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Thread: Basal clades of hg R

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    Basal clades of hg R

    Remember: By basal R, I mean any R that is not R1a1a1-M417 and R1b1a2a-L23, because those lineages take up 90%+ of R today. Looking at R(xL23, M417) can help learn about the origins of L23 and M417.

    I'm going to use this thread as....

    >An option for people to post information/discuss about basal clades of Y DNA hg R.
    >For myself to post any information I find on basal clades of Y DNA hg R. I'm going to make a Y DNA Atlas blog to put as much Y DNA data as possible, like I did for mtDNA.

    Among members here and even some academics it's unanimously believed that both R1a1a1-M417 and R1b1a2a-L23 were carried mostly by early Indo European speakers and expanded out of Russia/Ukraine starting in circa 3000 BC. Arguments nowadays revolve around where the ancestors of R1a1a1-M417 and R1b1a2a-L23 came from. Some of the best evidence you can give for an origin is diversity of R(xL23, M417). The R1b1 and R1a1 from Mesolithic Russia are dead-lineages. IMO, there's a high possibility both M417 and L23 are from West Asia.

    Here's some data I've gathered from online sources. I only have data from Near East, Caucasus, Iran, SC Asia, East Europe, and Sweden so far. Not all samples were tested at the same coverage.

    Basal R frequencies


    The string of R*(xR1, R2a) in Asia should be ignored because it is probably R2(xR2a), some might be R* who knows. There's a single R(xR1) from East Finland which might be R*. The only legitimate R* is a single sample from Kyrgz(Central Asia), it was negative for R1 and R2. The only R1, that is negative for basal forms of R1a and R1b, are from Oman in SW Arabia, Pakistan, Iran, and Ukraine(xR1a1a, R1b1a, could be R1b1c). Early forms of R1 are absent from Caucasus, India, SC Asia.

    2.7% of Iran Y DNA is of Basal forms of R1, R1b, and R1a1. And it's spread-out and not restricted to one of the three. You don't see this anywhere else in Asia and not in East Europe. The only other locations basal forms of R1, R1a, and R1b are found that are probably not R1b1c/R1b1a1 is in Pakistan(R1, xR1a1a, R1b1), NW Caucasus(R1a1, xR1a1a), and Ukraine(R1, xR1b1a, R1a1a). I have very little data, I think most importantly from Volga/Ural Russia and North Asia, but with what I have R1, R1a, and R1b basal forms are most popular in Iran.

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    The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known. Modern men are modern men, after all, not throwbacks to some bygone era. I think one has to look not to odd one-offs here or there but to where the major splits seem to have occurred. Better yet is to look at where the oldest ancient y-dna is showing up.

    Of course, the fact that these small "basal" results are showing up in Asia is no surprise really, since that is where the member clades of Super Group K are found all within relatively close proximity to one another.

    I think Mal'ta Boy turning up in Siberia near Lake Baikal is an important clue.
    Last edited by rms2; 10-17-2015 at 03:39 PM.

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    "The R1b1 and R1a1 from Mesolithic Russia are dead-lineages. IMO, there's a high possibility both M417 and L23 are from West Asia."

    The Karelian guy is only ancestral to M417. But I don't read Haak as ruling out the possibility of M417 also originating in that general area. I'm not sure whether the R1a's from Serteya have been fully analyzed or not. So unless you have some very good reason (other than a lack of data), excluding the territories north and west of Khvalynsk as potential R1a-M417 seems premature. There's been hardly any testing.

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    If you haven't already Krefter, check out Di Cristafaro et al.'s data for Central Asia (including Afghanistan). Some interesting Y-DNA R parahaplogroups emerged there. You could also check Arunkumar et al. for any South Indian R parahaplogroups, or the several SNP-confirmed papers done on Pashtun Y-DNA since 2012. I wouldn't bother using STR-only papers for this purpose (parahaplogroups behave strangely in subclade predictors for obvious reasons).

    The standard caveat regarding the fallacy of assuming modern population distributions can be reverse-transposed onto the past. The directional nature of time means the past generally explains the present and not vice versa.

    In the case of Iran, it's been apparent to me for some years that the Iranian plateau (and adjacent regions) are currently particularly rich in Y-DNA R parahaplogroups (my own R2a-M124 appears to be one of these for now).

    One possibility I anticipate may emerge is the derivation of early Y-DNA R1 across the steppes via HG's, with a few wayward branches happening to reach places like Iran, Afghanistan or Tajikistan in prehistoric times. Some of these lines may well have remained further north in Central Asia and then brought into these regions by European steppe derived populations.

    There's several explanations accounting for the Iranian R parahaplogroups which don't require an actual origin in Iran. At face value, their presence does not immediately agree with the aDNA we have so far (Mal'ta, various Neolithic and Mesolithic European steppe results). Some have proceeded to conclude the European steppe is the cradle of all things Y-DNA R1. In the absence of West Asian aDNA and the lack of an empirical explanation regarding the Iranian-Central Asian Y-DNA R parahaplogroup situation, that is a premature conclusion. There is no rational argument in favour of crystallising this view at present ("absence of evidence isn't evidence of absence" alone determines this).

    Having said that, the convenience of Y-DNA R* (Mal'ta), R1a* (Karelian HG), R1b* (Samara HG) and several R1a and R1b subclades residing on the steppes clearly makes this the favoured working scenario for now. All options are on the table until we have more data.

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    Quote Originally Posted by rms2 View Post
    The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known. Modern men are modern men, after all, not throwbacks to some bygone era. I think one has to look not to odd one-offs here or there but to where the major splits seem to have occurred. Better yet is to look at where the oldest ancient y-dna is showing up.

    Of course, the fact that these small "basal" results are showing up in Asia is no surprise really, since that is where the member clades of Super Group K are found all within relatively close proximity to one another.

    I think Mal'ta Boy turning up in Siberia near Lake Baikal is an important clue.
    I agree. The basal R1 branches in Iran for example are not proving much and I don't see how R1a-M417 or R1b is from West Asia especially when R1b and R1a were the dominant markers of EHG which were genetically between WHGs and ANEs so just an East European or maybe West Siberian origin makes sense for these PIE clades of R1a and R1b. We don't need to make it more complicated than it is is and R1 is obviously from Siberia/ the mammoth steppe.
    Last edited by Coldmountains; 10-17-2015 at 04:36 PM.

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    Quote Originally Posted by DMXX View Post
    . . . The directional nature of time means the past generally explains the present and not vice versa . . .
    Super quotable line! One of the best I've seen in a long while. I'll probably plagiarize it frequently.

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    Quote Originally Posted by Coldmountains View Post
    I agree. The basal R1 branches in Iran for example are not proving much and I don't see how R1a-M417 or R1b is from West Asia especially when R1b and R1a were the dominant markers of EHG which were genetically between WHGs and ANEs so just an East European or maybe West Siberian origin makes sense for these PIE clades of R1a and R1b. We don't need to make it more complicated than it is is and R1 is obviously from Siberia/ the mammoth steppe.
    Autosomal component associations aren't reliable.

    Before the aDNA era, some users on another forum found there was a "positive correlation" between the "Mediterranean" component of several ADMIXTURE calculators with R1b-M269.

    The conclusion was made that R1b-M269 was brought into Europe via a different, more "southerly" route than R1a-M17. A year into the aDNA era, I don't think that's even a minority view right now, even if some circles were firm proponents of it.

    For the sake of preventing another "house of cards" scenario, we'd be better off ignoring auDNA associations and focus squarely on SNP-guided MRCA calculations using a combination of ancient and modern samples.

    This is a matter of uniparental phylogeny, after all. What better way to answer Y-DNA questions than with Y-DNA data?

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    Quote Originally Posted by rms2 View Post
    The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known.
    "Basal" means it branched off before the main clade. It doesn't mean it is frozen in time. This is normal biological usage, e.g. one can refer to sea squirts as basal chordates, even though they are modern species that split from vertebrates many hundreds of millions of years ago.

    So no, this is perfectly correct usage, and the clades are truly basal. If some people are confused and think "basal" means "ancestral and unchanged", then educate them.

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    Quote Originally Posted by DMXX View Post
    Autosomal component associations aren't reliable.

    Before the aDNA era, some users on another forum found there was a "positive correlation" between the "Mediterranean" component of several ADMIXTURE calculators with R1b-M269.

    The conclusion was made that R1b-M269 was brought into Europe via a different, more "southerly" route than R1a-M17. A year into the aDNA era, I don't think that's even a minority view right now, even if some circles were firm proponents of it.

    For the sake of preventing another "house of cards" scenario, we'd be better off ignoring auDNA associations and focus squarely on SNP-guided MRCA calculations using a combination of ancient and modern samples.

    This is a matter of uniparental phylogeny, after all. What better way to answer Y-DNA questions than with Y-DNA data?
    Yes but I am talking about Mesolithic/Neolithic autosomal and Y-DNA , which is quite good correlating to each other. EHGs and Neolithic Farmers had totally different autosomal and Y-DNA for example but today autosomal and Y-DNA is not so good correlating with each other among modern populations. Ancient populations were genetically more homogeneous and their Y-DNA was often closely linked to their autosomal DNA (but of course not in every case).In the case of steppe R1b/R1a we see that EHG males lacking West Asian ancestry belonged to the same haplogroups and that later with the arrival of "teal" autosomal and mtdna PIEs became West Asian shifted so it is very unlikely that PIEs got their R1 from West Asia. But some R1 entering West Asia from the EHG steppe or Central Asia could of course very early exist there.
    Last edited by Coldmountains; 10-17-2015 at 05:06 PM.

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