Limitations of current genetic models

This map may help to put some (though not all) of Brotherton's findings into context:
Enceintes_MK_EAA_copie.jpg

It comes from an on-going joint French-German research project on the Michelsberg Culture (MK), ca. 4,300-3,600 BC, which followed on the Rössen culture in Western Germany and Northern France. The MK core is shaded bluish, its contact zone with neighbouring cultures (including Middle Elbe/ Saale to the east, marked yellow as MK/TRB) is highlighted. In Brotherton's chronology, MK corresponds to late Rössen - Schöningen - early Baalberge [Central European Neolithic chronology is an absolute mess, every author and every regional school appears to use a specific terminology and time scale, which makes it quite difficult to identify common patterns on a larger geographical scale].

Several (all?) of the settlements (triangles) may be interpreted as early cities - one of the best known and researched is the Glauberg north of Frankfurt. The Michelsberg near Karlsruhe, a 10 ha summit plateau, after which the culture was named, is another example.
http://en.wikipedia.org/wiki/Michelsberg
http://en.wikipedia.org/wiki/Glauberg

Two other large and fortified settlements were Halle-Döhlauer Heide, and nearby Salzmünde. They are represented by the two yellow triangles inside the dotted square around Halle, near the eastern end of the map. The Salzmünde earth walls encircled an area of 40 ha. As already indicated by the names (old German "Hall"=salt, see also "Hallstatt"), both places were important centres of salt extraction and trade. The same, btw, applies to other places that have lent their names to local cultures such as Bernburg and Schöningen (Schöningen is most likely the black "Rössen" star NNW of Halle, just on the border between Lower Saxony and Saxony-Anhalt). The earliest evidence for salt boiling north of the Alps (ceramic evaporation vessels, so-called briquetage, see photo below) was found in Halle-Döhlener Heide. Northern Saxony Anhalt is still today the most important salt production area inside Germany. Salt springs are indicated in white. The map also shows important Neolithic flint mines, including Lousberg near Aachen, and the recently discovered Bottmersdorf mine near Mansfeld in the Elbe-Saale region (though it does not include the Upper Bavarian mines near Kelheim, a bit SW of Regensburg).
25154659913.jpg


The on-going French-German research project tries to establish whether the MK evolved around a hypothesized central axis "Ile de France" - "Mosel" - "Rhein-Main-area (Glauberg)" - "Erfurt" - "Halle/ Saale" (shaded in pink on the map). It will pay special attention to tracking longer-distance trade, especially of salt, in this respect. Let's see what they will find out...

Glauberg is the burial places for the "royal" celtic chiefs ......IIRC this place has been excavated for more than 10 years

Nobody1 earlier in the year mentioned a new post from glauberg...IIRC 27 skeletons where found
 
@Angela

Do you have any links to papers that show radiocarbon dated HG sites that post-date the arrival of the Neolithic in the area? How many of them are there in relationship to the Neolithic sites? Is there other data that, in your opinion, would indicate that there were substantial numbers of WHG remaining in the area?

I haven't had a lot of time and this thread fills up with interesting responses. However, I feel I have an obligation to answer this as I, as an amateur, so pretentiously have called for attention to these cultures. I initially learned about from Dutch archeology books, books that I have all currently packed as I am moving. The original Vlaardingen finds, from a culture that seems related if not similar to Swifterband, are on display in Leidens museum of antiquity. They consist of a number of well preserved fish traps and a lot of freshwater fish remains. This is therefore not inconsistent with continuing mesolithic HG's using freshwater fisheries for sustenance.

The original Swifterband find is described in the link below and in the first map with an overview of Swifterband finds you again see them concentrated around freshwater systems.

http://dissertations.ub.rug.nl/FILE...evriendt/thesis_Izabel_Devriendt___proe_1.pdf

But you want dates off course, in order to check the impact of coexistence. This might be interesting: Hoge Vaart being a typical Swifterband site. Actually, on slightly more than a day's walk distance from the Swifterband site.

www.academia.edu/1231539/Radiocarbon_dating_of_Mesolithic_open-air_sites_in_the_coversand_area_of_the_north-west_European_plain_problems_and_prospects

There is quote in it that indicates something happened to HG's though:

The reliability of these samples for dating Mesolithic sites is corroborated by more than 404 dates for the Netherlands (Niekus 2005–6) and about 25 for Belgium (Van Strydonck andCrombé 2005). Except for a few isolated dates, all belong to the Mesolithic, with a sharp decrease during the Final Mesolithic (Swifterbant Culture) from c. 5800 bp onwards (Niekus2005–6). From then onwards, and during the entire Neolithic, hearth pits occur only very incidentally (Groenendijk 1987; Hamburg and Louwe Kooijmans 2006).
 
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@FrankN

In other words: The original, simple LBK design has survived with Germanics, while areas further south that had gotten under Celtic influence changed it. Shifting the load-bearing function from the central posts to the walls allowed to build higher (two-storey) and better-lighted houses, which also consumed less ground space. Since that innovation never reached the Germanics, they must have adopted the original LBK design rather early, at latest during the Bronze Age.

Dutch farms are similar. But there are local differences

A farmhouse called "Saksische boerderij", Saxon farmstead. The difference between the examples you give and these is that these regularly have the frontdoor on the small side.

Vragender_dorp.JPG


The Frisian type, which seems to be a worked out version of the former but is not considered a "hallenhouse":

800px-West-Beemster%2C_Jisperweg_130.jpg


and

1024px-Stjelp.jpg


The Frankish type, a clear "hallenboerderij":

800px-Gevel_-_Oirschot_-_20171901_-_RCE.jpg



And, just as in Germany, in the original LBK settlement area the farmhouses have changed considerably. Frams consist of houses around a central yard. The "carréboerderij":

800px-Sibbe-Dorpstraat_45_%284%29.JPG
 
@FrankN,
I don't think this is quite the thread for a detailed discussion of Lazaridis et al, and I'm very pressed for time as I'm about to go on “sabbatical” for about a six to eight week period, but I don’t want it to appear as if I am ignoring your post, and, frankly, I am loathe to let what I consider serious misunderstandings of the paper stand for those who may not be very familiar with autosomal analysis.

(I want to extend my apologies to Aberdeen and the moderators for continuing this hijacking of this thread. Please feel free to remove both of these extended posts about Lazaridis et al to a more appropriate venue.)


So, to begin, you stated that I misrepresented the findings of Lazaridis et al. Having said so, it would have been helpful if you had pointed out specific examples where I did that. I think I have been pretty scrupulous about quoting specifically from the text, and rather cautious about extrapolating from it.

As to the validity of the analysis itself, Lazaridis et al is a ground breaking study of the peopling of Europe. I hold it in high esteem, and it seems I am in good company, as 72 of the world's leading population geneticists have signed on as "contributing" authors, including Brenna Henn, Mark Thomas, George Busby, Christian Capelli, Toomas Kivisild, Joachim Burger, Wolfgang Haak (from the group that produced the paper we are discussing) to Qiaomei Fu and Svante Paabo. I hardly think they would have put their names to it if they thought there were serious methodological problems with it. Then, of course, there are the listed co-senior authors, Johannes Kraus and David Reich, although I’m sure as senior authors they have no problems with the conclusions of their own paper. If you wish to pit your expertise in population genetics, the new statistical algorithms that have been developed, and the new statistical tools created to assist in this analysis, that’s of course your prerogative. Far be it from me to suggest that the validity of a study should be determined by an appeal to authority.


The following are just a few thoughts from my non-professional population geneticist’s, “ lay person's” , perspective on the paper and the various tools used in the paper, a lay person who has, however, been reading autosomal analyses and papers since the publication of The History and Geography of Human Genes by Luca Cavalli-Sforza in 1994, (a book that is still invaluable as a primer in this area), so I have, I hope, some familiarity with the issues.

You state that you are concerned that the results from the ADMIXTURE software analysis are not valid because there are not dozens of samples from each population group. More samples are always better. However, autosomal DNA is not like uniparental DNA. There has been so much "mixing" that, from what I have seen, you don't need a lot of samples to get a statistically reliable number for a certain area. There are analyses that address this issue, but I don't have the time to search for them right now. Just as a simple example, there are numerous sample sources for Tuscans. One has 7 samples (HGDP), one has 20 (Hap Map 3) and one has 100 individuals in it (1000 Genomes Project). There is virtually no difference in the autosomal analysis results. For another example, again from the Italian population, the results for the people in the Bergamo HGDP sample are almost identical to the garden variety Northern Italian participants in Dienekes' Dodecad sample.

(Also, to your point about uniparental markers, they are good for tracking individual migration movements, but they are very poor indicators, particularly in the case of yDNA, of autosomal make-up, as I would think you would know. There is the often cited example of some pastoralists in western Sub-Saharan Africa who carry very significant amounts of R1b, and yet they are autosomally practically indistinguishable from surrounding non R1b tribes. Particularly as to your point about the ancient genomes, Loschbour is I2a, and La Brana is “C”, a haplogroup we now associate with eastern Asia. Yet, they form an autosomal cluster. )

Further, as to your point about the analysis with ADMIXTURE, if you re-read the paper and the supplement, it might refresh your recollection as to the fact that the Admixture software is just [FONT=&quot]one [/FONT]of the tools they used to reach their conclusions. They also used PCA analysis, f-statistical analysis and ADMIXTUREGRAPH, unsupervised Mix Mapper and Tree Mix software, plus IBD analysis and chromosome painting analysis to arrive at their conclusions.
.
Now, would it have given the consumers of the paper more information if more populations were tested? The answer is yes, of course. That doesn't invalidate the results, which state broadly that "these analyses allow us to infer that EEF ancestry in Europe today ranges from ~ 30% in the Baltic region to ~90% in the Mediterranean, a gradient which is also consistent with patterns of identity by descent sharing (IBD)(S118) and chromosome painting (S119)”

Those patterns would indicate, in my opinion, that the area from Czechoslovakia (which [FONT=&quot]was[/FONT] tested-.495 EEF), west through Germany and the Netherlands to Britain(which was also tested and had exactly the same EEF score-.495) hovers around a 49-50% rate on average, a fact that is borne out in the results from the calculator, with the number dropping a few points in far northern Germany from what I recall. (Although I have criticized that calculator, Central Europe, going by the correlation between the calculator results and the study results, is not one of the geographic areas of concern. ) Ukrainians score .46, by the way.


Of course, it’s unfortunate that more western and northwestern European populations were not included. I’m sure that they will be included in the future, since, as the authors speculate, that may be why their PCA does not exactly duplicate those of some prior studies. However, that is one, and not a particularly good tool, so this doesn’t in any way invalidate the findings of the paper or the percentages of these ancient genomes that show up in modern populations. It just means we don’t have the figures for some modern European populations.

From the figures that are provided, there seems to be a very narrow range in terms of these scores across the northern European plain and into at least part of the British Isles, which goes from about .46 for Ukrainians for EEF to about .49 in Britain. The number for EEF starts to increase in France, where a more northerly sample is .554 , but France_South is already .675 EEF. The EEF number of about 50% in Central Europe jumps to .715 in northern Italy, .713 in Spanish_North, .712 in Bulgaria and then to .745 in Tuscany, .81 in the Spanish etc. and so on. This all makes total sense in terms of prior autosomal analyses of modern Europeans.

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. Even since the period of the Indo-European migrations, you have the “mixing” that took place in this region as the result of the Germanic migrations, the Slavic migrations, the numerous wars like the Thirty Years War, the migrations brought about by industrialization, and then the dislocations of the First and Second World Wars. Many of these events did not impact populations in Iberia and the Italian peninsula to the same degree. If you've read all the pertinent papers, and followed the personal results as well, I don't understand how you can fail to see this pattern.

For those who have not seen them, these are some graphics of PCA’s based on autosomal results for Europeans that I think nicely illustrate the point:

http://upload.wikimedia.org/wikiped...tic_structure_(based_on_SNPs)_PC_analysis.png

http://2.bp.blogspot.com/_Ish7688voT0/R6Nt4XlfrwI/AAAAAAAAAFA/NzaQHAnUOvI/s1600-h/pc300k.jpg



http://s21.postimg.org/6pawkhkjb/russiangwafig3.png



You also make some statements that I think are very off the mark, given the reading that I have done on this subject. Why on earth, for example, would it be surprising that Icelanders have an EEF component? They are a mixture of settlers from Norway and Ireland, both areas that received genetic input from Neolithic farmers. (Norway has an EEF score of .41 and Scotland has an EEF score of .39. This makes the Icelandic score of .394 perfectly plausible.) The Neolithic farmers also spread to South Asia (a recent paper explored it in depth) and, yes, Africa, in the form of pastoralism, with some speculation that it's connected to the Cushitic speakers, as per your comment about the Afars of Ethiopia, who are pastoralists who indeed speak a Cushite language. Perhaps you haven't gotten around to reading the papers showing a large Southwest Asian autosomal component in Horner populations, some of which could indeed have entered their genomes with such a migration? Ukrainians also have, of course, an EEF component, as do far NWestern Russians, but the latter so called “ Volga Russian” population is a heavily Siberian admixed population, so their numbers will, of course, be quite different. You may also not be aware of the detail that the Algonquin, Cree and Ojibway are some of the most heavily European admixed populations among all Amerindian groups. There is speculation as well that they have a somewhat differential gene flow as shown by their levels of mtDNA “X”. These are all known relationships genetically speaking.

I also don't quite know how to respond to your complaint that Lazaridis et al doesn't tell us the fate of the WHG in the various areas of Europe. (Although they do, contrary to your assertion, speculate that the perhaps 20% WHG in EEF is attributable to the Mediterranean HGs. They obviously need ancient samples from them to be sure. Also, they did indeed try to fit the SHG into the model, but the statistical analysis refuted it.)


This is an incremental process...as more ancient data becomes available, from Mediterranean HGs, from Ancient Near Eastern farmers, from the first farmers in the Balkans, indeed, from Mesolithic samples in the Balkans, from Samara and from the new groups entering the Balkans around 3500 BC, I’m sure this group will adjust their analyses, just as they adjusted their findings as published in Moorjani et al in the Patterson et al paper.

The fact remains that, properly understood, this is a quantum leap forward in terms of genetics population studies, and, from what I have seen, is accepted as such in the academic and hobbyist communities.

For those who haven’t been tracking the analyses produced by the Reich Lab, I would suggest reading the following papers in the listed order:

Moorjani et al: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001373
Patterson et al: http://www.genetics.org/content/early/2012/09/06/genetics.112.145037.full.pdf
Lipson et al: http://arxiv.org/pdf/1212.2555v2.pdf

The following improvements in statistical analysis appeared in these papers:


  • Reich et al, 2009 (Indian Cline; introduction of f-statistics)
  • Green et al, 2010 (Neandertal genome; introduction of D-statistics)
  • Durand et al 2011 (elaboration on D-statistics)
  • Meyer et al, 2012 (high coverage Denisova; enhanced D-statistics)
  • Pickrell et al, 2012 (Khoisan origins; use of admixture LD with 1-ref)
  • Reich et al. (2012 (Native American origins; multiple waves of admixture)

The following tools were used in the following papers: Patterson et al (ADMIXTOOLS), Loh et al (ALDER), and Moorjani et al (updates to ROLLOFF)


I would also recommend a careful reading of Ralph and Coop:

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001555

To explore in detail what happened to the hunter-gatherers in each area of Europe, their number, where and when the admixture with farmers took place, whether it was from HG's who remained in place, or from later repopulation from the north, or with the Indo-European migrations, wasn't the [FONT=&quot]purpose [/FONT]of this paper. On the most basic level, what it is showing is that the genes of the WHGs (Loschbour and La Brana) appear in the genomes of modern Europeans in certain percentages. The same applies to the genes of the Stuttgart sample and the ANE sample. (And the Gok sample and Oetzi himself cluster with Stuttgart) The purpose of the paper is to show that the populations of [FONT=&quot]Europe[/FONT], not the Middle-East, can best be modelled as a mix of three ancient genome clusters. Other admixtures, when more ancient samples are available, are possible. I can't see how they can be faulted for not answering every detailed question we have about every minor as well as major migration flow and extinction that has taken place in a particular area of Europe over the last thousands of years.

Your comment about them "throwing out" certain groups also shows a fundamental misunderstanding, in my opinion, of this analysis. First of all, the Ukrainians can indeed be fit with the three population model. The Finns, the Mordovians, and the Volga Russians cannot, because they have, in the case of the Finns, for example, according to other autosomal analyses, [FONT=&quot]at least[/FONT] 5-6% "Eastern" admixture. (Siberian/East Asian, the percentages differing slightly by analysis) They weren't "thrown out". Nor were the Sicilians and the Maltese thrown out. They're all still Europeans. It's just that unlike all other Europeans, they don't fit the model because they have too much "other" admixture, which in the case of the Sicilians and Maltese is not yet properly understood, by the way. Said another way, they are not a statistical fit as a combination of Neolithic farmers from the Near East, Western Hunter Gatherers, and an ancient North Eurasian population that is also ancestral to Amerindians. The fact that the model doesn't fit a few groups at the periphery of Europe doesn't mean that the model is invalid. It [FONT=&quot]is[/FONT] valid for the vast majority of Europeans.

I don't have the time to address all your points, nor is this the thread for it, but I think I've posted enough to show that I strongly disagree with your analysis. People will have to make up their own minds after reading all the pertinent papers.
 
I haven't had a lot of time and this thread fills up with interesting responses. However, I feel I have an obligation to answer this as I, as an amateur, so pretentiously have called for attention to these cultures. I initially learned about from Dutch archeology books, books that I have all currently packed as I am moving. The original Vlaardingen finds, from a culture that seems related if not similar to Swifterband, are on display in Leidens museum of antiquity. They consist of a number of well preserved fish traps and a lot of freshwater fish remains. This is therefore not inconsistent with mesolithic HG continuing freshwater fisheries

The original Swifterband is described here, and in the first map you also see it concentrated around freshwater systems.

http://dissertations.ub.rug.nl/FILE...evriendt/thesis_Izabel_Devriendt___proe_1.pdf

But you want dates off course, in order to check the impact of coexistence. This might be interesting: Hoge Vaart being a typical Swifterband site. Actually, on slightly more than a day's walk distance from the Swifterband site.

www.academia.edu/1231539/Radiocarbon_dating_of_Mesolithic_open-air_sites_in_the_coversand_area_of_the_north-west_European_plain_problems_and_prospects

There is quote in it that indicates something happened to HG's though:

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. :)
 
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.
 
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 :)
 
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/ccc?key=0ArJDEoCgzRKedGR2ZWRoQ0VaWTc0dlV1cHh4ZUNJRUE#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/y-chromosome-haplogroup-q-and-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.
 
@Angela: Here is what I said:
@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!
Haplogroup-I2b.gif

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.
doggerland5.png
 
@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):

Paleografie%20Laat-atlanticum%205100%20j%20gel.jpg


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")

Paleografie%20Subboreaal%203000%20j%20gel.jpg



EDIT: http://www.historischekringdebilt.nl/bodemonderzoek/geologie/nederland.html
 
"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
 
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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.
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...
 
@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.


 
@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.
 
"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.


 
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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