Allentoft and Iron Age Sweden - Printable Version +- The GenArchivist Forum (https://genarchivist.com) +-- Forum: Human Population Genetics (https://genarchivist.com/forumdisplay.php?fid=21) +--- Forum: Ancient (aDNA) (https://genarchivist.com/forumdisplay.php?fid=181) +--- Thread: Allentoft and Iron Age Sweden (/showthread.php?tid=460) |
Allentoft and Iron Age Sweden - Anglesqueville - 01-16-2024 I started using data from the big Allentoft study. For me, they are of major interest in having been calculated (by Glimpse) by professionals. I have in fact always had reservations about my own imputations (by Beagle) for data with very low coverage. This is particularly the case for the Finnish Iron Age micro-group (Levänluhta). In addition, Allentoft has given us, among other things, a gift of valuable new data, in particular from the Swedish Falköping group (between 2000 BC and 1700 BC). This group is of major importance for at least three reasons: 1) It contains the first representatives of I-M253 which have a reasonable chance of corresponding to the roots of this haplogroup as we know it today (TMRCA and location). 2) Falköping is located in the heart of the Swedish corridor to which I have often alluded on the late proto-Germanic thread. This corridor, which links the Lake Mälaren region and the southwest coast of Sweden, is the area where most of the early iron industries were distributed, as well as the finds of Mälar axes. 3) Isotopic analyzes attest that most of the individuals from Falköping are not native to this area, but to regions located in the northeast of Sweden. (see: Open Archeology 2018; 4:1–35 Malou Blank*, Anna Tornberg, and Corina Knipper "New Perspectives on the Late Neolithic of South-Western Sweden. An Interdisciplinary Investigation of the Gallery Grave Falköping Stad 5"). I first carried out a PCA (by Plink2) by projecting onto modern populations the groups Falköping (Sweden_N), Sweden_IronAge (which includes the outlier individual of Levänluhta), Sweden-BattleAxes, and finally the micro-group of Levänluhta (which merges with that of the modern Saamis). This PCA reveals an indisputable cline, with an obvious shift of the Sweden_N group relative to the Falköping group in the direction of Levänluhta. I obviously wondered whether this shift was verifiable by qpAdm. I didn't have much hope, remembering the sad experiences I had previously had with Levänluhta. My pessimism was unwarranted, because what qpAdm gives me is nothing less than the best model I have ever gotten for Iron Age Swedes. This model absolutely converges with Allentoft's conclusions regarding the leading role of the Falköping group. As for the Iron Age, it undoubtedly points to a genetic influx from Finland. left pops: Sweden_IA.imputed_allentoft Sweden_N_Falköping.imputed_Allentoft Finland_IA.imputed_allentoft right pops: Russia_Ust_Ishim.DG Cameroon_SMA.DG Italy_North_Villabruna_HG Czech_Vestonice16 Belgium_UP_GoyetQ116_1 Russia_MA1_HG.SG Iran_GanjDareh_N Kazakhstan_Botai_Eneolithic.SG Russia_Kostenki14.SG Ukraine_Mesolithic Indian_GreatAndaman_100BP.SG Russia_Arkhangelsk_Veretye_Mesolithic.SG Israel_PPNB Georgia_Kotias.SG Turkey_N_I0707 best coefficients: 0.919 0.081 totmean: 0.919 0.081 boot mean: 0.919 0.081 std. errors: 0.033 0.033 fixed pat wt dof chisq tail prob 00 0 13 6.435 0.928885 0.919 0.081 01 1 14 12.129 0.595957 1.000 0.000 10 1 14 318.653 0 0.000 1.000 best pat: 00 0.928885 - - best pat: 01 0.595957 chi(nested): 5.694 p-value for nested model: 0.0170234 Samples: NEO221_A U Sweden_N_Falköping.imputed_Allentoft NEO223_A U Sweden_N_Falköping.imputed_Allentoft NEO224_A U Sweden_N_Falköping.imputed_Allentoft NEO225_A U Sweden_N_Falköping.imputed_Allentoft NEO226_A U Sweden_N_Falköping.imputed_Allentoft NEO227_A U Sweden_N_Falköping.imputed_Allentoft NEO228_A U Sweden_N_Falköping.imputed_Allentoft NEO259_A U Sweden_N_Falköping.imputed_Allentoft RISE174_A U Sweden_IA.imputed_allentoft VK522_A U Sweden_IA.imputed_allentoft VK523_A U Sweden_IA.imputed_allentoft DA234_A U Finland_IA.imputed_allentoft DA238_A U Finland_IA.imputed_allentoft Here for once is a model of easy interpretation: the p-value of the alternative model is too low for this alternative model to be admissible. The intervention of the Finnish group is clearly essential. The monumental tail-prob of the complete model left little doubt as to this in any case. RE: Allentoft and Iron Age Sweden - MrI1 - 01-16-2024 If the forefathers of modern I1 diverged apart from OST003 perhaps during the Ertebølle Culture at said time they would probably be primarily WHG. Perhaps when farming was introduced into Northern Europe the forefathers of Modern I1 moved to northeastern Scandinavia to completely avoid the Funnelbeaker Culture as opposed to the forefathers of Mr. OST003 who maintained their hunter-gathering lifestyle and genetics despite being surrounded by the farmers in Northern Germany for around 800 years? I guess a few questions I still have are when and where did the forefathers of Modern I1 encounter the Corded Ware Culture? By the time they show up in Falköping during the Late Neolithic they have primarily Corded Ware autosomal dna correct? Did they have early contact with the Corded Ware somewhere in the Eastern Baltic? At said point how did they maintain their I1 patrilineal lines despite absorbing primarily Corded Ware autosomal dna? RE: Allentoft and Iron Age Sweden - AimSmall - 01-16-2024 Nice work. You had me all excited thinking a new data drop was out there, but I see it's still 54.1.p1 RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-16-2024 (01-16-2024, 03:22 PM)AimSmall Wrote: Nice work. The data is from Allentoft: https://erda.ku.dk/archives/917f1ac64148c3800ab7baa29402d088/published-archive.html. I did a bit of work to make this data usable, and recently uploaded the resulting eigenstrat file to my dropbox, but had to delete it because I was running out of space. Kale and Teepean downloaded it, I think you can call them if you're interested. RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-16-2024 (01-16-2024, 03:08 PM)MrI1 Wrote: If the forefathers of modern I1 diverged apart from OST003 perhaps during the Ertebølle Culture at said time they would probably be primarily WHG. Perhaps when farming was introduced into Northern Europe the forefathers of Modern I1 moved to northeastern Scandinavia to completely avoid the Funnelbeaker Culture as opposed to the forefathers of Mr. OST003 who maintained their hunter-gathering lifestyle and genetics despite being surrounded by the farmers in Northern Germany for around 800 years? Where did the Falköping guys pick their I1? Honestly, I don't know, even if I have some secret ideas about this question. RE: Allentoft and Iron Age Sweden - teepean - 01-16-2024 (01-16-2024, 03:40 PM)Anglesqueville Wrote:(01-16-2024, 03:22 PM)AimSmall Wrote: Nice work. I converted the dataset to plink: https://drive.google.com/drive/folders/1mu_3Z50_u0JjLSsGhEbW3OWEgEqXWcw2 RE: Allentoft and Iron Age Sweden - AimSmall - 01-16-2024 Got is downloaded, thanks teepean. RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-16-2024 (01-16-2024, 06:52 PM)teepean Wrote:(01-16-2024, 03:40 PM)Anglesqueville Wrote:(01-16-2024, 03:22 PM)AimSmall Wrote: Nice work. You should have asked me, I made the Plink first too, and kept it of course. Tell me if you see weird things with the names. I used R to rename the samples. I think it's OK but one never knows. RE: Allentoft and Iron Age Sweden - AimSmall - 01-17-2024 I've been spacing out on this thread... doh! This Allentoft is the Neolithic discussion from last October. Totally wasn't making the connection. Here is a family file I modified at Davidski's request. It's not as inclusive as the one above, but has population names and lat long data. Code: Russia_Mesolithic_Romanov-Ilmurzin NEO100 0 0 0 NEO100 51.566 53.683 RE: Allentoft and Iron Age Sweden - ANIEXCAVATOR - 01-17-2024 (01-16-2024, 08:51 AM)Anglesqueville Wrote: I started using data from the big Allentoft study. For me, they are of major interest in having been calculated (by Glimpse) by professionals. I have in fact always had reservations about my own imputations (by Beagle) for data with very low coverage. This is particularly the case for the Finnish Iron Age micro-group (Levänluhta). In addition, Allentoft has given us, among other things, a gift of valuable new data, in particular from the Swedish Falköping group (between 2000 BC and 1700 BC). This group is of major importance for at least three reasons: Great work Anglesqueville! If we believe that the expansion of the final stage of the proto-Germanic took place with an subtle shift in the direction of Uralic populations, because of people migrating from Malaren, it will be even more convincing if you can show that Danish or Norwegian Iron Age samples around 0AD are shifted from Danish or Norwegian samples from the I1 cluster 4,000 years ago in the direction of Finns as well. Are there enough samples for you to do this? RE: Allentoft and Iron Age Sweden - Codaman - 01-17-2024 It's my understanding that some of these Levänluhta samples(specifically DA234 and JK1968, although not so much JK1970 and not at all DA238) which are of course ancestrally Saami have relatively high levels of Germanic ancestry which is in line with proto-Germanics being the primary contact group of ancestral Saami along with Baltic Finns and I wonder if this could affect the results presented. The following models may illuminate this. Target: Vologda_EIA:NEO538 Distance: 3.0806% / 0.03080646 41.0 Russia_Krasnoyarsk_BA.SG 24.2 Russia_Vologda_Veretye_Mesolithic.SG 19.4 Kazakhstan_MLBA_Karagash 9.8 Estonia_IA.SG 3.0 Estonia_BA.SG 2.6 Sweden_Motala_HG 0.0 Norway_N_HG.SG 0.0 Sweden_LN:NEO221 Target: FIN_Levanluhta_IA:DA234 Distance: 2.1313% / 0.02131308 52.2 Vologda_EIA:NEO538 27.6 Sweden_LN:NEO221 20.2 Estonia_BA.SG 0.0 Sweden_Motala_HG 0.0 Norway_N_HG.SG 0.0 Kazakhstan_MLBA_Karagash 0.0 Russia_Vologda_Veretye_Mesolithic.SG 0.0 Estonia_IA.SG RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-18-2024 (01-17-2024, 03:32 PM)Codaman Wrote: It's my understanding that some of these Levänluhta samples(specifically DA234 and JK1968, although not so much JK1970 and not at all DA238) which are of course ancestrally Saami have relatively high levels of Germanic ancestry which is in line with proto-Germanics being the primary contact group of ancestral Saami along with Baltic Finns and I wonder if this could affect the results presented. I doubt. If the sources (Falköping and Levänluhta) shared enough alleles for the qpAdm model presented to be disrupted, this would be seen in the standard errors. However, these standard errors are very low. No, I believe these sources are as close to orthogonal as possible. With qpAdm Levänluhta (at least the two proto-Saamis imputed by Allentoft) can be modelled very well as combinations of VolgaOka_IA, kra001 and Motala_HG, and the addition of Falköping to these sources does not bring anything good in terms of tail prob. That there was a proto-Germanic lexical contribution to Saami languages is indisputable. But that doesn't reflect in the autosomal constitution of the Saami-like guys from Levänluhta. RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-18-2024 (01-17-2024, 02:23 PM)ANIEXCAVATOR Wrote: Great work Anglesqueville! The Denmark_IronAge micro-group is represented by 4 individuals, who come from the Margaryan study. Nothing is simple with them. In fact, this quartet is as heterogeneous as the Swedes micro-group is homogeneous. Thus, among these two individuals we find two males, both I1, VK521 and VK532. VK521 could come from Sweden (perhaps we have isotopic analyses for him, we should check), in any case "my" model applies perfectly to him. But this is not the case with VK532, which cannot be modelled with any Scandinavian source. In any case, I didn't find anything convincing for him. For the Norwegians, I have to work. RE: Allentoft and Iron Age Sweden - Codaman - 01-18-2024 (01-18-2024, 06:51 AM)Anglesqueville Wrote: With qpAdm Levänluhta (at least the two proto-Saamis imputed by Allentoft) can be modelled very well as combinations of VolgaOka_IA, kra001 and Motala_HG, and the addition of Falköping to these sources does not bring anything good in terms of tail prob. That there was a proto-Germanic lexical contribution to Saami languages is indisputable. But that doesn't reflect in the autosomal constitution of the Saami-like guys from Levänluhta. The amount of Siberian ancestry from NEO538 to Levänluhta halves yet it is not due to an increase of 50% in SHG and certainly it's not Volga-Oka either because that makes no sense so what is the cause? the sources can not be chosen without considering their plausibility What if you instead of these you used the following sources NEO538 NEO62(Bolshoy Oleni Ostrov) NEO225 and any source from the BA/IA Baltics which has the highest coverage RE: Allentoft and Iron Age Sweden - Anglesqueville - 01-18-2024 ^^ I haven't been interested in NEO538 at all so far, so I don't have anything to say about it. As for using VolgaOka_IA as a source for the Saamis (including the two from Levänluhta) this is a perfectly justified choice if one follows Lang's theories (which is my case, at least on this point). This choice requires to be completed by a bonus from Krasnoyarsk_BA, and gives very satisfactory adjustments with qpAdm. |