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Thread: Population genomics of Bronze Age Eurasia (Allentoft et al. 2015)

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    Quote Originally Posted by Mikewww View Post
    I think it is incumbent on those using SNP counting to estimate ages across haplogroups to show the evidence that SNP branch lengths have a precise linear relationship with time.
    After comparing the numbers of SNPs found in ancient samples (for example in those from Ust’-Ishim, Mal’ta and Anzick), it is obvious that there is a relationship between the number of accumulated SNPs and the age, and there is nothing indicating that this relationship is not linear. The more ancient samples are studied, the more confidence we will get that this relationship is indeed linear, although we will probably always hear some voices saying that not all time periods (or not all geographical locations) were tested so far, so there is still a possibility that the mutation rate strongly depends on some unknown factors that make our reconstruction of the deep past totally unreliable.

    Quote Originally Posted by Mikewww View Post
    A 30% difference over 3000 years could be cause for alarm of wide variability.
    It all depends on the mutation rate and on the extend of the Y-DNA region studied. If we focus on a relatively small region of Y-DNA (let’s say 1 Mb) where one reliable SNP arises only once in 1500 years (on average), then even the 200% difference over 3000 years should not be counted as really surprising. When analyzing the 10 Mb region, a 30% difference over 3000 years is still statistically insignificant, as long as we are comparing just two independent lineages (and not two large groups of independent lineages from different haplogroups of exactly the same age).

    Quote Originally Posted by Mikewww View Post
    There is a big difference between honing in on a 200-300 year period 4000 years ago versus honing versus honing in on the correct millennium.
    This is why we need to analyze a series of independent lineages for estimating the reliable TMRCA ages, and this is what YFull tries to accomplish, only that in some cases the number of available independent lineages is very low (which strongly affects the confidence interval), not to mention that they probably use a slightly overestimated mutation rate, but this cannot be definitely verified until more ancient samples (of good quality) are studied.

    Quote Originally Posted by Mikewww View Post
    Again, I still think SNP age estimation methods are very valuable, but the precision is a question mark. I haven't seen the scientific studies and rebuttals like I have with Y STR methods yet. I would consider that we have initial studies but not rebuttals and/or broad agreement.
    Please note that despite so many publications on the STR mutation rates, all those published (and unpublished) STR-based ages show many inconsistencies, and there is actually no general agreement regarding the usefulness of different approaches applied to produce the STR-based age estimates. In fact, most people don't trust those STR-based ages anymore, especially in all those cases when relatively old clades are considered. I can show you multiple examples of STR-based estimates that have been initially questioned by the first SNP-based estimates before being definitely discredited by the ancient DNA results.

    The fact that ancient Y-DNA samples are used with great success to significantly refine the Y-DNA SNP mutation rate makes the SNP-based method (especially for older clades) just a method of choice. Having said that, I don't think the STR-based estimates are not useful. Let me cite what I wrote elsewhere on this subject:

    Having two independent (though nearly equally reliable) ways of calculating TMRCAs (using either STRs or SNPs) would be a great thing, as in case of any coincidental aberration related either to significantly skewed SNP rate or to some unusual level of STR homoplasy, the other method will alarm us that something is going wrong (and thus we should apply a much larger margin of error than usually)
    Last edited by Michał; 07-14-2015 at 09:22 PM.

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    Interesting conclusion graphs from David on Eurogenes. Regarding bell beakers he states that bell beaker and corded ware are like twins except that the non-steppe genes they picked up differed and perhaps went back to the same source steppe population taking two different routes west.

    http://eurogenes.blogspot.co.uk/2015...ronze-age.html

    Certainly that could have parallels in the P312/U106 split albeit that Corded Ware seems to have a lot more R1a than R1b. Might make sense if they both arose in what had been a long term contact zone with each other - which might explain how some L11 derived got into the mainly R1a CW population. The elite strata of two populations with a tradition of friendly relations and marrying each others women could come to look genetically very similar after a number of generations. I have a strong suspicion that the R1a CW group and the L11 group were separate but long bordering populations with fairly close relations with each other. Its hard to place that anywhere other than the Dnieper-Dniester zone. What I dont know is whether the idea that south Poland as the area of genesis of CW is still safe or whether to look a bit east to the Middle Dniester. Regardless it does seem likely that any contact zone between the proto-CW R1a rich population and whoever was carrying L11 seems surely to have taken place at some place between those two rivers, probably actually one of the rivers. If the genesis of CW in south Poland is maintained that would seem to point towards the Dniester. Anthony believed in some sort of link to the origins of CW using that valley (albeit he was playing down migration). However, I would seriously wonder if the complex cultural mix along the Dniester around the couple of centuries either side of 3000BC is compatible with the genetic evidence from CW . I would tend to think that the Middle Dnieper would fit the genetic evidence from CW better than the Dniester.

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    Quote Originally Posted by alan View Post
    Interesting conclusion graphs from David on Eurogenes. Regarding bell beakers he states that bell beaker and corded ware are like twins except that the non-steppe genes they picked up differed and perhaps went back to the same source steppe population taking two different routes west.

    http://eurogenes.blogspot.co.uk/2015...ronze-age.html

    Certainly that could have parallels in the P312/U106 split albeit that Corded Ware seems to have a lot more R1a than R1b. Might make sense if they both arose in what had been a long term contact zone with each other - which might explain how some L11 derived got into the mainly R1a CW population. The elite strata of two populations with a tradition of friendly relations and marrying each others women could come to look genetically very similar after a number of generations. I have a strong suspicion that the R1a CW group and the L11 group were separate but long bordering populations with fairly close relations with each other. Its hard to place that anywhere other than the Dnieper-Dniester zone. What I dont know is whether the idea that south Poland as the area of genesis of CW is still safe or whether to look a bit east to the Middle Dniester. Regardless it does seem likely that any contact zone between the proto-CW R1a rich population and whoever was carrying L11 seems surely to have taken place at some place between those two rivers, probably actually one of the rivers. If the genesis of CW in south Poland is maintained that would seem to point towards the Dniester. Anthony believed in some sort of link to the origins of CW using that valley (albeit he was playing down migration). However, I would seriously wonder if the complex cultural mix along the Dniester around the couple of centuries either side of 3000BC is compatible with the genetic evidence from CW . I would tend to think that the Middle Dnieper would fit the genetic evidence from CW better than the Dniester.
    So you think R1b came via the Danube? And R1a through via the Dneiper?
    Modifying Anthony you would shift 3b further north-east?
    Fig. 1. The Proto-Indo-European homeland and the first three migrations, paralleling the phylogeny of Ringe et al. 2002
    http://www.jolr.ru/files/(104)jlr2013-9(1-21).pdf

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    Quote Originally Posted by parasar View Post
    So you think R1b came via the Danube? And R1a through via the Dneiper?
    Modifying Anthony you would shift 3b further north-east?
    Fig. 1. The Proto-Indo-European homeland and the first three migrations, paralleling the phylogeny of Ringe et al. 2002
    http://www.jolr.ru/files/(104)jlr2013-9(1-21).pdf
    I just feel that the way Anthony describes the interaction of Usatovo, TRB in the creation of CW (which appears to involve the Dniester) is not only clearly wrong but the genetics of CW seem not to fit the very noisy amount of cultures in that zone. I would expect a far larger old European farmer element in CW in that scenario. Even Usatovo itself looks a complex mix of steppe elite and C-T farmers. To me CW looks like it comes from a steppe group with the same prior ancestry as Yamnaya that also seems to have avoided the sort of heavy mixing with European farmers that you would expect in several of the western steppe groups like Usatovo, Kemi Oba, Lower Mikhaelovka, and others on the Dniester, at the lower end of the Dnieper, the north-west Black Sea coast etc. I tend to think CW looks like it was isolated from that. I wonder if it has links with Post-Mariupol on the east side of the Dnieper which retained more pure steppe type skulls compared to the cultures I have just mentioned.

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    by the way, the genesis of Yamnaya from late Repin and its inclusion of a Caucasus component makes perfect sense when one considers that the Don in immediate pre-Yamnaya centuries included Repin with the Maykop linked Konstantinovka culture just to its south on the Lower Don. They would have interfaced on the middle Don around 3500BC and some people think Maykop influence was important in the evolution of Yamnaya (metallurgy, wheels, rich mega kurgans etc). So, it makes perfect sense to me if the Yamnaya culture and its genetic mix arose from Repin on the Don with Konstantinovka relations and expanded east then west. One of the main thrusts of Caucasian influence seems to have followed the Don. However there seem to have been other influences nearer the Dnieper and Azov areas too.

    I just found this book online and it has some really handy summaries of copper age/Yamnaya on the steppes. It seems pretty recent judging by quotes and has some nice maps

    https://books.google.co.uk/books?id=...ulture&f=false

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    I think one should look to Northern Belarus and Russia for Corded Ware beginnings. We already have a few R1as there.

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    Quote Originally Posted by alan View Post
    by the way, the genesis of Yamnaya from late Repin and its inclusion of a Caucasus component makes perfect sense when one considers that the Don in immediate pre-Yamnaya centuries included Repin with the Maykop linked Konstantinovka culture just to its south on the Lower Don. They would have interfaced on the middle Don around 3500BC and some people think Maykop influence was important in the evolution of Yamnaya (metallurgy, wheels, rich mega kurgans etc). So, it makes perfect sense to me if the Yamnaya culture and its genetic mix arose from Repin on the Don with Konstantinovka relations and expanded east then west. One of the main thrusts of Caucasian influence seems to have followed the Don. However there seem to have been other influences nearer the Dnieper and Azov areas too.

    I just found this book online and it has some really handy summaries of copper age/Yamnaya on the steppes. It seems pretty recent judging by quotes and has some nice maps

    https://books.google.co.uk/books?id=...ulture&f=false
    it does strike me looking at the map of the many Yamnaya variants on page 14 that we already have Yamnaya DNA from at least two of the variants and, despite these being from almost opposite ends of the Yamnaya distribution and with several untested Yamnaya variants lying in between them, they are both Z2103. That is a major strike against people who see it as a broad horizon more than a migration. However, there is no way Z2103 can explain the IE languages in most areas so either there is a horizon aspect to Yamnaya or PIE pre-dates Yamnaya and indeed Repin because Repin doesnt have the sort of spread needed.

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    I'm afraid it's still too early to reach the "desired"(?)(:=)) conclusions... It's pretty obvious that Yamna is a cultural horizon rather than a unified culture. There are some pretty important differences between its variants and significant archaeologists refuse to see Repin as its single starting point or as a kind of "expander" group. So that is still very much open. As indeed is the Y-DNA signatures of the various Yamna groups. Lots of R1b's of course, but also I2a's (of the M-436 variety it seems). So one still cannot rule out the presence of R1a's (et al.) even on the south route. We must wait a little longer for answers to this and other questions.

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    Quote Originally Posted by Chad Rohlfsen View Post
    I think one should look to Northern Belarus and Russia for Corded Ware beginnings. We already have a few R1as there.
    I think there is a possibility that PIE needs to have commenced in a horizon shared by several steppe cultures and non just the Repin-Yamnaya grouping. It is possible that pre-Yamnaya networks such as the Skelya elites of the Sredny Stog culture (who controlled the supply of Balkans metal in the steppes) could be responsible for preventing dialect divergence in the way would would expect. Repin apparently emerges c. 4000BC or soon after from the easternmost area they controlled on the Don and is said to have at least significant Sredny Stog roots. However they are just one group who emerged from one end of the Sredny Stog horizon which extended to the Dnieper. It seems Repin leading to Yamnaya only became important when important influences started to reach them from Maykop related Konstantinovka culture who settled downstream on the Don c. 3500BC. I figure that was what over a few centuries essentially created the Yamanaya culture and the generic signature we see in Yamnaya east of the Don to date.

    The question is whether Yamnaya was the source of fully developed PIE or whether it was a subset of it. I am not convinced that knowledge of the wheel helps us distinguise between Yamnaya c. 3300BC and some other steppe culture who may also have got knowledge of the wheel (probably available from 3500BC) from a similar sources (influences from the Caucasus can also be seen further west In the Ukraine steppes (north of the Sea of Azov) but did not use it to develop classic Yamnaya mobile pastoralism.

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    Quote Originally Posted by Chad Rohlfsen View Post
    I think one should look to Northern Belarus and Russia for Corded Ware beginnings. We already have a few R1as there.
    certainly its very hard to see how the idea (based on RC dating) of it originating in southern Poland can be correlated with the genetic signature of CW found to date. A position further east somewhere like north-east Ukraine on the opposite side of the Dnieper from Kiev would seem logical. That is not so far from southern Belarus and part of Russia where R1a hunters have been found. My feeling at the moment if P297 derived R1b could go back to some very distance link to the hunting element who were adapted to dry southern and eastern Euro-steppe environments where hunting may have been based on chasing horses etc while R1a may have essentially during the hunting period got their hands on the better hunting lands slightly further north and west on the forest steppe area. However in Ukraine the steppe, forest steppe and forest areas moved up and downstream significantly over time as aridity oscillated and this meant people moved too as their adapted environment did - so its not easy to generalise.

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