tag:blogger.com,1999:blog-3023805782808412230.post6609007912290477333..comments2024-03-09T15:46:44.638+01:00Comments on For what they were... we are: Autosomal DNA of NE EuropeansMajuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.comBlogger35125tag:blogger.com,1999:blog-3023805782808412230.post-40467843171964228702013-04-20T11:59:38.335+02:002013-04-20T11:59:38.335+02:00If you read the discussion, beginning by the main ...If you read the discussion, beginning by the main entry, I have been arguing that endogamy/bottlenecks are distorting everything here especially because Finno-Ugrics are oversampled, so they begin coping most K levels (or eigenvector positions, same logic) very early on. This adds a level of cryptic difficulty to interpretation. <br /><br />So you have in account:<br />1. Sample size matters (a lot) because every individual sample weights the same<br />2. Distinctiveness or affinity are not absolute values but are often enhanced by endogamy and/or ancient bottlenecks, both factors which seem to be very important in the Far North, where population densities were always necessarily very low. <br /><br />So in fact Finno-Ugric peoples do cluster with each other at eingevector 1: they are all far to the left. Same with ADMIXTURE's K=3: they are all very high in the red component. But, because of their intrinsic peculiarities and the very large size of their sample, they cope eingeverctor 2 and it's ADMIXTURE equivalent at K=4. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-30519424665631899402013-04-20T09:00:00.924+02:002013-04-20T09:00:00.924+02:00Sorry, i meant on the right !Sorry, i meant on the right !France_LGChttps://www.blogger.com/profile/08169145428521942518noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-81033894410057384722013-04-20T08:57:22.170+02:002013-04-20T08:57:22.170+02:00As regard Figure3, I understand that we have the &...As regard Figure3, I understand that we have the "Average Europeans" on the left in the positive values.<br />What surprises me is that Uralic people do not seem to add up to a real group. Logically Komi people are closest to unmixed Finno-Ugric people, so it would seem that the Balto-Finnic people + "Arctic" pseudo-Russians are another population that was Uralicized.<br />Is this a possible scenario in light of data?France_LGChttps://www.blogger.com/profile/08169145428521942518noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-87801490102622213592013-03-18T19:27:17.609+01:002013-03-18T19:27:17.609+01:00I've read your detailed comment this morning a...I've read your detailed comment this morning and I've been chewing on it all day but I don't see anything on it that would not cause a highly endogamous set of similar populations, such as the dramatically oversampled Finno-Ugrics in this set, from dominating the vectors/PCs (or components in ADMIXTURE equally) easily: having low genetic diversity just weights a lot in creating a vector. <br /><br />I still do not understand well why that equation because I get for the various values:<br />· p(j)=0.9 → w(j)=3.33<br />· p(j)=0.5 → w(j)=2.00<br />· p(j)=0.2 → w(j)=2.50<br /><br />How can a relatively rare marker with a frequency of 20% weight more than a marker with a 50% frequency? Is this what you meant to explain above? I think so. Freaky algorithm this one! I don't find this correct because intermediate frequencies are punished against and that seems to distort the matter even more in favor of "freak" populations with extreme values. <br /><br />"And those scenarios with the high weight are what you would expect from an ancient contribution"...<br /><br />Not really. Any kind of "bottleneck" process can cause it. Actually ancient contributions should be more diluted in general (because of the "balming effect" of recent cosmopolitanism in most populations) while more recent bottlenecks, such as those caused by recent endogamous drift, are necessarily enhanced. <br /><br />So it's actually doing the exact opposite of what you expect. Maybe I should look more frequently at the algorithm definitions instead of just the results (I admit that integers scare me). <br /><br />... "heavily drifted populations largely have randomly lost markers, or have an unusual build-up of decently common (but not extremely rare) markers (if they were rare, then that is of significance even without subsequent drift)"...<br /><br />On the contrary: they will accumulate a collection of rarities because their whole genome tend to converge at highly accelerated pace towards variants that are rare in other populations. This is very obvious, for example, in the Sámi haploid DNA, concentrated (fixated) in few lineages shared with nobody else. Exactly the same happens in the autosomal DNA, just that SNP by SNP: p(j) values close to 1 or 0 will be the rule, not the exception among such heavily drifted populations (this of course also has effects in concentration rare illnesses as is known among Ashkenazim, for example, even if selection weights against them to some extent). Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-88004767991497788942013-03-18T09:59:54.922+01:002013-03-18T09:59:54.922+01:00Maju,
This is my interpretation of EIGENSOFT; hop...Maju,<br /><br />This is my interpretation of EIGENSOFT; hopefully this is at least roughly correct: <br /><br />The matrix elements are weighted with the function w(j) = 1/sqrt[p(j)*(1 -p(j))], where j is the SNP marker index, and p(j) is the allele frequency calculated as 1/2 of the average for that site. For autosomal data, a site can have the values 0, 1 (only one copy) or 2 (both copies carry the SNP). In the end, the square of the Matrix elements (after projection onto the eigenvectors) enters, so, roughly speaking, w^2 = 1/[p(j)*(1 -p(j))] is more relevant. Now, this is where the number of populations comes in: say, you have 10 different populations, and for simplicity, all populations are fairly homogenous. The most extreme scenarios are that only one carries the marker, and only once - or that all but one population carries the marker, but that one still once. Then p = 1/20 or 19/20 and w^2 ~20 in both cases - that is, the calculation is heavily weighted in favor of such scenarios. On the flip side, a case in which SNPs are all over the place in the different populations, say 3 have the marker twice, 4 once, and 3 don't have it, p = 1/2 and w^2 = 4, i.e., a factor 5 difference in weight. This weight difference keeps increasing with the number of (different) populations included, and increases with the number of individuals if the populations are not homogenous. So, if 1000 individuals are studied, in the extreme case, the weight can be 2000!<br /><br />And those scenarios with the high weight are what you would expect from an ancient contribution: an SNP left over but long gone in all comparison populations (individuals), or a rare new mutation, or not being part of a sweep. On the flip side, heavily drifted populations largely have randomly lost markers, or have an unusual build-up of decently common (but not extremely rare) markers (if they were rare, then that is of significance even without subsequent drift). Both such cases do not yield a high weight. In general, drift occurs at a rate sqrt[p(j)*(1 -p(j))] - that is, it occurs most swiftly at sites that receive the lowest weight in EIGENSOFT.<br /><br />This is what I base my claim on that properly weighted PC analysis is fairly insensitive to drift, but extremely sensitive to ancient markers or the lack of participation in sweeps and the like.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-51390937119017800832013-03-18T08:59:50.910+01:002013-03-18T08:59:50.910+01:00It's not the number of populations as much as ...It's not the number of populations as much as the number of individuals in each population and the distinctiveness of their genetic pool. Also Europeans are quite homogeneous, what does not help here: all but Italians (to some extent) are very similar (Poles, Czechs, Germans, mainstream Russians... all look about the same in the genetic analysis), both in ADMIXTURE as in the EV graph. Instead the pools of Finno-Ugric ancestry peoples are all very characteristic and that is, in this case, because of endogamy: a distorting effect hard to compensate for with such large numbers. <br /><br />"PC analysis also calculates higher components"...<br /><br />Sure but it's roughly the equivalent of deeper K-values in ADMIXTURE. I can tell you that the EV3 in this case shows a polarity defined by Central-East Europe, the yellow component (deduced from the ADMIXTURE data of course). Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-29699351839338160932013-03-18T08:48:18.776+01:002013-03-18T08:48:18.776+01:00Yes, having a good number of external populations ...Yes, having a good number of external populations is important - and there were eight, here, which is not bad: Italians, Germans, Czechs, Poles, Latvians, and three Southern Russians.<br /><br />PC analysis also calculates higher components - but many don't bother showing the results. I'd like to see at least PC3, best in a 3-D plot or as color or with "height markers." Then one can at least tell if there is useful additional information.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-18316452380206257342013-03-17T21:41:42.552+01:002013-03-17T21:41:42.552+01:00This you mention about a rather sharp distinction ...This you mention about a rather sharp distinction in the mtDNA pools of Finnish and Swedes is very interesting and agrees with my interpretation of the autosomal and archaeological data in my reply to Eurologist above. <br /><br />As for the difficult to understand origins of V among Sámi, etc. (which you mention in other comments) we must have in mind that bottlenecks, even in relatively recent times (very small numbers and extreme environmental conditions) seem to have shaped that genetic pool very intensely, with highly randomized results. This applies to all the Far North but maybe more to the Sámi than anyone else. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-6512956532690593432013-03-17T20:17:14.435+01:002013-03-17T20:17:14.435+01:00I completely forgot the Saami R1a! Finnish Saami h...I completely forgot the Saami R1a! Finnish Saami have only 4.5% of R1a, but Swedish Saami have 20% and Kola Saami 21.7%. Swedish average is 17%. Northern Norwegians have 27.1% and the Southernmost Norwegians only 13.2%, but I don't know their type and I have no idea whether they form a cluster of their own. <br /><br />Now I am wondering if Mtdna V that has extreme frequencies among Saami is somehow connected to an old type of R1a. According to Family Tree search (https://my.familytreedna.com/snp-map.aspx), there is an old Pan-European R1a1a M198 that is found also in Northern Norway. For example, Poles have a lot of pre-V Mtdna.<br /><br />Then, I noticed that the only R1a sub-cluster that might be old enough to be connected with Corded Ware culture in Finland, is R1a1a1b1a2 - Central Eastern European branch, Southern Baltic type. According to Family Tree, it forms a special Finnish cluster. Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-70709473673964432312013-03-17T18:05:12.437+01:002013-03-17T18:05:12.437+01:00As for my understanding of the Saami roots, forget...As for my understanding of the Saami roots, forget the "recent" geneflow from the Eastern Arctic area. If this Eastern geneflow (D and Z1a) is from Bol'shoy Oleni Ostrov, dated 3,500 uncal. yBP, it is not very recent! In this study of ancient Mtdna in North Western Russia, it is however pointed out that these Bol'shoy Oleni Ostrov people were not the ancestors of modern Saami people.Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-40142052127221122092013-03-17T15:38:58.440+01:002013-03-17T15:38:58.440+01:00As haplogroup H is very important around the Balti...As haplogroup H is very important around the Baltic Sea, I took a careful look at the median-joining networks found here:<br />Fig. 3 http://mbe.oxfordjournals.org/content/21/11/2012.long<br />Fig. 4 http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.2007.00429.x/full<br /><br />The root of H* seems well anchored in Carelia. The route of H2 (age estimate 11,000) to Finland seems to go through Eastern Slavs and the entrance is again through Carelia. It seems instead that Western H3 (age estimate 16,000) arrived in Finland through the Baltic region. Also the route of H5 seems to be Turkey - Eastern Slavs – Finland. Haplogroup H1 (age estimate 23,800) seems to be well anchored in Carelia, but looking at the map, it seems that it might have arrived in Finland from the East (even from Volga-Ural area where it has a high frequency). <br /><br />It is highly interesting that the first study says that ”in contrast to that found in Europeans, sub-Hgs H6 and H8 among Central Asian/Altaian populations are characterized by distinctly divergent haplotypes This finding may reflect a long-time separation of Asian and European H6 and H8 mtDNA pools and/or an earlier expansion of H6 in the eastern part of its present range. Indeed, the coalescence age of H6 in Central Asians is very deep—40,400 years.”<br /><br />As for Sweden, H2 may have arrived to Sweden through Poland - Germany (these countries are not included in the study, in the map there is only a Lithuanian circle). Based on Fig 4, you would say that H3 arrived to Sweden through Latvia, but the route through Germany is probably more plausible, as the haplogroup came from Iberia. H5 is quite rare in Sweden, and based on the map you would say that it came to Sweden from the Baltic region (Latvia-Estonia). H1 arrived in Sweden probably from the South, and also H1a and H1b, and in fact, these two sub-clusters are not found in Finland! In the median-joining network, I really was not able to find any case where a H-haplotype arrived in Finland from Sweden. <br /><br />As for the old U5a, I am not sure how to read the map. I am wondering if U5a is derived from U5b and if U5b has come to Finland through the Baltic region (Latvia). Anyway, the Saami motif U5b1b1 seems to have taken the Eastern route to Lapland through Carelia.<br /><br />I studied carefully also the instances of R1a in Finland (http://www.familytreedna.com/public/r1a/default.aspx?section=results) and noticed that for the most part, it arrived in Finland from the East, possibly through Carelia. This applies for Central European R1a1a1g1. This applies also for Carpathian-Russian R1a1a1b1a2. R1a1a1b1a2 - Central Eastern European branch, Southern Baltic type is found also in Northern Finland. R1a1a1b1a2d East Slavic I is found only in Carelia. The only Scandinavian R1a cluster is R1a1a1b1a3 - Scandinavian branch and it is also found in Russia.<br /><br />According to Wikipedia, ”the Corded Ware culture (in Middle Europe ca. 2900–2450/2350 cal. BC), alternatively characterized as the Battle Axe culture or Single Grave culture, is an enormous European archaeological horizon that begins in the late Neolithic (Stone Age), flourishes through the Copper Age and culminates in the early Bronze Age. Corded Ware ceramic forms in single graves develop earlier in Poland than in western and southern Central Europe, already 3000 BC.” The Corded ware culture arrives in Southern and South Western Finland from North Western Poland and the Baltic region in c. 2500 BC. By looking at the haplogroup routes above, you would say that at least part of ydna R1a must have arrived in Finland during the Corded Ware period through the Baltic area. I suggest that mtdna W arrived also from Poland during that period, as its highest frequencies in Europe are in Poland, Latvia and Lithuania. Also the majority of mtdna H3, I and T might have taken that route to Finland.<br />Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-13840114501413184982013-03-17T15:37:59.986+01:002013-03-17T15:37:59.986+01:00Eastern haplogroups, D and Z1a, were found at a 3,...Eastern haplogroups, D and Z1a, were found at a 3,500 year old burial site in extreme North (Bol'shoy Oleni Ostrov). Also U4a1, U5a and U5a1, T and C and C5 were found. I would say that Saami people combine recent geneflow from the Eastern Arctic area in an old Northern European population (Mtdna U5b and ydna I1, + ydna N1c). They lack all Neolitic or Southern haplogroups that Finns have, but they have a lot of Mtdna V, and I do not quite understand the route of this haplogroup.Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-73638861931503890812013-03-17T13:09:18.118+01:002013-03-17T13:09:18.118+01:00Now that I think of it, a reason why you may belie...Now that I think of it, a reason why you may believe that PCAs are "much less sensitive to drift / endogamy" could be that, normally, the two main PCs are not described by one such endogamy-caused polarity (as would be most commonly also with ADMIXTURE K=3 clusters, depending on sampling strategy always) but this is not any rule, just an accident caused by, in most cases, having ample and diverse samples, which define these poles/components on more realistic grounds. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-35366873268404246422013-03-17T13:05:40.774+01:002013-03-17T13:05:40.774+01:00If you look at the substance of the eigenvectors t...If you look at the substance of the eigenvectors they are identical to K=3 and K=4 components (after excluding the Chinese). EV1 shows the Italian vs. Finno-Ugric duality of K=3 (blue vs red) and EV2 shows the Komi-Izh vs Finns-Ku polarity (red vs purple at K=4). <br /><br />They are the same thing in essence, just that shown differently. The results are nearly identical. I don't have any reason to believe, as you suggest, that PC analyses are "much less sensitive to drift / endogamy". Never heard of that before and never noticed it in the many many PC/EV graphs I have seen in my life: they behave almost identically to ADMIXTURE/STRUCTURE analysis, just that with much lesser depth (2D, sometimes 3D constraint), what is a clear limitation. What ADMIXTURE-like analysis does is to add more and more dimensions until, if done properly, an optimal clustering level is reached. But both seem equally sensible to the distorting effects of highly endogamous populations - this AFAIK only depends on sampling strategy, which is the human factor. An astute analysis will seek to minimize these anomalies, if not in one analysis A, then in a complementary analysis B, by properly balancing the numbers of each of the populations studied in order to get a most realistic result and minimize endogamy-caused artifacts. A shallow one will not and that is a failure. <br /><br />Whatever the case this issue needs more research, that we do agree on.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-47298014360397121222013-03-17T11:29:12.418+01:002013-03-17T11:29:12.418+01:00Kristiina,
Thanks for listing that.
Do you suspe...Kristiina,<br /><br />Thanks for listing that.<br /><br />Do you suspect that Saami have <i>less</i> admixture with ancient local northerners (vs. Uralic Reindeer herders) than Finns (proper)in Finland?<br /><br />Of course there could be drift at work, again, but the percentages of V and Z are astonishing.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-66631911441991316392013-03-17T11:11:52.003+01:002013-03-17T11:11:52.003+01:00Maju,
Not to beat a dead horse, but I was talking...Maju,<br /><br />Not to beat a dead horse, but I was talking about the PC analysis - not ADMIXTURE. It is my understanding (but perhaps I am wrong?) that properly weighted PC analysis is much less sensitive to drift / endogamy. I mean, it is constructed such as to find and use the SNPs that are most meaningful to properly structure (find the highest correlation in) <i>all</i> populations in the study.<br /><br />And again, I don't doubt that drift is very important in this context - I just think that the PC analysis indicates that both the Finnish and Komi component directions are "real" in the sense that they point to an ancient connection rather than to some idiosyncratic drift of run-of-the-mill northerners over the past thousand years, or so.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-75267110745304360972013-03-16T17:20:11.110+01:002013-03-16T17:20:11.110+01:00The biggest haplogroups in Kainuu, Northern Finlan...The biggest haplogroups in Kainuu, Northern Finland are the following: H 37%, V 9%, U 36%, W 10 % and M 6% (in the whole country H 39.3%, V 5.1%, U 27.9%, W 10,1%, M 2.5%. Kainuu Finns seem to be admixted with Saami people, as Finnnish Saami have 37.7% of V and 15,9% of Z and D5. It is noteworthy that there is no difference in the amount of W and, in fact, the share of older haplogroup U is bigger in Kainuu than in the South. On the other hand, the share of H is bigger in the South, as is expected as the frequencies of H are in Estonia 41,1%, 35,2% in Latvia and 45,6 in Sweden (according to Lappalainen et al.)<br /><br />Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-41514394480261433302013-03-16T15:45:22.345+01:002013-03-16T15:45:22.345+01:00Okay, it is Nelis et al research! It seems that Sw...Okay, it is Nelis et al research! It seems that Swedes, Estonian and Russians are on the same plot while Helsinki Finns and Lithuanians are on the same plot and Kuusamo Finns stand apart. During the bronze age (and later?) there were close contacts between Southern Finland and Baltic area and there was surely admixture. Perhaps there were also very close contacts between Russians, Estonians and Swedes and these contacts were not unidirectional, initially there may have been more contacts and admixture from East to West and later on more from West to East.Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-16465281750914477312013-03-16T15:10:23.991+01:002013-03-16T15:10:23.991+01:00Eurologist, you say that half of the Helsinki Finn...Eurologist, you say that half of the Helsinki Finns are closer to Swedes (or Estonians) than they are to extreme Finns. Where do you get that, as I can't find Swedes in this reasearch?<br />Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-44481402632668637302013-03-16T15:03:45.505+01:002013-03-16T15:03:45.505+01:00Okay, Finns proper may have a small amount of rece...Okay, Finns proper may have a small amount of recent Swedish admixture, but it is probably Finland Swedes who have more. The haplogroup frequencies I listed above represent however whole Finland and not Helsinki Finns!<br /><br />Anyway, I do not know how this pool of Helsinki Finns is gathered in this Kruhmin et al research, but if there is a bigger share of Finland Swedes in this Helsinki component, then of course the difference between Kuusamo Finns and Finns proper is smaller than in this study. Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-74363406289993729902013-03-16T14:24:46.110+01:002013-03-16T14:24:46.110+01:00"And Swedes and Estonians are admixed with Fi..."And Swedes and Estonians are admixed with Finns, but Finns are not admixed with them?"<br /><br />First of all, some Finns do show a deviation towards Swedes, but it surely corresponds to recent times (Swedish occupation, Viking Era, admixture with Finland-Swedes). Second, I don't think that Estonians and Finns are admixed among them (at least not notably so) but rather that they share a common origin, at least partly. Third, Swedes are probably admixed with Finnic peoples other than Finns proper, more like Sámi. <br /><br />"What's the semantic difference I don't get, here?"<br /><br />Well, it's the same as saying that Mexicans are (natives) admixed with Spaniards but Spaniards are not (significantly) admixed with Mexicans. There's a difference and a quite clear one.<br /><br />"Half of the Helsinki Finns are closer to Swedes (or Estonians) than they are to extreme Finns".<br /><br />That's because Northern Finns seem to be not just less cosmopolitan but also a different (albeit related) population re. Southern Finns. Also "drift" (or endogamy) plays a role here: Southern Finns were for sure all the time a larger population and a more cosmopolitan one than Northern ones. <br /><br />"We know for certain that agricultural Swedes settled along the Baltic coast of Finland. Some still speak Swedish, there. Why is it so difficult to imagine that they intermixed?"<br /><br />I'm not rejecting that but that seems obvious only in a small fraction of Helsinki Finns who are divergent (and not too much) towards Swedes. It's anyhow likely that the impact of this recent admixture is more obvious in Finland Swedes than in Finns proper. <br /><br />"The main question to me is: was this originally a local Uralic population (probably not), or a local, extreme NE population that got elite-dominated by a Uralic-speaking population before becoming known as Finns (possible, IMO)".<br /><br />I suspect that the first (Epipaleolithic) substrate population of Finland was of Central-Eastern European origins but were later assimilated but Combed Pottery peoples arrived from further East, who spoke (proto-)Finnic and exerted a patrilocal centrality of some sort. Probably the "elite dominance" of this second wave was determined by "Reindeer Neolithic" (i.e. a pastoralist economy). <br />Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-45980699111201111852013-03-16T14:06:03.436+01:002013-03-16T14:06:03.436+01:00Not sure what to say - perhaps mentally try to rot...Not sure what to say - perhaps mentally try to rotate the axes for better seeing what is going on (while compensating for the fact that the two scales are different)?<br /><br />And Swedes and Estonians are admixed with Finns, but Finns are not admixed with them? What's the semantic difference I don't get, here? Half of the Helsinki Finns are closer to Swedes (or Estonians) than they are to extreme Finns. How does that argue against them being admixed with Swedes and Estonians? <br /><br />We know for certain that agricultural Swedes settled along the Baltic coast of Finland. Some still speak Swedish, there. Why is it so difficult to imagine that they intermixed?<br /><br />The Estonians, on the other hand, prove my point: namely, that there was a genuine, genetically distinct Finish population that intermixed with both Swedish and Baltic populations.<br /><br />The main question to me is: was this originally a local Uralic population (probably not), or a local, extreme NE population that got elite-dominated by a Uralic-speaking population before becoming known as Finns (possible, IMO).eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-20955490845160501702013-03-16T13:46:13.964+01:002013-03-16T13:46:13.964+01:00Sardinians do. If you get only European samples, S...Sardinians do. If you get only European samples, Sardinians often define one of two clusters at K=2. <br /><br />Also in my example (linked above), Ashkenazim and Moroccan Jews took over 2/4 clusters at K=4 (I don't recall how they behaved at lower values). I had to scrap them off for that very reason. <br /><br />I'm saying "drift" (or more precisely "endogamy", "inbreeding") because there are other reasons that support that conclusion in this case: the ROH table. It is very clear that they are highly endogamous populations which do not behave normally in the ADMIXTURE analysis and distort everything. It happens (for example the Tunisian Berbers of Henn - she admitted that they were clearly too inbred to be informative after using them twice), so it is a lesson we must take in account and very seriously so. <br /><br />If you want to mess around with the word "drift", then I'd rather scrap it out and use "endogamy" or "inbreeding", because (while drift is of course involved and intensified by these phenomena, it is not the underlaying cause: the isolation of a small sized population is). Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-36064485042360677722013-03-16T13:35:36.579+01:002013-03-16T13:35:36.579+01:00But, Eurologist, look at the PC graph: Finns only ...But, Eurologist, look at <a href="http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0005472.g002&representation=PNG_M" rel="nofollow">the PC graph</a>: Finns only slightly tend, in some cases, towards Sweden, while Swedes have a general clear deviation towards Finns and in some cases they much more Finnish than Swedish, genetically speaking. <br /><br />Also from the viewpoint of archaeology or material prehistory, while Southern Scandinavia was populated from mainland Europe since the Epipaleolithic, there's absolutely nothing that suggests those peoples migrating far northwards, much less towards Finland (i.e. not before the Viking Era). <br /><br />Finns stand as much closer in that graph to Estonians and in PC1 (which weights 2x PC2) they are clearly closer to Russians and other East Europeans, only appearing closer to Swedes in PC2 (half that weight). As I said before, Swedes are not even a realistic comparison because they are themselves a mix of mainstream Central-North Europeans and Eastern Europeans (Pitted Ware + Kurgans). <br /><br />More genetic data: in table 2, Finns do not appear either particularly close to Swedes but rather (Southern Finns) to (1) Estonians and (2) Poland (only 3. Sweden), and (Northern Finns) to (1) Poland and (2) Hungary (and then again 3. Sweden). Their relation with Sweden may well be caused more by Swedish Finnic admixture than vice-versa anyhow. <br /><br />They do not look "Russian" either (distances are not large but larger than to Poles and other peoples from East-Central Europe. So I can only imagine that the earliest substrate may be rather from the East-Central European Paleolithic, etc.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-46733478317511079132013-03-16T13:27:11.402+01:002013-03-16T13:27:11.402+01:00Maju,
I was talking about the principal component...Maju,<br /><br />I was talking about the principal component analysis - not admixture. We do not see Sardinians, Irish, Orcadians, Icelanders, or Jews define the first couple of eigenvalues in that type of analysis in a reasonably wide study. Those components persist even removing such populations.<br /><br />Some people look at studies like the one I cite below and say: "Look! It's all drift! PC1 is due to Italians drifting from CEs and Balts drifting from CEs, and then there are Finns drifting from CEs in PC2!"<br /><br />Of course, we know that is not true. Drift explains everything and nothing. Ignoring Neanderthals, I could state non-Africans are just people that drifted away from Africans, West-Asians and Europeans are just people that drifted away from South Asians, and Europeans are just people who drifted away from West Asians. <br /><br />But we know that hidden in all of this is a complex pre-history of European and extreme West Asian homogeneity, but with an important gradient during the Gravettian, drift and changes during several distinct LGM refugia, neolithic and bronze age migrations from the same general areas (emphasizing the northern Levant, western Anatolia, and the CE Balkans), and very little thereafter from the outside.<br /><br />We have a chance to resolve the above by combining ancient DNA studies with models of populations genetics within Europe - but not if the prevailing notion is; "Oh well, it's all just drift" (which we know to be untrue for many reasons, including the uniparental markers Kristiina mentions).eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.com