope it's deliberate. I used all the M, N and R haplogroups with long tails. Surely you're not going to claim that what holds true for one haplogroup cannot possibly hold true for other two. Unless you've already decided what it is you wish to see and are wishing to use different criteria when considering the data.

    "And there is where you arrive after all that esoteric rambling: to a pointless fictitious conclusion about long-stemmed haplogroups".

    Fictitious? Surely the fact is that no haplogroup with a long tail can be shown to have moved anywhere from where its undifferentiated ancestor haplogroup arrived.

    In fact I have actually found several cases where members of the same haplogroup, or closely related haplogroups, are separated geographically. This is the situation you claim for M and N in relation to L3, and for the western N haplogroups. They are mostly M, with just one R:

    1) R14, in New Guinea and the Nicobar islands. A gap through SE Asia.

    2) M31, in the Andamans and Northeast India. A gap through Burma.

    3) M42'74, M42 in Australia and M74 in China. A gap through SE Asia.

    4) M32'56, M32 in the Andamans and M56 in Central India.

    Unfortunately no N haplogroups fall into this category and so presumably you going to indulge in your usual special pleading. But note that the gaps between the haplogroup branches all involve a water crossing, missing coastal regions and islands along any possible route.

    So there you have it: haplogroups can move quite long distances without leaving descendants along the way. But such journeys always involve crossing bodies of water, and you have claimed that expansion through islands is not comparable in any way with expansion over land.

    ReplyDelete
  40. Man, it's been months, or rather years of this endless discussion in circles, almost every day. Even if now and then you make a criticism worth considering or introduce some information I may have missed, most of what you say is waste of letters. Mind you: reading your one-liners and finding the context and trying to understand and, normally, debunk them takes much of my time - too much. It's a discussion for the sake of discussion, which you may be fond of but I can only find tiresome and pointless.

    I know your hypothesis (even if you have bothered explaining it formally nowhere) and I know that it does not hold at all. There is no "bread crumbs" trail from the origin of L3 but actually an explosion from a shared center after a "private level" (small) migration.

    You may still disagree but you cannot persuade me unless you'd find more, many more, basal N subhaplogroups in West Eurasia and Africa. Considering that there are 11 of those along the Pacific Ocean, such a turnover is effectively impossible.

    Do you want for N to migrate back to West Asia via Altai (the only possible alternative route to South Asia)? That might be a reasonable claim where we could disagree very reasonably and gentlemanly... but you want to revert the arrow of that flow, and that is extremely unreasonable, considering the evidence and the fundamental logic of the "apples" (with long legs) that requires that most lineages remain as close as possible to where the real origin (the "tree") was.

    ...

    ReplyDelete
  41. ...

    So the discussion is pointless and all what you say here is nagging self-contradictorily about nothing of substance. Example:

    "Not as finished haplogroups but maybe as intermediate stages (when more than one mutation exists in a stem)".

    Ridiculous. S cannot have migrated as an intermediate stage
    .

    I repeat: "when more than one mutation exists in a stem" and "maybe" (which is different from "must" and is used to indicate uncertain territory).

    About 80% of our discussions are like that. You must understand that I'm uninterested.

    "You are being deliberately stupid here".

    I'm tired of trying to unravel your logic behind every sentence of esoteric meaning.

    "I used all the M, N and R haplogroups with long tails".

    You should explain yourself better and that's why you probably want to write longer, more elaborate and better thought articles at your own blog.

    Anyhow, your insistence on the "tails" is pointless, we have excellent examples of haplogroups which must have migrated in the "long stem" phase in M and N themselves. Not even you would claim they coalesced in Africa or that L3 was diffusely extended all the way to East before equally diffuse N and M (and R) could coalesce in geographies so indeterminate that seem to belong to quantum mechanics.

    And yet you insist:

    "Surely the fact is that no haplogroup with a long tail can be shown to have moved anywhere from where its undifferentiated ancestor haplogroup arrived".

    Where is all the L3* in Asia? Either you are very wrong or you explain yourself extremely poorly. Or, most likely, both.

    Your "diffuseness" hypothesis requires massive culling everywhere all the same and not just loss to drift locally in harsh conditions. Why don't we have 20 or 200 lineages basally derived from L3 (or any other widespread macro-lineage)?

    Because the migrations were 'private' and the stem-pruning drift happened locally before the expansion of the derived haplogroup. Whether they traveled a lot or remaining static is rather pointless and in the second case we get stuff like R (in my model at least) or M4'67 but in the first case we get M and N themselves.

    However I think that all long-stemmed lineages which show signs of notable expansion share one thing: they all expanded in frontier areas, often far away from their ancestors. Not checked for every lineage but it does work for all I can think of right now: M and N in relation with L3 and X, N2 and A in relation with N. So they should have followed similar processes of migration-and-expansion (pre-node-post).

    In any case, I have already wasted too much time here today.

    ReplyDelete
  42. "Man, it's been months, or rather years of this endless discussion in circles, almost every day".

    Because you decided long ago what you wanted the data to reveal and you keep twisting your interpreatation to support that belief. You are not prepared to look at the raw data and interpret it in a consistent manner.

    "In any case, I have already wasted too much time here today".

    I'm still prepared to help you discard your stupid theories.

    "About 80% of our discussions are like that".

    I agree. As shown by this stupid comment:

    "I repeat: 'when more than one mutation exists in a stem' and 'maybe' (which is different from 'must' and is used to indicate uncertain territory)".

    How can you possibly insist that S arrived in Australia a little before O (with two mutations), in turn both had been there for some time before N13 (6 mutations) arrived, followed some time later by N14 (10 mutations). Doesn't make sense. Surely it's time for you to alter your hypothesis.

    "an explosion from a shared center after a 'private level' (small) migration".

    'Small migration'? From Africa to SE Asia? Come on now.

    "Do you want for N to migrate back to West Asia via Altai"

    Why do you insist on a 'back migration' to SW Asia? There is absolutely no evidence for such a migration, except in your imagination. A 'long stem' does not automatically mean a 'long migration'. In fact usually not, as all the examples of non-N haplogroups with long stems demonstrate. But you insist on claiming N as a special case. The reason being that it fails to fit your belief unless you claim it as such.

    "fundamental logic of the 'apples' (with long legs) that requires that most lineages remain as close as possible to where the real origin (the 'tree') was".

    Exactly. And that's why I find it impossible to believe that either M or N moved very far from the other L3s before eventually being able to undergo their own independent expansions.

    "Not even you would claim they coalesced in Africa or that L3 was diffusely extended all the way to East before equally diffuse N and M (and R) could coalesce in geographies so indeterminate that seem to belong to quantum mechanics".

    I most certainly do not claim that either M or N coalesced anywhere in 'the East'. It is you who are claiming that. However it is obvious both haplogroups reached far to the east before their subclades coalesced, many undergoing secondary expansions of their own. And M and N almost certainly expanded eastward independently. Their distributions are quite different from each other. They did not expand together from some Paleolithic garden of Eden.

    "Where is all the L3* in Asia?"

    Surely even you accept that it became M and N. The long stems in both haplogroups indicates a period of drift, during which L3* became extinct in SW Asia.

    ReplyDelete
  43. "Your 'diffuseness' hypothesis requires massive culling everywhere all the same and not just loss to drift locally in harsh conditions".

    I don't see how you conclude that. In fact it is your hypothesis that 'requires massive culling everywhere all the same and not just loss to drift locally in harsh conditions' in the case of haplogroup N through India. Very difficult to come up with any possible explanation for such loss.

    "Because the migrations were 'private' and the stem-pruning drift happened locally before the expansion of the derived haplogroup".

    Yes. The drift happened locally, not during any migration to or from anywhere.

    "However I think that all long-stemmed lineages which show signs of notable expansion share one thing: they all expanded in frontier areas"

    Agreed. But they arrived at those frontier areas' as part of an earlier expansion from an earlier frontier area. They were prevented from immediate expansion by the same factors that had prevented their 'ancestor' haplogroup from further expansion. Their eventual expansion was made possible by changing climatic conditions or improved technology. Surely it is simple to understand.

    "often far away from their ancestors".

    I can't see how you can believe that at all. Surely their ancestors must have arrived at the point of the derived haplogroup's eventual departure.

    "it does work for all I can think of right now: M and N in relation with L3 and X, N2 and A in relation with N".

    I can see how if those four are the only haplogroups you've checked you could maintain that belief. But surely it is unlikely thay would be the only haplogroups that fit such a scenario.

    "we have excellent examples of haplogroups which must have migrated in the 'long stem' phase in M and N themselves".

    Those two haplogroups, along with A and N2, are the only possibilities. And they are only 'possibilities' because your pre-existing belief demands they must have done so. If they in fact did migrate 'in the long stem phase' they would be absolute exceptions. I found not a single example of any haplogroup having 'migrated in the 'long stem' phase ' in the list I provided. Perhaps you may be able to find some other examples that support your belief. I'm sure the only ones you can come up with are A, M, N and N2, the very ones that your pre-existing belief demands must have done so. And N2 is hardly a good example. N1'5 is nearby so N2 most probably arrived with it.

    It is difficult to avoid the conclusion that you use the 'long stem' explanation for those haplogroups because any other conclusion would fail to fit your pre-existing belief.

    ReplyDelete
  44. At the site of our other prolonged argument you suggested 'Burma, Cambodia...' as a possible site for N's coalescence. I said the that as far as I was aware no N was present in either place. Turns out I was wrong. N21 may have originated in Thailand/Cambodia. Until now I thought that N21 was Sumatran. You may find the following link interesting for other reasons as well:

    http://mbe.oxfordjournals.org/content/27/10/2417.full#F2

    ReplyDelete
  45. "You are not prepared to look at the raw data and interpret it in a consistent manner".

    You have the arrogance and lack of self-criticism of saying THAT. "Mirror, mirror..."

    "I'm still prepared to help you discard your stupid theories".

    I don't need your "help", I don't want your "help" and I

    "How can you possibly insist that S arrived in Australia a little before O"...

    I dare you to find a quote by me saying that. Much of our continuous misunderstanding is that you insist in reinterpreting what I say according to what you think I might have meant, what is almost always wrong.

    "'Small migration'? From Africa to SE Asia?"

    From Africa to South Asia. The N phenomenon surely happened under the ominous clout of much larger M (and maybe relates with Toba somehow, but I can't say exactly how) and it probably happened in a context of *rapid* and maybe also *coastal* migration by which some peoples were highly nomadic, easily marching to yet another undiscovered beach, jungle or whatever, almost every new generation. Not all were so dynamic (the peoples of mtDNA M and Y-DNA F(xMNOPS) appear to have lived more relaxed lives).

    You say they migrated through freezing Altai and not the coast... I dare you to prove it somehow. Not a single piece of genetic evidence, not a single piece of archaeological one... instead presumably unfriendly hominins with Mousterian lived there.

    "Why do you insist on a 'back migration' to SW Asia?"

    The centroid says quite unmistakably that N coalesced in or near SE Asia, so it must have back-migrated to the West. As most Western subclades are long-stemmed, this should pose no problem (there is time, marked in the phylogeny as notches). The exceptions are R and N1'5, which appear to have back-migrated via South Asia.

    That's why.

    "A 'long stem' does not automatically mean a 'long migration'".

    It does not preclude it either. In many cases they do correlate with quite clear long migrations in fact, in others maybe not. But in all cases something must have changed from a period when expansion was not possible (stem) to one when expansion did happen. Just staying put is not a way to change: either climate or geography (or both) changed and the easiest way to achieve that is via migration to a better land (but I don't say it is always the case, just quite common).

    ...

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  46. ...

    "In fact usually not, as all the examples of non-N haplogroups with long stems demonstrate".

    I'll have to counter-demonstrate this "demonstration" of yours (where is it? just some appeals, no graphs not schemes, no counts, no anything). See how you make me waste my time?!

    "But you insist on claiming N as a special case".

    Not at all.

    "I find it impossible to believe that either M or N moved very far from the other L3s before eventually being able to undergo their own independent expansions".

    Well, the facts deny your "finding" because it's obvious that neither M nor N coalesced in Africa.

    Your mental wall is not evidence of anything: look at the damn fucking facts!

    "Surely even you accept that [Asian L3*] became M and N".

    Indeed but that implies that there was one population (or two at the most) which migrated in small numbers into Asia before they found an occasion to expand, quite apparently in Southern Asia (with or without SE Asia), carrying the L3m and L3n haplotypes (and maybe others that went extinct or stayed put near the Red Sea). Otherwise you can't explain the relative lack of L3 in Asia, where M and N coalesced without doubt.

    This is a narrative, a reconstruction of prehistory, that can't be successfully challenged unless you measure reason with the ruler of madness.

    And you do just that: insist in nonsense beliefs of you, by which humankind would have never moved from certain river bank of East Africa... One wonders what the explorers and migrants of all times would think about that static apple nonsense.

    If, say, you have 4 mutations and each mutation corresponds with, say, 300 generations and if each generation moves 100 km (70 miles), in a "short stem" of just one mutation you can have a migration of 30,000 kilometers, somewhat less than the circumference of Earth by the Equator line (40,000 km). So in order to migrate from Addis Ababa to Dacca (less than 6000 km), we only need 60 generations that migrate 100km each or 300 generations (one notch) migrating some 20 km each (a local distance).

    We have five times that time in the case of N, so plenty for all kind of pauses and what not.

    "Turns out I was wrong. N21 may have originated in Thailand/Cambodia".

    See how splitting hairs bring us nowhere? There's plenty of small-size data in less well studied regions. You can't expect me to know every detail about each lineage but roughly enough to get a more than decent approximate result indeed.

    It is a very interesting paper that I did not know about either, thanks again.

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  47. "I don't need your 'help', I don't want your 'help' and I'

    You may not want it, but I think you need it.

    "The centroid says quite unmistakably that N coalesced in or near SE Asia, so it must have back-migrated to the West".

    Centroids are almost certainly very unreliable in indicating source.

    "As most Western subclades are long-stemmed"

    As are many eastern and Australian ones.

    "In many cases they do correlate with quite clear long migrations in fact, in others maybe not".

    I can see no examples of where they need 'correlate with quite clear long migrations'. Surely we should first examine all haplogroups from the same perspective before adaopting any other stance.

    "But in all cases something must have changed from a period when expansion was not possible (stem) to one when expansion did happen. Just staying put is not a way to change: either climate or geography (or both) changed and the easiest way to achieve that is via migration to a better land"

    But we see quite clearly the periods of expansion and diversification. To me it is obvious that long stems are exactly the result of 'Just staying put'.

    "Much of our continuous misunderstanding is that you insist in reinterpreting what I say according to what you think I might have meant, what is almost always wrong".

    I think I now get what you believe. I'll cover it next.

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  48. "Your mental wall is not evidence of anything: look at the damn fucking facts!"

    OK. Here we go. You brought up the subject of N2 and its stem. That encouraged me to go back and have a closer look at it.

    As you will already be aware N2 really consists of two haplogroups: N2a and W. N2a, with a stem of 7 mutations, has not formed any recognised subclades but W, also with a stem of 7 mutations, has diversified into a multitude of subclades. So N2's expansion is really W's expansion.

    In the McDonald map W is shown as being most common amoung the Kurds. Wikipedia claims its highest concentration is in North Pakistan. From Phylotree we see that W's spread is almost instantaneous at 7 mutations from N2. N2 in turn is 4 mutations from N. And N is 5 mutations from L3.

    Using your hypothesis that a long stem indicates a period spent moving through a huge variety of habitats allows us to claim that L3 had left africa and moved to SE Asia. Along the route generations of women accumulated those 5 mutations in N's stem, but they left no descendants along the way. Next, women carrying N left SE Asia and moved into South Asia. Along the route generations of women accumulated those 4 mutations in N2's stem. Then women carrying N2 moved out of India to SW Asia. Along the route more generations of women accumulated those 7 mutations in W's stem, as well as the 7 mutations in N2a's stem. Some W clades are found in South Asia, which you claim is evidence in support of your hypothesis.

    Examining the data using the hypothesis that a long stem indicates a period spent isolated in a particular habitat allows us to construct a different, and simplrer, story.

    Haplogroups W and N2a endured a period of drift 7 mutations long in separate, but presumably neighbouring, regions. Perhaps at opposite ends of the region in which N2 had spread through at some time. These two regions must have been close to where the two haplogroups had first coalesced from N2. N2 is 4 mutations removed from N, so that region would also be close to where N2 had first coalesced from N. N has a stem of 5 mutations from L3 so the region would also be close to where N had first coalesced from L3. That region would appear to be somewhere between Kurdistan and Northern Pakistan.

    All the N haplogroups are the product of a group of N-carrying women who escaped from that region at the 5 mutation level. Haplogroups N2a and W developed from those women who remained behind, and were only able to escape 11 mutations later. When we turn to N in the east we find that no N haplogroups with long stems diversified once they had arrived. They arrived as N and have remained isolated.

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  49. "You may not want it, but I think you need it".

    That sums it up. I'm not reading much less replying anymore to your replies until you cease and desist with that psychotic stalker attitude.

    ReplyDelete
  50. Well. You just keep on believing that humans can move long distances while undergoing drift, and you will keep on being mystified as to the spread of haplogroups around the earth's surface. And you will continue to be forced to make things up to explain what you see as anomalies.

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  51. I am a social scientist interested in creating a layman's narrative to the map provided by one of the genetic laboratories that illustrates the migration and mitochondrial DNA haplogroup of my ancestors. Can you explain, in layman's terms, how MtDNA L3, N) became YDNA? Before starting the research I ad assumed that they were all MtDNA.

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    Replies
    1. They are mtDNA and never became Y-DNA. I'm not sure which is the source of your confusion but I never said nor implied what you seem to have (mis-)understood.

      Just to be completely clear: Y-DNA and mtDNA are completely different "animals": Y-DNA is the one in the Y-chromosome, transmitted from father to son (women are XX, so they do not carry it); mtDNA is the relatively short chain found in the mitochondria, cell organelles of probable bacterian origin, which are passed from mother to daughter and son (sperm does not carry any mitochondria, only the ovule does). They do not mix, much less transform in each other.

      I wonder if the source of your confusion is that some lineage names are similar in both cases. That's just because they use letters and numbers but they have no relation whatsoever. For example mtDNA N is a major non-African macro-haplogroup including about half of Humankind and ancestral to many others, while Y-DNA N is a not-so-important East and North Eurasian lineage (typical of Buryats or Finns for example). Similarly mtDNA L1 is an African lineage typical of Pygmies and some other West-Central Africans (the Fulani for example) while Y-DNA L1 is typical of Pakistan instead. They just share name by mere chance.

      Delete
    2. PS- The up-to-date mtDNA and Y-DNA trees can be found in the following reference sites:

      → mtDNA: http://www.phylotree.org/
      → Y-DNA: http://www.isogg.org/tree/

      For more details I would suggest to begin your search in Wikipedia for example, although the articles are never good enough they may be a good starting point for a basic understanding in most cases.

      See also the "links" page:
      → http://forwhattheywereweare.blogspot.com/p/links.html

      And feel free to drop a question if in doubt, sure.

      Delete

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