tag:blogger.com,1999:blog-1820243696969815052.post5066184362076623078..comments2022-04-02T11:11:39.133+02:00Comments on Fennoscandia Biographic Project: La Braña 1 closest to Basque, Sardinians and Lithuanians in geneologyAnders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.comBlogger22125tag:blogger.com,1999:blog-1820243696969815052.post-80737367110931965832015-08-05T00:26:52.375+02:002015-08-05T00:26:52.375+02:00My gedmatch says I have a lot of La Brana 1. Does ...My gedmatch says I have a lot of La Brana 1. Does this help?Ancient Bloodlineshttps://www.blogger.com/profile/02484680463822399367noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-28863570100812030142014-06-10T09:56:03.425+02:002014-06-10T09:56:03.425+02:00Thanks. No I have not run any Saami individuals vs...Thanks. No I have not run any Saami individuals vs the Eurogenes K13.Anders Pålsenhttps://www.blogger.com/profile/13444056522800105747noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-57110659824101558662014-05-13T04:02:58.420+02:002014-05-13T04:02:58.420+02:00Anders, your blog is very informative and interest...Anders, your blog is very informative and interesting, thanks for posting this stuff. I have one question, do you have any Eurogenes K13 results of Sami people? Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-10766421985608136522014-04-08T15:52:08.555+02:002014-04-08T15:52:08.555+02:00Eskimos (from East Greenland) are more like normal...Eskimos (from East Greenland) are more like normal East Asians and Siberians, so Russians and Mordovians show more shift towards them. They probably are more recent than mainstream Amerindian migration.<br /><br /> http://fennoscandia.blogspot.no/2014/02/europeans-and-native-americans.html<br /><br />"If we zoom on the European panel we see as expected that especially Saamis, Mordovians and Vologda Russians pulls left toward the common East-Asian, Siberian and Native American dimension 2. Note that Finns doesn't show the same level of pull towards left as the Saamis, Mordovians and Vologda Russians."<br /><br />"However if looking at dimension 3 /(vertical) we clearly see Saamis and Finns pulling towards the Native Americans dimension at about same level of intensity. It appears to be lacking among Vologda Russians and Mordovians who pull toward the common East-Asian, Siberian and Native American dimension 2 (horizontal). This seem to suggest (also noted by commentators of this blog from ealier posts) that there is different influences from the East in Europe."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-63244358343567563552014-04-08T14:49:37.198+02:002014-04-08T14:49:37.198+02:00It would be interesting to see how much eskimos ha...It would be interesting to see how much eskimos have of the amerindian component.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-86582873237528053122014-04-07T16:42:36.898+02:002014-04-07T16:42:36.898+02:00The eastern influence in finns and russians is nat...The eastern influence in finns and russians is native american and Han. Finns have more of the native american one and probably indicate a far north ancient gene flow along the coastline of barents sea.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-55990984830713497372014-04-06T18:00:52.937+02:002014-04-06T18:00:52.937+02:00Yes, but that can be increased by many things like...Yes, but that can be increased by many things like a different and older type of gene flow, or including the fact that there are two individuals in the sample who cluster with Mordovians and Vologda Russians in heatmap at page 152, unlike others who cluster with Estonians or Lithuanians.<br /><br />There are also the f3 signal differences between strength and type for Finns and Russians/Mordovians, page 81 and 82:<br /><br />"In a case where admixture was previously detected, e.g.,<br />the French for the pairing (Sardinian, Karitiana), a much lower f3-statistic (Zdiff=4.3 standard errors)<br />is produced by the pairing (Stuttgart, MA1) involving two ancient samples."<br /><br />Similar thing happens with Finns, for whom admixture is detected for pairing (Sardinian, Karitiana), but a much lower f3-statistic (Zdiff 4.1 standard errors) is produced by the pairing (Abkhazian, Loschbour). This is the same as with Icelandic or Estonians or Lithuanians, but not for Russians:<br /><br />"The strongest decrease in the value of the f3-statistics when we including ancient genomes is observed<br />for Europeans, for which Zdiff>3 except for three cases:<br />(i) Ashkenazi Jews where the (Stuttgart, MA1) pairing produces Zdiff=2.3 lower statistic than the<br />(Basque, Dinka) (the Dinka may reflect small recently gene flow from Africans4).<br />(ii) Maltese where the (Stuttgart, MA1) pairing is Zdiff=2 lower than the similar (Basque, Esan)<br />(iii) Russians where the (Loschbour, Chuckchi) pairing is Zdiff=2.7 lower than (Chuckchi, Sardinian)."<br /><br />Mordovian signal is barely >3, and Russian signal doesn't even involve Amerindians but Chukchis.<br /><br />Also when compared to amerindians and different types of East Asians including Han, Finns don't plot with Mordovians or Russians:<br /><br />http://fennoscandia.blogspot.no/2014/02/europeans-and-native-americans.htmlAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-11815200413395978742014-04-06T17:46:51.411+02:002014-04-06T17:46:51.411+02:00Yes, but not missing.
Page 121 Table S14.13
&q...Yes, but not missing.<br /> <br />Page 121 Table S14.13<br /> <br />"but the three populations violating our <br />model (Table S14.13) are clearly to the right, <br />sharing relatively more alleles with the Han"<br /><br />Finns is one of the population that sharing more alleles with the Han and therefore deviate from the main Europeans that form a cline from Stuttgart to Estonia.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-11367899300046819132014-04-06T15:39:00.512+02:002014-04-06T15:39:00.512+02:00Yes, the three populations with a significant (Z&g...Yes, the three populations with a significant (Z>3) curve were Mordovians, Russians and Chuvash (table S14.14)<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-56169152539247588322014-04-06T14:39:05.899+02:002014-04-06T14:39:05.899+02:00????
http://arxiv.org/ftp/arxiv/papers/1312/1312.6...????<br />http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf<br /><br />page 121<br /><br />"using the Han as a reference and found a significant<br />(Z>3) curve for three populations (for Finnish, Z=1.27, w"<br /> Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-5148873076738665802014-04-05T17:53:03.321+02:002014-04-05T17:53:03.321+02:00True, it will have to wait until Loschbour genome ...True, it will have to wait until Loschbour genome is released to see if different modes produce different results.<br /><br />The study also contains additional evidence for different sources of "easterness" in Finns, Mordovians and Vologda Russians, in addition to the ALDER run where the latter two showed a Han admixture signal that was missing from Finns. They compared strongest two-way admixture signals for different populations from fits involving at least one ancient genome and from fits involving only modern genomes. For Finns, Lithuanians, Estonians and Icelandic the strongest ancient signal came from "Loschbour and Abkhazian" fit, and the strongest modern signal for all of them was "Sardinian and Karitiana". The ancient signal was clearly stronger for them all. <br /><br />The difference between signal strenghts would probably have been even bigger for Finns if the two individuals clustering with Mordovians and Vologda Russians in their FINESTRUCTURE run would have been removed from the sample (which had 7 individuals total).<br /><br />For Mordovians the strength of ancient signal (also Loschbour + Abkhazian) and modern signals (Sardinian + Surui) were almost the same. For Vologda Russians, who all clustered with Mordovians in their FINESTRUCTURE run, the strongest ancient signal was "Loschbour + Chukchi", and the modern signal "Sardinian + Chukchi" was clearly stronger for them than the ancient signal. Unfortunately they didn't test the single Saami sample they had.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-4556202458840777552014-04-05T09:50:42.532+02:002014-04-05T09:50:42.532+02:00As I understand it the Chromopainter-Finestructure...As I understand it the Chromopainter-Finestructure analysis used there was with the linked model. In the case of La Braña 1 the clustering is different between the linked and unlinked model.Anders Pålsenhttps://www.blogger.com/profile/13444056522800105747noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-41397376757517034412014-04-03T13:29:15.936+02:002014-04-03T13:29:15.936+02:00The Chromopainter/FineSTRUCTURE analysis Lazaridis...The Chromopainter/FineSTRUCTURE analysis Lazaridis&co did on Loschbour and Stuttgart aligns with these results. <br /><br />Loschbour joins a Northeast European group that contains three subgroups, one group with Lithuanians, Estonians, some Finns and Belorussians, one group with all Vologda Russians and Mordovians and some Finns, and one group with all Ukrainians and some Belorussians (and single individuals from Czech and Finland).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-43448580654194067622014-03-18T22:14:19.998+01:002014-03-18T22:14:19.998+01:00Hi Anders,
Thanks!
If possible, could I email yo...Hi Anders,<br /><br />Thanks!<br /><br />If possible, could I email you my raw-data? I'm not European, but from South Central Asia, so I was wondering if you'd be willing to use my raw-data? I'd truly appreciate this. Thank you in advance.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-70633984522353304392014-03-18T09:03:21.464+01:002014-03-18T09:03:21.464+01:00I plan to use MA-1 in the next ordinary run + a im...I plan to use MA-1 in the next ordinary run + a imputed La Braña 1 genoem to match the remaining 289k of SNP in the standard run.Anders Pålsenhttps://www.blogger.com/profile/13444056522800105747noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-39954776948099869442014-03-18T09:01:58.573+01:002014-03-18T09:01:58.573+01:00No its from chunkcounts alone. There is very high ...No its from chunkcounts alone. There is very high correlation between chunkcount and chunklenght anyway but might be worth checking out.Anders Pålsenhttps://www.blogger.com/profile/13444056522800105747noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-75716095550239850942014-03-15T06:22:05.988+01:002014-03-15T06:22:05.988+01:00Anders,
Is it from the segment size that you esti...Anders, <br />Is it from the segment size that you estimate the time depth in unlinked and linked form, small segment = older, large segment = younger connection?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-14194639922252793002014-03-14T20:26:20.352+01:002014-03-14T20:26:20.352+01:00Hi Anders,
If possible, could you try this with M...Hi Anders,<br /><br />If possible, could you try this with MA-1, using only Asian (Middle Eastern, Caucasian, Central Asian, South Asian, East Asian, Southeast Asian, Northeast Asian-Siberian, and Oceanian) populations. It seems ANE peaks in Asia, rather than Europe, so it would be very interesting to see him analyzed in an Asian context. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-8817913925085126922014-03-11T18:39:17.438+01:002014-03-11T18:39:17.438+01:00By the way, could you check La Braña against Siber...By the way, could you check La Braña against Siberians, East Asians and Amerindians?<br /><br />This f3 test suggests he is in line with most europeans in Karitiana affinity but more shifted towards Han (between Adygei and North Russians, the populations are from HGDP) than most of them.<br /><br />http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature12960_SF5.htmlAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-73616936523008942742014-03-11T15:29:10.335+01:002014-03-11T15:29:10.335+01:00Interesting results! would it be possible to get P...Interesting results! would it be possible to get PCA's with individual codes, it is difficult to distinguish different groups with those colored dots.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-7357286963358109402014-03-10T15:11:47.942+01:002014-03-10T15:11:47.942+01:00I think its the "mask" effect of recombi...I think its the "mask" effect of recombination. In the linked mode it looks for the closest haplotype when it comes to distance in mutations and in recombination and the linked mode doesn't find these among the Saamis but among Basque.Anders Pålsenhttps://www.blogger.com/profile/13444056522800105747noreply@blogger.comtag:blogger.com,1999:blog-1820243696969815052.post-39300900819384169792014-03-10T14:33:48.665+01:002014-03-10T14:33:48.665+01:00The affiliation to North Saamis especially seems t...The affiliation to North Saamis especially seems to change a lot between unlinked and linked mode, from what looks to be the closest to Braña to one of the most distant, which may indicate much drift there's been since.<br /><br />Does dimension 1 in the PCA's reveal anything?Anonymousnoreply@blogger.com