October 31, 2012

Finally some improved knowledge of haplogroup R1a1 (Y-DNA)

Haplogroup R1a, most of which is R1a1, dominant in Northern South Asia and Eastern Europe, as well as in much of Central Asia, has been giving headaches to population geneticists, academic and amateur alike, because key markers were not identified, making most of the haplogroup look like an amorphous goo, the same in India as in Europe. It seems that this may change now:

Horolma Pamjav et al., Brief communication: New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1. AJPA 2012. Pay per view ··> LINK [10.1002/ajpa.22167]

Abstract


Haplogroup R1a1-M198 is a major clade of Y chromosomal haplogroups which is distributed all across Eurasia. To this date, many efforts have been made to identify large SNP-based subgroups and migration patterns of this haplogroup. The origin and spread of R1a1 chromosomes in Eurasia has, however, remained unknown due to the lack of downstream SNPs within the R1a1 haplogroup. Since the discovery of R1a1-M458, this is the first scientific attempt to divide haplogroup R1a1-M198 into multiple SNP-based sub-haplogroups. We have genotyped 217 R1a1-M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the “1000 Genomes Project”.
The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub-haplogroups. R1a1-M458 and R1a1-Z280 were typical for the Hungarian population groups, whereas R1a1-Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages. This pattern implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a-M82 is their only discernible paternal lineage of Indian heritage.

Not having access to the paper right now, I can't say much more but I believe that the abstract alone is very informative already.

Distribution of R1a per Underhill 2010
 


Update:

Fig. 1 - MJ trees
(click to expand)
A reader already sent me a copy of the paper and I think that it has two aspects:

On one side the paper effectively detects these markers and study them, as well as R-M458 in Hungarians and related ethnic groups (Csangos, Szeklers, Hungarian Roma), as well as in Malaysian Indians, Uzbeks and Mongols. This part is informative, even if the selected Asian populations may not be the best choice (Mongols are low in R1a and so are Tamils who make up the bulk of Malaysian Indians).

On the other side, the authors attempt to read too much, not just on these haplogroups but specially on molecular-clock-o-logic estimates, (based on the Zhivotovsky mutation rate, now considered obsolete even by molecular clock enthusiasts). A corrected age estimate would be roughly doubly old[ref 1, ref 2] and that means that neither the Kurgan expansion nor the Neolithic one could account for its arrival to Europe.

Even using Underhill age estimates, they'd imply at least LGM dates for the arrival to Europe after the due correction. Their own dates, after due x2 correction, give Late Upper Paleolithic dates for the haplogroups researched here. 

Also the authors insist on arguing against a South Asian origin of R1a1 (Underhill 2010) on what sound like weak and fallacious arguments:

Previous publications have pointed out that regions of highest haplogroup frequencies do not always indicate the territory of origin (Cinnioglu et al., 2004) and high STR diversity may not be exclusively an indicator of in-situ diversification but could also be the consequence of repeated gene flow from different sources (Zerjal et al., 2002; Sharma et al., 2009).

Basically they are nagging: "Underhill could hypothetically be wrong in his conclusions but we have no evidence whatsoever that he is - just saying". 

The real reason is that they seem to hope to find a more westerly origin for the lineage and attribute it again to Indoeuropean expansions, in line with classic speculations for which the high South Asian STR diversity levels are a big problem. However it is most unlikely that a bunch of horse-riding nomads could so radically alter the genetic landscape of the whole subcontinent, more so when its agriculture was already fully developed, sustaining no doubt high densities. 

But notwithstanding all those highly questionable opinions, the discovery of new haplogroups adding to our comprehension of this major lineage is a great advance.


Update: 

It seems that some of the data exposed in this paper was already floating around in some circles because ISOGG already includes the "new" haplogroups in its phylogenetic synthesis. Most interestingly the two "European" clades (along with a third one, whose geography I ignore so far) make up a larger haplogroup (R1a1a1b1a - S198/Z282), which is "brother" of the "Asian" one (R1a1a1b2 - S202/Z93).

As I was just commenting elsewhere the key to the origins of R1a is not so much in these low level haplogroups but in the higher "asterisk" paragroup, which (from memory) used to be concentrated in Pakistan and nearby areas of India, etc.

But once reached the level of R1a1a1b1 (S339/Z283), this lineage seems to have split in two: one which we can describe as "European" and another which we can describe as "Indian".

The European half is treated in this paper as two of its subclades only and separately, what may be confuse. Hence I am adding here a synthesis of the current ISOGG phylogeny of R1a, with some annotations, for easier reference:

  • R1a* ··> Iran, Persian Gulf, Turkey
  • R1a1  (L120/M516, L122/M448, M459, Page65.2/SRY1532.2/SRY10831.2)
    • R1a1* ··> Iran, Caucasus, Greece, Scandinavia
    • R1a1a (L168, L449, M17, M198, M512, M514, M515)
      •  R1a1a* ··> where? (not clear)
      •  R1a1a1 (M417, Page7)
        • R1a1a1* ··> where?
        • R1a1a1a (L664/S298)  ··> where?
        • R1a1a1b (S224/Z645, S441/Z647)
          • R1a1a1b* ··> where?
          • R1a1a1b1 (S339/Z283)
            • R1a1a1b1* ··> where?
            • R1a1a1b1a (S198/Z282)
              • R1a1a1b1a*
              • R1a1a1b1a1 (M458) ··> Central & East Europe
              • R1a1a1b1a2 (S204/Z91, S466/Z280) ··> Europe, Central Asia
              • R1a1a1b1a3 (S221/Z284, S443/Z289) ··> where?
          • R1a1a1b2  (S202/Z93) ··> India, Central Asia

All the data on the geography of top level "asterisk" paragroups is from Underhill 2010, already mentioned above. It suggest a West Asian origin for R1a overall and spread to West and East since the R1a1a level or lower.

I used colors to emphasize the clades discussed here (purple for the larger haplogroup, blue for the European-leaning clade and red for the Indian-leaning one).

Clades in cursive are "proposed", not yet consolidated.

67 comments:

  1. Maju you're full of it, as usual.

    Europe has much higher R1a SNP diversity than South Asia, where only Z93 is found.

    Z280, M458 and ancestral lineages of Z93 all overlap in Europe. Not even in Inner or Central Asia as this paper claims.

    Therefore, R1a expanded deep into Asia from somewhere in Europe.

    Here's the latest tree you clown.

    http://img543.imageshack.us/img543/4425/r1am198.jpg

    ReplyDelete
    Replies
    1. I'd appreciate if you tone down your comments a bit.

      Anyhow, what percentage of South Asian R1a belongs to the sub-haplogroups that we know are mostly from that region? Because research bias is important in discerning subhaplogroups existence altogether (you know or should know that well).

      IF you can show me as a matter of fact that most South Asian R1a or R1a1 belongs to the haplogroups already discovered, I would be the first to acknowledge because, when research is throughout, basal haplogroup diversity should be most informative, well above STR structure or estimated diversity.

      So far I don't see that and instead there have been two papers (Underhill's and another one which had found that the deepest apparent R1a sublineages were from South Asia as well - can't recall the author right now but I'm sure you will).

      I understand that R1a expanded in the Upper Paleolithic, the same as relatives R1b and Q, in the context of the colonization of West Eurasia (including Central Asia). But prove me wrong, of course.

      I believe we already discussed that, in parts of Europe, it looks like R1a-M458 could be related to Kurgan expansion (Corded Ware specifically), specially because it's found at higher frequencies in Greek Macedonia than in all the Slavic Balcans, what make it a very unlikely "Slavic" clade.

      Anyhow, how can be a lineage that allegedly expanded c. 2500 BCE a "Slavic marker" when the Slavic expansion only happened around 700 CE, 3200 years later? You should try to be more internally consistent at the very least.

      Delete
    2. There's nothing but Z93 (L342+) in South Asia (India + Pakistan). There's definitely no confirmed R1a* there at this stage.

      Europe has Z283 (which includes M458, Z280 and Z284), L664, Z93 (L342-), and R1a*.

      So you would need a major shift in results to back up what you'd like to see.

      I think the theory that R1a originated in South Asia is a dud, and it's only around due to the fact that STR diversity was wrongly assumed to mean anything in this context. R1a most likely comes from West Asia, and R1a-M417 from Europe. That probably means Z93 also comes from Europe.

      Delete
    3. Actually it was easier than I thought to find the top level paragroups data, because Underhill 2010 already worked that (see supp. tables).

      R1a* is only found in West Asia (Iran, Turkey, Gulf emirates).

      R1a1* is found also in Iran and, additionally in Caucasus, Greece and Scandinavia.

      R1a1a* is widespread (from India to Europe).

      So it'd seem that the expansion happened at the R1a1a level and also (maybe at the same time) at the immediately lower levels. But I see no signature of IE expansion in it, sincerely.

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    4. Correction: R1a1a* in Underhill 2010 is probably not R1a1a(xR1a1a1) but some other category. Whatever the case R1a obviously originated in West Asia from where it spread to Europe and South Asia. I see no data supporting a Europe-to-India pattern, sorry but a radial from West Asia one instead. You could argue for a Neolithic origin, I guess.

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    5. Don't worry, you'll get it eventually when more stuff comes out. No point arguing about it now.

      Delete
    6. I worry that you state claims without evidence. It's not just annoying but says little about the quality of your assessment.

      Delete
  2. It must be from the Punjabi diaspora in Malasia

    ReplyDelete
    Replies
    1. It must be, it is in fact a random sample of Indians from Malaysia taken from the 1000 genomes project, who are 85% Tamil.

      I have no idea why they did not use other 1000 genomes' samples like Gujaratis from Houston (GIH) or the several Pakistani ones but worry not someone will and soon. I just don't have the means/know-how but the data is there stored in public access database and is all about someone checking it.

      Delete
    2. The GIH have been checked. They're Z93+.

      All the 1000 Genomes samples have been checked. That's how many of the new SNPs have been found.

      Delete
  3. could you please send me a link to the site.

    ReplyDelete
  4. my email is clusteredmaps@aol.com
    and I could put the site on the blog clusteredmaps.blogspot.com

    ReplyDelete
    Replies
    1. Uh? The site? What site?

      Your blog has not updated in two years incidentally.

      Delete
    2. THat is because I need new info, in addition to this I have R1a so I would really appreciate the data.

      Delete
    3. What I don't understand is the nature of your request. Do you want a copy of the paper or what?

      Delete
    4. Just a copy of the PDF paper or the infortion about the frequency of R1a1 in all of the popualtions studied, a list of the popualtions studied and the frequency of the R1a in all populations the supplementary data is sketchy. For example who is 728/05 in http://onlinelibrary.wiley.com/store/10.1002/ajpa.22167/asset/supinfo/AJPA_22167_sm_SuppTab2.xls?v=1&s=86bbd2fd32edea0a235d3ff2ff3ff87ac873d07d

      Delete
  5. "R1a1a1a (L664/S298) ··> where?"

    Northwestern Europe.

    "On the other side, the authors attempt to read too much, not just on these haplogroups but specially on molecular-clock-o-logic estimates, (based on the Zhivotovsky mutation rate, now considered obsolete even by molecular clock enthusiasts). A corrected age estimate would be roughly doubly old[ref 1, ref 2] and that means that neither the Kurgan expansion nor the Neolithic one could account for its arrival to Europe."

    You seem pretty confused. Pedigree estimates of autosomal SNP mutation rates have nothing to do Y STR mutation rates, which have their own pedigree estimates (leading to dates much younger than with Zhivotovsky).

    ReplyDelete
  6. "R1a1a1a (L664/S298) ··> where?"

    Northwestern Europe.

    "On the other side, the authors attempt to read too much, not just on these haplogroups but specially on molecular-clock-o-logic estimates, (based on the Zhivotovsky mutation rate, now considered obsolete even by molecular clock enthusiasts). A corrected age estimate would be roughly doubly old[ref 1, ref 2] and that means that neither the Kurgan expansion nor the Neolithic one could account for its arrival to Europe."

    Pedigree estimates of autosomal SNP mutation rates have nothing to do Y STR mutation rates, which have their own pedigree estimates (leading to dates much younger than with Zhivotovsky).

    ReplyDelete
    Replies
    1. "Northwestern Europe".

      Why? Source?

      Also, only there? How can we know?

      ...

      As for the other aspect, are you saying that the authors counted every single SNP in the Y chromosome (of some people) and are not using anymore STR-based estimates?

      And, if so, which is their calibration point, because the SNP-based estimates I have seen have totally wrong calibration points usually, like attributing 50 Ka to the OoA when it is 125-80 Ka - depending what part of the episode: 80 Ka would be for F or CF, already in South Asia. If you calibrate the B/CF'DE at 50 Ka when it must be before 125 Ka, you get the wrong results also.

      But it would be nice to clarify if they are counting all SNPs in some individual lines, something that is indeed possible nowadays, and, if so, which is their calibration reference.

      Delete
  7. I am an Indian with r1a1 as determined by the National Geographic Genographic project, so the comment above by davidski is weird.

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    Replies
    1. Hi Ash, but have you been tested downstream of R1a1, for example for M17 or Z39?

      Genographic Project, AFAIK, is an old (and a bit "pop") reference anyhow, for more than a decade now the Y-DNA quasi-official reference for nomenclature has been YSOGG, which is kept up to date to the latest genetic research (or almost).

      What is exactly what you find "weird" in Davidski's comment?

      Delete
  8. Is it not logical that R1a originated in Northwestern Europe when the core area for the R haplogroup is obviously there?

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    Replies
    1. What do you mean by NW Europe? There's very little basal diversity of this lineage in places like Britain or th Netherlands.

      The most obvious apparent origin of R1a would seem to be Iran because R1a* is not found in Europe (only West Asia) and only at the level of R1a1 we begin to see some presence in Europe (Greece, Norway) but also in West Asia.

      The intermediate levels between R1a1 and R1a1a1b1 are not well documented but at this level we see a split between a European branch (R1a1a1b1a) and a South Asian branch (R1a1a1b1b).

      So R1a as such originated in West Asia (Iran probably) as did maybe R1a1, which began migrating to Europe. Much later two specific major branches, one European and the other South Asian, coalesced. I'm not sure of which process or time-frame this stage corresponds to.

      Delete
    2. I noticed that the R* haplotype is found mostly in Cameroon/Sudan and in eastern India/Central Asia. As far as I understand, also the R2 and R1* are found in the same areas. To my understanding, these R*, R2 and R1* are old haplotypes of the R haplogroups. The areas they are found in are in the outskirts of the distribution area for the R haplogroup.
      My instinctive assumption a priori was that the place where the haplogroup originally developed should have the oldest haplotypes as well as the newest ones because it should in theory have the highest diversity.
      However upon examening the available data, my initial assumption seems wrong.
      The R haplogroup seems to have a clear core in NW Europe. After all R1B is common in Western Europe and R1A is commonly found going east from Scandinavia/Germany. So now it looks a lot more like the R haplogroup originally developed in NW Europe. R1b and R1a must have developed in the same area. The older versions seem to have been 'displaced' to the fringes of the distribution area for the haplogroup. Some times initial assumptions are disproved by the data.
      I suspect that some of the basic assumptions used in arguing for geographical locations of origin for haplogroups and haplotypes could very well be wrong.
      It is early days yet in the understanding of DNA, and we will know much more in the future. I realize there are probably few people who have the same opinion as I do.

      Delete
    3. I don't understand your logic, Miraculix. Basal diversity refers to the number of older branches, those stemming directly from the root; the newest sublineages must be considered separately as autonomous entities with their own processes (which happened necessarily AFTER the oldest ones).

      Therefore
      → (phase 1, 2 and 3) P, R and R1 appear to originate in South Asia
      → (phase 4) R1a and R1b (as well as Q) appear to originate in West Asia
      → etc. for lower tier sublineages

      This seems to fit well with the overall pattern of Eurasian colonization: first Southern Asia, then Australasia and finally West Eurasia and NE Asia. Based on this R1a, R1b and Q should have coalesced around 50-60 Ka ago in West Asia, within the process of colonization by our species of "the Neanderlands".

      Later on there must have been other flows and back-flows, one of them brought R1a1a1b2 to Northern India (possibly Neolithic but Kurgans may be argued for, even if I'm skeptic).

      As for R1* in Sudan/Cameroon, all I know is of R1b, most of which should be R1b-V88 specifically.

      Delete
    4. I agree that the older versions of R and R1 are found in South Asia.
      Also that the basic R1a is most common in West Asia/ Iran.
      So the basic logic of your reasoning is that the older versions in South Asia and West Asia did not mutate and change over time, while the ones who supposedly migrated into Europe did mutate and change over time so that we can tell them apart from the older ones?
      Why do you suppose that the ones who move geographically are also the ones who develop new subclades? By the estimated rate of mutation the older versions should also have changed? So why haven't they? And should we automatically assume that they stayed in the very same spot generation after generation for thousands of years in every single case just because one individual has been tested and ancestry proved going back 500 years?

      Delete
    5. Look: the asterisk only means "others": usually lineages that are rare enough not to have been grouped in any described haplogroup (emphasis in "group"). All them mutated at about the same pace, but these asterisk catch-all groups (paragroups, i.e. pseudo-groups) are barely researched at all and/or have so few known members that they necessarily fall in the "others" (asterisk) category.

      If you don't understand this, you don't understand anything about the nomenclature, phylogeny or population genetics.

      "Why do you suppose that the ones who move geographically are also the ones who develop new subclades?"

      Clades or more precisely haplogroups are human terminology, what we have in nature are lineages. The issue is that while R1a is one sublineage of R1, as is R1b, R1* (i.e. R1-others) may include several sublineages (at the very least one but probably many). So, simplifying, the R1 great-grandfather had several sons, two of which (R1a and R1b) had very numerous descendants, while the others (R1*) did not. Why did R1a and R1b grandfathers had so numerous descendants? Maybe because they colonized new niches (founder effect). This last is debatable and may vary depending on cases but a new colonization is clearly one such opportunity to leave a strong biological inheritance.

      Delete
    6. I agree with you the basic facts, that the P, R1 and R* are found in India/South Asia and that because these are not common in Europe, that means South Asia has a higher basal diversity.
      The question is does higher basal diversity necessarily mean the haplogroup R originated in South Asia?
      After all, human populations can migrate. So we can't be entirely sure that the R* and R1 have stayed in the same place ever since they came into existance?
      But I agree that if we assume that higher basal diversity automatically indicates place of origin, then your analysis is entirely reasonable.
      The only way to be sure of how these populations have originated, grown and emigrated is after all to have DNA from dated human remains, but I guess that could take some time...
      I don't mean to be difficult, but I am having trouble accepting some of the underlying assumptions.
      Is it for instance impossible that the P haplogroup spread to NW Europe before mutating into R?

      Delete
  9. "... does higher basal diversity necessarily mean the haplogroup R originated in South Asia?"

    Basal diversity is the best indicator we have to track the prehistory hidden in the haploid phylogenies. It's not 100% certain, I guess we can always imagine extreme catastrophes that brutally reduced the diversity in some places or maybe the differences between this and that other region are not clear and conclusive enough but otherwise...

    When migration happens it is always a subset which migrates, not ALL lineages from the homeland. This has been confirmed from recent data many times. So the colony tends to have less basal diversity than the motherland. There may be confounding factors if the motherlands are several (increasing the diversity because of the various sources) but common sense and careful parsing of the data should also reveal that.

    "But I agree that if we assume that higher basal diversity automatically indicates place of origin, then your analysis is entirely reasonable".

    Thanks.

    "The only way to be sure of how these populations have originated, grown and emigrated is after all to have DNA from dated human remains, but I guess that could take some time..."

    Ideally it should be that way but: (1) human remains do not always exist, (2) DNA does not always survive (this applies especially to hot humid areas) and (3) the desirable work of extraction and sequencing of the DNA does not always happen (or is done with too cheap means that don't reveal the whole data). In the case of Y-DNA it is much harder to survive than mtDNA, so we normally have much better info for the matrilineages.

    "I don't mean to be difficult, but I am having trouble accepting some of the underlying assumptions. Is it for instance impossible that the P haplogroup spread to NW Europe before mutating into R?"

    Nothing is "impossible" as in "100% impossible" but there are other principles in science known as parsimony or Occam's razor: i.e. what makes good sense and what seems extremely unlikely.

    So the only thing (and is not little thing) that we can say about your question is that it is extremely unlikely.

    Also you should consider archaeological data, which is not really supportive of your hypothesis, which implies ancient mass migrations from Europe into West and South Asia nowhere to be seen.

    ReplyDelete
    Replies
    1. I would like to point out that mass migrations from Europe to West and South Asia were theorized already before DNA was discovered. The term 'Arian Invasions' has been used for it, and the theory is supported by both archaeology and linguistics and so on. However it is a controversial theory.

      And the DNA does seem to indicate an initial origin for the haplogroup R in India/South Asia then?
      So the haplogroup P changes into R there, and the more successful strains migrate to Europe, while the others(R1, R*) stayed in India.
      What the scientists used to call the Arian invasions seem then to be backflow into India of mostly R1a1a varieties and some R1b varieties?
      And this backflow has occurred over thousands of years it would seem?
      I still think it's odd how NW Europe is clearly divided between R1a and R1b.
      It makes it appear as if that's where they originated, since they are so neatly positioned next to each other.
      So even if NW Europe doesn't have the R1a*, but only from R1a1 and up, I still suspect that NW Europe is the place where R developed into R1b and R1a.
      And I realize that if we assume the place that still has the simple R1a is the place they initially developed, it is in Iran or thereabouts.

      It seems risky to assume that the R1a* could not migrate from NW Europe to Iran for instance?
      I think everybody has to agree that there has been SOME backflow from Europe back into India, the question is how much and for how long.
      Is it from R1a1a level or from R1a* level would be interesting to know.

      Delete
    2. I have been tested as R1a1a1g3b - Old Scandinavian R1a1a
      That's why I find this stuff interesting.
      From your analysis, the R1a1 is the first level in which we see migration back to India then?

      Delete
    3. "I still think it's odd how NW Europe is clearly divided between R1a and R1b."

      Again not sure of what you call NW Europe. Britain and Ireland for example are clearly dominated by R1b (two main variants: one from NW Europe and the other from SW Europe). Even much of Germany is. R1a seems to be in those areas a rather recent arrival from the Corded Ware period on.

      Considering the data, I can even imagine an R1 split in West Asia instead of South Asia (imagining that R1* is not-so-diverse there) but not in Europe.

      "It seems risky to assume that the R1a* could not migrate from NW Europe to Iran for instance?"

      R1a* as such does not even exist in Europe, it seems, what leaves us with only one half-serious possibility about its origins.

      "I think everybody has to agree that there has been SOME backflow from Europe back into India, the question is how much and for how long".

      The only opportunity for that is the Indoeuropean expansion and it seems to me that this one was not so strongly impacting. IMO the R1a of India is mostly from Neolithic or older backflows from West Asia (not Europe). Notice please that India (South Asia) and Europe are not even in direct contact.

      Maybe you imagine mass migrations across the Central Asian deserts and very low population densities in South Asia, unable to absorb them. But I reconstruct the exactly opposite scenario: not so large migrations through South Asia, assimilation of many native Afghans, Pakistanis, etc. into the early Indo-Aryan genetic pool, and large demographic densities in a South Asia (North) that had been practicing agriculture for as long as Europeans.

      "From your analysis, the R1a1 is the first level in which we see migration back to India then?"

      Then why all Indian R1a is R1a1a1b2? Shouldn't start diverging locally in India already from that R1a1 level? Yes, of course it should. But it does not.

      Your speculation is so easily demonstrated wrong...

      Delete
    4. By NW Europe I mean the area facing the Atlantic from Portugal to Spain, France, Britain, Holland, Belgium, Germany, Poland, Scandinavia.
      So your conclusion is that R developed in South Asia and has since spread to Europe. Basically all migration has been from East to West then?
      But you say that in the 'IndoEuropean expansion'there was some migration from Europe into India then?
      The next section I am a little confused whether you are still talking about the Indoeuropean expansion or the initial migrations out of India?
      And the population assimilated many Afghans and Pakistanis native haplogroups into the early Indo-Aryan gene pool. Does not India have many haplogropups that do not occur in Europe(C, H, L, O, T1, E1b1a)? If the R haplogroup came from South Asia, why aren't they also to be found in Europe? Would not the R have assimilated these haplogroups into their gene pool before arriving in Europe?

      According to Wikipedia,
      http://en.wikipedia.org/wiki/Indo-Aryan_migration#Genetic_anthropology

      quote; 'Furthermore, the majority of researchers have found significant evidence in support of Indo-European migration and even "elite dominance" of the northern half of the Indian subcontinent, usually pointing to three separate lines of evidence: the previously widespread distribution of Dravidian speakers, now confined to the south of India; the fact that upper caste Brahmins share a close genetic affinity with West Eurasians, whereas low caste Indians tend to have more in common with aboriginals or East Asians; and the comparatively recent introgression of West Eurasian DNA into the aboriginal population of the post-Neolithic Indo-Gangetic plain.'

      But you say it is not so?

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    5. Also, certain Vedic hymns, Avestic passages, Vedic chronology and Vedic calendars indicate that the Aryans migrated from a location close to the Arctic circle to India early in their history.
      I don't know if this is a widely held view in India or not.
      http://en.wikipedia.org/wiki/The_Arctic_Home_in_the_Vedas

      Delete
    6. "By NW Europe I mean the area facing the Atlantic from Portugal to Spain, France, Britain, Holland, Belgium, Germany, Poland, Scandinavia".

      I'd call that North and West Europe (but not NW Europe). In any case, much of that area is very low in R1a. Only Central-North Europe falls out of this general rule.

      "Basically all migration has been from East to West then?"

      In the Eurasian colonization process South Asia (and to lesser extent SE Asia, incl. Southern China) was the core of everything. After a preliminary settlement of Arabia, which had very limited other effects, it was Southern Asia which acted as second cradle of Humankind (after Africa, of course), being at the origin of all humans outside Africa (excepted some minor 'recent' flows directly from Africa). Most of West Asia, as well as Central Asia and Europe came later, at the beginnings of the Upper Paleolithic.

      There were surely some secondary flows and backflows but we have to carefully locate and measure them. In many cases it's not too clear and don't seem overwhelmingly important.

      So yes, the general trend of settlement by H. sapiens was Africa → Arabia → India (and possibly SE Asia) → West Asia → Europe. And that fits well with what I see for P (incl. both R and Q), as well as other lineages. The only exceptions in the case of Europe are "recent" flows from Siberia (essentially Y-DNA N) and Africa (essentially Y-DNA E1b), which may well be dated to Epipaleolithic times (or Neolithic or, in the case of E1b-M81, maybe even Solutrean).

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    7. "The next section I am a little confused whether you are still talking about the Indoeuropean expansion or the initial migrations out of India?"

      Now I'm also confused but I guess that the later. There's no known migration out of India of any meaningful size or influence in "recent" times (post-LGM). When I said out of India I was no doubt thinking about some 50-60 Ka ago (roughly).

      "Does not India have many haplogropups that do not occur in Europe(C, H, L, O, T1, E1b1a)? If the R haplogroup came from South Asia, why aren't they also to be found in Europe?"

      Is E1b1a Indian? I don't think so but feel free to teach me something new. O is found in India but arrived only in "recent" post-Neolithic times, it seems. H and LT are indeed aboriginal to the subcontinent, I believe.

      Whatever the case it's clear that, as in any migration, not the whole motherland was represented but just a subset. This subset was essentially made up of (Y-DNA): G, IJ R1 and Q, (also some lesser F* and others). This was the West Eurasian founder effect.

      By the time of the settling of Europe there was another founder effect (or maybe two in sequence): I and R1 subclades (R1b for sure, R1a possibly too). All the rest (roughly) seems to have arrived only in the Neolithic, a secondary wave. A different founder effect took place in another West Asian derived settlement: Altai, where the main (or only) Y-DNA lineage was Q, which later expanded to NE Asia and America.

      ...

      Regarding the Indo-Aryan migration (or rather conquest), I adhere very tightly to the mainstream model which shows it originated in Easternmost Europe and Central Asia (Andronovo culture and such). I have no doubts about that.

      What I have very serious doubts are about its genetic impact. After all Northern India was Neolithic (and even highly civilized in many areas) since long before that invasion but then we see LOTS of R1a and not just among the upper castes (not at all, although it may be more common, and is even found among Dravidians). So if all Indian R1a arrived at that time it'd mean a massive demic replacement (almost only in the male side however) but a bunch of nomads never were able to shatter so much the genetic landscape of agricultural peoples which they wanted to conquer as essentially serfs. So I think it must be older, even if the Indo-Aryan invasion also helped to move lineages around, these were mostly previously consolidated South Asian lineages.

      A clear example of the absence of meaningful population replacement we find in Balochistan, where Balochis (Indo-Aryans) and Brahuis (Dravidians) have almost identical genetic pools. This clearly tells us that Balochis are nothing but aculturized Brahuis (just like Gascons are romance-speaking Basques) and also that Dravidian was surely spoken at the IVC.

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    8. I find the current model which insists that the common human ancestor lived a mere 70k years ago is a very strange theory, when archaeology suggests modern humans have been around for at least 1,93 million years, and the volcanic eruptions 70k years ago were not as serious as the ones in Iceland lasting 1000 years from 12000 bp to 11000 bp. During the latter, skeletal finds show that the muscle mass of humans was roughly halved. Humans changed from Cro.Magnon to modern Sapiens. The changes to the physique of humans seem to have occurred simultaneously in all populations world wide.
      To me the 'origin' of human evolution is not in Africa.
      My thought is that humans developed in Australia over 2 million years ago.
      Haplogroup A spread to Asia and Africa, then B evolves and displaces the A haplogroup people. Then at the start of the ice-age, which started 2 million years ago, deserts developed in Eastern Africa/Arabia and the Sahara. That isolated the haplogroups A and B in Africa. Since Australia changed from green rainforest to dry deserts, the centre of human evolution moved to the islands north of Australia...
      Haplogroup C then displaces both A and B haplogroup people in all of the world except in Africa, where they remained isolated by deserts. The D haplogroup develops in the Western range of the C haplogroup, and the E haplogroup further West still. The action in terms of genetic seems to have moved slowly north and the newer haplogroups appear in South Asia and India.That's F and G in India, then H, I, J also in India.
      The K(xLT) appears from India to Papua New Guinea, and is the ancestor of the MNOPS group. As to where the P haplogroup appeared, I would guess India or north of there.
      So for me the story of humans begins in Australia. Africa is little more than an isolated region which is home to the oldest haplogroups, but these originally developed in Australia and South Asia.
      As for the fact that so many 'experts' have a different opinion, I would say that it's early days in genetics still. We have only learned to recognize the basic recipes our cells use to make proteins and amino acids. That's only 3% of the total mass of DNA. The remaining 97% are thought by many to be 'trash' DNA, even though it is perfectly obvious that this is not the case.
      To simply assume that humans are from Africa(this is based on absolutely nothing) is amateurish. The fact that so many experts make the same mistake, doesn't make it more correct. The oldest found human remains are 1,93 mill yrs and are from Java. So why just assume that we 'came out of Africa'? It is an outdated theory from the 70s.
      I think simple models that do not account for one group displacing another
      I still think the R haplogroup appeared somewhere like in France or northern Spain initially, and I find the interpretations of mainstream science on this subject very much lacking in depth and consistency.
      So my view is not a commonly held one, but I have to say that according to Occam's razor it is the right one.
      But I find all the information useful even though my view is so different.

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    9. Correction;
      *I think simple models that do not account for one group displacing another, are simply too simple.

      Also I think the R1b developed in the Spanish Ice Age refuge, and that R1a appeared before the LGM 30k years ago, somewhere around the English Channel.
      At the beginning of the current inter-glacial period which started about 18500 years ago, and not 11 k years ago as so many people mistakenly think.
      During this time the R1a would have inhabited the then above sea level North Sea, which was a giant plain with huge rivers and fertile sediments.
      Wwhen the Ice age ended, the huge body of water located south of the ice in Russia, drained into the the Atlantic in a series of enormous floods at intervals of thousands of years. Of course, the R1a people living on the North Sea plains would have been in the way of this series of floods and consequent rising sea levels. Which sounds eerily similar to the myths of the Arians in India. Also the Levites among the jews claim to be descended from survivors of a giant flood, making it more than circumstantial. Since that time, R1a1a has migrated eastwards to India, south to the Levant and Italy and to every other place the R1a are currently found.
      The way it looks to me the current mainstream interpretations on our DNA has many 'migrational arrows' pointing the opposite way of what they should. And the fault is in their basic assumptions.

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    10. "I find the current model which insists that the common human ancestor lived a mere 70k years ago is a very strange theory"...

      It is becoming very apparent that this is about the first time you reached to this blog and also that your overall knowledge of Prehistory is a bit sketchy. Let's see:

      Per the extant paleontological data, H. sapiens has existed since c. 200 Ka ago, not just a mere 70 Ka. The first known H. sapiens is Omo 1, which is found along another specimen, Omo 2, which is not classified as such (would be H. rhodesiensis or similar). Omo 1 is dated to c. 190 Ka ago. The next known H. sapiens specimens (Herto, Jebel Irhoud) are dated to c. 160 Ka ago.

      The dates we are currently considering for the colonization of Greater Asia are of c. 125 Ka for Arabia and Palestine, c. 100 Ka for South and SE Asia (this bit is pretty new), maybe 60 Ka for Australasia, 55 Ka for Palestine UP (Emirian) and 50-45 Ka for European and Altaian UP.

      "... archaeology suggests modern humans have been around for at least 1,93 million years"...

      That would be Homo as genus, not what is often described as "anatomically modern humans" (AMH), which corresponds with our species H. sapiens, which is about 200 Ka old only.

      "To me the 'origin' of human evolution is not in Africa".

      Then you have serious problems with all the archaeology, genetics, etc.

      "My thought is that humans developed in Australia over 2 million years ago".

      Just because? There's no archaeological nor genetic data that might even suggest that. Furthermore there used to be not even placentarian mammals there, let alone primates.

      Get your facts straight, read a bit, learn... before you can debate.

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    11. You are just repeating your original arguments, and the remains that are 1,93 mill years old from Java, are actually completely modern anatomical humans.
      http://www.athenapub.com/13intro-he.htm
      is one useful link to show this of many.
      They should be haplogroup A, B or C according to my theories.
      The Lucy remains from Kenya are pre- homo erectus and are more than 3 mill years old. The skeletons found in Java are like I said completely modern humans in the homo erectus family.
      Just because I don't agree with your theories, which are not really yours because all you do is to take the experts word for everything, does NOT mean that I am wrong. It is a known fact that 90% of what 'science' believes to be true at any given time, is then later shown to be completely false.
      So don't give me tired old propaganda about how the experts of course always must be right, because this has been shown to be untrue countless times in the past. The scientific community is mainly comprised of cowards who do not dare to think a single independent thought for themselves. And some people are naive enough to think that if the scientific community are agreed on something, that means that it must be true.
      I think you are the one who needs to read a little, and much more to think for yourself instead of assuming that what you have been told is true.
      I will admit that there is currently very little to indicate Australia specifically as the definitive origin, after all it COULD still be in Africa, given that the oldest haplogroups(A, B) are still to be found there. But then it is strange that all the new haplogroups develop outside Africa, and the African genetics then is frozen in time compared to the rest of the world.
      Also, it is strange that the emigrants from Africa then seem to mutate just as soon as they set foot outside Africa. I would expect some of the A and B haplogroup people to make it to the Middle East then? Maybe even Europe?
      I mean what kind of theory is that?
      So I have 'Serious problems' with the established truths as long as they are not based on a sound logical reasoning. I have actually read a bit about these topics, I understand the mainstream view I think just as well as you do, it's just that I don't believe in them like you do. I think that because scientists in the 70s said they thought we came from Africa, nobody has the guts to say anything else. They would be afraid that other people would say exactly what you said to me above. That I must be stupid and uninformed, and so the scientists don't dare to say it. But I do. Maybe because I can't lose my job as a scientist, because I don't work as a scientist?
      I think that people in the future will be better informed, and that they will agree with me eventually.
      And the idea that the remains from Java are not modern humans, really shows that you don't know how to differentiate humans from their ape-like pre- homo erectus ancestors, they really are modern humans. What are they doing there if it is as you say, that humans are only 200 k years old?
      It is perplexing to me why someone would put forward that theory, when we know we are at least 1,93 mill yrs old as a the human race. An axe was found in England believed to be more than 700 k years old from the strata it was found in. Are you saying Aliens made that axe?
      In any case I am sure humans have been aroud longer than 200 k yrs.

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    12. In order to have theories, you first need to have knowledge. It seems obvious to me that you don't. They say: "ignorance is daring" but I am not really interested in so extremely unfounded wild speculations.

      Whatever the case Homo erectus is not Homo sapiens. And if you look at the skulls in your link, you should be able to realize that.

      The multiregional hypothesis was popular in some corners until recently but nowadays with all the genetic evidence, there is absolutely no doubt: Neanderthals and Erectus only influenced modern humankind in very minor fractions of our genome (Neanderthals to all non-Africans and Erectus only to Australasians).

      If you wish to learn something I'll be glad to point you to somewhere to look but if you're going to just rant with totally obsolete hypothesis like multiregionalism or absolutely nonsense ones like "Australian origin", I will ask you to spare me, please.

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    16. Well Maju, this is beyond any doubt;

      1. Anything after the so-called 'Missing Link' is by definition HUMAN!
      Homo Erectus is therefore HUMAN!

      2. When the 'out of Africa' theory was postulated, the oldest known homo erectus that had been found, had been found in Africa.
      3. That was used as the definitive 'proof' that the 'out of Africa' theory was true. 'Humans must be from Africa because the oldest human remains are from there'.

      4. When they found Homo Erectus outside Africa which were older than the ones in Africa, the followers of the 'out of Africa' theory proceeded to 'redefine' what being human is, instead of admitting that humans are not from Africa.

      The 1,93 mill years old remains in Java are an average height of 1,79 meters. This should tell you that they must be chronologically after haplogroup A, because haplogroup A are shorter than the remains in Java.

      Because Homo Erectus is HUMAN by definition, then your current assumption should then be that humans are from Java, is that not correct?
      Then you can argue all you want that "Anatomically Modern Humans" as the followers of the out of Africa theory call it, are from Africa.
      But humans do not seem to be from Africa according to the evidence.

      The missing link mutations involving loss of fur, development of sweat glands, changes to the ancle joint, drastic changes to the mandible, allowing for increased brain size and so on, are all present in the Homo Erectus. AMH is just an attempt to cloud the issue and save a dead theory.

      It is very good of you in any case to allow me room in this blog, as I know my topics are a little divergent from the intended topic of your blog(R1a1).
      But I felt it necessary to examine the basic assumptions that are at the foundations of the debate and point out the flaws before even discussing the specifics of R1a1. Don't worry, I will not write any more comments now, as I believe I have made my point :)
      Check.... and mate.

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    17. Do I look like I care about "missing links", do I look like doubting the humanity of H. erectus? But human or whatever, H. erectus is not H. sapiens. The difference may be subtle to you you may even want to argue that those are not different species but subspecies or whatever but the fact is that we can discern pretty well between one and the other. And we are not them (excepted the small Australasian introgression).

      "When the 'out of Africa' theory was postulated, the oldest known homo erectus that had been found, had been found in Africa".

      And is still the case. But we do not care here about H. erectus but about H. sapiens primarily, and oldest H. sapiens is African and African are also the only known H. sapiens for many hundred thousand years.

      What's the problem with Africa? No idea but I'm guessing that people like you are driven by unconfessed racism against Black People. You guys can't bear to have black ancestors and desperate look for any other impossible alternative. And in some cases you don't even know it!

      "'Humans must be from Africa because the oldest human remains are from there'".

      Pretty solid, right? Also there's other evidence like artifacts, genetics... all adds up.

      "When they found Homo Erectus outside Africa which were older than the ones in Africa"...

      It's not the case in fact. African remains of H. habilis and H. erectus are still older than Asian ones. It is not very clear how the many branches of H. habilis, erectus, ergaster, etc. are related but the Erectus OoA stands not just on the skulls and bones but on the Olduwayan (chopper industry) chronology, the existence in Africa and nowhere else of extensive "missing links" like H. habilis and all the Australopithecus family, never mind key Pan-Homo divergence fossils like Toumaï who, following your dubious logic, was "human" (in scientific terminology it's said "hominid" instead).

      Anyhow is not like H. erectus is a well defined category but rather a catch-all term for most Homo before the Sapiens and Neanderthal stages. Nobody agrees if H. georgicus is erectus or habilis or something in between, many anthropologists differentiate Asian H. erectus from African H. ergaster, which is the actual ancestor of AMHs and Neanderthals, but the difference seems more techno-cultural than biologically well defined and others keep using H. erectus for all.

      But regardless of your speculations about H. erectus, what is 200% sure is that H. sapiens appeared first in Africa and expanded from there. Actually the H. sapiens migration is the third such "out of Africa" migration we can clearly identify: first it was the expansion of H. erectus/georgicus with Olduwayan (chopper ind.) technology, then, about a 700,000 years later the expansion of H. ergaster with Acheulean technology and finally the expansion of H. sapiens with African technologies (MSA, Aterian... but also ill-defined flake industries).

      ...

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    18. ...

      "The 1,93 mill years old remains in Java"...

      AFAIK it's just 1.8 Ma and would be of similar age as those in Africa. This is a 1994 press note: http://www.nytimes.com/1994/02/24/us/redated-fossil-upsets-map-of-man-s-evolution.html

      Even if you'd be right (what I seriously doubt) and Java Man is older than the contemporary H. erectus of East Africa:

      1. All other previous human evolution fossils, including H. habilis, A. sediba and all the other Australopithecines (and all other hominids since Toumaï), the oldest evidences of an intentional stone industry, of use of fire, etc. belong to Africa.

      2. I am essentially concerned about H. sapiens and the OoA I normally discuss about is the H. sapiens OoA (third OoA), so whatever happened earlier is a bit out of my radar. There is absolutely no doubt that H. sapiens appeared first in Africa with the oldest fossils being in Ethiopia (Omo 1, Herto) and Morocco (Jebel Irhoud). Transitional fossils from H. rhodesiensis are also in Africa (for example Lake Eyasi, Tanzania). The toolkit is pretty much unmistakable as well.

      "Because Homo Erectus is HUMAN by definition"...

      I don't care much if H. erectus is "human" or not. That's a philosophical and not biological nor archaeological discussion. Was Toumaï (Sahelanthropus tchadiensis) human with its small chimp-sized but human-like-wired brain and bipedal locomotion? Would we consider H. erectus "human" if they existed today? Hard to answer. Probably there is not one correct answer because the answer can only be subjective.

      "The missing link mutations involving loss of fur, development of sweat glands, changes to the ancle joint, drastic changes to the mandible, allowing for increased brain size and so on, are all present in the Homo Erectus".

      We have no idea if H. erectus was furry or sweated. I doubt that the jaw is important re. brain development. Actually our sapiens tendency to very vertical facial features is not yet present in H. erectus nor in H. neanderthalensis: it's exclusive of our species (and clearly related to the existence of a chin). Neanderthals at least (and also many within the H. erectus catch-all category) were able to develop very large advanced brains while keeping prominent jaws (and the corresponding browbone).

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    19. "It is very good of you in any case to allow me room in this blog, as I know my topics are a little divergent from the intended topic of your blog(R1a1)".

      Actually I was just noticing how out-of-topic you had diverged and I must say that:

      === NO MORE OFF TOPIC COMMENTS HERE ===

      === THEY WILL BE DELETED ===

      Feel free to search and find a more appropriate thread if you wish to continue this philosophical discussion. Something in the category "human evolution" for example.

      Thanks.

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  10. Hi

    I noticed that in the Family Tree DNA database 'R1a and all subclades' there are now two test results from England that have been confirmed by SNP testing as R1.
    They are on page 1 under the header 'ungrouped'.
    The names are Pickering and Cates.
    Still the only place the simple R has been found is in Pakistan and the area around there. Do you expect that the simple R will also be found in Europe, or not?

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    1. Notice that NW European ancestry peoples tested by companies like FTDNA are counted in the many many thousands, hence you will find rare cases of almost everything, amounting to maybe one per 10,000. This is hardly comparable to samples of merely hundreds or dozens used in academic papers or even with the same companies' samples from less affluent or genetics-interested peoples like, say, Turks, Indians or even most continental European populations. Therefore a warning about comparing apples and oranges: rather than counting individuals it'd be wise to count percentages.

      "Still the only place the simple R has been found is in Pakistan and the area around there. Do you expect that the simple R will also be found in Europe, or not?"

      Everything is possible if you search enough. There's always the odd exception amounting to maybe one per million or whatever. Is this meaningful? Nope. Individual erratics at such frequencies should not be considered at the same level as greater apportions.

      In any case the R* found only in Pakistan is not "simple R" but R(xR1,R2), we can imagine it as "R3", or "R3, R4 and R5" or "R3, R4, R5, R6, R7, R8, R9, etc." It's anything but simple: it is "other", unclassifiable by our knowledge so far.

      So it's probable that the Pickering and Cates haplotypes' conjectural haplogroup could be described as "R1a2" (quite probably both are related), which is probably shared with other Eurasian peoples, much as the "Sardinian" R1b-V88 (first found in that island, where it has significant frequencies, unlike your example) is shared with Africans from the Chad Lake area, as well as other peoples from West Eurasia and Africa (something discovered only a decade later because Africa is not as high as Europe in the priorities of universities and researchers, much less commercial testing companies, which only test those who pay).

      There is a bias in the amount and quality of the available data, so we have to correct for it, for example rounding to "per thousand" figures (three decimal points in absolute or "per one" value), when your erratics clearly vanish into nothingness. Hence it's most likely that this "English" "R1a2" is shared with other peoples in Europe and Asia and that, in Asia, other lineages (let's say "R1a3, R1a4, R1a5, etc.") also exist - but not in Europe (or at such extremely low levels that they become irrelevant erratics).

      What you say is like talking of mountains and comparing the Everest with a hill of a mere 100m height, or talking of seas and comparing the Pacific Ocean to the Dead Sea, etc. Just because someone may be obsessed with the Dead Sea, it does not make it an ocean.

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  11. I thought that the R-M207* was the earliest version found of the R haplogroup. According to Wikipedia 'Y-chromosomes which possess the marker M207 that defines Haplogroup R-M207 but neither of the markers for its subgroups, are categorized as belonging to group R-M207*.' But according to what you are saying there is no such 'simple' version of the R haplogroup that doesn't have markers for any subgroup. If that is true, then it seems very difficult to sort the different haplotypes of the haplogroup in terms of chronology then?

    It is clear that the R-M207* has only been found in Pakistan and the area surrounding Pakistan, and so these results do indicate an initial appearance for the R haplogroup there. And unless the results should change significantly with time, this means that if we assume that the oldest versions of the haplogroup are still living in the same area as they were living when they first came into existance, then the haplogroup originated in Pakistan/India.
    Does that not make sense?
    Then we can of course endlessly debate whether the above mentioned assumption is reasonable or not. But if the R-M207* are not an older version of R, then it doesn't make much sense to say that the R are from there?
    I also thought that the R1 haplotype is a simmple version of R1 without any of the markers for any subgroups. Otherwise it doesn't make much sense to call it R1, then they would have to find the subgroup. After all the same problem of chronology would apply to this as does to the simple R? We could not say it is older unless it is a simpler version?

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    1. That's it: there's no such thing as "ancestral R1a" (nor any other haplogroup) because, in Y-DNA particularly (much much longer than mtDNA), mutations never stop happening (not sure of the exact frequency but at least one SNP every generation, possibly more). If we could work with full Y-DNA sequences (so far highly impractical and expensive but maybe easier in the near future) we would get extremely rich and nuanced trees, what would be a nightmare for the nomenclature, already overly complicated. What we have is a simplified (and occasionally even too simple) scheme of the real phylogenetic tree based on the known SNPs. The tree is correct but not nearly as complete as the actual thing. The map is not the reality.

      In mtDNA instead mutations seem to happen much more sparingly, maybe one every thousand or even several thousand years, so you can actually have vast star-like nodes (M, H) which are very real, although the various mutations may have happened at different moments. Also in mtDNA you can sometimes find the ancestral sequence of some haplogroups underived, "frozen in time", for the very same reason. But not in Y-DNA.

      "If that is true, then it seems very difficult to sort the different haplotypes of the haplogroup in terms of chronology then?"

      We can only know at each phylogenetic level (hierarchical node), where we find the greatest basal diversity. This greater diversity surely indicates where the haplogroup (the ancestral node) may have coalesced first, because with each new migration it is normal to lose diversity (founder effect). Although it will be created forged again at lower phylogenetic levels as the descendants of those founders spread around.

      "It is clear that the R-M207* has only been found in Pakistan and the area surrounding Pakistan, and so these results do indicate an initial appearance for the R haplogroup there".

      Yes but don't forget that R2 is rather concentrated in India than Pakistan and you should also consider these sublineages (R1 and R2, as well as R*). Also considering the relative lack of research for these kind of rarities (i.e. R*) and that P* seems to be concentrated around Bengal, I tend to consider R as originally South Asian in general. As you put it: "the haplogroup originated in Pakistan/India".

      "But if the R-M207* are not an older version of R, then it doesn't make much sense to say that the R are from there?"

      It still makes sense because of R2. Anyhow R* is not a preserved old version of R but it may well include several and not just one sublineages of R (i.e. "R3, R4, R5, etc.") so it weights at least as one of the other more common sublineages and probably more. So it's still important evidence regardless that you misunderstood its meaning.

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  12. Yes I know that R* represents a collection of subgroups.

    So the assumption is basically that because R2 are found in India/Pakistan then that is the place R is from, and then the basal diversity seems to back that up?
    And other than that it is hard to say anything about the chronology of the haplotypes in Y-DNA?

    Well, it will be interesting to see how interpretations may change when researchers start working with full Y-DNA sequenses as you mentioned above. I have also heard rumours about a new technique that is capable of extracting human DNA from archaeological sites that contain human excrement. Apparently they can still find DNA in really old samples. If that is true, they could yield a lot of historical DNA information. I have only been told of this new technique so I don't know yet if it's really as revolutionary as it sounds.
    But new technologies can make for much improved knowledge in this field in the future, that's for sure.

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    1. Not just R2 but all taken as a whole: within R, R1 (West Asian?) weights 1, R2 (South Asian) weights 1 and R* (South Asian) weights at least 1, probably more. What conclusion can you reach? Please do it yourself.

      Then consider also the roots of R, i.e. P. Here R weights 1, Q (West Asian) weights 1 and P* (South Asian) again weights at least 1 and probably more.

      Going even higher in the phylogenetic hierarchy, MNOPS (aka K(xLT)) has a clear tendency towards the Pacific Ocean regions (East Asia and Melanesia) other than P. The exact hierarchy within MNOPS is not yet well understood but it's at least plausible that the lineage coalesced in or near SE Asia.

      Etcetera (K looks South Asian, F as well). Try to look at the whole and not just the parts, don't let the tree hide the forest.

      "But new technologies can make for much improved knowledge in this field in the future, that's for sure".

      I look forward to that.

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  13. R1a1a is widespread throughout Indian Sub continent

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    1. It is much more common to the North (as apparent in the accompanying map) and also, in most cases at least, seems to have a positive correlation with upper caste (especially in the South, where Brahmins appear to be of Northern origin to at least a very large extent).

      For example, in a study of Tamils and Southern Tribals, R1a is very low (<2%)in tribals (excepted the ones who cremate their dead ones), rather low (8-12% among "low" castes: scheduled and dry land farmers), middle (20%) among the warrior-artisan castes and clearly very high (42%) among Brahmin-type groups.

      So "widespread" depends on what you mean. It is more or less in the frequencies shown in the map above.

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  14. Please analyse www.harappadna.org (or single p)data which has more representative sample analysis for this region of Indian subcontinent

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    1. Can you direct me to a more clear, specific link? AFAIK Harappa DNA is mostly interested in autosomal DNA, which is a different "animal" than Y-DNA.

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  15. The link provided by Davidski in the first comment at the top is a very good link.
    http://img543.imageshack.us/img543/4425/r1am198.jpg
    The image shows the branches of the tree for R1a1a.

    I also found another website with some interesting information about the R* in India, claiming that they all probably are R2 or R2a.
    http://r2dnainfo.blogspot.no/2010/08/all-r2s-may-now-be-known-as-r2a.html
    The site also has a new Haplogroup R tree that covers the entire R haplogroup.
    Although the results indicate the R* in Pakistan/India is mostly R2 the results are not completely final, as more testing is needed.
    But I think the tree that is presented is very useful, and relevant to the above discussion, don't you agree?
    Doesn't this mean that the argument that haplogroup R is from Europe just got stronger?
    My personal opinion is that the tree presented at the website makes it well possible that Europe is the place. But I also see that India is still a possibility, and no absolute conclusion has been made by me yet. Given all the haplogroups that have appeared in India it would not surprise me if India was the origin, however the division of Europe into West(R1B) and East(R1a) still makes me doubt the Indian origin.
    As for your above comments on me about Africa, I would say it is rather rude to insinuate that I am a racist just because I think the human species originated outside Africa. In any case the oldest haplogroups A and B are found in Africa today, so the fact that those people are in a sense 'who our ancestors were' is of course not changed by the fact that the earliest humans may have appeared outside Africa. A and B are still the oldest haplogroups. So screaming racism(!) is just not called for.

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    1. That tree in the link above is from 2010 so you may have seen it already?
      The site also has an article from 2012 on R2 frequencies in Afghanistan.
      Most of the comments on the site concerning the Aryan Invasion theory are in agreement with your view, that R is from India, and that all the migration has been from east to west.
      But still it seems quite possible that much of the R* in India/Pakistan/Afghanistan could well be R2, or would you discount that?

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    2. ... "the division of Europe into West(R1B) and East(R1a) still makes me doubt the Indian origin".

      It has nothing to do with the origin of R or R1 or even R1a and R1b. These areas are dominated by high frequencies of very much derived lineages of R1b and, for what we are seeing here, also R1a. So this must be the effect of two or three different demographic colonization processes, in which founder effects in SW (R1b-S116), NW (R1b-U106) and Eastern Europe (R1a-S198) were clearly decisive.

      You may interpret these colonizations-cum-founder-effects happening at various times in prehistory, I guess, but what is clear is that these three haplogroups, originating in these three founders (along with the one of I) are the initiators of the vast majority of European patrilineages, which are all them exclusive of Europe in practical terms. So you have to look at them for the origins of the E-W genetic division of Europe.

      This initial European duality (or multi-polarity) was in any case sharpened or diluted by later intra-European migrations, after the basic lineage distribution had been established. Hence it's still possible that, long after R1a-S198 was established as Eastern European lineage, it expanded thanks to Kurgan conquests, and/or other other intra-European flows. IMO the Chalcolithic Kurgan expansion sharpened the duality, while the Bronze/Iron expansions (from Central Europe westward and south into Italy) had only limited consequences instead, but subjective preferences clearly weight here on how to interpret these details.

      Subjectivity should play no role however in the clear identification of the founder effects, which is straightforward and hardly questionable. So I beg you to understand these founder effects in R1b, R1a and I before you jump to the interpretative phase. What we see in Europe, especially in large numbers, is not all R1b nor all R1a but clearly descendants of these. That we used the labels "R1a" and "R1b" often for short instead of the more precise names of these sublineages should not confuse you, I hope.

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    3. "I also found another website with some interesting information about the R* in India, claiming that they all probably are R2 or R2a.
      http://r2dnainfo.blogspot.no/2010/08/all-r2s-may-now-be-known-as-r2a.html"

      The blog looks somewhat interesting and I did not know of it before, so thanks for the link. However there's no specific data about how R* (and how much of it: most is not all) became R2 and the link to the reference study is broken.

      "The site also has a new Haplogroup R tree that covers the entire R haplogroup".

      Not new AFAIK. The reference for this is ISOGG, unless some study is slightly more advanced and being that post from 2010, it should not.

      "But I think the tree that is presented is very useful, and relevant to the above discussion, don't you agree?"

      Well, it's the same I knew before, not sure about you. R splits into R1, R2 and the mysterious R*, then R1 splits into R1a, R1b and R1*. Downstream of R1 the tree is not complete so I'd rather lead you to the scheme posted in the update of this entry (for R1a) and to the article on R1b-M269 linked in my last comment (although it's from 2010 it's pretty much unchanged as of now). For the rest of R1b, ISOGG and maybe Wikipedia (for where the various sublineages are found, etc.)

      "Doesn't this mean that the argument that haplogroup R is from Europe just got stronger?"

      Sincerely, not at all: you are using incomplete data and putting the cart before the horses (i.e. your pet hypothesis before the facts.

      "As for your above comments on me about Africa, I would say it is rather rude to insinuate that I am a racist just because I think the human species originated outside Africa".

      Well, I think people often have that kind of motivations, even if unbeknown to them, when they happily jump to defend totally unsubstantiated "alternative models" to the out of Africa or to the centrality of Tropical Asia in the later phase. I think I must suggest that so you can make your own self-analysis of your real deep, possibly unconscious, motivations.

      Sorry for my bluntness but, well, really not: it's not a bug but a feature. As someone raised under the chords of Punk music, I don't think bluntness as a defect but as virtue of truth, while I tend to consider excessive politeness a defect of deceit and cowardice instead. As they say: if you don't like the heat, get out of the kitchen.

      Whatever the case I think you should meditate about the real reasons behind your conjectures (all of which are obviously wrong - yes, they are) because they do stink to Eurocentrism. I sincerely believe I'm making you a favor by stating what you may not be aware of about yourself.

      On the other hand, do not worry too much about it: we all have biases (although some of us try to fight against them) and ethnocentrism is a very common one.

      "But still it seems quite possible that much of the R* in India/Pakistan/Afghanistan could well be R2, or would you discount that?"

      I do not know. AFAIK there is still R*(xR1,R2) in Pakistan and R1*(xR1a,R1b) in West Asia and Pakistan. I'm recalling from databases but I do not have all the data so only very careful parsing of it may decide this matter. I just do not have enough time.

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    4. I see your point, Maju.
      And I have been aware of these things all along as I have tried to tell you before. The only point I am making here, is that the founder effects could also be explained by early migrations going from west to east, the R developing into R2 as the R spread to India during the ice-age. We have to admit that we don't know the pattern of migration yet, and therefore this could easily explain the pattern of distribution seen in the R haplogroup.
      I guess you think I am twisting the DNA results to fit a 'Eurocentric' ideology or something, but I assure you I will not feel heartbroken at all if proof is given that the current interpretations putting the origin of the R haplogroup in S Asia is correct.
      I am not trying to say that the model with R originating in India and all migration since going west from there is necessarily wrong, I am only saying that both theories are entirely possible. But of course you have to be able to change your basic assumptions and look at the DNA results with fresh eyes, even if only as a hypothetical theory. You don't really seem willing to do that. And therefore you just dismiss it as impossible.
      So R2 is not found in Europe, and logically I assume that R2 developed when the R migrated to India. You say that R1 and R2 developed in India and for some reason(conveniently for your theory) the R2 decided not to emigrate.
      India has little R1b and lots of R1a, which makes me think the direction of migration is west to east. The R1a in Central and Eastern Europe moving east along the rivers into Asia. You say the R1b / R1a developed in W Asia and then migrated into Europe where they for some mysterious reason decided to sort themselves with R1b in the West and R1a in the East, even if it seems much more logical that they would have been more mixed if they originated in W Asia and then migrated to Europe. Do remember that I am aware of the basic reasoning of basal diversity and founder effects when I am saying these things.

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    5. There are many other lineages which come from Southern Asia, essentially all, at this or that level, with the rare East Asian or African exception. The bulk of West Eurasian ancestry is (distantly in time but directly anyhow) from South Asia. So it would be very exceptional if it'd be like you say, and exceptional claims need exceptional evidence, you know.

      But I still think that the evidence is for MNOPS coalescing in SE Asia (or close to it), P and R coalescing in South Asia and R1 maybe in West Asia (but not in Europe). Why not in Europe? Because the basal diversity is concentrated in West Asia and it is also the geographical center of a rich radial (or quasi-radial) expansion. This applies not just to R1 but to R1a and R1b as well.

      "I assure you I will not feel heartbroken at all if proof is given that the current interpretations putting the origin of the R haplogroup in S Asia is correct".

      Well the evidence has been provided in this discussion and yet you insist. And you are not pushing it westward just a bit (to West Asia, after all Iran borders Pakistan... there could be something missing) but a lot: to Europe and even NW Europe if I recall your initial words correctly. Sorry but Europe (and most of West Asia, i.e. "the Neantherlands") was colonized after most of Asia and the bulk of European ancestry comes from elsewhere and that elsewhere is most directly Southern Asia.

      It was some 50,000 years ago... or maybe 30,000 if we imagine R subclades expanding with Gravettian and not Aurignacian (or just 7000 years if we would accept, that I don't, the Neolithic mass-replacement hypothesis) but, whatever the time frame, the vast majority of European ancestors came from Asia. It is very apparent in the genetics and everyday more apparent also in the archaeology.

      What do you have? Nothing but your pet speculation. I already have relatives who seem unable to differentiate between degrees of certainty: between what is merely possible, what is probable and what is certain, jumping from possible to certain by the magic of self-deceit, of faith, or mere believing (and therefore are undergoing treatment), I don't need any more such logical mess, thanks.

      "You say that R1 and R2 developed in India"...

      R1 may have coalesced in West Asia. I'm not sure about it. Maybe in the border areas, in AfPak... whatever. In fact, if you think of it, it's a bit pointless to argue about where exactly R1 coalesced, because what matters is the overall pattern MNOPS→P→R→R→etc., which is clearly East to West.

      "India has little R1b and lots of R1a, which makes me think the direction of migration is west to east."

      Of R1a yes, surely so. But that does not make R1a European by origin: it is still original from West Asia, as I argued several times before, including the update of this entry.

      Seriously: I get tired of going in circles. I suggest you to not try my patience with this kind of vicious discussion dynamics and bring your obsessions to some discussion forum instead of my blog. I have a good deal of patience but I'm not here to pay attention to every commenter who does not know when to stop.

      ...

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    6. ...

      "You say the R1b / R1a developed in W Asia and then migrated into Europe where they for some mysterious reason decided to sort themselves with R1b in the West and R1a in the East"...

      Mysterious reason no: founder effects.

      For example, IF these lineages spread in Europe with Aurignacian or Gravettian (both original from West Asia), they would have naturally created such two zones East around the Dniepr-Don region and West around the Franco-Cantabrian region (and maybe Doggerland as secondary zone). The Last Glacial Maximum would have reduced the Central European populations to almost nothing and then there was re-expansion from the West. Later, in the Chalcolithic, there were also expansions into Central Europe from East and West.

      No big mystery here, if you know your prehistory and your population genetics. Whatever the case it is not anymore R1a and R1b but some highly derived subclades, exactly the same that R1a and R1b are not anymore F. What you should focus is on those European-specific subclades and which are the differences between them and what is found of R1 elsewhere. For example there is much more R1b basal diversity in West Asia and there are major R1b top-tier sublineages which are more common in Africa or Central Asia. So for R1b (better studied than R1a) there is no doubt: West Asia is the origin and the only debate is when and how did the subordinated expansions happened. Much of the same for R1a, with the exception that there are a bunch of intermediate layers described only by SNP but not by location(s), at least with the data we are all managing here.

      "... it seems much more logical that they would have been more mixed if they originated in W Asia and then migrated to Europe".

      It does not seem logical to me at all. Eastern and Western Europe experienced totally different Upper Paleolithic since Gravettian and only remixed a bit with the (E→W) Kurgan invasions of the Metal Ages. Even the Neolithic was very different, only linking via West Asia, if at all.

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