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ANALYSIS STATUS: FILE PREPERATIONS!Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.comBlogger73125tag:blogger.com,1999:blog-1820243696969815052.post-50661843620766230782014-03-10T12:03:00.001+01:002014-03-10T15:02:37.306+01:00La Braña 1 closest to Basque, Sardinians and Lithuanians in geneologyThis is the second look at the recently released La Braña 1 diploid genome. The <a href="http://fennoscandia.blogspot.no/2014/02/la-brana-1-diploid-genome-vs-europeans.html" target="_blank">previous analysis</a> was done using Plink MDS tool and gave a limited overview. This time I am using first the Chromopainter-Finestructure unlinked model and second the Chromopainter-Finestructure linked model.<br />
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<b>Unlinked model</b><br />
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The unlinked model appear to show a result consistent with the previous analysis with the La Braña 1 in the same heatmap box as Finns and Saamis especially what appear to be East-Finns and North-Saami. However also notice that the La Braña 1 in the heatmap show affiliation to Basque, Lithuanians and a mixed group of Scandinavians and Finns. This affiliation is interesting as particular Saami and Finns do not show much sharing to Lithuanians and Basque. It may be that La Braña 1 is "ancestral" to these modern populations but through the generation or 7000 years the populations may have drifted and/or mixed with other populations..<br />
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<a href="https://sites.google.com/site/fennobga/screenshotEurope200tUNL-100304.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/screenshotEurope200tUNL-100304.png" width="320" /></a></div>
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ChunkCount 54k unlinked aggregated</div>
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The PCA plot generated from Finestructure shows a slightly different plotting in the previous analysis Plink MDS plotting (may be due to pruning). In dimension 3 (horizontal) the La Braña 1 still cluster with Finns and Saamis but in dimension two (vertical) the La Braña 1 is at the same height as the Basque.</div>
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<a href="https://sites.google.com/site/fennobga/PCAUnl-100304.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/PCAUnl-100304.png" width="320" /></a></div>
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ChunkCount 54k unlinked PCA </div>
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<b>Linked model</b></div>
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As I understand from the authors the unlinked and linked model may give different time depths in the analysis with the unlinked model showing the most ancient time depth and the linked analysis more recent ancestry. This analysis may confirm this statement. The difference between the linked and unlinked model may be the "masking" effect of recombination that may hide ancient relationships seen in the unlinked model. This is to my knowledge the first haplotype based analysis of the La Braña 1 as the La Brãna 1 was phased.</div>
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As we can see the linked analysis shows a very different clustering of the La Braña 1. He is in the same heatmapbox as with Western Europeans and in particular with Basque and Sardinians. The La Braña 1 also show strong "heat" to the Lithuanians but the strong affiliation to Finns and Saami we so earlier is in the linked model much weaker but still quite easy to see.. </div>
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<a href="https://sites.google.com/site/fennobga/screenshotEuroLinked2-100314.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/screenshotEuroLinked2-100314.png" width="320" /></a></div>
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ChunkCount 54k aggregated linked</div>
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We can also see in the heatmap that there is strong divergence between haplotypes painted vs haplotypes donated for the La Braña 1. The La Braña 1 find related haplotypes among the modern populations but the modern populations find closer related haplotypes among themself. This suggest La Braña 1 have haplotype variation that no longer exists in the modern populations and also due to recombination the modern populations would make the La Braña 1 haploblocks very small.</div>
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The PCA for the unlinked model shows a different clustering from the unlinked model. This time at the center of the plot between the Scandinavians and Vologda Russians.</div>
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<a href="https://sites.google.com/site/fennobga/PCALinked-100304.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/PCALinked-100304.png" width="320" /></a></div>
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ChunkCount 54k linked PCA</div>
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<b>Conclusion</b></div>
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As we can see the different models appear to give different results and its due to that <i>in geneology</i> the La Braña 1 closest to Basque, Sardinians and Western Europeans but in ancient ancestry closest to Finns and Saamis.<b> </b>The clustering in geneology with Basque, Sardinians and Western Europeans in the linked model make sense as the La Braña 1 individual was found in today northern Spain. This means that the La Braña 1 like haplotypes is still much present among Western Europeans of today suggesting continuity in the autosomes.<b><br /></b><br />
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As a sidenote to this also notice the change of clustering for the Saamis, Mordovians and Vologda Russians between the unlinked and linked model. In the linked model Saamis and Finns cluster together and the Vologda Russians and Mordovians cluster with Easern Europeans, but in the unlinked model Finns are seperatae from the Saamis, while the Saamis cluster with Mordovians and Vologda Russians. Also in the unlinked mode the Mordovians and Vologad Russians is part of a greater cluster also including Saamis and Finns.<b><br /></b></div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com22tag:blogger.com,1999:blog-1820243696969815052.post-61868561485881211182014-02-18T15:42:00.001+01:002014-02-20T11:54:42.686+01:00La Braña 1 diploid genome vs Europeans first lookI finally got my hand on the latest La Brána 1 diploig genotype from the <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12960.html" target="_blank">Iñigo Olalde et al.2014 paper.</a> In previous analysis of the La Braña 1 and other ancient genomes they have only been the available in a "haploid" state meaning that it has not been possible to phase it and analyze using high resolution linked haplotype based models but instead using only unlinked single SNP models. I also had to "haploidize" all the other indnviduals I compared him with both in Chromopainter-Finestructure, ADMIXTURE or in Plink runs. It could possibly have affected the analysis as this seem to show at least for the La Braña 1 part.<br />
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I initially used a 1.1 mill SNP diploid La Braña 1 genotype and of these to 54k SNP matched by current 289k standard panel used in most of the project standard runs. I further LD pruned in PLINK down to 25k and run in PLINK's own MDS plotting function. It gave the following very familiar "V" shape with Saamis and Finns at one branch and Vologda Russians, Mordovians and Lithuanians on the other branch.<br />
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Please note this is a preliminary analysis and not the state of the art analysis but as we can see from the positioning the La Braña 1 without much doubt cluster with Saamis and Finns in dimension 1 (horizontal) and 2 (vertical) but not in dimension 3 where Scandinavians and Lithuanians cluster closest. <br />
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My first impression is that it is North Saamis and Eastern or Northern Finns who cluster closest in these two first dimensions but not in dimension 3 where they cluster closest with Scandinavians and Lithuanians but the distance appears huge. It may suggest that the La Braña 1 have a variation in this dimension that very much dissappeared but still exists to some extent among Scandinavians and Lithuanians.<br />
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The haplotype based analysis that will for certain come later will be able to give a better image of clustering.. The La Braña 1 individual will be included in all future Chromopainter-Finestructure haplotype based analysis and very probably the 24 000 year old individual from Siberia as well.<br />
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<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="248" src="https://sites.google.com/site/fennobga/MDSLaBrana1180214.png" width="320" /></a></div>
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La Braña 1 diploid genome 25k Plink MDS D1-D2<br />
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<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214D1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="286" src="https://sites.google.com/site/fennobga/MDSLaBrana1180214D1-D3.png" width="320" /></a></div>
La Braña 1 diploid genome 25k Plink MDS D1-D3<br />
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If assuming that this position also will be at this location in the future Chromopainter-Finestructure haplotype analysis (<a href="http://fennoscandia.blogspot.no/2013/12/updated-europe-analysis.html" target="_blank">as seen in the last run</a>)we may get an idea of what have happening genetically speaking in Europe since 7000 year before present. Please note that the below is not made from the above MDS run but from a earlier Chromopainter-Finestructure run.</div>
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<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214-PCAhaployD1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/MDSLaBrana1180214-PCAhaployD1.png" width="318" /></a></div>
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Dimension 1 - Agricultural expansion</div>
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<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214-PCAhaployD2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="245" src="https://sites.google.com/site/fennobga/MDSLaBrana1180214-PCAhaployD2.png" width="320" /></a></div>
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Dimension 2 - Expansion from the East<br />
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<a href="https://sites.google.com/site/fennobga/CCEuropeD2map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="304" src="https://sites.google.com/site/fennobga/CCEuropeD2map191213.png" width="320" /></a></div>
Dimension 3 - Expansion from Northern and Southern edges <br />
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<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214IND.png" target="_blank">Individual results D1-D2</a><br />
<a href="https://sites.google.com/site/fennobga/MDSLaBrana1180214D1-D3IND.png" target="_blank"> Individual results D1-D3 </a></div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com5tag:blogger.com,1999:blog-1820243696969815052.post-34367284544977586492014-02-13T23:23:00.001+01:002014-02-14T18:42:02.932+01:00Europeans and Native Americans<em>Updated 14/02/2014 with individual results PCA plots</em><br />
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This is a furter investigation of the previous posts about East-Asian influences in Europe. This time I have extended the earlier studies by adding Native Americans. The results appears as expected but also contain unexpected results.<br />
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The first dimension in this new Finestructure run we have seen before several times in the previous run and peak on one side among Northern Europeans and the other among South-East Asians and especially Papuans/Melanasians. It will not be discussed more here.<br />
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The second dimension (X-asis below) on the other hand clearly separate Europeans from Native Americans, Siberians and East-Asians. The third dimension separate on the other hand Native Americans from East-Asians with the Siberians between.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD2D3-130214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/PCAD2D3-130214.png" width="320" /></a></div>
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Dimension 2 (X-axis/horizontal) and 3 (Y-axis/vertical)</div>
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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.</div>
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<a href="https://sites.google.com/site/fennobga/PCAD2D3-130214EuropeZoom.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/PCAD2D3-130214EuropeZoom.png" width="320" /></a></div>
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Dimension 2 (X-axis/horizontal) and 3 (Y-axis/vertical) zoomed Europe<br />
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<a href="https://sites.google.com/site/fennobga/PCAD2D3-130214EuropeZoomInd.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="316" src="https://sites.google.com/site/fennobga/PCAD2D3-130214EuropeZoomInd.png" width="320" /></a></div>
Individual results D2-D3 as above</div>
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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.</div>
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If we move on to dimension 4 (vertical, keeping dimension 2 at horizontal). This is the same dimension as seen in the usual European PCA plot regularly seen on this blog with the charactaristic "V" shape. This is the branch (top) with Finns and Saamis and with Sardinians and Basque at the root (bottom). As we can see Siberians, East-Asians and Native Americans appear to cluster consistent separately vertical along the "European" dimension. I would guess the informed reader would agree without much thought what we see on the top with Siberians being placed at the same level with Saamis and Finns at the upper part of vertical dimension in the plot.</div>
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<a href="https://sites.google.com/site/fennobga/PCAD2D4-130214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/PCAD2D4-130214.png" width="320" /></a></div>
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Dimension 2 (X-axis/horizontal) and 4 (Y-axis/vertical) zoomed Europe<br />
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<a href="https://sites.google.com/site/fennobga/PCAD2D4-130214IND.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="315" src="https://sites.google.com/site/fennobga/PCAD2D4-130214IND.png" width="320" /></a></div>
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Individual results D2-D4as above zommed into Europe<br />
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However if we move down to the middle we see the cluster of East-Asian group. If we from this vertical level move horizontally toward right we see that this "East-Asian" level actually end up with the Mordovians, Vologda Russians, Russians and many Lithuanians with other Eastern Europeans in close proximity. This clustering is also difficult to explain but its striking that the East-Asians appear to fix among at least certain Eastern Europeans given known history of the area.</div>
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If we move even further down we reach the Native Americans and if we move right from the vertical level of the Native Americans we will meet Southern European populations like Italians, Basque and Sardinians. This appears to me to a big surprise I find difficult to explain. I have been thinking the thought of post-1492 admixture among Native Americans but these samples have been screened for outside admixture before included in the analysis.</div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com4tag:blogger.com,1999:blog-1820243696969815052.post-8471602475070096002014-02-05T11:25:00.001+01:002014-02-05T12:44:45.745+01:00Europeans, East-Asians and AfricansThis is a continuation of the <a href="http://fennoscandia.blogspot.no/2014/01/is-there-east-asian-influence-in_29.html?" target="_blank">previous post</a> where I investigated haplotype variation between Europeans, East-Asians and Siberians. This time investigate further by including Africans as it shed some more light on the haplotype variation seen between Europeans, East Asians and Siberians.<br />
<a href="https://sites.google.com/site/fennobga/Afr-PCAD1-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><br /></a>
The <b>first</b> dimension is surprising as I would expect there to be greatest haplotype variation in the dataset The first dimension is not to my suprise between Africans and non-Africans but strangely enough Europeans cluster by themself peaking among northern Europeans while Africans appear to show similarity with the East-Asians. Notice here that the PCA distance between Africans and East-Asians appear rather small.<br />
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<img border="0" height="188" src="https://sites.google.com/site/fennobga/Afr-PCAD1-040214.png" style="cursor: move;" width="320" /></div>
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Dimension 1 - brown Finns/Saami - blue Africans
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This gradient map appear strikingly similar to <a href="https://sites.google.com/site/fennobga/Euroasia191213-D1.png" target="_blank">dimension 1</a> in the previous <a href="http://fennoscandia.blogspot.no/2014/01/euroasian-variation-gradiation-maps.html" target="_blank">Euroasian analysis</a>. My interpretation of this connection between Africans and East-Asians I believe is remnants of a Papuan or/and Melanasian like population among todays East-Asians. I have earlier suggested that Africans and Papuans/Melanasians still shows a genetic connection especially to San and Pygmyes from a <a href="http://fennoscandia.blogspot.com/2013/01/oceania-influence-in-east-asians.html" target="_blank">earlier post</a> suggesting that it was a San/Pygmy like population that first migrated along the southern coast in Asia..<br />
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The <b>second</b> dimension dimension is also surprising as it instead of showing African vs non-African variation instead shows a common African-European variation vs East Asians and Siberians.</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD2-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="185" src="https://sites.google.com/site/fennobga/Afr-PCAD2-040214.png" width="320" /></a></div>
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Dimension 2 - brown - Africans/Europeans - blue - East Asians/Siberians</div>
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This gradient map also shows a very striking similarity to <a href="https://sites.google.com/site/fennobga/Euroasia191213-D2.png" target="_blank">dimension 2</a> in the previous <a href="http://fennoscandia.blogspot.no/2014/01/euroasian-variation-gradiation-maps.html" target="_blank">Euroasian analysis</a>. As we can see here this dimension does not only seperate Europeans and East-Asians/Siberians but seperate Europeans-Africans from East-Asians-Siberians. I am very unsure about the interpretation but as dimension 1 it appear to be ancient.</div>
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These two dimensions can be summed up into two dimensions and as we can see this plot is identical to the <a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB.png" target="_blank">PCA plot dimension 1 and 2</a> in a <a href="http://fennoscandia.blogspot.no/2014/01/is-there-east-asian-influence-in_29.html" target="_blank">previous analysis</a> investigating relationship between Europeans, East Asians and Siberians. This may sugggest that the previous indication of East-Asian ancestry among Southern Europeans may be due to shared Papuan-Melanasian ancestry among East-Asians.and Southern Europeans.</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD1D2Overview-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="281" src="https://sites.google.com/site/fennobga/Afr-PCAD1D2Overview-040214.png" width="320" /></a></div>
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PCA Dimension 1 (horizontal) and 2 (vertical) Overview</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD1D2OverviewZoomEuro-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="293" src="https://sites.google.com/site/fennobga/Afr-PCAD1D2OverviewZoomEuro-040214.png" width="320" /></a></div>
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PCA Dimension 1 (horizontal) and 2 (vertical) Overview Europe</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD1D2OverviewZoomEuroIndiv-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="317" src="https://sites.google.com/site/fennobga/Afr-PCAD1D2OverviewZoomEuroIndiv-040214.png" width="320" /></a></div>
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PCA Dimension 1 (horizontal) and 2 (vertical) Overview Europe individual results </div>
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The third dimension finally appear to be a true African vs non-African dimension. The PCA coordinate distance between Africans and non-Africans is very large and outside Africa the haplotype variation appears rather uniform in comparison suggesting a bottleneck or/and foundereffect after leaving Africa. The fact that this dimension first appear as number tree suggesting this variation to be less than the previous dimensions make the previous dimensions intriguing. Maybe its just the effect of oversampling from the European region or maybe its traces of ancient migrations or mixing from earlier than out of Africa events. </div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD3-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="182" src="https://sites.google.com/site/fennobga/Afr-PCAD3-040214.png" width="320" /></a></div>
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Dimension 3 - blue - Africans, brown - Non-Africans.</div>
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This maybe make dimension 2 and 3 best for investigation of African and East-Asian/Siberian minority ancestry among Europeans. As we can see Spanish and Sardinians appear to have the most African like minority admixture while Saamis, Mordovians and Vologda Russians shows the most East-Asian or Siberian admixture.</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD2D3Overview-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="277" src="https://sites.google.com/site/fennobga/Afr-PCAD2D3Overview-040214.png" width="320" /></a></div>
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PCA Dimension 2 (horizontal) and 3 (vertical)</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD2D3OverviewEurope-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://sites.google.com/site/fennobga/Afr-PCAD2D3OverviewEurope-040214.png" width="320" /></a></div>
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PCA Dimension 2 (horizontal) and 3 (vertical) Europe Overview</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD2D3OverviewEuropeInd-040214.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="312" src="https://sites.google.com/site/fennobga/Afr-PCAD2D3OverviewEuropeInd-040214.png" width="320" /></a></div>
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<b>European zoomed gradient maps:</b></div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD1-040214-Euro.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="311" src="https://sites.google.com/site/fennobga/Afr-PCAD1-040214-Euro.png" width="320" /></a></div>
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Dimension 1 - Europe</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD2-040214-Euro.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://sites.google.com/site/fennobga/Afr-PCAD2-040214-Euro.png" width="320" /></a></div>
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Dimension 2 - Europe (Note Saamis should be blue)</div>
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<a href="https://sites.google.com/site/fennobga/Afr-PCAD3-040214-Euro.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="317" src="https://sites.google.com/site/fennobga/Afr-PCAD3-040214-Euro.png" width="320" /></a></div>
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Dimension 3 - Europe </div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com17tag:blogger.com,1999:blog-1820243696969815052.post-13532837307688166502014-01-29T10:37:00.001+01:002014-01-29T11:08:19.645+01:00Is there a "East-Asian" influence in Continental Europeans? Part IIThis post goes further in the the previous post "Is there a <a href="http://fennoscandia.blogspot.no/2014/01/is-there-east-asian-influence-in.html" target="_blank">"East-Asian" influence in Continental Europeans?"</a>. It further elaborate on the separate run Finestructure using European, Siberian and East-Asian samples shown at the down part of the previous blogpost. In that part we only looked at the first dimension 1 and 2 and here we move further to the higher dimensions.<br />
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The third dimension is actually the same dimension we have seen many times when doing the PCA plot for the European panel in this project giving the characteristic "V" shape where South Europeans cluster at the root while Finns, Saamis cluster on one branch while Eastern Europeans branch on the other. This dimension is the Saami-Finnish branch variation vs South Europe. This variations peaks on one side among Saamis and Finns and as we can see from the gradient map it also exists consistently among the Siberians but not among the East-Asians. On the other side it peaks among Sardinians, Basque and Italians and the East-Asians cluster here with the South-Europeans. I am very unsure about the interpretation here but as both Siberians and East-Asians is not at the extreme on either side of the variation I tend to believe it may represent a gene flow from Europe towards Siberia and East-Asia. Maybe the northern spread represent a geneflow of Saami/Finnish like hunter gatherers eastward into Siberia and the lower part a geneflow from Europe towards East-Asia through todays India.<br />
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<a href="https://sites.google.com/site/fennobga/EuroasiaD3-270114.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="132" src="https://sites.google.com/site/fennobga/EuroasiaD3-270114.png" width="320" /></a></div>
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Dimension 3 - peaks among Saami, Finns vs Sardinians and Basque</div>
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Dimension 4 is the equivalent to the other branch of the "V" in Europe. On one extreme we found the Lithuanians, Mordovians and other Eastern European populations (actually here there is a Chukchi individual that a very little higher value than the top Lithuanian). The other extreme is Basque, Western Europeans, Saamis, Scandinavians and also the East-Asians. Also here I am unsure about the interpretation but it appear to show consistency as in dimension 3 but this time with a different spread. It may be a geneflow spread from Eastern Europe eastward through Siberia.<br />
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<a href="https://sites.google.com/site/fennobga/EuroasiaD4-270114.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="137" src="https://sites.google.com/site/fennobga/EuroasiaD4-270114.png" width="320" /></a></div>
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Dimension 4 - peaks among Lithuanians vs Basque </div>
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Dimension 5 appear to be a dimension that peaks among East-Asians on one side and Siberians on the other with the Europeans between. As we can see there is tendency to Siberian like influence in western part of Europe.<br />
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<a href="https://sites.google.com/site/fennobga/EuroasiaD5-270114.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="137" src="https://sites.google.com/site/fennobga/EuroasiaD5-270114.png" width="320" /></a></div>
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Dimension 5 - peaks among Siberians vs East-Asians</div>
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This dimension appear interesting with regard to the question if there is any East-Asian influence among continental Europeans. So if we zoom to Europe and remove the PCA elements from outside Europe leaving only the European PCA elements we cen a more detailed view.</div>
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<a href="https://sites.google.com/site/fennobga/EuroasiaD5-270114-EuropeZoom.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="276" src="https://sites.google.com/site/fennobga/EuroasiaD5-270114-EuropeZoom.png" width="320" /></a></div>
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Dimension 5 - peaks among Siberians vs East-Asians
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What is very striking here is that it appear to peak among Eastern Europeans and to some degree also Finns but appear least among the Basque, Western and South-West Europeans and among Norwegians and Saamis. It may suggest a gene flow from East-Asia that have divided in half an earlier haplotype distribution that may have gone from Western Europe to Siberia but now only remains among Western Europeans Scandinavians and Siberians. This dimension has a striking resemble to <a href="https://sites.google.com/site/fennobga/CCEuropeD4map191213.png" target="_blank">another dimension</a> in Europe I have earlier believed to be internal European variation.<br />
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The PCA coordinates for all individuals and all dimensions can be <a href="https://sites.google.com/site/fennobga/CCPCASIBEAEURO-270114.csv" target="_blank">downloaded here</a>.<br />
.Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com55tag:blogger.com,1999:blog-1820243696969815052.post-32326843793555990902014-01-24T13:36:00.000+01:002014-01-27T11:06:20.046+01:00Is there a "East-Asian" influence in Continental Europeans?<i>Updated 27/01/14</i><br />
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This question have been following me since the last previous blogpost where I found this geographical distribution of chunkcounts PCA dimension 4 between Euroasian populations.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://sites.google.com/site/fennobga/Euroasia191213-D4.png" width="320" /></a></div>
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Everybody would probably agree about the northern distribution shown in blue and green apparently showing a genetic connection between North-East European populations like Saamis and Finns and Northern Siberian populations all the way from Fennoscandia to Beringia in Eastern Siberia as shown many times in this blog, from university research and from other bloggers. However if we look closer at the color distribution for the map:<br />
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<a href="https://sites.google.com/site/fennobga/ColorRange.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://sites.google.com/site/fennobga/ColorRange.png" /></a></div>
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We should of course not take this color distribution to literally as PCA plots distirbutions can be affected by many things but as we can see the red grade is close to the brown. This probably means the whole area from western continental Europe to East- and South-East Asia appear to show haplotype similarity. So it appears not only to have been a northern East-West influence but also a southern East-West influence as well.<br />
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To investigate this further I did a seperate run Chromopainter using 23k linked SNP at Chromosome 1 with a selection of individuals that had been phased together with over 2000 individuals using a high number of iterations in BEAGLE minimizing the error rate to a minimum. I used Chromopainters admixture functionality to design a admixture test using the relevant East-Asian, African and Siberian populations. As far I know from previous screening using ADMIXTURE all these individuals appear unmixed without any European admixture.<br />
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakADMIXLINKED.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/HanAndKoryakADMIXLINKED.png" width="237" /></a></div>
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As we can see North-East Europeans appears to score low on East-Asian influence while continental Europeans from western and central Europe appear to score rather high vs the East-Asians. As expected we see the largest African like influence among the more southern populations and the North-Siberian influence in the more North-East European populations. Please note as this result is based on only 1 chromosome it doesn't always correlate 100% with the result of a whole genome analysis. There is a strong negative correlation between the East-Asian and Siberian component at -0.56 and there is even a stronger negative correlation between the Siberian and African component. The correlation between the East-Asian and Siberian component is weak at -0.17.<br />
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We can further see this using a area plot for the same data. The continental European populations from western and central Europe appear quite consistent to be closer to the East-Asian populations.<br />
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakADMIXLINKEDAREA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://sites.google.com/site/fennobga/HanAndKoryakADMIXLINKEDAREA.png" width="320" /></a></div>
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In Finestructure (from the previous run with the whole genome using superindividuals) the clustering appear to confirm what was observed above. The East-Asian influence appear rather consistent for all European populations included. In the North-East European populations this East-Asian influence appear to be lacking or less but the North-Siberian influence appear as expected from earlier analysis.<br />
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakCCheatmapSnapshot.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="16" src="https://sites.google.com/site/fennobga/HanAndKoryakCCheatmapSnapshot.png" width="320" /></a></div>
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<b>Individual results for project participants for PCA dimension 4 shown in the first image above. The first column show the actual PCA plot value and the second the ranking seen from top as in East-Asian and bottom as in Siberian.</b><br />
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD4-IndividualResults.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD4-IndividualResults.png" width="9" /></a></div>
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<b>This is a seperate PCA run using Europeans, East Asians and Siberians as reference. The X axis (horizontal) shows dimension 1 and the Y-axis (vetical) shows dimension 2. The X axis shows the European vs East-Asian influence, the Y-axis shows the European vs Siberian influence.</b></div>
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB.png" width="320" /></a></div>
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Europe vs East Asia and Siberians overview</div>
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB-Europe.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="296" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB-Europe.png" width="320" /></a></div>
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Europe vs East Asia and Siberians zoomed at Europeans</div>
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB-Europe-detailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="315" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-D2-OverviewEAvsSIB-Europe-detailed.png" width="320" /></a></div>
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Europe vs East Asia and Siberians zoomed at Europeans detailed </div>
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-EuropeGradientvsEA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="295" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD1-EuropeGradientvsEA.png" width="320" /></a></div>
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Gradient map of PCA dimension 1 - blue most East-Asian, brown least East-Asian like.</div>
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<a href="https://sites.google.com/site/fennobga/HanAndKoryakPCAD2-EuropeGradientvsEA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="287" src="https://sites.google.com/site/fennobga/HanAndKoryakPCAD2-EuropeGradientvsEA.png" width="320" /></a></div>
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Gradient map of PCA dimension 2 - blue least Siberian like, brown most Siberian like </div>
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<a href="https://sites.google.com/site/fennobga/ColorRange.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://sites.google.com/site/fennobga/ColorRange.png" /></a></div>
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<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com29tag:blogger.com,1999:blog-1820243696969815052.post-38032532226672796102014-01-10T09:37:00.001+01:002014-01-16T14:12:19.155+01:00Euroasian variation gradiation mapsThis is a graphic presentation of the 7 Euroasian haplotype based (chunkcount) PCA plots from the latest project run using 289k linked SNP's. The average number of SNP in each segment chunk in the world panel is 13 (with a heavy overweight of Europeans and Northern Europeans in particular). This analysis is at this stage experimental. Please ignore coloring in Africa, Australia and Greenland as no populations are included from these continents.<br />
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The first dimension peaks on one side among Finns and Saamis (brown), and on the other side among Panya, Chukchi and Cambodians (light blue or blue). It appears all Fennoscandians in general belongs to this brown component.. This component appear identical to <a href="https://sites.google.com/site/fennobga/CCEuropeD1map191213.png" target="_blank">dimension 1</a> in the previous analysis. As this is the first dimension it also explain the largest variation in haplotypes between the populations. As the "blue side" here appear mostly at the coast peaking among populations that show affiliation to Papuans and Melanasians I suspect it seperate this ancient population from old European hunter gatherers.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="https://sites.google.com/site/fennobga/Euroasia191213-D1.png" width="320" /></a></div>
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Euroasian dimension 1</div>
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The second dimension peaks on one side among Lithuanians and Scandinavians and on the other side among the "The Others" containing the remaing individuals, but in the remaining panel it is peaks among Miao and some other East-Asian population. It seem to show a clear division of West and East Euroasian populations. All Fennoscandians belong in general to this western cluster.</div>
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="https://sites.google.com/site/fennobga/Euroasia191213-D2.png" width="320" /></a></div>
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Euroasian dimension 2</div>
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The third dimension peaks on one side among the "Others" and secondary at Bedouins and other Middle East populations and on the other side among North Siberian populations. It seem to represent influence from the African continent. This influence have reached as far north as South-Scandinavia but to less extent among Saamis and Finns. This dimension may be related to <a href="https://sites.google.com/site/fennobga/CCEuropeD3map191213.png" target="_blank">dimension 3</a> in the previous analysis.</div>
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="https://sites.google.com/site/fennobga/Euroasia191213-D3.png" width="320" /></a></div>
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Euroasian dimension 3 </div>
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The fourth dimension peaks among Dai, Cambodian and Han in South-East Asian on one side and among Koryak, Yugagir and Nganassans in North-Siberia. Saamis, Finns and to a degree Scandinavians seems most similar in variance to the North-Siberian group while Continental-Europeans appears more similar to the South-East Asian group.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://sites.google.com/site/fennobga/Euroasia191213-D4.png" width="320" /></a></div>
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Euroasian dimension 4 </div>
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The fifth component peaks among Saamis, Finns and some South-East Asian populations on one side and among Northern Siberians on the other. Scandinavians appear less related to this dimension. This dimension may be related to <a href="https://sites.google.com/site/fennobga/CCEuropeD3map191213.png" target="_blank">dimension 3</a> in the previous analysis. <br />
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This component appears more difficult to explain as other analysis have shown no connection between Saamis, Finns and South-East Asians but to North-Siberians as in dimension 4. It may be an effect of having large sample of Europeans and small sample of other populations however its striking that the clustering appears consistent among the various non-European populations and not spread out randomly as if there was no structure. As far as I know and can remember there has not been done such wide scale analysis before using linked haplotypes so it may be something not seen before.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D5.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="180" src="https://sites.google.com/site/fennobga/Euroasia191213-D5.png" width="320" /></a></div>
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Euroasian dimension 5 </div>
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The sixth dimension peaks among East-Asians on one side and the Indian subcontinent on the other. Saamis Finns appear a little closer to the Indian subcontinent than Scandinavians.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D6.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://sites.google.com/site/fennobga/Euroasia191213-D6.png" width="320" /></a></div>
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Euroasian dimension 6 </div>
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The seventh dimension peaks among the Lithuanians and Koryak on one side and among the Chukchi, South-Indians and among some North-Siberians. In more general terms as the heatmap shows similarity between Eastern Europe and South-East Asians. This dimension as dimension 5 appears difficult to explain and the same stated about this there apply here as well.<br />
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<a href="https://sites.google.com/site/fennobga/Euroasia191213-D7.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://sites.google.com/site/fennobga/Euroasia191213-D7.png" width="320" /></a></div>
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Euroasian dimension 7</div>
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The remaining higher dimensions appear to show local variation between Siberian groups. </div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com1tag:blogger.com,1999:blog-1820243696969815052.post-91024983764795461782013-12-22T12:19:00.000+01:002014-01-16T14:13:14.718+01:00Updated Europe Analysis(Updated 26/12-2013) This is the first updated Europe analysis using the "superindividual" approach where all individuals not of interest is group into the "other" group. Just as in the Fennoscanda analysis it appear to give added resolution to the results.<br />
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The chunkcount heatmap show much the same as in previous analysis but the new cluster seen in the Fennoscandia analysis also appear here. Chunkcounts is the total number of identical and related segments of DNA between any individual. The intensity of the colors on the heatmap and the closeness in the tree branch indicate relatedness to other individuals or groups.<br />
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<a href="https://sites.google.com/site/fennobga/EuropeCCAggr191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/EuropeCCAggr191213.png" width="320" /></a></div>
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CC Aggregated Europe linked 289k</div>
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<a href="https://sites.google.com/site/fennobga/EuropeCCRaw191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/EuropeCCRaw191213.png" width="320" /></a></div>
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CC Raw Europe linked 289k </div>
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The PCA overview of Europe appears to be better than previous analysis by using superindividual grouping for "others". We can now for example see a clear differentiation between Finns and Saamis in dimension 3 horizontal and dimension vertical 4. The differentiation in dimension 4 appears to be that Saamis pull to the same level as the Basque and Sardinians in this axis. </div>
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<a href="https://sites.google.com/site/fennobga/EuropeCCPCAOverview191213D3-D4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/EuropeCCPCAOverview191213D3-D4.png" width="320" /></a></div>
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CC Europe PCA Overview linked 289k</div>
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<a href="https://sites.google.com/site/fennobga/EuropeCCPCAAIND-D3D4-191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="310" src="https://sites.google.com/site/fennobga/EuropeCCPCAAIND-D3D4-191213.png" width="320" /></a></div>
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CC Europe PCA Individuals linked 289k</div>
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<b><u>The PCA components presented in geographical heatmaps:</u></b></div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD1map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="315" src="https://sites.google.com/site/fennobga/CCEuropeD1map191213.png" width="320" /></a></div>
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Dimension 1 - external peaks in Finns. Opposite Spanish, Sardinians and Romanians. What source "Others" is is not known but appears to be close.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD2map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="304" src="https://sites.google.com/site/fennobga/CCEuropeD2map191213.png" width="320" /></a></div>
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Dimension 2 - external peaks in Albanians, Mordovians, Vologa Russians and Saamis. Opposite Scandinavians. May suggest a non-European influence that have arrived far north and far south into Europe or/and foundereffect among Scandinavians.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD3map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/CCEuropeD3map191213.png" width="318" /></a></div>
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Dimension 3 - internal peaks in Finns and Saamis. Opposite Basque and Sardinians. May reflect expansion of agriculture to Europe.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD4map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="245" src="https://sites.google.com/site/fennobga/CCEuropeD4map191213.png" width="320" /></a></div>
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Dimension 4 - internal peaks in Lithuanians, Mordovians, Belorussians, Ukranians. Opposite Basque Sardinians and Saamis. May reflect Eastern European expansion and/or foundereffect. The ancestry sharing along the Western European shores from Iberians to the Saamis may suggest old coastal migrations from the south to the north.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD5map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="306" src="https://sites.google.com/site/fennobga/CCEuropeD5map191213.png" width="320" /></a></div>
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Dimension 5 - internal peaks among Scandinavians and Saamis. Opposite Basque, Sardinians, Spanish and Finns. This may show an agricultural expansion from South-East Europe to Finland.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD6map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="259" src="https://sites.google.com/site/fennobga/CCEuropeD6map191213.png" width="320" /></a></div>
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Dimension 6 - internal peaks among Basque and secondary Saami. Opposite Sardinians. May suggest a common autosomal link between Saamis and Basque.</div>
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<a href="https://sites.google.com/site/fennobga/CCEuropeD7map191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/CCEuropeD7map191213.png" width="320" /></a></div>
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Dimension 7 - internal peaks among Saamis and secondary Sardinians. Opposite British and Vologda Russians. Appears specific to Saamis as rest of Europe appears quite uniform except for the Sardinians.</div>
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(Analysis in progress)<br />
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<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com9tag:blogger.com,1999:blog-1820243696969815052.post-69918215576795434122013-12-19T21:39:00.000+01:002013-12-26T14:09:48.238+01:00Updated Fennoscandia Analysis(Updated 26/12-13) Its finally time for updated Fennoscandia analysis. Its been over a half year since the last update. We have more than 53 new participants most of these are Swedes.<br />
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We do as usually look first at the heatmap that catches the main structure of the data. CC is ChunkCounts and is the total number of shared segments including identical and related segments. CL is ChunkLenght and is the total shared (both identical and related) segments in cM (centimorgans).<br />
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CC Linked Aggegated 289k </div>
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CC Linked Raw 289k
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<a href="https://sites.google.com/site/fennobga/FennoCLAggr191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="266" src="https://sites.google.com/site/fennobga/FennoCLAggr191213.png" width="320" /></a></div>
CL Linked Aggregated 289k<br />
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<a href="https://sites.google.com/site/fennobga/FennoCLRaw191213.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="266" src="https://sites.google.com/site/fennobga/FennoCLRaw191213.png" width="320" /></a></div>
CL Linked Raw 289k<br />
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The most different we see from previous Fennoscandia level analysis is the huge influx of Swedes creating a bigger cluster especially for the northern part (Norrländingar) of the country. This cluster of Swedes at the middle of the heatmap appears to show affiliation to the Southern Saami cluster consisting of SWE7 and SA3. So it appears like there must have been some kind of founder effect and maybe drift in this process that have made them look more related to each other than other Swedes and other Scandinavians from further south. This foundereffect appear to have included a Saami population or Saami like population. </div>
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There is also a secondary cluster consisting of mostly Swedes but also some Norwegians in the upper part of the heatmap below the Saami. These appears to show affiliation to the Northern Swedish cluster, Finns and individuals of mixed Scandinavian and Finnish ancestry.</div>
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<b><u>External influenced varuation</u></b><br />
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The PCA plots can as seen before be divided into external influenced variation and internal variation. Dimension 1 and 2 appear to be very similar external variations that peaks in "Others" and with Danish and Scandinavians and lowest among Finns. That this variation peaks among Danish suggest a central-European origin of this external influence. These two dimension effectively divide Scandinavians and Finns.<br />
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<a href="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="309" src="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D2.png" width="320" /></a></div>
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CC Linked PCA D1-D2 289k </div>
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Dimension 3 on the other hand reflect an external variation from "Others" that peaks among Finns and to large extent Saami and the least among Scandinavians suggesting a Eastern European continental origin for this influence. As we can see also this dimension appear to be effective to differentiate Finns and Saamis from Scandinavians but it doesnt appear so clear cut as dimension 1 and 2 above.<br />
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<a href="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="308" src="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D3.png" width="320" /></a></div>
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CC Linked PCA D1-D3 289k </div>
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<b><u>Internal influenced variation</u></b><br />
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As dimension 1 horizontal axis appears to differentiate so well the Scandinavians and Finns at each extreme we will continue to use this dimension. All the dimensions above 3 appear to show internal variation. The dimension 4 vertical axis appears to show the Scandinavian-Finn and Saami at each extreme.</div>
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<a href="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="304" src="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D4.png" width="320" /></a></div>
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CC Linked PCA D1-D4 289k</div>
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We clearly see from the new participants that NO25, SWE56, SWE62, SWE53 and SWE52 very clearly pull out of the Scandinavian cluster towards the Saamis and to some lesser degree also SWE59 and SWE55. Most of the appear to belong to the " Norrländingar" cluster.</div>
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Of individuals going away from the Finnish cluster towards the Scandinavians we can mention FI35, FI40. Of Scandinavians moving towards Finns we can mention NO21, SWE65, SWE54, NO26, SWE45, SWE55, SWE59, SWE50, SWE68.</div>
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As we can see from the heatmap the north-Swedish cluster appear to be much closer related to each than the normal Swede. This also shows in the PCA plot dimension 1-5 with dimension 1 at the horizontal and dimension 5 at the vertical.</div>
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<a href="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D5.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="307" src="https://sites.google.com/site/fennobga/FennoCCPCA191213D1-D5.png" width="320" /></a></div>
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CC Linked PCA D1-D5 289k </div>
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The "Norrländing" cluster appears to peek in Norrbotten area. As we can see the South-Saamis (SWE7+SA3) appears to attract the most of other groups to this cluster.<br />
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DImension D1-D6 appears diffcult to explain. It appears to be Finnish variation as its more dispersed among Finns than others.<br />
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CC Linked PCA D1-D6 289k</div>
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I will need some more research about this dimension. It doesnt seem to reflect the structure of Finnish subgroups in the heatmaps.<br />
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CC Linked PCA D1-D7 289k</div>
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In this plot the horizontal dimension 1 is the same as above while the dimension 7 appears to peak among the South-Saami individuals SWE7 and SA3. As we can see that both some Finns and Scandinavians climb towards these individuals. However the top other individuals closest to these South-Saamis appears to be from Västergotland and Skania area. On the Finnish side I am not sure but maybe coastal areas of Finland or from Karelia. </div>
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This clustering make me unsure and it maybe will not be cleared out properly with higher marker resolution, something I have been planning to do at least for the Fennoscandia analysis to higher power of differentiation. </div>
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I have also been looking at dimension 6 and it doesn't make sense to me currently so it add further uncertainty to the interpretation of dimension 7 a higher dimension than dimension 6 as higher dimensions means more uncertainty as individual variation become more visible in the data than in the lower dimension that capture more at the group level. </div>
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(Work in progress)</div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com1tag:blogger.com,1999:blog-1820243696969815052.post-25471733714281703412013-11-13T13:56:00.000+01:002013-11-20T12:54:19.135+01:00Ajv70 and modern European variation II<b><i>Updated: 20 Nov 2013. </i></b>This is a updated analysis of the <a href="http://fennoscandia.blogspot.no/2013/08/ajv70-and-modern-european-variation.html" target="_blank">previous</a> Ajv70 analysis. See previous blogpost about the improvements. This analysis is based on 444k SNPs after all filtering (mostly imputed for all the modern populations, for Ajv70 all SNP are actuals).<br />
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Ajv70 appears different from Ajv52 who in the <a href="http://fennoscandia.blogspot.no/2013/11/ajv52-and-european-variation-ii.html" target="_blank">previous analysis</a> appeared to be of mixed ancestry between what appeared to be a Saami like and a Baltic like or Eastern European like population. Ajv70 on the other hand in large cluster with Saamis, Vologda Russians and Mordovians and in particular with Saamis.<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70CC-091113.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/Ajv70CC-091113.png" width="320" /></a></div>
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CC Euro Overview 444k SNP<br />
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As we can see the heatmap ancestry profile for Ajv70 and for the other close clustering groups seem resemble each other. Note that Mordovians and Vologda Russians doesnt cluster with Saamis and Finns in Chromopainter-Finestructure linked mode on the heatmaps but with Eastern Europeans. This is likely due to the linked mode reflect more recent ancestry and that the unlinked mode shows more ancient ancestry and Vologda Russians and Mordovians do seem to have more recent Eastern European admixture and in the past being part of the Finnic and Volga Finnic language area. This is seen both in linked and unlinked mode but probably weights more in linked mode than in the unlinked mode making them cluster with Eastern Europeans in the linked mode. The unlinked mode also give a lower resolution as its based only on allele frequencies adding to uncertainty.<br />
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The low affiliation for Ajv70 vs the Mediterranean populations on the heatmaps is only matched by Saamis and Finns among the modern populations. Finns appears more influenced by Eastern European populations and Scandinavians than the Ajv70 while Vologda Russians and Mordovians appears more influenced by Eastern European populations. Saamis show less affiliation to Scandinavians and Eastern Europeans than both Finns and Ajv70, but Ajv70 heatmap profile do seem to resemble the Saami most. </div>
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The PCA dimensions dimension 4-5 showing internal European variation does not at first glance support the common heatmap clustering of Ajv70 vs Saamis, Vologda Russians and Mordovians as the Ajv70 appears among Scandinavians on the PCA and the Saami/Finns and Vologda Russians/Mordovians appear on very different locations on the PCA, However the heatmaps neither indicate any Scandinavian like ancestry for Ajv70 even the individual's variation is plotted in this cluster. What could explain this seemingly contradictory result that Ajv70 resemble Saamis on the heatmap but not on the PCA is the fact that Ajv70 is not <i>close in geneology</i> to the populations it cluster closest with on the heatmap and that the Saamis, Finns, Mordovians and Vologda Russians are more dissimilar to "Others" and similar to "Others" than the others, however what this dissimilarity and similarity could be can be different..<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70CCPCAD4D5-091113IND.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="277" src="https://sites.google.com/site/fennobga/Ajv70CCPCAD4D5-091113IND.png" width="320" /></a></div>
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CC Euro PCA 444k D4-D5</div>
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First about "not close in geneology". It can be best observed if we on a Europe PCA included related Orcadians and unrelated British. The Orcadians would form a clear outgroup on the PCA from the British even their ancestry profile on the heatmaps for the Orcadians wouldnt look much different from the British except for their internal sharing due to close relatedness and would else branch close to the unrelated British. <br />
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For the same reason Ajv70 would not cluster with Saamis and Finns on the PCA plot even they do cluster on the heatmap and else shows very similar profile with Finns and especially Saami. The explanation would therefore be that Ajv70 was not part in the founder effect that made the modern day Saamis and Finnish cluster due to closer relatedness to each other and therefore Ajv70 appears among the next best they could cluster with, the Scandinavians on the PCA plot (In earlier linked analysis Scandinavians shows both Saami and Finnish admixture) compared to continental Europeans so it would make sense.<br />
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Second about "dissimilarity" and "similarity" vs external influences or "Others". In dimension 1 and 2 vs the "Others" (the rest of the world panel) we seem to catch variation that could also explain why the Ajv70 heatmap clustering also include Mordovians and Vologda Russians even the European PCA dimension 4-5 do not support this clustering.</div>
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<a href="https://sites.google.com/site/fennobga/Ajv70CCPCAD1D2-091113IND.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="289" src="https://sites.google.com/site/fennobga/Ajv70CCPCAD1D2-091113IND.png" width="320" /></a></div>
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CC Euro PCA 444k D1-D2</div>
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This PCA plot describe the degree of similarity and dissimilarity vs the "Others". As we can see here Lithuanians, Scandinavians and many more form the upper left extreme and middle of the plot showing variation closest to the "Others" while the Saamis showing variation most distant to the "Others" in the lower right. The Ajv70 is within the range of the Saamis in this plot. There is also one Vologda Russian within this range too else the Vologda Russians and Mordovians is the next to follow up to the left after the Saamis and Ajv70. In PCA dimension 3 we also have a dimension where the Saamis, Vologda Russians, Mordovians and to some extent Finns is closest to the "Others" (not shown). The position on these dimensions can have have multiple explanations whatever each individual have been or been not influenced in various degree by the category "Others" and the very diverse panel included in this. So this means the dissimilarity for Saamis, Mordovians and Vologda Russians not necessarily is the same dissimilarity just more dissimilar than "Others" category, for example the Saamis probably pull high towards "Others" dimension 3 due to what appears as Siberian like minority ancestry while the Ajv70 who shows no such similar pull probably pull towards the "Others" because of what may be minority Afircan like ancestry (may also be erroneous affiliation due to contamination). This could affect the Finestructure tree clustering in unlinked mode giving adding Vologda Russians and Mordovians to the Saami, Finns and Ajv70 cluster.<br />
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<b>Conclusion: </b>Ajv70 appear to have the most similar heatmap profile to the Saamis but this individual do not seem to have been part of the same founder effect that made the higher genetic sharing between modern Saamis and Finns and therefore do not cluster together with the Finns and the Saamis on the PCA instead making Ajv70 cluster "incorrect" with their closest neighbors Scandinavians. Ajv70 neither show any significant degree of influence from the Baltic or Eastern European populations like Ajv52 who made Ajv52 appear to <a href="http://fennoscandia.blogspot.no/2013/11/ajv52-and-european-variation-ii.html" target="_blank">shift away</a> into open space from Ajv70 position among Scandinavians closer to the Eastern European populations. The Ajv52's clustering with Scandinavian-Saami mixed individuals when adding some Baltic like admixture seem to further support that Ajv70 mostly resemble a Saami like population. Next it would make sense to check if Ire8 may have been part of the common modern Saami-Finns foundereffect. Earlier analysis may suggest it to certain degree.<br />
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<b>Edit 19/11-13 </b>broader overview with more European and Middle-Eastern populations. It is again very clear that Ajv70 cluster with Uralic or earlier Uralic populations and especially the Saami.<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70CC-091113V2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/Ajv70CC-091113V2.png" width="320" /></a></div>
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CC Euro Overview extended 444k SNP <b><br /></b></div>
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<b>Individual results:</b><br />
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CC Euro haploid 444k</div>
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CC Euro diploid 444k</div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com1tag:blogger.com,1999:blog-1820243696969815052.post-91088275981212426682013-11-08T13:20:00.001+01:002013-11-20T13:21:00.676+01:00Ajv52 and European variation IIThis is a updated analysis of the <a href="http://fennoscandia.blogspot.no/2013/08/ajv52-and-european-variation.html" target="_blank">previous</a> Ajv52 analysis. In the previous analysis it was difficult to find any proper affiliation of the Ajv52 individual. The reason for seems now to be that I only did the mapping- and base quality filtering but not the additional filtering needed to remove what could be contamination. This would as suggested to me by the author of Skoglund 2012 make the ancient genomes appear more African like than they really were. So this time I followed the remaining contamination procedure except for gap filtering as this wasn't described in detail in the supplementary and I removed all positions with multiple reads (author randomly chosed one random if multiple). I also this time didn't do any LD prunning in PLINK as the authors of Chromopainter-Finestructure commented LD would be taken into consideration in the Chromopainter unlinked mode. I also grouped all individuals not of interest into superindividuals ("others") in Finestructure also as recommened by the Chromopainter-Finestructure authors. This analysis is therefore based on 261k SNP after contamination filtering.<br />
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As we can see below the Ajv52 have made an interesting clustering at large together with other groups of mixed Scandinavian and Saami or Finnish ancestry and in particular to the group of mixed Scandinavian-Saami ancestry (NOR-SAM). This is interesting if one sees this in light of my earlier <a href="http://fennoscandia.blogspot.com/2013/08/ire8-and-modern-european-variation.html" target="_blank">Ire8</a> analysis (Ire8 will be reanalyzed using similar approach later) where Ire8 very clearly clustered with the Saami-Finnish group. If looking at the heatmap we can see that Ajv52 shows an increased affiliation to the Baltic populations compared to others in the larger group at the same time as Ajv52 shows increased affiliation to Saamis and Finns the Baltics continental Europeans and even Scandinavians doesn't have. <br />
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<a href="https://sites.google.com/site/fennobga/OverviewEuropeAjv52-081113.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><br /></a></div>
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<img border="0" height="288" src="https://sites.google.com/site/fennobga/OverviewEuropeAjv52-081113.png" style="cursor: move;" width="320" /></div>
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CC Europe Overview 261k SNP </div>
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This suggest that Ire8 may have represented the receiving population of ancient Gotland who had similarity to modern day Saamis and Finns while Ajv52 may represent a mix with this population and a population migrating across from the Baltic region.<br />
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<b>EDIT 9 Nov 13:</b> have added individual results. I have added heatmap results both in haploid and diploid mode as the Ajv52 analysis is Chromopainter have been done in haploid mode (Ajv52 have only "homologus" data). Diploid mode have been made by using superindividuals.<br />
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In diploid mode we see that Ajv52 cluster with NO6, NO7 and SWE40. In haploid mode we see Ajv52 cluster with SWE40_A, SWE40_B, NO7_A, NO7_B, NO6_A, NO6_B, SWE7_A and SWE11_A. All these individuals are of mixed Scandinavian-Saami ancestry.<br />
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<a href="https://sites.google.com/site/fennobga/Ajv52haplo081113.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/Ajv52haplo081113.png" width="320" /></a></div>
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CC Europe Haploid 261k SNP</div>
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CC Europe Diploid 261k SNP </div>
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<b>Edit 11 Nov 13:</b> The PCA plot for dimension 4 and 5 clearly shows that Ajv52 have a shift toward Eastern Europe compared to <a href="http://fennoscandia.blogspot.no/2013/11/ajv70-and-modern-european-variation-ii.html" target="_blank">Ajv70</a> who is in the Scandinavian cluster. See discussion about Ajv70 position on PCA vs heatmap in the Ajv70 post as it relates to Ajv52 as well.</div>
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CC Europe diploid D4-D5 261k SNP<br />
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<b>Edit 19 Nov 13</b>: Extended Overview of Ajv52's clustering with European populations. We still see that Ajv52 cluster with Scandinavian-Saami mixed ancestry individuals.<br />
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<a href="https://sites.google.com/site/fennobga/OverviewEuropeAjv52V2-081113.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/OverviewEuropeAjv52V2-081113.png" width="320" /></a></div>
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CC Europe extended Overview 261k SNP </div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com2tag:blogger.com,1999:blog-1820243696969815052.post-30809458848673892902013-10-15T23:29:00.000+02:002013-10-15T23:31:36.235+02:00Digging deeper in Fennoscandian ancestry IIThis is a continuation of the <a href="http://fennoscandia.blogspot.no/2013/10/digging-deeper-in-fennoscandian.html" target="_blank">previous analysis</a> (not a new analysis run!) and this time we look at the analysis possibilities of differentiating Scandinavians (Swedes, Norwegians, Danes). This time all individuals who shows considerable Saami (both North-Saami like or South-Saami like) or Finnish admixture in the previous analysis was removed from further analysis to keep any outside influence reduced to a minimum and lumped into the "other" group containing the rest of the world.<br />
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The data was run through Finestructures clustering processing but it was unable to differentiate the remaining Scandinavians meaning it appeared by the software to be one population. However in the PCA plot it was possible to infer structure. As we so in the previous analysis the first two dimensions of the PCA plot appears to reflect level of external influences in Scandinavians. In both dimensions the Norwegians clustered in the upper left corner closest to the "others" while Swedes clustered in much of the lower right corner but with a huge spread over large part of the plot. The single Danish individual appear to cluster with the Norwegians.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD1-D2ScandOthers151013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="279" src="https://sites.google.com/site/fennobga/PCAD1-D2ScandOthers151013.png" width="320" /></a></div>
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PCA dimension 1(horizontal) and 2 (vertical)</div>
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Dimension 3 on the other hand appears to be internal between Norwegians and Swedes, below together with dimension 2 and seem to give a better clustering. The Danish individual still in the Norwegian cluster but closer to the Swedes.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD2-D3ScandOthers151013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="283" src="https://sites.google.com/site/fennobga/PCAD2-D3ScandOthers151013.png" width="320" /></a></div>
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PCA dimension 2(H) and 3 (V)</div>
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So the Chromopainter-Finestructure pipeline appears to be able to differentiate Norwegian and Swedish ancestry even only using 289k SNP's. The division isnt entirely clear cut but there have been populations movement between these countries for many centuries so the classification labels may not be entirely correct and some individuals also have mixed backgrounds.Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com13tag:blogger.com,1999:blog-1820243696969815052.post-20926052195119401782013-10-05T10:17:00.002+02:002013-10-05T10:35:37.152+02:00Digging deeper in Fennoscandian ancestry II have been the last few months become more aware by the authors of Chromopainter-Finestructure that I have not been doing the analysis completely "according to book" even the software manuals have not being saying it explicitly.<br />
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I have from the start had this practice of running the Chromopainter-Finestructure analysis with the whole world panel and then later extracted from the output file the subdata from each run into a European panel and into a Fennoscandian panel for more detailed local analysis. However actually you should use the "superindividual" and "continent" functionality in Finestructure to get the analysis right and no file editing necessary and you also need to do a new ChromoCombine run with the forcefiles with these superindividuals.<br />
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I have been testing the difference using my earlier practice in the last standard run (this is NOT a new run!) data with these new settings to compare the results. It appears that after the advice from the authors its possible to extract even more information from the run with the current resolution than I was aware of even at Fennoscandiia level. I have in this reanalysis grouped all others than Fennoscandia into the superindividual "Others".<br />
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First the heatmaps. As we can see as before the heatmap identify a range of main clusters as before, some may notice that the numbers of identified clusters seem to be lower than from previous runs.<br />
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<a href="https://sites.google.com/site/fennobga/FennoCCAggr041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/FennoCCAggr041013.png" width="320" /></a></div>
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CC Fennoscandia 289k Aggregated</div>
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CC Fennoscandia 289k Raw</div>
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We then turn the attention to the PCA plots to see if we can infer more resolution than the standard heatmaps. As the superindividual "Others" contain much of the rest of the world it appears quite distant in both heatmap tree and the PCA. The "Other" group dominate the first 3 PCA dimensions as it appears far away from the Fennoscandia group in sum. The direction of "Others" are indicated on the plot.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD1-D2Others.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="276" src="https://sites.google.com/site/fennobga/PCAD1-D2Others.png" width="320" /></a></div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D2041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="250" src="https://sites.google.com/site/fennobga/PCAD1-D2041013.png" width="320" /></a></div>
PCA D1-D2 Fenno vs Others</div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D3Others.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="266" src="https://sites.google.com/site/fennobga/PCAD1-D3Others.png" width="320" /></a></div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D3041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="249" src="https://sites.google.com/site/fennobga/PCAD1-D3041013.png" width="320" /></a></div>
PCA D1-D3 Fenno vs Others </div>
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As I understand it these PCA D1-D3 reflect level of external influences on Fennoscandinans possibly from continental Europe as DK1 is closest "Others" in both dimensions. Scandinavians are closest to "others" on both dimension 1 and 2 while Finns and Saamis are closest "others" in dimension 3 especially FI18. In any way all these 3 dimensions can be used to differentiate Scandinavians vs Finns and Saamis. We had a similar dimension in the earlier local Fennoscandia analysis.</div>
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In dimension 4 we get a dimension that is able to differentiate Saamis from Finns and Scandinavians. We see North-Saami individuals at the extreme. If we combine this dimension with any other two dimensions we would get a plot differentiating Scandinavians, Finns and Saamis. Notice that we now also get a better grouping of the Finns.</div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D4Others.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="272" src="https://sites.google.com/site/fennobga/PCAD1-D4Others.png" width="320" /></a></div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D4041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="245" src="https://sites.google.com/site/fennobga/PCAD1-D4041013.png" width="320" /></a></div>
PCA D1-D4 Fenno vs Others</div>
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At this point from previous analysis we would not get any more information using my earlier method, however using these new setting we can dig even deeper in the PCA plot. This can be shown below as we move to dimension 5. <br />
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As we can see below SWE7 a South-Saami individual clearly stand out in a own dimension separately from dimension 4 peaking in North-Saami. What this mean that using this new method the project can explicit differentiate South-Saami ancestry from North-Saami ancestry.<br />
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In earlier analysis the South-Saami ancestry appear to blend in somewhere between North-Saami and Scandinavians but as this show they are in a dimension of their own even they do share ancestry with North-Saami in dimension 4. However the North-Saami share very little of this South-Saami specific component but it appears far more common among other Fennoscandians both Scandinavians and even some Finns than the North-Saami specific component.</div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D5Others.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="255" src="https://sites.google.com/site/fennobga/PCAD1-D5Others.png" width="320" /></a></div>
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<a href="https://sites.google.com/site/fennobga/PCAD1-D5041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="252" src="https://sites.google.com/site/fennobga/PCAD1-D5041013.png" width="320" /></a></div>
PCA D1-D5 Fenno vs Others </div>
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This means that we can combine dimension 4 and 5 to map further explicit for Saami ancestry both North and South in Finns and Scandinavians.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD4-D5041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="275" src="https://sites.google.com/site/fennobga/PCAD4-D5041013.png" width="320" /></a></div>
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PCA D4-D5 Fenno vs Others<br />
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There are more dimensions after dimension 5 but they appear to become more unclear and increasingly reflect individual variation. However dimension 6 (vertical axis) may be something worth looking at in the future as it appears populated with what seem to be western Finns, central Swedes and two Saamis depending on where you set the borderline.<br />
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<a href="https://sites.google.com/site/fennobga/PCAD1-D6041013.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="250" src="https://sites.google.com/site/fennobga/PCAD1-D6041013.png" width="320" /></a></div>
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PCA D1-D6 Fenno vs Others </div>
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CONCLUSION: This study shows that using superindividuals one can extract even more detailed ancestry information from autosomal genetic data within Fennoscandia. This new knowledge will be used in future project updates.</div>
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<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com0tag:blogger.com,1999:blog-1820243696969815052.post-80330089138241174772013-09-18T13:56:00.000+02:002014-10-08T09:51:58.704+02:00Saami ancestry and the MDLP Oracle-x Population Fitting<span style="color: red;"><strong>Update</strong> 08.10.2014: The MDLP calculators have been updated and now do not give the results as shown below. This post is then considered outdated and should not be used as guide vs the MDLP calculators.</span><br />
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This is a short test of MDLP Oracle-x Population Fitting at <a href="http://www.gedmatch.com/" target="_blank">Gedmatch</a> ability to catch Saami ancestry. Only MDLP calculators have been tested as these are the only one with Saami population reference. <br />
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As the test shows finding Saami ancestry using these calculators may give very different and even erroneous results (no Saami ancestry or minor Saami ancestry when there is actually major Saami ancestry) but one stand clearly out as the preferred choice. The "test subject" (with consent) is a North-Saami individual participating in the project with mostly Saami ancestry.<br />
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<i>Absent</i> = Saami ancestry not detected.<br />
<i>Minor</i> = Saami ancestry detected but as minority ancestry.<br />
<i>Top but minor</i> = Saami ancestry detected as top population but with less than 50%.<br />
<i>Top majority</i> = Saami ancestry detected as top population with more than 50%.<br />
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<a href="https://sites.google.com/site/fennobga/MDLPComparisment.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="24" src="https://sites.google.com/site/fennobga/MDLPComparisment.png" width="320" /></a></div>
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As the result shows using <i>MDLP K=5 Oracle X "Pct. Calc. Option 1"</i> appears to be the preferred choice to detect Saami ancestry.<br />
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<b>EDIT 20/9-13</b><br />
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Please note that all the other functionalities of the different versions of the MDLP calculators like Oracle and Oracle-4 was neither able to find that the Saami individual had majority Saami ancestry. Some where able to infer Saami minority ancestry and some didnt detect anything at all. The exception again is the MDLP K=5 that managed in Oracle to get a Saami population as number two and 3 of 4 in Oracle-4. Thie MDLP 27 calculator (not in Gedmatch) managed using Gaussian method 1 population mode to infer the correct population but failed in the 2,3 and 4 approximations.<br />
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<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com28tag:blogger.com,1999:blog-1820243696969815052.post-5992388820666078042013-09-11T11:50:00.001+02:002013-09-20T16:57:28.647+02:00La Braña 2 and modern European variationThis is a reanalysis of the La Braña's but this time separately. The La Braña 2 matched the 1000 genome reference panel with 56k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 56k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 26k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 21k SNP's.<br />
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The heatmap, tree structure and PCA plot below shows somewhat different result than for the La Braña 1 as La Braña 2 appears to have a position that cluster around with the Scandinavian-Saamis (individuals with both Scandinavian and Saami background).<br />
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This means that the <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">original analysis</a> of the composite La Braña need to be adjusted after the findings here. La Braña 2 appears most similar to individuals of mixed Scandinavian and Saami ancestry..<br />
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<a href="https://sites.google.com/site/fennobga/EUROCCBRA2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/EUROCCBRA2.png" width="320" /></a></div>
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CC Euro unlinked 21k</div>
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CC Euro unlinked 21k detailed </div>
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CC Euro unlinked 21k D1-D2</div>
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<a href="https://sites.google.com/site/fennobga/EUROBRA2PCAD1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/EUROBRA2PCAD1-D3.png" width="320" /></a></div>
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CC Euro unlinked 21k D1-D3<br />
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EDIT: 20/9-13</div>
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<a href="https://sites.google.com/site/fennobga/BRA2INDIVIDUALS.xls" target="_blank">Download BRA2 individual results</a></div>
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Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com3tag:blogger.com,1999:blog-1820243696969815052.post-80846458967824633252013-09-09T10:51:00.000+02:002013-09-23T08:35:46.585+02:00La Braña 1 and modern European variation.This is a reanalysis of the <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">La Braña's</a> but this time separately. The La Braña 1 matched the 1000 genome reference panel with 129k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 129k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 47k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 38k SNP's.<br />
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The heatmap and tree structure below shows somewhat different result than for the composite La Braña individual consisting of both La Braña 1 and La Braña 2. As we can see the La Braña 1 do not completely cluster witht the Finns and Saamis anymore but appears to have a more intermediate position between the Saami-Finnish cluster and the Eastern European cluster.<br />
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<a href="https://sites.google.com/site/fennobga/BRA1CCEUROt2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/BRA1CCEUROt2.png" width="320" /></a></div>
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CC Euro 47k unlinked La Braña 1</div>
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This is also reflected in the PCA D1-D2 (horisontal and vertical) where La Braña 1 appears to appear in the middle between the Finnish-Saami cluster and Eastern Europeans.<br />
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<a href="https://sites.google.com/site/fennobga/BRA1CCEUROt2detailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="141" src="https://sites.google.com/site/fennobga/BRA1CCEUROt2detailed.png" width="320" /></a></div>
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CC Euro 47k unlinked La Braña 1 detailed </div>
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<a href="https://sites.google.com/site/fennobga/BRA1PCAD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="318" src="https://sites.google.com/site/fennobga/BRA1PCAD1-D2.png" width="320" /></a></div>
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CC Euro 47k PCA unlinked D1-D2</div>
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<a href="https://sites.google.com/site/fennobga/BRA1PCAD1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="318" src="https://sites.google.com/site/fennobga/BRA1PCAD1-D3.png" width="320" /></a></div>
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CC Euro 47k PCA unlinked D1-D3</div>
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The analysis of La Braña 2 will follow later<br />
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EDIT 23/9-13<br /><br /><a href="https://sites.google.com/site/fennobga/BRA2INDIVIDUALS.xls" target="_blank">Download individual results</a><br /></div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com5tag:blogger.com,1999:blog-1820243696969815052.post-80549226160086988812013-08-29T09:37:00.001+02:002013-11-08T13:22:34.828+01:00Ajv52 and European variationEDIT: This analysis is outdated and have been reanalyzed <a href="http://fennoscandia.blogspot.no/2013/11/ajv52-and-european-variation-ii.html" target="_blank">here</a>.<br />
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The Ajv52 like <a href="http://fennoscandia.blogspot.no/2013/08/ajv70-and-modern-european-variation.html" target="_blank">Ajv70</a> and <a href="http://fennoscandia.blogspot.no/2013/08/ire8-and-modern-european-variation.html" target="_blank">Ire8</a> individual belonged to a 2800-2000 BC <a href="http://en.wikipedia.org/wiki/Pitted_Ware_culture" target="_blank">Pitted Ware Culture</a> complex found in Ajvide, Gotland, Sweden. Ajv52 belonged to mtDNA hg V. The PWC was a hunter gatherer culture.<br />
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The Ajv52 genome had in common 281k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for <a href="http://fennoscandia.blogspot.no/2013/08/ajv70-and-modern-european-variation.html" target="_blank">Ajv70</a>, <a href="http://fennoscandia.blogspot.no/2013/08/ire8-and-modern-european-variation.html" target="_blank">Ire8</a>, <a href="http://fennoscandia.blogspot.no/2013/08/gok4-and-modern-european-variation.html" target="_blank">Gok4</a>, <a href="http://fennoscandia.blogspot.no/2013/08/ste7-and-modern-european-variation.html" target="_blank">Ste7</a> and <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">La Brañas</a> (se earlier posts) imputed using BEAGLE with the same reference panel as before using both project individuals and public reference populations. The populations was further LD pruned in PLINK down to 77k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panel was extracted from a world Chromopainter run output files resulting in about 61k SNP's for Finestructure analysis. The high number of SNPs should give good resolution for further analysis.<br />
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The result seems mostly similar for Ajv52 as for Ajv70. In the above heatmap appears not to give a clear clustering to any modern European populations as Ajv52 doesnt fit into any heatbox clusters and branch out very early from the rest of the European tree, in other words no more systematic affiliation as we have seen in the analysis of the Ire8, Gok4, Ste7 and the La Brañas. There is however no doubt that Ajv52 belongs to the more northern populations in Europe if looking at the PCA plots below.<br />
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In the heatmap it seems like CR1, NO6 and NO7 appears to affliate strongest on the heatmap, this can however be the effect of these groups beeing of only one individual, but if looking at more systematic affiliation with larger samples one sees.some weaker affliation to northern and northeastern continental European populations and to south-west populations. So it might appear like Ajv52 may have some more southern ancestry than Ajv70 even they appear similar.On the PCA D1-D3 it seems Ajv52 cluster with Scandinavians but not in D1-D2.<br />
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<a href="https://sites.google.com/site/fennobga/Ajv52CCEuro.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/Ajv52CCEuro.png" width="320" /></a></div>
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CC Europe 61k unlinked</div>
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<a href="https://sites.google.com/site/fennobga/Ajv52CCEuroDetailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="142" src="https://sites.google.com/site/fennobga/Ajv52CCEuroDetailed.png" width="320" /></a></div>
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CC Europe 61k unlinked detailed</div>
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<a href="https://sites.google.com/site/fennobga/Ajv52PCAD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="318" src="https://sites.google.com/site/fennobga/Ajv52PCAD1-D2.png" width="320" /></a></div>
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CC Europe PCA 61k unlinked D1-D2</div>
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<a href="https://sites.google.com/site/fennobga/Ajv52PCAD1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="315" src="https://sites.google.com/site/fennobga/Ajv52PCAD1-D3.png" width="320" /></a></div>
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CC Europe PCA 61k unlinked D1-D3<br />
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EDIT 20/9-13</div>
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<a href="https://sites.google.com/site/fennobga/Ajv52INDIVIDUALRESULT.xls" target="_blank">Download individual results</a></div>
</div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com0tag:blogger.com,1999:blog-1820243696969815052.post-49405921189338760522013-08-26T12:55:00.001+02:002013-11-13T21:35:52.494+01:00Ajv70 and modern European variationEdit: I now consider this analysis outdated please look at the updated analysis of <a href="http://fennoscandia.blogspot.no/2013/11/ajv70-and-modern-european-variation-ii.html" target="_blank">Ajv70</a>.<br />
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The Ajv70 like <a href="http://fennoscandia.blogspot.no/2013/08/ire8-and-modern-european-variation.html" target="_blank">Ire8</a> individual belonged to a 2800-2000 BC <a href="http://en.wikipedia.org/wiki/Pitted_Ware_culture" target="_blank">Pitted Ware Culture</a> complex found in Ajvide, Gotland, Sweden. Ajv70 belonged as Ire8 to mtDNA hg U4. The PWC was a hunter gatherer culture.<br />
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The Ajv70 genome had in common 421k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for <a href="http://fennoscandia.blogspot.no/2013/08/ire8-and-modern-european-variation.html" target="_blank">Ire8</a>, <a href="http://fennoscandia.blogspot.no/2013/08/gok4-and-modern-european-variation.html" target="_blank">Gok4</a>, <a href="http://fennoscandia.blogspot.no/2013/08/ste7-and-modern-european-variation.html" target="_blank">Ste7</a> and <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">La Brañas</a> (se earlier posts) imputed using BEAGLE with the same reference panel as before using both project individuals and public reference populations. The populations was further LD pruned in PLINK down to 105k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panel was extracted from a world Chromopainter run output files resulting in about 85k SNP's for Finestructure analysis. The high number of SNPs should give good resolution for further analysis.<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70CCEuroV1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/Ajv70CCEuroV1.png" width="320" /></a></div>
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<b>Ajv70 CC unlinked Europe 85k</b></div>
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<a href="https://sites.google.com/site/fennobga/Ajv70CCEuroV1detailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="141" src="https://sites.google.com/site/fennobga/Ajv70CCEuroV1detailed.png" width="320" /></a></div>
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<b>Ajv70 CC unlinked Europe 85k</b>
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<a href="https://sites.google.com/site/fennobga/Ajv70CCEuroV2detailed.png?attredirects=0" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="144" src="https://sites.google.com/site/fennobga/Ajv70CCEuroV2detailed.png?attredirects=0" width="320" /></a></div>
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<b>Ajv70 CC unlinked Europe 85k (changed color scale to emphasise more subtle differences)</b>
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The result for Ajv70 above heatmap appears not to give a clear clustering to any modern European populations as Ajv70 doesnt fit into any heatbox clusters and branch out very early from the rest of the European tree, in other words no more systematic affiliation as we have seen in the analysis of the Ire8, Gok4, Ste7 and the La Brañas. There is however no doubt that Ajv70 belongs to the more northern populations in Europe if looking at the PCA plots below..<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70CCEuroPCAD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="319" src="https://sites.google.com/site/fennobga/Ajv70CCEuroPCAD1-D2.png" width="320" /></a></div>
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<b>Ajv70 CC PCA D1-D2 unlinked Europe 85k</b></div>
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As we can see from the main variation in thie first dimension D1 (horizontal) Ajv70 appears to cluster in the same middle area of the plot as many populations from especially northeastern continental Europe and some of the Scandinavians. The secondary dimension D2 (vertical) appears more difficult to explain. Ajv70 and one of the Saami SA2 appear alone on the upper part of the plot.but when moving further down the plot looking at the upper part of the major cluster not only other Saamis shows up but also some of the Vologda Russians, Mordovians, Belorussians, Bulgarians and Sardinians..The reason for this could be that there are individuals in continental Europe that to larger extent have Ajv70 like ancestry in this dimension than many other individuals of their own population. Scandinavians and Brits appears to show the most distant to Ajv70 in this dimension D2.</div>
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<a href="https://sites.google.com/site/fennobga/Ajv70CCEuroPCAD1-D3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="315" src="https://sites.google.com/site/fennobga/Ajv70CCEuroPCAD1-D3.png" width="320" /></a></div>
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<b>Ajv70 CC PCA D1-D3 unlinked Europe 85k</b> </div>
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If looking further to dimension D3 (vertical) on the PCA plot above we get a more familiar plot also seen in other analysis. Here we can see Ajv70 appears to locate between the Scandinavians in the middle of the plot and Vologda Russians, Russians and Mordovians.</div>
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<b>Conclusion:</b> </div>
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Ajv70 appears not to fit very well any specific modern European population but appears for certain northern, but at group level (infered from 289k analysis) from the heatmap colours Ajv70 appears to be somewhere between SA4, SWE-SAM, AUS1, NO6 and EST.<br />
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This analysis also oppose the following claim about Ajv70 made by other genome bloggers:<br />
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<a href="http://eurogenes.blogspot.no/2012/04/prehistoric-scandinavians-genetically.html" target="_blank">"Prehistoric Scandinavians genetically most similar to modern Poles</a>"<br />
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EDIT 23/9-13<br />
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<a href="https://sites.google.com/site/fennobga/Ajv70INDIVIDUAL.xls" target="_blank">Download individual results</a><br />
<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com5tag:blogger.com,1999:blog-1820243696969815052.post-33401840855738553652013-08-18T22:15:00.000+02:002013-09-23T09:21:02.015+02:00Ire8 and modern European variationThe Ire8 individual belonged to a 2800-2000 BC <a href="http://en.wikipedia.org/wiki/Pitted_Ware_culture" target="_blank">Pitted Ware Culture</a> complex found in Ajvide, Gotland, Sweden. Ire8 belonged to mtDNA hg U4. The PWC was a hunter gatherer culture. <br />
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The Ire8 genome had in common 51k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for Gok4, Ste7 and La Brañas (se earlier posts) imputed using BEAGLE with the same reference panel as before using both project individuals and public reference populations. The populations was further LD pruned in PLINK down to 22k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panal was extracted from a world Chromopainter run output files resulting in about 19k SNP's for Finestructure analysis.<br />
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As the results shows from Finestructure heatmap Ire8 appears to give an clear clustering to a commom Saami-Finnish box, and at the group level appears to be closest to SA1-SA2, Swe-Sam (equal) and Finns3. However we do not see a clear clustering as with the La Braña's vs the Saamis in the tree structure.<br />
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It seems from the heatmap coloring like Ire8 appears to have more southern ancestry than both the Saamis and the Finns suggesting contact with early farmers.<br />
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<a href="https://sites.google.com/site/fennobga/CCEuroIre8.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuroIre8.png" width="320" /></a></div>
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CC Euro Ire8 unlinked 19k</div>
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<a href="https://sites.google.com/site/fennobga/CCEuroIre8Detailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="142" src="https://sites.google.com/site/fennobga/CCEuroIre8Detailed.png" width="320" /></a></div>
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CC Euro Ire8 unlinked detailed 19k</div>
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<a href="https://sites.google.com/site/fennobga/CCEuroIre8PCAD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="318" src="https://sites.google.com/site/fennobga/CCEuroIre8PCAD1-D2.png" width="320" /></a></div>
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CC Euro PCA unlinked 19k<br />
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EDIT 23/9-13</div>
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<a href="https://sites.google.com/site/fennobga/Ire8INDIVIDUALS.xls" target="_blank">Download individual results</a></div>
</div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com3tag:blogger.com,1999:blog-1820243696969815052.post-34155688537147902222013-08-14T12:58:00.001+02:002013-09-23T09:48:41.179+02:00Gok4 and modern European variationThe Gok4 individual is as the earlier analysed <a href="http://fennoscandia.blogspot.no/2013/08/ste7-and-modern-european-variation.html" target="_blank">Ste7</a> individual in the previous posts belonging to the Funnelbeaker culture finding in Gökhem, Sweden and the first farmers in Fennoscandia. Gok4 belonged to mtDNA haplogroup H. However the autosomal DNA coverage is for this ancient individual far better than for Ste7. I managed this time to match 294k SNPs vs the 1000 genome autosomal panel that I used to impute the missing markers for a standard selection of project participants and reference populations using phasing and imputation software Beagle. These was further LD pruned down to 76k in Plink to get a set of unlinked SNPs. The data was then run in Chromopainter-Finestructure pipeline unlinked mode using a world panel and then the European panel was extracted from the outpul files giving around 63k remainng SNPs for analysis.<br />
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As the results belows shows Gok4 appears to resemble quite much the earlier Ste7 individual. The strongest affiliation is with the Sardinians, then to Italians, Iberians, Albanians, Croat and Spanish. We also see an increased affiliation with populations in Central and Northern Europe like British, Scandinavians and Austrians. The most distant populations appears to be Saamis, Mordovians and Finns.<br />
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This appear to suggest some continuity between the first farmers of Fennoscandia and the modern Scandinavians. This was not seen in the earlier Ste7 analysis but may be due to the low number of markers (6k SNPs) giving high margin of error and possible partly different ancestry in Ste7 (possible Saami like or La Braña like ancestry). This analysis however has 63k SNP's used in the analysis comparable to the earlier La Braña of Northern Spain using 68k.<br />
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<a href="https://sites.google.com/site/fennobga/CCEuroGok4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuroGok4.png" width="320" /></a></div>
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CC Euro Unlinked 63k</div>
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<a href="https://sites.google.com/site/fennobga/CCEuroGok4Detailed.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="140" src="https://sites.google.com/site/fennobga/CCEuroGok4Detailed.png" width="320" /></a></div>
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CC Euro Unlinked 63k detailed</div>
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<a href="https://sites.google.com/site/fennobga/CCEuroPCAINDGok4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="265" src="https://sites.google.com/site/fennobga/CCEuroPCAINDGok4.png" width="320" /></a></div>
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CC Euro PCA Unlinked 63k (haploid individuals)<br />
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EDIT 23/9-13</div>
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<a href="https://sites.google.com/site/fennobga/Ire8INDIVIDUALS.xls" target="_blank">Download individual results</a></div>
</div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com2tag:blogger.com,1999:blog-1820243696969815052.post-58713387457131071052013-08-02T10:09:00.000+02:002013-09-20T14:13:44.715+02:00Ste7 and modern European variationI have this time followed the same procedure as for the <a href="http://fennoscandia.blogspot.no/2013/05/la-brana-and-saamis.html" target="_blank">La Braña analysis</a> and extracted in total 13k SNP's that matched the 1000 genome reference SNP's. I further imputed these markers to a panel of project participants and reference populations, and then linkage pruned these down in Plink to 7k SNP's. I then run the data through the unlinked Chromopainter-Finestructure pipeline editing out the European populations from the output file resulting in 6k of European panel SNPs.<br />
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Again because of the very small number of SNP's the inferred structure can be both noisy and inaccurate especially for the defined groups that consists of only one individual. I also again used the "superindividuals" functionality in Finestructure for all individuals except Ste7 based on earlier 289k SNP haplotype linked clustering.<br />
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The Ste7 individual was found in <a href="https://en.wikipedia.org/wiki/Funnelbeaker_culture" target="_blank">Funnelbeaker culture</a> context in Gökheim, South Sweden and appears to represent the first farmers in Fennoscandia.<br />
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The result shows not unexpected that Ste7 shows strongest affiliations to Europe's more southern populations like especially Sardinians and Iberians, then Bulgarians, Albanians. Also some other close by populations shows stronger affiliations like Romanians, Hungarians, French, Austrian, Polish and Croat. Strangely neither the single Greek individual, Basque, Italians and Spanish shows any larger affiliation but this could be an artefact of the low resolution and large variation at individual level for the Greek individual but not for the Basque, Italians and Spanish overall. <br />
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<a href="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7.png" width="320" /></a></div>
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CC Europe Unlinked 6k<br />
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Also Ste7 shows a surprising strong sharing to the two mixed Norwegian individuals with party Saami ancestry "NOR-SAM" and two of the North-Saami individuals "SA1-2" as the more Central-European populations. This link is not seen between the Saamis and the Central-European populations so it could reflect part ancestry with a more Saami or La Braña like populations. This finding could also be the result of large individual variation (error margin) due to the low resolution (only 6k SNPs).<br />
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Other populations that show less affiliation than the above of the more southern populations are Basque, Spanish and Italians. Further north the British, Germans, Danish, Finns and Scandinavians. Further east also Ukraine, Russians, Lithuanians, Mordovians and Vologda Russians shows less affiliation.<br />
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<a href="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7Details.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="142" src="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7Details.png" width="320" /></a></div>
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CC Europe Ste7 detailed<br />
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<a href="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7PCA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="316" src="https://sites.google.com/site/fennobga/CCEuroUnlinkedSte7PCA.png" width="320" /></a></div>
CC Europe Ste7 PCA D1-D2<br />
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<b>Conclusion</b>: It appears like Ste7 are mainly of southern European ancestry but may also have "local" or ancient ancestry (se La Braña posts) as there appears to be affiliation with part of the Saami samples as well.<br />
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EDIT 20/9-13<br />
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<a href="https://sites.google.com/site/fennobga/Ste7INDIVIDUAL.xls" target="_blank">Download individual results</a></div>
Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com0tag:blogger.com,1999:blog-1820243696969815052.post-55550357571816263562013-07-04T09:28:00.001+02:002013-07-11T13:03:18.613+02:00La Braña and modern World variation III have done a new analysis of the La Braña, now using ADMIXTURE with only 4k SNP's (both LD pruned and MAF 0.05 filtered in PLINK) and over 2200 samples worldwide from different reference sets and because of the large sample size it was possible to increase the numbers of K up to 8. As a caution please remember that compared to earlier analysis the number of SNP's are very low and so the resolution is low and the individual variation large especially for the minority components compared to earlier analysis linked and unlinked, but by pooling individuals into populations this is to some extent made more even.<br />
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As we can see from the enclosed admixture bars the La Braña appears (given the considerations above) to have a very high level of North European like affiliation similar to the ones we see from the northernmost populations in Europe and is consistent with <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">earlier analysis</a> but ADMIXTURE is here not able to differentiate between them as Chromopainter-Finestructure did. The Middle-Eastern like admixture is close to 0 very different from the modern Iberian peninsula populations who reach levels up to 34%.<br />
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We further see that the Central Asian like admixture is close to zero similar to todays Iberian populations and Saamis (please note that the CA admixture in the Saami is due to only 1 individual, the rest shows close to 0 admixture), so is the affiliation to Siberians and Native Americans.<br />
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The implication of this result may be that large part of Europe was populated by hunter gatherers who mostly resembled todays North-Europeans and <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-saamis-ii.html" target="_blank">especially the Saamis</a>. Later Middle-Eastern farmers moved westward and northwards. Their genetic impact was minimal in the fringe populations in the far north. Later Central-Asian like populations moved west from the east but their genetic impact was minimal in the Iberian populations and among Saamis in Fennoscandia. The Finns, Mordovians and especially the Saami on the other appears to have received considerable Siberian like admixture from the arctic.<br />
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First in alphabetical order:<br />
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<a href="https://sites.google.com/site/fennobga/BRA-K8-ALPHA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://sites.google.com/site/fennobga/BRA-K8-ALPHA.png" width="320" /></a></div>
Then in order of North-European (NE) admixture:<br />
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<a href="https://sites.google.com/site/fennobga/BRA-K8-NE.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://sites.google.com/site/fennobga/BRA-K8-NE.png" width="320" /></a></div>
Then in order of Middle-East (ME) admixture:<br />
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<a href="https://sites.google.com/site/fennobga/BRA-K8-ME.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://sites.google.com/site/fennobga/BRA-K8-ME.png" width="320" /></a></div>
Then in order of Central-Asian (CA) admixture:<br />
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<a href="https://sites.google.com/site/fennobga/BRA-K8-CA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://sites.google.com/site/fennobga/BRA-K8-CA.png" width="320" /></a></div>
Then in order of Siberian (SIB) admixture:<br />
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<a href="https://sites.google.com/site/fennobga/BRA-K8-SIB.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="95" src="https://sites.google.com/site/fennobga/BRA-K8-SIB.png" width="320" /></a></div>
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This ADMIXTURE study appears to show similartity to the study of Hughe 2011.<br />
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<a href="https://sites.google.com/site/fennobga/Huyghe.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="84" src="https://sites.google.com/site/fennobga/Huyghe.png" width="320" /></a></div>
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<br />Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com4tag:blogger.com,1999:blog-1820243696969815052.post-36981691545416999752013-06-20T09:32:00.000+02:002013-09-23T09:50:56.653+02:00La Braña and the Saamis IIEDIT 23/9-03. I now consider this analysis outdated. Please see the new individual analysis for <a href="http://fennoscandia.blogspot.no/2013/09/la-brana-1-and-modern-european-variation.html" target="_blank">La Braña 1</a> and <a href="http://fennoscandia.blogspot.no/2013/09/la-brana-2-and-modern-european-variation.html" target="_blank">La Braña 2</a>.<br />
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In a <a href="http://fennoscandia.blogspot.no/2013/05/la-brana-and-modern-european-variation.html" target="_blank">earlier post</a> I showed that the La Braña have variation that fit the common Saami-Finn Plink MDS based cluster. I have now again done the same analysis with the exact same populations and markers using a different method unlinked Chromopainter-Finestructure pipeline.<br />
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<a href="https://sites.google.com/site/fennobga/FinestructurePCAEuropeD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="256" src="https://sites.google.com/site/fennobga/FinestructurePCAEuropeD1-D2.png" width="320" /></a></div>
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Finestructure PCA 68k</div>
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As we can see in the Finestructure PCA D1-D2 above the La Braña individuals also here do cluster with the Saami-Finns as in the Plink MDS analysis. If we further define superindividuals representing different population clusterings found in <a href="http://fennoscandia.blogspot.no/2013/04/updated-europe-analysis.html" target="_blank">earlier 289k analysis</a> we can see the La Braña also correctly located in the tree in the heatmap below. <br />
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<a href="https://sites.google.com/site/fennobga/CCEuropeUNLINKED68K.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuropeUNLINKED68K.png" width="320" /></a></div>
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Finestructure tree and heatmap 68k</div>
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However we do not still see a clear clustering of the La Braña to either Finns or Saamis. We see in the above that Finns actually split into two branches seperate from each other. This is probably due to the effect of different external influences included in this analysis as the La Braña have shown African minority admixture and Saamis and Finns have shown Siberian like minority admixture. If we take the 68k dataset from the <a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-modern-world-variation.html" target="_blank">earlier world analysis</a> and extract from the output file the same European populations we used here we end up with ca 55k SNP and get a much better clusterings of both the Finns, Saamis and the La Braña.<br />
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<a href="https://sites.google.com/site/fennobga/CCEuropeUNLINKED55K.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuropeUNLINKED55K.png" width="320" /></a></div>
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Finestructure tree and heatmap 55k</div>
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By removing these it appears like the common component for Finns and for Saamis have been revealed and so the La Brãna now cluster with the population its closest to after removing external influences, the Saamis.<br />
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Other related posts in chronologial order, most recent first:<br />
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<a href="http://fennoscandia.blogspot.no/2013/06/la-brana-and-modern-world-variation.html"><span style="color: #ff9900;">La Braña and modern World variation</span></a> <br />
<a href="http://fennoscandia.blogspot.no/2013/05/la-brana-and-modern-european-variation.html"><span style="color: #ff9900;">La Braña and modern European variation</span></a> <br />
<a href="http://fennoscandia.blogspot.no/2013/05/la-brana-and-saamis.html"><span style="color: #ff9900;">La Braña and the Saamis</span></a> <br />
<a href="http://fennoscandia.blogspot.no/2013/05/la-brana-individuals-and-1000g-european.html"><span style="color: #ff9900;">La Braña individuals and the 1000G European populations</span></a><br />
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Edit 1: This is the same run as above but with all the Saamis (incl. SWE7) and Finns except "Finn-Sam" joined together in each group. NO6 and NO7 joined into "Nor-Sam".<br />
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<a href="https://sites.google.com/site/fennobga/CCEuropeUNLINKED55KV2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuropeUNLINKED55KV2.png" width="320" /></a></div>
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Finestructure tree and heatmap 55k</div>
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Edit 2: This is the original run but the North-Saamis SA1-SA4 have been grouped and all Finns except Finn-Sami have been grouped. We now see that when taking into consideration external influences the La Braña move together with the South-Saamis (SWE7) and Scandinavians with Saami ancestry (both Scandinavians with North-Saami and South Saami ancestry). The North-Saamis (SA1-SA4) group with Finns and Finns with Saami ancestry when taking into account external influences. This make sense as North-Saamis and many Finns shows elevated Siberian like ancestry compared to SWE7 and other individuals of Scandinavian-Saami ancestry.<br />
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<a href="https://sites.google.com/site/fennobga/CCEuropeUNLINKED68KV2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/CCEuropeUNLINKED68KV2.png" width="320" /></a></div>
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Finestructure tree and heatmap 68k</div>
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(Updated 22/6-2013)Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com6tag:blogger.com,1999:blog-1820243696969815052.post-56106906897216551232013-06-06T11:20:00.000+02:002013-06-06T11:56:33.313+02:00La Braña and modern World variationThe previous analysis of the La Brãna was based on a two dimensional MDS plot. In this analysis using a wider word-panel I will atempt to analyse them using the unlinked Chromopainter-Finestructure pipeline using what the Finestructure calls "superindividuals" and is similar to the "supervised" method used in ADMIXTURE. I used as before 68k unlinked SNPs in this analysis.<br />
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As we can see the substructures makes a lot of sense vs the previous analysis but more detailed. As we can see the La Braña is put into a larger branch containing Saamis, Finns, Vologda Russians and Mordovians. Further they are clustered into a subbranch shared only with Vologda Russians and Mordovians. I am not entirely sure why it has this branching as there is not doubt from the heatmap that there is huge sharing with the Finnish-Saami cluster.<br />
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What is different between the La Braña individuals vs the Saami-Finns is first of all the obvious larger African like minority admixture. Second we see smaller East-Asian, Siberian minority like admixture. Third we also seem to see smaller West-Asian influence.<br />
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In the more subtle it seems the La Braña shows affiliation to the Vologda Russians that the Saami-Finn group dont have possibly explaining some of the clustering. There is also appears to be affiliation to Basque and a Croat.<br />
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There also finally appears to be a larger asymmetry in the chromopaints received vs donated suggesting the affiliation between the groups is differentiated in time.<br />
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<a href="https://sites.google.com/site/fennobga/screenshot.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://sites.google.com/site/fennobga/screenshot.png" width="320" /></a></div>
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This also rise the question about where this common component seen in La Braña and the Saamis and Finns really come and what time the different infleunces from Africa and Asia arrived.Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com2tag:blogger.com,1999:blog-1820243696969815052.post-7936058841280358832013-05-23T14:32:00.001+02:002013-05-24T17:01:45.613+02:00La Braña and modern European variationThose who have followed this blog or participated in this project would been used to seeing the below linked PCA plot of European variation on this blog from Chromopainter-Finestructure with the charactaristic ">" or "<" shape where the more south-western European populations usually cluster close to the root while the Central and East European populations form on one branch while Scandianvians, Finns and Saami form on the other. Like the one below<br />
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<a href="https://sites.google.com/site/fennobga/CCEUROPCAD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://sites.google.com/site/fennobga/CCEUROPCAD1-D2.png" width="320" /></a></div>
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Probably many have wondered why it has this shape and how old it is. I have now done more analysis with my ancient La Braña dataset and done a unlinked MDS plot analysis (more analysis under way) in PLINK. It has been PLINK pruned down to 69k using all participants and reference populations. As we can see there *absolutly* no doubt where the ancient La Braña cluster with at the two main dimensions.<br />
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<a href="https://sites.google.com/site/fennobga/AncientIberianEuriopeD1-D2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="249" src="https://sites.google.com/site/fennobga/AncientIberianEuriopeD1-D2.png" width="320" /></a></div>
So this probably means that the ancient La Braña Iberians had a major genetic variation that resembled Finns and Saamis today found only in Fennoscandia, variation that largely have disappeared further south and west, however as the previous post indicate there are probably components that further separate the La Braña from the Finns towards the Saamis.Anders Pålsenhttp://www.blogger.com/profile/13444056522800105747noreply@blogger.com6