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Thread: Limitations of current genetic models

  1. #26
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    Once people start discussing the more academic aspects of autosomal analysis, etc., I find it best to sit back and read, rather than showing my lack of background in the more esoteric aspects such stuff by commenting too much. But I think that in critiquing such material, it's useful to go back and remind oneself of what the author was and wasn't addressing. And I think it's also useful to remember what certain terms mean - for example, although the early European farmers came to Europe from the Middle East during the Neolithic, we all know that EEF doesn't equate to modern Middle Eastern Farmers, because of genetic changes in that area since the Neolithic. However, knowing that and keeping it in mind are sometimes two different things.

    I do think that some of the discussion of Lazaridis et al that has appeared in this thread so far is useful and on topic up to a certain point, but any further analysis of that material might be more useful in a separate thread devoted to that subject. And while I certainly find the lesson material on modern German and Dutch farmhouses to be fascinating, I'm not sure how relevant it is to the thread. A similarity of design with Neolithic structures may mean continuity of of design, but it could also simply be a demonstration of the fact that people who have similar problems to address often create similar designs without continuity. (I think only the Atlantis crowd would argue that the similarity between Egyptian and Mesoamerican pyramids showed a flow of cultural continuity between the two areas.)

    The main issue I want to address is that, even if one accepts the view of the authors of the paper that the specific locale shows that the current pattern of mtDNA H in the area was already primarily set 6000 years ago and was only somewhat affected by Bell Beaker and the Bronze Age folk (and I don't agree), that still tells us nothing about Europe as a whole. And yet the paper does appear to be extrapolating on that basis. So even if you agree with its conclusions for that specific area, so what?

    I hope you enjoy your vacation, Angela. But I'll miss your learned and well written comments.

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    Quote Originally Posted by Angela View Post
    Thanks for the links, Epoch, and I will definitely read them carefully. Unfortunately, I won't be posting much, if at all, for the next 6-8 weeks. Perhaps when I return, if this is still being discussed, I can add my two cents. :)
    Go away. There is a lot more in life than posting on the internet: Go and enjoy it :)

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    Quote Originally Posted by FrankN View Post
    Unfortunately, no. All that I have is the Lazarides study with the Supplemental Information. I browsed it again, but it seems they only published admixture estimates (WHG/EEF/ANE) for Europeans. There are quite a number of hints on the transatlantic gene flow scattered across the various supplements, ...
    I don't doubt it. That topic has piqued my interest for some time now. I read Stanford and Bradley's book "Across Atlantic Ice" and have since made lots of posts on the Solutrean Hypothesis thread further down here in this "Ancient DNA Studies" sub-forum. My current thinking is that there may have been three separate waves across the Atlantic in prehistoric times. There are lots of hints out there in this DNA data world. For instance, in this ADMIXTURE breakdown for k=13: https://docs.google.com/spreadsheet/...ZUNJRUE#gid=24 it lists a sample of 17 Mayans as being: 96.9% Amerindian, 2.1% Mediterranean, 0.8% North European, and 0.2% Siberian. There's also this paper: http://dienekes.blogspot.ca/2013/08/...nd-native.html that has found ydna Q1b in Central and South America. There's an interesting discussion in the comments on that article, where a commenter says that the closest STR match is from Morocco. It might be a stretch to suggest that a Q1b once had those Mediterranean/North European/Siberian admixture proportions, but you never know - La Brana was ydna C. Sorry to go off topic there.

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    2 out of 2 members found this post helpful.
    @Angela: Here is what I said:
    Quote Originally Posted by FrankN View Post
    @Angela: I think you (and possibly a few other posters) are over- or misinterpreting Lazarides findings. Or, maybe I better say: Amidst the various highly interesting results Lazarides has delivered, serious methodical flaws of his work tend to be overlooked.
    And you are correct - I shouldn't have used the word "misinterpreting", it put a wrong notion to my post. I also shouldn't have addressed that remark specifically to you - it was actually geared towards a number of "conclusions" from Lazarides drawn by various posters, and I lumped your position together with others, which was unfair. My apologies!

    I nevertheless stand to the second sentence. There is neither a need to be a genetic expert for that, nor for in-depth technical discussion - Lazaris et al. are pretty open themselves on various methodological shortcomings, as put forward in their Supplemental Materials No. 10, 12, and 14. I just intended to sum up these shortcomings for those here that haven't taken the time to look through all the Annexes.

    The main problem is the model itself. A three-way mixture model implies the following:
    1. There has only been one North-Eurasian population inflow. As you state yourself, that is against everything we know about Russians, Chuvash, Finns etc.
    2. There has only been one population inflow from the Near East. Well, their admixture analyses clearly point at two such inflows, one Levantine, and one Caucaso-Gedrosian. Existence of these two, different flows seemed to be generally accepted before they published their study.
    3. There only has been one European LGM refuge. That would actually have been worthwhile to be examined. Unfortunately, they haven't. Instead, they overloaded their population sample with Iberians and Western Mediterraneans, which automatically pulled the European HG towards the Cantabrian refuge [The problem with the sampling sizes is not the reliability of the results for each country/ region. The problem is that all of the various methods that are used try to find the best fit to all samples. And if over 25% of all samples are from Spain or Sardinia, but 0% from Central Europe (figures taken from p.77 of their Supplemental Analysis), you get a result that fits well in the Western Mediterranean, but not necessarily elsewhere.]

    But, didn't they prove that their three-way mixture works? Look at their Supplementary Information 12 (p. 88):
    The finding of at least 4 ancestral populations is seemingly at odds with our modeling approach which assumes 3 populations, so we sought to determine the cause of the added complexity. We removed each of the populations of R in turn and repeated the analysis over all 23 subsets. If the 4th ancestral population has largely affected only one of the populations in R, the evidence for four populations should disappear or greatly weaken when one of the affected population is removed.
    We find that the P-value for rank 2 remains <10`\ for 22 subsets, but for the subset R-{Spanish} it becomes 0.019, which is not significant after correcting for multiple hypothesis testing.
    (..)
    A different approach is not to start with the full set of populations, but to choose a “small” R as:
    R = {Belorussian, Bulgarian, Croatian, Czech, English, French, Hungarian, Icelandic, Norwegian, Orcadian, Sardinian, Scottish}
    This set of populations includes members of the main south-north European cline (Fig. 1B), and avoids most Mediterranean and Baltic populations where there may be more complex history involving Near Eastern, African, or East Eurasian ancestry.
    (..) We find that rank 1 is excluded (P < 10-12), and thus there must be at least 3 source populations related to the outgroups even for this restricted set of European populations (Table S12.3)
    What they have proved is that one can fit the 12 populations above into a 3-way WHG / EEF / ANE split. For these 12, the model is valid. For all the others, it is at best a statistical not significant hypothesis, at worst not tested at all.

    So, what happens when you try to squeeze six (maybe seven, a bit from North Africa seems to also have reached the Western and Southern Mediterranean Europe) admixtures into three groups? You end up with some strange proxies that try to combine 2-3 fairly unrelated components into one "hyper component". And suddenly, Sardinians are the prototypical EEF. Stupid as I am, I always thought yDNA I2a1a to be an indicator of WHG from the Cantabrian refuge...

    Why do I think that neglecting Central Europe might be problematic? Well, wasn't it you who just told us a few days ago that Tuscans are quite different genetically from other Italians? The map below (btw pertinent to the original focus of the thread) indicates where, in the absence of autosomal data, I would expect to find elevated HG concentrations - for example in the Middle Elbe- Saale region, or in northern Sweden. Both are places that are not too far away from Motala!

    If there had been a Black Sea LGM refuge, I would also expect some autosomal traces of it to still pop up, maybe in Moldova or Romania (both not sampled). Getting from the Black Sea by boat to the Baltic Sea and then into Central Sweden shouldn't have been that difficult for a Mesolithic HG (actually, the Baltic Sea wouldn't even have been there initially). In fact, it is probably much easier to get into Central Sweden from the Black Sea than from Cantabria. Unfortunately, Lazarides et al didn't investigate whether there may have been more than one European LGM refuge, so this is all speculative.

    I would be absolutely shocked if there is much difference in the scores for people from different areas on the Northern European plain. That would be contrary to every result I've ever seen from personal or academic autosomal genetic analysis of these groups. There is a great deal of homogeneity in this area, which crosses national borders.
    Do you have a link to these analyses (especially, of course, to any relating to the Elbe-Saale region and its periphery)? What I have seen so far for Germany (but data is pretty scarce) doesn't at all point to homogeneity, but to strong regional differentiation (and mind you, not all of Germany, and also not all of the Elbe-Saale region, is on the Northern European Plain).

    Anyway, enjoy your holiday. I don't expect an answer now, we can continue discussion when you are back.

    @Aberdeen:
    And while I certainly find the lesson material on modern German and Dutch farmhouses to be fascinating, I'm not sure how relevant it is to the thread. A similarity of design with Neolithic structures may mean continuity of of design, but it could also simply be a demonstration of the fact that people who have similar problems to address often create similar designs without continuity. (I think only the Atlantis crowd would argue that the similarity between Egyptian and Mesoamerican pyramids showed a flow of cultural continuity between the two areas.)
    I think we are trying to establish whether there has been some kind of population inflow between LGM and Bronze Age, and from where. Our knowledge of the middle- and late Neolithic is pretty thin - just look at Maciamo's migration maps for that period (hint: There aren't any!) Wikipedia is also a mess in that respect - sometimes the region in question is MK, sometimes stroke-ornamented culture, sometimes Lengyel, sometimes TRB, and when you start checking German papers, it gets even messier (among others as the region was divided by the Iron Curtain, and West and East German archaeologists obviously didn't communicate much with each other during that period) So the main message of the study seems to be: "Hey guys, something important has been going on during that period that we all have overlooked so far, but we also don't really have a clue what that could have been".
    I am trying to figure out what might actually have happened. And since I am better in looking at houses than in looking at pot sherds (and also think houses may tell us more about how the people lived and where they might have come from), I thought I place a kind of baseline here. Whether housing changed, and in which way, and if any of that will really be meaningful - no idea yet..

    The main issue I want to address is that, even if one accepts the view of the authors of the paper that the specific locale shows that the current pattern of mtDNA H in the area was already primarily set 6000 years ago and was only somewhat affected by Bell Beaker and the Bronze Age folk (and I don't agree), that still tells us nothing about Europe as a whole. And yet the paper does appear to be extrapolating on that basis. So even if you agree with its conclusions for that specific area, so what?
    First of all, the study never claimed to speak about Europe at a whole, they speak about Central Europe. But if some major, so far largely unnoticed change has been going on in a region that somehow is being linked to all other major cultures from Normandy to Eastern Poland, and down to the Danube, some of that change should also have affected those related cultures. And those people with new and additional mtDNA H must ultimately have come from somewhere..

    @epoch: Thanks for the links. The first paper seems to indicate that the main sites near the Ijsselmeer were submerged sometimes around 4,300 BC. You don't happen to by chance have seen any maps on changes of the Dutch North Sea coast over that period? Those Doggerland maps only date to 9,000- 5,000 BC, and are anyway a bit speculative and with little detail about the continent. While there is quite good German cartography tracing land loss since the 2nd century AD, I haven't yet found any research or modelling on the times before.

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    Quote Originally Posted by FrankN View Post
    @epoch: Thanks for the links. The first paper seems to indicate that the main sites near the Ijsselmeer were submerged sometimes around 4,300 BC. You don't happen to by chance have seen any maps on changes of the Dutch North Sea coast over that period?
    5000 year ago (Purple is peat):



    3000 year ago (A lake starts to appear. The name in the Middle Ages of the expanding lake was "Almere", all lake. After a while it turned to a estuary, then a sea, the Zuiderzee. After this was dammed parts were reclaimed which is why they made the finds. Currently one of the new cities in these polders is called "Almere")




    EDIT: http://www.historischekringdebilt.nl...nederland.html

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    "I would be absolutely shocked if there is much difference in the scores for people from different areas on the Northern European plain. That would be contrary to every result I've ever seen from personal or academic autosomal genetic analysis of these groups. There is a great deal of homogeneity in this area, which crosses national borders."

    The I2a2 hotspot on the DNA map above would be the Harz mountains so just south of the Northern European plain.

    edit: above may be an unwarranted assumption, see post below from FrankN
    Last edited by Greying Wanderer; 12-07-14 at 02:53.

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    Quote Originally Posted by Greying Wanderer View Post
    "I would be absolutely shocked if there is much difference in the scores for people from different areas on the Northern European plain. That would be contrary to every result I've ever seen from personal or academic autosomal genetic analysis of these groups. There is a great deal of homogeneity in this area, which crosses national borders."The I2a2 hotspot on the DNA map above would be the Harz mountains so just south of the Northern European plain.
    That's where the problem starts. The hotspot on the map would actually be south of the Harz, in Thuringia, somewhere around Erfurt. Several non-scientific German texts talk about the hotspot extending from the Harz northwards to around Luneburg. I have been looking for more details for quite some time already, but it seems this is al based on the old study by Rootsi et al (2004), which also (at least not the main body) doesn't give specific information on the sampling area, but instead just comes up with a map showing the European hotspot somewhere in Central Germany. Harz of course sounds good, because the Lichtenstein cave is located nearby (though neither to its south, nor to its north, but to its west).http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181996/

    Anyway, after Rootsi, it appears that nobody has again looked systematically into the I2a2 distribution inside Germany. The regionalised studies that I have seen typically lump all yDNA I together, which isn't really helpful, as I1 is of course very common in Northern Germany (and, btw, also not really homogenically distributed over an east-westerly cline, say Central Ukraine to Paris basin). A recent comparison between German border regions and Poland shows I2a2 at 2% in Bavaria and 5% in Mecklenburg, that's about it.

    I don't know whether it is any better in the Netherlands - Rootsi has them at 10% I2a2, Underhill (2007) at 5.4%, but Maciamo in his map appears to have only used the second figure. Now, one might think that such a difference between two studies could indicate quite a differentiation inside the Netherlands, but I am not sure if anybody ever looked into it...

    For the Czech republic, I have seen figures ranging from 1% (Rootsi) to 6.4% (Underhill). I guess it all depends how near or far away your sampling locations are from the "big river" (Elbe, Rhine) and/or loess plains, but that's just a guess...

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    @FrankN

    "The hotspot on the map would actually be south of the Harz, in Thuringia, somewhere around Erfurt. Several non-scientific German texts talk about the hotspot extending from the Harz northwards to around Luneburg."

    Ah, that was just me assuming then.


    "Now, one might think that such a difference between two studies could indicate quite a differentiation inside the Netherlands, but I am not sure if anybody ever looked into it..."

    Yes I wonder if prior assumptions effect this more generally? If a researcher's premise is this dna migrated from somewhere else (and maybe a lot of it did) then the exact current distribution might not seem to matter much. However if a researcher is looking for possible indigenous survival in specific likely areas then the precise location of hotspots of specific clades matters a lot.



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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Greying Wanderer View Post
    @FrankN

    "The hotspot on the map would actually be south of the Harz, in Thuringia, somewhere around Erfurt. Several non-scientific German texts talk about the hotspot extending from the Harz northwards to around Luneburg."

    Ah, that was just me assuming then.


    "Now, one might think that such a difference between two studies could indicate quite a differentiation inside the Netherlands, but I am not sure if anybody ever looked into it..."

    Yes I wonder if prior assumptions effect this more generally? If a researcher's premise is this dna migrated from somewhere else (and maybe a lot of it did) then the exact current distribution might not seem to matter much. However if a researcher is looking for possible indigenous survival in specific likely areas then the precise location of hotspots of specific clades matters a lot.


    That's exactly the question I wanted to bring up. As British and Irish are much more into individual DNA testing than Germans (or central Europeans in general), we now have a pretty good picture of yDNA differentiation inside the British isles, and it has turned out that patterns are far from being homogenous or following simple geographical clines. The same is becoming apparent in the Alps. As to I2a-Din, what was once assumed to be a West Balkan pattern has now been shown to have specific concentrations on Dalmatian islands and in some valleys in Herzegovina and SW Bosnia, while I2a-Din is far less present along the Danube. If researchers started to look into the Carpathians, or the Massif Central, at a geographic resolution similar to the one that has already been used in Spain and Italy, I wonder what they would find.

    That leads of course into a general problem. Big cities tend to be excluded for methodological reasons (you ideally want your test sample to have been resident in the area for at least three generations). Depending on the country in question, this implies that something like 50-70% of the current population are a priori excluded. That's ok as long as one assumes that mobility is unrelated to genetics, but is that really the case? Mobility has to do with education, with has to do with parental professional background, which may relate to socio-economic patterns that already have been established long ago. Then there is the issue of mining, which has a millennium-long tradition in several of the areas that have been studied intensively (Sardinia, NW Spain, Bosnia-Herzegovina), or not that intensively (Harz, Erzgebirge, Carpathians). Field-crop farming along the rivers vs. specialised tree-crops (viticulture, olives etc.) vs. transhumating cattle-herding vs. fishing? We are starting to getting some glimpses of a possible differentiation, especially on the Balkans, but so far, systematic evaluation hasn't been done. However, when looking at the archaeological record, the assumption that EEF would rather go into field-crop farming, while HGs might switch towards cattle herding or specialise on fishing is anything but implausible.

    We are rightfully happy about any ancient DNA coming in. But do we really know which "culture" that DNA may be assigned to? All available evidence points to Ötzi the Iceman not being an EEF, but engaged in metal exploration and/or trade. A spectacular "royal grave" with lots of precious artefacts is uncovered next to simple collective burials. Surely the local leader. But, take for example the Amesbury Archer, who was born somewhere in the NW Alps. Was he really the local leader, or rather a long-distance trader, who happened to die far away from his home, and was buried together with all of his belongings since there were no relatives nearby to claim the heritage? Unlikely that a stranger will be given an exquisite burial? Check out this case from the High Medieval:
    http://en.wikipedia.org/wiki/Nicholas_the_Pilgrim

    In summary - while we all agree that more DNA testing, and especially of ancient DNA, will be required, we may still be much too confident about the state of knowledge that apparently has already been achieved. What we have so far consists of relatively regionalised DNA data around the Mediterranean and on the British Isles, but comparatively poor sampling of central & eastern Europe, which excludes cities (including those that have been existing already for millenniums). The data is analysed under the assumption of homogenous regional clines, without paying attention to (pre-)historic economic specialisation of the sampled regions. That analysis is combined with ancient DNA that is again just grouped according to simplified geographical and economic criteria (Med / West/ North; HG vs. EEF). And ultimately, we are applying the results of this genetic analysis to an archaeological record that is far from being complete, especially when it comes to the middle and late Neolithic.

    I realise that I have been getting a bit off topic again - maybe we should open a new thread for a general discussion on the limitations of current genetic models. Let me also add that I in general prefer an incomplete model to not having a model/analysis at all. I am grateful for all those new studies, including the Lazarides one, but we need to be aware that much more work may be needed until we arrive at a half-way complete picture.

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    1 out of 1 members found this post helpful.
    "So I had the impression that mtDNA should follow autosomical DNA more than Y-DNA."

    These kind of mismatches can provide clues to what happened. IIRC there are countries in South America (Argentina?) where the mtdna is largely native while the autosomal dna is largely European. This is a result of multiple waves of mainly male migration so the first wave marry native women resulting in 100% native mtdna and 50/50 autosomal but then as further male migrants arrive some of the mixed women marry mixed men and some marry the new arrivals. Over time the European autosomal percentage keeps going up while the percentage of native mtdha stays the same. In theory a situation like that could eventually lead to 100% native mtdna and 90%+ European autosomal.



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    Quote Originally Posted by LeBrok View Post
    That's pretty high level of "contamination". Can't wait for Ancient Near Eastern sample to clean up this issue. I think there might be some EEF farmer gene flow in Loschbour WHG admixture. It would be a surprise if Loschbour was completely pure Hunter Gatherer at 6k BC, only 150 km and 500 years from Stuttgart farmer.
    why would it be so surprising, Lebrok?
    6000 BC is old enough - the 2 pop's didn't melt together so easily - agriculture didn't take a huge place in N and NW Europe before about 5000/4500 -
    let's remember Michelberger-"neolithical"-s had seemingly a strong remnant of mesolithic genes

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