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Thread: How it was all clear from the beginning

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    How it was all clear from the beginning

    In this post, I will talk about R1b and how the truth about it could have been deduced many years ago and is now more and more being confirmed by ancient DNA. If you all remember, early studies seemed to give more attention to frequency rather than diversity and for this R-M269 was once believed to have been the genetic signature of the very first Europeans due to its high concentration in the western portion of the ''continent'' and especially among the Basques whose language was thought to be a remnant of the first paleolithic Europeans.

    However, the data back then was already clear in that it was not supportive of this agenda-driven scenario. Looking at the various haplotypes of R-M269 from all around Europe, it was clear that the clade lacked in diversity but you could only know it if you actually cared to compare the data with that of Haplogroup I and especially I2. Looking at I2, it was possible to notice how it was made up of multiple distinct branches represented by different modal haplotypes and with much more internal diversity, indicating the haplogroup's more ancient diversification. On the other hand, the different divisions within R-M269 not only somewhat lacked in diversity but also more often than not did not have distinct modals and thus could not really be distinguished on the basis of Y-STRs, the main tool we had back then. This off course meant that no long bottleneck events led to those branches and that R-M269 instead differentiated quickly into its various sub-clades, in a starlike fashion. That was of course indicative of a more recent expansion and clearly very far from being in agreement with the absurd belief that it was Cro-Magnon's line.

    All of the above was of course confirmed when the SNP revolution happened in the beginning of the current decade and when ancient DNA emerged. Even shortly before that, there were new theories proposing a neolithic arrival together with other allegedly neolithic lines from the Near-East and many people switched to this scenario. This was when papers started to become increasingly obsessed by diversity, not yet knowing that it is rather basal diversity that is more important since Y-STR diversity on itself could be misleading, especially when not understood properly. The diversity of M269 in Armenia and Anatolia made a lot of people think that this was evidence for this new scenario. But if the time aspect was now closer to the truth as it was no longer question of Cro-Magnon or any absurd stuff along those lines, there was more to it if one payed enough attention. Europe also had its big share of basal R-M269, and R-L23(xL51) looked rather european and was all over the place. Gioiello made countless efforts trying to persuade people about the role Italy played in the evolution of M269 and R1b as a whole, but most people didn't want to listen, despite him being very insightful. People cared more about their own personal conviction and opted for either a neolithic arrival or a link with the diffusion of indo-european languages.

    However, the data was also not in favor of any of that, which further shows how fast are people, be them actual scientists or not, jumping to conclusions. No matter how people tried to ignore Italy and Europe, the fact remained that there was definitely something of great importance over there and someone had to provide a sound explanation. The indo-european migrations didn't make sense and were easy to dismiss for it was recorded that not only ''basque'' but quite a few pre indo-european languages were spoken in Iberia not so long ago. Or were these people thinking that all of iberian M269 came with the Celts or the Romans ? Very silly indeed... The near-eastern theory was also very speculative, nothing indicated that M269 could be from there, its distribution as well as internal structure are not similar to other clades that were thought to have diffused during the neolithic. It was primarily because of R-V88 that people insisted on this otherwise poor scenario. Indeed, everyone was of the opinion that V88 entered Africa from the Levant because that was the most obvious route. But did it really make sense that various clades of R1b would have migrated from the Near-East at very distinct times without the Near-East preserving any initial diversity even though - given that M269 and V88 are fairly divergent from each other - it stayed there for many thousand years and that instead each branch migrated to very different places (M269 to Europe, M73 to the north into Eastern-Europe/Central Asia and V88 to Africa) and during different eras, without being associated with other clades along the way ? At least in my head, it always looked very unlikely that R1b was ever in the Middle-East.

    If you really looked close enough, there was more to R-V88 than this very simplistic scenario. Browsing through the data made it clear that there was something european about V88. Its presence in many regions across the ''continent'' (Italy, Balkans, Iberia, British Isles...) was certainly against some kind of african diffusion. V88 in Africa has a ''chadic'' diffusion, not maghrebi. Even if it came from the Maghreb, how come it made it to so many places then and why would Sardinia have this elevated frequency of almost 3% and have specific non-african sub-clades ? This was without even looking at the diversity, for which european V88 seemed to have much by looking at the haplotypes. When we came to know more about R-V88's phylogeny, it of course became obvious that it is Europe and not Africa which harbored basal lines and thus was its most likely place of origin. I was and still am from the view that it entered Africa from Italy since it is more common there and is very rare in Morocco (about 0.2%) and almost non-existent in more western areas of Africa thus making an iberian route very unlikely, whereas it is relatively common in Tunisia, Libya and Egypt (roughly 2% or more each) making it more likely that it quickly went to the south following ancient libyan rivers from there until it reached lake Chad. Today we know from Yfull that this is a nicely fitting model since the TMRCA of sub-saharan V88 corresponds to the intense aridification process associated with the 5.9 kiloyear event. Quite frankly, the near-eastern scenario never made sense...

    But apparently, all of this was not enough to convince the majority of people. Now when ancient DNA came into play and that R-M269 failed to show up in various neolithic remains, most people became even more clueless. The followers of the near-eastern neolithic origin quickly switched their minds and started adhering to the indo-european arrival from the East, especially when it appeared in Yamnaya, not acknowledging that V88 is most likely european thus not being concerned with the fact that Europe/Italy have basal representatives for both V88 and M269, which would be a little bit too coincidental to happen through unrelated migrations to Italy. Hey but they had R-M73 to back them up in their claims right !? Here comes the most interesting part which should end the debate. Indeed, the sister-clade of R-M269, R-M73, would appear eastern to the unfamiliar observer given that it is mostly diffused in central Asia and even managed to reach much farther east as far as western China. Well, that's only true for one of its two sub-clades, R-M478, which is further divided in two. The first cluster, now known as R-Y14051, is lacking in diversity due to a more pronounced bottleneck and can easily be spotted by a multi-step deletion at DYS390 for which it has a value of 19, while the second cluster, now R-Y20750, is more diverse and ancient. M478 as a whole seems to be associated with turkic speaking people and is almost completely absent in Europe.

    But here is what most people are not aware of : R-M478 has an european brother. And not only european but western european. This R-M73 sub-clade is definitely not linked to any turkic migration or whatsoever, as it is not seen outside of western Europe, where it is found everywhere albeit at low frequencies. While it is now merely a shell of its former self, YHRD used to be a great tool for allowing the user to search for haplotypes in their massive database, with more than 7000 samples from Germany, 4000 from Poland, 2000 from Czech republic, 5000 from Iberia and so on. Thanks to it, I've found a lot of stuff and this, coupled with FTDNA, was what enabled me to see just how widespread and above all very diverse this sub-clade is. Hopefully it has a distinct enough modal to be identified, you just had to enter the three main discriminating values [DYS438=10, DYS392=13, DYS393=12] and then add a couple more to narrow down the possibilities such as DYS390=25. YHRD will then give you every corresponding haplotype and neighboring haplotypes (which are one mutation away from what you entered). Doing a few searches, the haplogroup showed up in a bunch of different regions within western Europe, reaching even previous associated colonies. It is found as far south as Portugal where it is also represented by a small cluster with DYS390 = 9 that also made it to Brazil, and as far north as Mecklenburg in northern Germany ! Everywhere in western Europe but never in the east, not even in Poland, with the easternmost case I know of being czech ! As can also be observed at FTDNA, its diversity is kind of high and I estimate its expansion time to be around 5000 years old. It happens to be concentrated just north of Italy : in the alpine mountain range of Switzerland and Austria, where it is found at about 0.3 - 0.5% on average. So we are again brought to the same area, an area which seemingly played a major role in the history of R1b no doubt (for example, remember the concentration of R-L23* in Switerland was known for many years).

    But I guess some could argue that pre-M73 was found in a hunter-gatherer from Samara, dating from about 7.6 kya. I wonder what actually made them think that M478 and M73 are equivalent SNPs while they're not as I've just told you about this non-M478 european cluster ! So the case from Samara is pre-M478 and now we know that M478's MRCA lived some 7.3 kya and would thus represent an eastern migration of M73. I'd estimate european R-M73* to have diverged from M478 about a thousand years earlier or two, putting the overall TMRCA of R-M73 at around 8-9000 years. We would need a sample submitted to Yfull to refine the estimate.

    So here is what I wanted to say : that everything was already clear, but only if you cared enough to dig extensively through every piece of data made available. It was clear based on all the above observations that Europe, especially the area around Italy/Switzerland, was very important to understand R-M269 and even R1b as a whole, pointing to some kind of alpine refugium. Back then, while not defined by any SNP yet, even the much rare sub-clades such as R-L389(xP297) and the basal R-L278*/PH155 could easily be noticed to also have european representatives. Now that we have a better understanding of haplogroups thanks to the SNP revolution, we can estimate ages with much more accuracy and it just so happens that most R1b sub-clades expanded at similar dates centered at about 7500 years ago, thus indicating a more or less common bottleneck in support of a refugium scenario. With ancient DNA, it is now case closed I think, with V88 popping up everywhere in Europe, taking away any last hope from the proponents of an extra-european coalescence. R1b, while clearly not the first european haplogroup, is not of neolithic or post-neolithic arrival either : it occupies an intermediate position between the two claims. It was already clear from the start and if you're not convinced, I suggest you re-read all of the above.

    But it was not clear for people who rushed to conclusions to support their own convictions. I cannot believe that the likes of Davidski spend a lot of time dealing with different charts, graphs and statistics but are still clueless. I've noticed that many people are saying that modern DNA is not informative, and it is not informative when you refuse to admit that Y-DNA K2 is south-east asian and instead argue that it's central asian, or think that E is not african... Lesson to be learned : never underestimate modern DNA and study every hidden bit of it while staying objective if you really want to discover the truth, else prepare to get your own little world destroyed when ancient DNA is given the right to speak.
    Last edited by Squad; 02-01-2018 at 02:27 PM.

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    Quote Originally Posted by DeathStranding View Post
    Yeah K2 is most likely south asian or southeast asian, however E is clearly non african, or at least originated in a population that was more related to eurasians compared to sub-saharan africans. Considering natufians did not look phenotypically like negroids/Sub-saharan africans at all and had no admixture from them either, while still carrying E old clades. Same with IAM in North africa, no SSA admixture and they didnt look black/ SSA in phenotype.

    Kostenki makes me wonder if there is some australoid substratum in modern Europeans.
    That's not even the intended purpose of my R1b post, but clearly non-african you say? Show your evidence then. The ONLY E sub-clade with non-african representatives is E-M35. I never understood how come people base themselves one one very downstream sub-clade to infer the origin of E as a whole. Even worse than that is that E-M35 itself is mostly african ! No one talked about modern sub-saharan Africans, they have nothing to do here as it is obvious that if the population which gave rise to CT was separated from B ''paleo-Africans'', the east-african population that was responsible for the spread of E would be closer to eurasian pops than to ''paleo-Africans''. People should stay objective and stop trying to distance themselves from Africans for a while !
    Last edited by Squad; 02-03-2018 at 04:40 PM.

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    Amusing as usual. I wonder what else in genetics is a conspiracy against the truth. First J1 and now R1b. To what you said about V88 I can agree slightly.
    Last edited by mephisto; 02-03-2018 at 07:41 PM.

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    Did I just read that E-M35 is European in origin? Now that's comical
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    Quote Originally Posted by mephisto View Post
    Amusing as usual. I wonder what else in genetics is a conspiracy against the truth. First J1 and now R1b. To what you said about V88 I can agree slightly.
    Many things I'd say. What I wrote about R1b actually is based on extensive research and observations and seems much closer to the truth, and now with ancient DNA it is becoming more and more obvious. What I specifically said regarding R-M73 is the most overlooked/hidden fact and the most important at the same time. As for J1, my concern was with its sub-clade J-P58 and also its parent L136, rather than the whole haplogroup.

    Quote Originally Posted by Tz85 View Post
    Did I just read that E-M35 is European in origin? Now that's comical
    Who said so ? In case you are referring to me, I said that out of all haplogroup E sub-clades, E-M35 is the only one which has some non-african representatives.
    Last edited by Squad; 02-03-2018 at 08:36 PM.

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    Quote Originally Posted by DeathStranding View Post
    Yeah K2 is most likely south asian or southeast asian, however E is clearly non african, or at least originated in a population that was more related to eurasians compared to sub-saharan africans. Considering natufians did not look phenotypically like negroids/Sub-saharan africans at all and had no admixture from them either, while still carrying E old clades. Same with IAM in North africa, no SSA admixture and they didnt look black/ SSA in phenotype.
    The only Natufians whose craniofacial traits I've seen tested did actually show a "Negroid" shift:

     


    This is why some chaps online were shouting from the roof-tops that Lazaridis et al. didn't notice SSA autosomal input in them because, as even the Lazaridis paper noted, some expected them to show such ancestry because of the small amount of craniofacial data (about 4 samples, I recall). And I still don't get how some think them not showing ancestry akin to modern non-Eurasian admixed SSAs while carrying E-Z830, a single subclade of E-M35, somehow informs on the overall origins of E as a whole or why this even matters. E originated around 65,000 years ago. It would pretty much date to a time when the lines between some African clusters and "Eurasians" were thoroughly blurred and still forming when the world was yet entirely inhabited by a relatively small number of Hunter-Gatherer bands that probably didn't even look substantially distinct phenotypically. Yet you still see weird folk projecting all this modern "Africa Vs. Eurasia" stuff into such a distant past. Quite odd... :-|

    Quote Originally Posted by DeathStranding
    Same with IAM in North africa, no SSA admixture
    Where are you getting this? The only results I recall from the Neolithic North-Africa pre-print on them were the ones shared in the supplementary and all I recall learning from those was that:

    * They have lowered Neanderthal ancestry.

    * They might be more basal than Natufians.

    * F-stats show they're much closer to Neolithic and Epipaleolithic Levantines than to various populations across Sub-Saharan Africa.

    * Their Fst distance from SSAs is comparable to their Fst distance from WHGs and EHGs. In fact, they're closer by 0.033 in this respect to Yorubas than to WHGs.

    Nowhere do I see a formal-stat test to confirm if they have some gene-flow from some Sub-Saharan groups when compared to Natufians, unless I've missed something? Even if they lack such admixture; they show a lot of it in ADMIXTURE and have a strong shift toward SSAs in the global PCA which, if this isn't direct recent East or West African-like ancestry, implies, in my humble opinion, that this could be caused by them being even more Basal-Eurasian than Natufians (who show similar but less significant shifts in ADMIXTURE and PCAs). So, we basically have our most Basal group yet and they're in North-Africa with a Fst distance closer to Yorubas than to WHGs... I wonder what that says to someone without an agenda about the possible origin place of Basal Eurasian (North-Africa?). I mean I think it could still be in West-Asia itself (the gulf oasis?) and I don't really care either way but we'll see.

    ---

    Anyway, sorry for having interrupted your thread with some OT content, Squad. As you were...
    Last edited by Awale; 02-04-2018 at 12:28 AM.
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    Squad, I think you're becoming one of my new favorite posters This place gets pretty dull honestly when there aren't interesting new papers coming out to stimulate disucssion.

    Back to the topic, if you're assuming a kind of mild Giollelo-esque position regarding R1b and the Alpine/Italian refugium, how do you envisage the correlation between the contemporary distribution of R1b in Europe and the Indo-European invasion?

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    Villabruna has bow been “promoted” to P297, making it the earliest attested on that line, and on the way to M269.
    However, I don’t think Italy was a refigium rather a relict Zone
    The main core of late glacial expansion was east Central Europe

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    The advantage the original post in this thread has it that it is too long. Most people, including me, don't want to read crap that long. I won't read long posts here unless they are from someone whom experience has taught me probably has something worthwhile to say, like Jean M, Generalissimo, or Alan, among a few others.

    But when "Squad", whom I'm guessing is someone who has been banned here before, said Gioiello was "insightful", that was it for me, I was done. Gioiello is a horrible anti-Semite and Italian chauvinist who lacks the sense God gave a piss-ant.

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    Quote Originally Posted by rms2 View Post
    The advantage the original post in this thread has it that it is too long. Most people, including me, don't want to read crap that long. I won't read long posts here unless they are from someone whom experience has taught me probably has something worthwhile to say, like Jean M, Generalissimo, or Alan, among a few others.

    But when "Squad", whom I'm guessing is someone who has been banned here before, said Gioiello was "insightful", that was it for me, I was done. Gioiello is a horrible anti-Semite and Italian chauvinist who lacks the sense God gave a piss-ant.
    Well, Squad whoever he is deserves a little less rudeness
    Anyhow, Jean Alan and all the Sibero-Steppe squad didn’t exact hit the nail on the about R1b, anyhow
    Last edited by Gravetto-Danubian; 02-04-2018 at 02:11 AM.

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