tag:blogger.com,1999:blog-7785493.post2044722555017307254..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: Human genetic variation: 124+ clusters with the Galore approachDienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger25125tag:blogger.com,1999:blog-7785493.post-63345781927618203842014-02-10T02:15:53.390+02:002014-02-10T02:15:53.390+02:00If Mclust can distinguish Moroccan Jews from Sepha...If Mclust can distinguish Moroccan Jews from Sephardic Jews, could it be used to determine the source of the Mediterranean component in the Melungeon population? The presence of Mediterranean ancestry is confirmed by some Melungeons being diagnosed with Familial Mediterranean Fever. Some Melungeons believe this is the traditionally claimed Portuguese, but there are also claims of Sephardic Jewish or Crypto-Jewish ancestry, or Moorish or Morisco, or Turkish or Spanish. MikeNassauhttps://www.blogger.com/profile/12368998887074749581noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53264988715265796512010-12-17T19:44:02.596+02:002010-12-17T19:44:02.596+02:00I'd love to see an analysis of Irish, Scottish...I'd love to see an analysis of Irish, Scottish, English, Welsh, French, Netherlands, Belgium, Norway, Denmark - with maybe Sweden, Germany and Finland thrown in - to get a better understanding of who the Anglo-Saxons were, or were not?!pconroyhttps://www.blogger.com/profile/10312469574812832771noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-54916101840449272992010-12-17T19:40:16.405+02:002010-12-17T19:40:16.405+02:00Also, was the one South_Italian_Sicilian who clust...Also, was the one South_Italian_Sicilian who clusters with the Sephardic Jews, submitted by me?pconroyhttps://www.blogger.com/profile/10312469574812832771noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-86769044361677578892010-12-17T19:33:39.701+02:002010-12-17T19:33:39.701+02:00The S_Italian_Sicilian sample doesn't seem to ...The S_Italian_Sicilian sample doesn't seem to split along that direction for the time being.<br /><br />I need 1 more Irish.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-1713245835655531022010-12-17T17:54:03.843+02:002010-12-17T17:54:03.843+02:00Dienekes,
I'd be very interested in how the S...Dienekes,<br /><br />I'd be very interested in how the Sicilians fare after a split from South Italians, as apart from Calabrians, I think the Sicilians have more Semitic ancestry and North African ancestry - at least this is what I'm seeing for the Sicilian samples I submitted.<br /><br />Also, are you still assigning a population level grouping, when you have 5 samples from that group? If so how many more do you need to form and Irish group - as I submitted 3 Irish samples?pconroyhttps://www.blogger.com/profile/10312469574812832771noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-68303497698035421892010-12-15T01:13:18.538+02:002010-12-15T01:13:18.538+02:00Foreseeable and very nice plot also.
Pre-Ashkenazi...Foreseeable and very nice plot also.<br />Pre-Ashkenazim Jews belonged at one of the three nucleus of Jewish ancient populations, that evolving the called "Syrian-European<br />nucleus" (Greek and Roman times of profuse and lavish proselytism with genetic inlays) like Sephardim are still today. <br />The "Babylonian and Persian nucleus" and "The Coptic nucleus" are the others of these three Ancient centers.<br /><br />The Ashkenazim Jews Europeans Components (around 35 to 50%), are, a half from South Europe acquired in ancient times, while the named “Hellenistic Proselytism” in Greek, Anatolia and Rome including Women and Men (“mtDNA” and “Y” markers) as well.<br />The other half: a 1/4 of the Whole DNA markers was shared and inlaying with E. Europe and host populations along the Galut or Diaspora life also Y and mtDNA from these Jews Kazhars descendant as well. The other 1/4 part was mainly from converted women and it could be seen in the mtDNA almost exclusively.<br />The West Asian markers represents the time when A. J. were living in E. Europe and the contact with Turkish Jews Khazars – a mixed Jews<br />people with West and Central Asia ancient components and I call "Medieval Age Four Nucleus East Europe" - and the inbred<br />into religious restrictions in Middle Ages, and Modern Era, that was the norm, modifying the profile patterns from a “Coptic” - “European Syrian” Jewish ancient mix -Alexandria and other M.E.- returning and resulting take in part to a more "South East European Syrian like". We need to study and compared the DNA markers of Cristhians Coptos from Egypt, with Ashkenazim and Ethiopians and others groups of Jewish and non Jewish origin and too bones or teeth of Jews graves of Alexandria and others ancient Jews communities, because the losing<br />and take up of haplotypes reveled ancient Egypt and Abyssinian components in moderns A.J. like mtDNA N1b (12% A.J.and 48% Ethiopians Jews and only 0.2% or minor in whole Europe) or “Y” DNA marker E3b1 Ashkenazim have 24% more than Sephardim 19%-20% as well. Note that “East African Y chromosomes in haplogroup E3b1-M78 which is abundant (38%), and may have originated in Ethiopia (Cruciani et al. 2004; Luis et al. 2004). East Africans E3b1 may have carried the latter to Egypt and, farther, to Europe via the Levantine corridor.<br /><br /> The Jews pre Ashkenazim arrived to Rome and Tuscany from Alexandria and others M. East regions mainly when the Muslims arrived to Egypt en the VII century AE, and from there to the North, they were heading to the Rhine river to the nowadays Lorena and Alsace, they got to oriental Europe where they mixed and got in contact with Khazars Jews.<br />Remember that the hyperhaploydia present in Ashkenazim is only<br />compatible with a most ancient population about 8500 years -not<br />beyond 1200 years like they are-, or a mixed with people along the<br />Diaspora life without religious restriction that is not the case.<br />The A.J. hyperhaploydia and heterozygosis, - practically almost absent in Sephardic - as well a great L.D. That could cluster these A.J. populations everywhere you want (not common in isolated population, or for mtDNA coming in great rate from host population, and endogamy practice that Ashkenazim hold), That is showed and explained easily by MDS,at four Dimensions and more visible with a number samples over 400 for each population, the same for PCA.horaciohhttps://www.blogger.com/profile/08177107320272273468noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-48375566557518944852010-12-14T19:15:52.932+02:002010-12-14T19:15:52.932+02:00I may split Sicilians from South Italians when I h...I may split Sicilians from South Italians when I have enough numbers.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-7067882608684300842010-12-14T18:41:20.180+02:002010-12-14T18:41:20.180+02:00Now that I think about it, why are Sicilians and S...Now that I think about it, why are Sicilians and Southern Italians pooled together?<br />In other studies seen on this website the two were separate. I wonder if next time these two populations could be analyzed separately.<br />How about Serbs and Cretans if the latter are not included in the Greek sample.Jackhttps://www.blogger.com/profile/01148345006852811881noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-38028180026500612242010-12-14T18:17:26.683+02:002010-12-14T18:17:26.683+02:00Dienekes, would it be a good idea to ask Dodecad p...Dienekes, would it be a good idea to ask Dodecad participants to list their geographic origin within their country? If you decide to continue doing Dodecad and your database grows, it would be interesting to see different patterns within countries. This can be done without revealing the identities of the participants.Deanhttps://www.blogger.com/profile/10753416265954000609noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-87714959748330867842010-12-13T19:48:29.670+02:002010-12-13T19:48:29.670+02:00but I simply dont understand why I see so many dif...<i>but I simply dont understand why I see so many different result on MDS-plots using ALMOST SAME data. It can be explained by a comment that it is because the data is different, but then we agree that results are not trustworthy.</i><br /><br />I have no idea what "different results" you see. Like I said, everyone is free to try their hand at this with the publicly available datasets. And, I certainly do not agree that "results are not trustworthy".Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-12590435766002837162010-12-13T19:45:26.470+02:002010-12-13T19:45:26.470+02:00Dienekes "So, this approach is quite good bec...Dienekes "So, this approach is quite good because it helps MCLUST by giving it aspects of the data (the first few dimensions) that capture most of the variation of the data, and that are known (empirically) to present clusters."<br /><br />I am not trying to prove that there could be better way, but I simply dont understand why I see so many different result on MDS-plots using ALMOST SAME data. It can be explained by a comment that it is because the data is different, but then we agree that results are not trustworthy. Hey, I am only saying that I had to wait until I can feel myself confident what I see now (I am not blaming you), because now cannot do it.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-4992930439918012882010-12-13T16:28:18.298+02:002010-12-13T16:28:18.298+02:00Interestingly, the two Hungarians who form cluster...Interestingly, the two Hungarians who form cluster #11, which is the most divergent one are the ones who have a bit of the "Altaic" component, in the Hungarian "population portrait"<br /><br />http://dodecad.blogspot.com/2010/11/admixture-analysis-of-eurasian.htmlDienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-4073646220850160532010-12-13T16:20:53.026+02:002010-12-13T16:20:53.026+02:00Hey Dienekes, can you post a phylo tree of the Nor...<i>Hey Dienekes, can you post a phylo tree of the North Euro clusters in that last image?</i><br /><br />http://tinypic.com/r/be91eb/7<br />http://tinypic.com/r/262tufn/7Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-40580959021954250202010-12-13T15:49:03.197+02:002010-12-13T15:49:03.197+02:00Hey Dienekes, can you post a phylo tree of the Nor...Hey Dienekes, can you post a phylo tree of the North Euro clusters in that last image?<br /><br />I'd run the "clusters galore" on my own data sets, but I can't do so now until the New Year.Unknownhttps://www.blogger.com/profile/00519828882672012862noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-25907011058450565942010-12-13T15:32:23.811+02:002010-12-13T15:32:23.811+02:00Thanks - but it would have been better without the...Thanks - but it would have been better without the Lithuanians, Belorussians, and Russians for the question I asked. On that matrix, the populations I mentioned are not well distinguished, at all - due to introducing yet more variables. The results are almost trivial: Germans group with French, Scandinavians, and Hungarians. Who would have thought... <br /><br />Of course, the very low number of Germans compared to others is a problem, as well.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-38073112431020523142010-12-13T13:59:21.160+02:002010-12-13T13:59:21.160+02:00Would be interesting to do the same with cluster D...<i>Would be interesting to do the same with cluster D. Germans and Hungarians often come out very close together, and then you have the Utahns, Orcadians, half of French, and 1/3 of Scandinavians in that mix.</i><br /><br />http://tinypic.com/r/be91eb/7<br /><br />5 MDS dimensions, 13 clustersDodecad Projecthttps://www.blogger.com/profile/10447516703222698752noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-84101459181594122642010-12-13T09:55:27.282+02:002010-12-13T09:55:27.282+02:00I read this blog casually on a regular basis; as a...<i>I read this blog casually on a regular basis; as a non-geneticist, I don't really understand how your snp data is "coded" for statistical analysis, nor do I understand how such coding translates into principal components (what do the axes represent?).<br /></i><br /><br />MDS is a technique that takes a distance matrix between all individuals (1-IBS distance matrix) and projects the individuals into a D-dimensional metric space. By looking at the distances in that D-dimensional space, you can reconstruct (with loss) their original distances. The good thing is that individuals tend to be clustered in the first few dimensions...<br /><br />http://dienekes.blogspot.com/2010/12/human-genetic-variation-first-50.html<br /><br />... and hence by doing this you are jump-starting any clustering algorithm you apply to the data.<br /><br /><i> Also, is mclust utilizing pca? A simple explanation or a relevant paper would be much appreciated and would greatly expand my appreciation of this blog.</i><br /><br />Mclust is not utilizing PCA itself. It is applied on data generated by MDS (which is a technique similar to PCA).Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-72341469120216396382010-12-13T09:48:54.346+02:002010-12-13T09:48:54.346+02:00The MCLUST is as good as the input data, reminding...<i>The MCLUST is as good as the input data, reminding about an old truth in computing. It could be good if the MDS data and dimensions are reasonable. <b>Anyway, MDS never represent the whole data.</b> What I am waiting is a method that uses directly IBS-data for clustering without any modelling with data losses. Until that straightforward IBS-comparisons are only good for me.</i><br /><br />Ergo, you don't need the whole data to cluster unlabeled individuals into clusters that largely correspond to their population labels.<br /><br />You also seem to misunderstand what clustering does. Clustering always prefers certain aspects of the data, namely the aspects in which individuals form detectible blobs. <br /><br />A good clustering algorithm will identify these aspects if it is "given all the data", but it is just as likely to be lost in the noise. This is quite visible in my experiments when increasing the number of MDS dimensions retained does not, in general, improve the algorithm's ability to detect clusters.<br /><br />So, this approach is quite good because it helps MCLUST by giving it aspects of the data (the first few dimensions) that capture most of the variation of the data, and that are known (empirically) to present clusters.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-71266657973994835362010-12-13T07:15:11.331+02:002010-12-13T07:15:11.331+02:00Would be interesting to do the same with cluster D...Would be interesting to do the same with cluster <i>D.</i> Germans and Hungarians often come out very close together, and then you have the Utahns, Orcadians, half of French, and 1/3 of Scandinavians in that mix. <br /><br />I have no doubt that they can be separated as well, but it would be interesting to see how easily and cleanly.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-82987403512119451092010-12-13T01:27:34.665+02:002010-12-13T01:27:34.665+02:00I read this blog casually on a regular basis; as a...I read this blog casually on a regular basis; as a non-geneticist, I don't really understand how your snp data is "coded" for statistical analysis, nor do I understand how such coding translates into principal components (what do the axes represent?). Also, is mclust utilizing pca? A simple explanation or a relevant paper would be much appreciated and would greatly expand my appreciation of this blog.Unknownhttps://www.blogger.com/profile/06609656795972246431noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-63194671927339872852010-12-13T00:53:30.468+02:002010-12-13T00:53:30.468+02:00Interesting to see that in this analysis Greeks fi...Interesting to see that in this analysis Greeks fit into three clusters. I would expect the one who fits into the Romanian cluster to be a Vlach, and the two who cleave to Sicily Cretans, whereas the mainlanders would cluster with Tuscans. Is this so?Auditor George Danoshttps://www.blogger.com/profile/15451291978096556616noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-59073644302415230032010-12-13T00:29:04.332+02:002010-12-13T00:29:04.332+02:00The MCLUST is as good as the input data, reminding...The MCLUST is as good as the input data, reminding about an old truth in computing. It could be good if the MDS data and dimensions are reasonable. Anyway, MDS never represent the whole data. What I am waiting is a method that uses directly IBS-data for clustering without any modelling with data losses. Until that straightforward IBS-comparisons are only good for me.Maurihttps://www.blogger.com/profile/03670078523265515878noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-46984638559514197532010-12-12T20:33:55.799+02:002010-12-12T20:33:55.799+02:00I am still trying to disentagle my neurons...I am still trying to disentagle my neurons...Jackhttps://www.blogger.com/profile/01148345006852811881noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-46785377203274799612010-12-12T18:49:51.781+02:002010-12-12T18:49:51.781+02:00As I've mentioned before, this type of analysi...As I've mentioned before, this type of analysis is not an admixture test, so it doesn't really try to estimate admixture in populations. It does, however detect population distinctiveness, and this might be due to a number of factors, such as isolation and/or a unique pattern of admixture.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-20747318267308399772010-12-12T15:15:51.552+02:002010-12-12T15:15:51.552+02:00What have you demonstrated by this? Of course Ashk...What have you demonstrated by this? Of course Ashkenazi Jews haven't only a "Southern European component", that you find in Southern-Italians-Sicilians and Greeks (anyway the Greek component cannot be 100% as you probably likes if you knows history: it could be also 0%), but also many other European components and probably North Africans etc. and this carries Ashkenazim a little far, very little indeed.Gioiellohttps://www.blogger.com/profile/13578860964923773647noreply@blogger.com