tag:blogger.com,1999:blog-7606098424948502460.post8541803583645681252..comments2023-10-31T06:00:32.091-04:00Comments on Ethio Helix ኢትዮ:ሒሊክስ: Intra African Genome-Wide AnalysisAnonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.comBlogger30125tag:blogger.com,1999:blog-7606098424948502460.post-4390297524135375722012-03-19T03:16:41.244-04:002012-03-19T03:16:41.244-04:00I applied the Studantize >2 method to remove ou...I applied the Studantize >2 method to remove outliers in the All Africa Dataset, this filtered out 295 individuals when I rerun the dataset, the West-Central Africa cluster disappeared and the Sandawe formed their own cluster, of which a significant amount was found in East/Horn Africans. This procedure also reduced the overall stDEV of each population-to-cluster significantly. I don't have time to detail/plot out the results but any body interested can take a look at the Median cluster Matrix and the stDEV cluster Matrix, below<br />http://dl.dropbox.com/u/42082352/Africa_Rev5.pdfEtyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-42273355270854817512012-03-03T14:02:35.349-05:002012-03-03T14:02:35.349-05:00The reason for my claim is that all those componen...The reason for my claim is that all those components are within normal Fst distances of West Eurasian clusters with each other (very loosely around 0.1), while their Fst distance to Tropical African is normally near 0.2. <br /><br />In the table I published in my exercise, the distinctly local Ethiopian and Fulani components already show up and have intermediate distances but, for example, before K=9 Ethiopians appeared as a mix of Arabian and Mandenka components (i.e. they appear as like 60% Arab-like, 30% Mandenka-like and 10% other). This is in agreement with the K=11 Ethiopian-specific component, once it shows up, showing Fst=0.101 for Ethiopian/Arab components but Fst=0.115 with the Mandenka one. <br /><br />Even if you don't wish to interpret it as demic/genetic backflow (what I think is very hard to question, specially for North Africa), it clearly indicates a most intense (West) Eurasian affinity. <br /><br />Do you know how can this disagreement be tested? Introducing an East Eurasian control population (like CHB or Papuans or whatever). IF the affinity is only or mostly because of East African ultimate ancestry of Eurasians in general (which I understand is what you are proposing), then West Eurasians and East Asians should be more or less similarly close to North Africans or, specially, these East African groups like Ethiopians or Maasai. <br /><br />But I have some good feeling by now of how the various components and Fst distances behave in North African (and to lesser extent Sahelian) populations, so my prediction is what I stated above: that the component indicates genetic back-flow from Eurasia, which can be old in most cases but not older than the Aurignacoid cultures of c. 50 Ka ago (which should be at least 30 or 40 Ka older than the Out of Africa migration giving origin to the large but less diverse "Eurasian" macropopulation).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-43316086048939794782012-03-03T12:42:53.561-05:002012-03-03T12:42:53.561-05:00According to this source Omotic and Cushitic rough...According to this source Omotic and Cushitic roughly split around 8 kya. <br /><br />http://www.phil.muni.cz/jazyk/files/AAmigrationsCORR.pdf<br /><br />So there probably existed a Cush-Omo meta-population around 10-8 kya, a branch of this group could have spread to the Southern Rift Valley, or perhaps later around 6 kya with the South Cushites (Iraqwoids).<br /><br />By the way what do you think of that Beja and Agew are the earliest branches of Cushitic, would this indicate that Cushitic spread from the Northwest (e.g. Northeast Sudan/Red Sea hills)? Some of the uniparental markers possibly indicate this (E-M78, E-M123, T-M70, and also many maternal lineages).jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-91773155056775687672012-03-03T12:21:57.884-05:002012-03-03T12:21:57.884-05:00"So the North African component should be con..."So the North African component should be considered the West Eurasian component in Africa without hesitation"<br /><br />Actually Maju, this is what Henn (2011) said regarding the cluster that was found in the Tuscans, proxy for West Eurasians, in relation to some East African populations:<br /><br />“At k = 4, we see a western African/Bantu-speaking cluster, an eastern African cluster, a cluster representing Europeans <b>that likely also signifies ancestral variation maintained in eastern Africa (e.g., Maasai and Sandawe populations)</b>, and finally, a cluster that links all our HG populations.”<br /><br />So there is no need to consider the 'North African' cluster as a “West Eurasian” component 'without any hesitation', as one should hesitate to contemplate on the fact that West Eurasian genetics is in essence a subset of that of Africa's, as well as the uniparental evidence of migrations out of Africa post-OOA.<br /><br />The 'North-Africa' cluster likely has a gradient of indigenousness to Africa, decreasing in the degree of its indigenousness, both temporally and spatially, in a direction going from East to North-Africa.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-35195806998874424892012-03-03T06:30:08.689-05:002012-03-03T06:30:08.689-05:00The North African component is the West Eurasian c...The North African component is the West Eurasian component: it shows up that way also in <a href="http://forwhattheywereweare.blogspot.com/2011/12/north-african-genetics-through-prism-of.html" rel="nofollow">my</a> and <a href="http://forwhattheywereweare.blogspot.com/2012/01/north-african-autosomal-genetics-again.html" rel="nofollow">Henn's</a> North African comparisons at low K levels. At deeper Ks other more local components shade this but, with the partial exceptions of the Ethiopian and Fulani components (which look old Eurasian-African mixtures, being similarly Fst-distant from Tropical Africans and West Eurasinans) and some small exotic "OoA-remnant" components (very Fst-distant from all), the North African local components are much closer (by Fst distances) to West Eurasians than to Tropical Africans. <br /><br />So the North African component should be considered the West Eurasian component in Africa without hesitation (and any European or West Asian control will show up as nearly 100% within that component in an analysis like this one).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-18822026894248308412012-03-03T01:27:52.921-05:002012-03-03T01:27:52.921-05:00Yea Eze, cosign with what you said for the most pa...Yea Eze, cosign with what you said for the most part, i'm just not sure on the possible dates of the split between omotic and Cushitic, it could have happened >10KYA if I recall, do you have any info on that?<br /><br />Regarding K=8 , I just run it for the exact same Dataset out of curiosity of Andrew's inquiry. In essence, what happened was that the 'East-Africa 1' and the 'West-Central Africa' clusters disappeared, the PCA FST plot looks pretty much like the K=10 run except those 2 clusters were gone.<br /><br /><a href="http://img26.imageshack.us/img26/6941/fstk8pca.png" rel="nofollow">PCA Plot for the FST Distances @ K=8</a><br /><br /><a href="http://dl.dropbox.com/u/42082352/K8_Median.pdf" rel="nofollow">Here is a PDF file with the Median proportions for all the pops</a>Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-35693311334857867432012-03-03T00:44:57.770-05:002012-03-03T00:44:57.770-05:00'that is part of the reason why I think that t...'that is part of the reason why I think that the North African cluster is a composite of European, Near Eastern and East African elements, with the composition proportions changing with geography, i.e. more of the indigenous elements in East Africa, and less so in North Africa.'<br /><br />I would agree with this last bit. IMO, it looks like the E1b1b1 found in these groups was spread by proto-Cushites (or possibly Omotic people), which explains their Northern affinities. E-M293 is not that old and fits the scenario of South Cushitic expansions. Also, L3x1 in the Sandawe looks like a Horn African lineage. The Sandawe to me seem mostly like a mixture between Bantus, South Cushites, and Paleo-Africans. I would say the Hadza are similar but with a higher Paleo-African component.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-21027539207234949862012-03-02T21:14:30.727-05:002012-03-02T21:14:30.727-05:00Andrew, you wrote a lot interesting things both he...Andrew, you wrote a lot interesting things both here and at your blog that I can not address all at the moment, but I will try to as time permits. One thing that caught my immediate attention however was this statement that you made : "The lower level of the North African component in Oromo speakers in Ethiopia relative to other Ethiopians is consistent with the notion that there was a meaningful demic component to the transition from a prior language to Ethiosemitic languages in Ethiopia. "<br /><br />The relevant Cushitic speakers that you want to compare Ethiosemitic speakers to before making such an assessment are those categorized as Central Cushitic speakers rather than Lowland East Cushitic Speakers. Since we do not have any genome-wide data from current Central-Cushitic speaking populations from the highlands of Ethiopia, we have to use the Ethiopian Jews or Beta Israel as a proxy since they were known to Historically speak Central Cushitic, or otherwise known as Agew languages, and as you can see, there is very little difference in cluster proportions between the Ethiopian Jews and the other Highland Ethiopians (EtT and EtA).<br /><br />Another point Re: Hadza and Haplogroups is that Henn(2011), from which the samples for this analysis came from, did report the haplogroups of the Hadza samples as follows:<br />mtDNA<br />L0a2*: 6% (1)<br />L3h: 11% (2)<br />L4g: 56% (10)<br />L2a: 22% (4)<br />L3b: 6% (1)<br /><br />YDNA<br />E1b1b1: 10% (1)<br />B2b: 10% (1)b<br />B2b4*: 50% (5)<br />E1b1a7a3a: 30% (3)<br /><br />For The Sandawe:<br />mtDNA<br />L0a2*: 20% (6)<br />L3x1: 13% (4)<br />L4g: 37% (11)<br />L2a: 10% (3)<br />L3e3: 17% (5)<br /><br />YDNA<br />A3b2*: 12% (2)<br />B2b4*: 29% (5)b<br />E1b1b1: 18% (3)<br />E2b1: 6% (1)<br />E1b1a7a3a: 24% (4)<br />E1b1a8a: 12% (2)<br /><br />And for the SAN<br />mtDNA:<br />L0d1a: 43% (14)<br />L0d1b: 50% (16)<br />L0a’b’f*: 7% (2)<br /><br />YDNA:<br />A3b: 26% (5)<br />A3b1: 32% (6)<br />B2b4*: 5% (1)b<br />E2b1: 5% (1)<br />E1b1a7a3a: 10% (2)<br />E1b1a8a: 10% (2)<br />R1b1b2a1a: 10% (2)<br /><br />In addition, since the Sandawe don't show any exogenous (relative to Africa that is) Paternal or Maternal lineages, but at the same time show ~12.3% of the 'North African' cluster, that is part of the reason why I think that the North African cluster is a composite of European, Near Eastern and East African elements, with the composition proportions changing with geography, i.e. more of the indigenous elements in East Africa, and less so in North Africa.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-10936961659880016092012-03-02T15:27:56.653-05:002012-03-02T15:27:56.653-05:00A more general comment that arose as I considered ...A more general comment that arose as I considered your post <a href="http://dispatchesfromturtleisland.blogspot.com/2012/03/genome-bloggers-get-sophisticated.html" rel="nofollow">here</a>:<br /><br />It isn't really clear to me that it makes sense to do this analysis at K=10 rather than K=8 in admixture. Presumably, at K=8, you would end up collapsing East Bantu, Central West Africa and West Africa into a single ancestral population since the Fst distances between those populations are negligable relative to the other populations. This would make the other patterns in the data stand out better, and my intuition is that the extra two ancestral populations may be carrying a lot of noise relative to the signal it is producing.<br /><br />Maju and I have also discussed the possibility that the extreme outlier status of the Hadza is a product of extreme inbreeding rather tha genuine genetic distance. Where would a typical individual Hadza individual show up on the PC charts if the rest of them were removed from the sample?<br /><br />Another analysis that would be interesting would be to compare admixture rates from the Admixture frappe charts and compare them to the inferred admixtures you would see from uniparentals. Indeed, I'd find it quite interesting to see side by side uniparental and autosomal data.<br /><br />Most of the Pygmy component in non-Pygmy populations looks like just minor components of an expanding Bantu mix. But, it seems like there is more at work than that in the Alur, which makes that population's history an interesting puzzle. Could there have been a third pygmy population in pre-historic Africa which was absorbed into the Alur? Is this just an exaggerated founder effect legacy of Bantu expansion? Or what?andrewhttps://www.blogger.com/profile/08172964121659914379noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-72757482595773366052012-03-02T15:14:55.234-05:002012-03-02T15:14:55.234-05:00Weird on the Mada point. The first page said &quo...Weird on the Mada point. The first page said "Their native language, also called Mada, belongs to the Niger-Congo language family.", but I agree with Maju that Ethnologue is more trustworthy and a high R1b frequency is a very strong predictor of Chadic linguistic affiliation in Africa. The fact that Hasua and Mada show a similar pattern makes lots of sense in this context.andrewhttps://www.blogger.com/profile/08172964121659914379noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-76461134411874524992012-03-02T02:50:26.659-05:002012-03-02T02:50:26.659-05:00I just find it fascinating, that's all. I wond...I just find it fascinating, that's all. I wonder how old it is in most of these populations, this should be an interesting subject for research.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-39819503806941580432012-03-02T02:38:49.664-05:002012-03-02T02:38:49.664-05:00I don't doubt their distinctiveness. However, ...I don't doubt their distinctiveness. However, if two siblings or a parent-child pair are within a particular group it can easily 'spark' a high Fst cluster. Without this the Fst might be slightly lower.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-67441336890422904142012-03-02T01:20:13.449-05:002012-03-02T01:20:13.449-05:00Ethnologue, which is usually a very trustworthy so...<a href="http://www.ethnologue.com/show_map.asp?name=CM" rel="nofollow">Ethnologue</a>, which is usually a very trustworthy source and regularly updated, classifies the Mada as Afroasiatic speaking and also they show up <a href="http://www.ethnologue.com/show_map.asp?name=CM&seq=30" rel="nofollow">in the midst of Afroasiatic speaking peoples</a>, what, in principle would be consistent with their R1b and East African relatedness (which I imagine expanding from Sudan with Chadic speakers).Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-21335575780220386512012-03-01T21:37:55.813-05:002012-03-01T21:37:55.813-05:00Why surprised? If you believe that 'Cushitic&#...Why surprised? If you believe that 'Cushitic' influence reached to as far as the tutsi who live in Rwanda(which I'm not even sure if it is really Cushitic or some very Ancient North East-African), the Hema are found even further North of Rwanda and Burundi. The Massai in Tanzania are even further south, we also know that E-M293 traveled to as far south as Southern Africa.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-57825078314698263852012-03-01T21:36:50.891-05:002012-03-01T21:36:50.891-05:00Actually, that is incorrect, the source you provid...Actually, that is incorrect, the source you provided says the Language of the Mada is part of the Chadic branch of Afroasiatic : http://www.ethnologue.com/show_lang_family.asp?code=mxu<br /><br />With respect to the Mada lacking in the 'North African' cluster that is true, it is however to be noted that they carry a significant amount of the 'East-African2' cluster, in fact, they are the Westernmost population to carry that particular cluster in appreciable amounts. Thus the 'East-Africa2' cluster can be used as a proxy for Afroasiatic just as much as the 'North African' cluster, a case can actually be made that the North East African axis seen in C1 Vs. C3, that is the diagonal Axis that the EtO, EtA, EtT samples lie on and leading all the way up-to Egypt, is the 'nucleus' for Afroasiatic.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-1175920945778446062012-03-01T21:35:16.792-05:002012-03-01T21:35:16.792-05:00Well, as far as the Divergence of the Hadza, this ...Well, as far as the Divergence of the Hadza, this run only just confirmed what Tishkoff (2009) found amongst the Hadza, and her find was even more extreme as they were divergent even on a GLOBAL level.<br /><br />“PC 3 (3.5%) distinguishes the Hadza hunter-gatherers from others”. <br /><br />“Finally, the Hadza are the sole constituents of a sixth cluster (yellow) consistent with their distinctive genetic structure identified with PCA and STRUCTURE.”<br /><br />“These results suggest the possibility that the SAK, Hadza, Sandawe, and Pygmy populations are remnants of an historically more widespread proto-Khoesan- Pygmy population of hunter-gatherers.”<br /><br />So I don't think the behavior of the Hadza in this run or any other similar runs can be easily just explained away by just 'relatedness'.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-68237136999591162782012-03-01T18:10:30.551-05:002012-03-01T18:10:30.551-05:00What I find the most interesting of this run is th...What I find the most interesting of this run is that the Hema carry the 'North African' component while their close neighbors the Alur and Mbuti completely lack it. The Alur and Hema apparently even speak the same language (Lendu). This probably means that the Hema are not ethnically Nilotic, but mainly Bantu with Cushitic (likely similar to the Tutsi). I'm kinda surprised that Cushitic admixture traveled that far.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-5239725188952635052012-03-01T17:46:12.380-05:002012-03-01T17:46:12.380-05:00Ironically the Mada have extremely high R1b freque...Ironically the Mada have extremely high R1b frequencies.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-20335895095759646912012-03-01T17:43:20.086-05:002012-03-01T17:43:20.086-05:00If you do start filtering the samples I would say ...If you do start filtering the samples I would say use a 0.2 pi-hat removal threshold for agriculturalist groups and a 0.4 pi-hat threshold for khoisan & pygmy groups, since there are fewer hunter-gatherer samples or otherwise you'll end up with too few of them. For example, the majority of the Hadza group has very high pi-hat scores with each other, there are even siblings in that group.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-80639293788323598632012-03-01T17:35:25.031-05:002012-03-01T17:35:25.031-05:00This source takes the position that the Mada peopl...This <a href="http://www.joshuaproject.net/people-profile.php?peo3=13193&rog3=CM" rel="nofollow">source</a> takes the position that the Mada people speak a Niger-Congo language rather than an Afro-Asiatic language, which would resolve one of the two outliers associated with the fact that the Hasua and Mada are the only two populations lacking a significant North Africa component that speak Afro-Asiatic languages.andrewhttps://www.blogger.com/profile/08172964121659914379noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-13531499163372270642012-03-01T15:14:19.320-05:002012-03-01T15:14:19.320-05:00I did use the pi-hat, but it took a while for my c...I did use the pi-hat, but it took a while for my computer to process it so I abandoned it, I will try it again for the next run.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-37918646562136480272012-03-01T15:13:45.028-05:002012-03-01T15:13:45.028-05:00Yea, it was me that recommended GNU octave, it is ...Yea, it was me that recommended GNU octave, it is a powerful computational software similar to MATLAB but with the difference that it is free and open source, it probably can do some numerical interpolation based on geo spatial positions/coordinates, but I would have to program something, I am sure there is something easier and already customized for this particular task out there.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-8453844632298216612012-03-01T15:13:15.785-05:002012-03-01T15:13:15.785-05:00Numbers, i.e. Quantity of samples, may indeed have...Numbers, i.e. Quantity of samples, may indeed have an influence on cluster formation, however the degree of influence I'm not so sure, for instance, take a look at the number of Maasai , Yoruba and Luhya samples in the above run, so it may not just be the total number of Mozambiqans that is influencing the creation of an independent cluster, there could be something in their population history that we may not be clear about. I have updated this post with the locations of the reference samples for this dataset by the way.Etyopishttps://www.blogger.com/profile/17311733086301215105noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-7244514537084985962012-03-01T05:32:23.890-05:002012-03-01T05:32:23.890-05:00Interesting analysis. I would just want to add tha...Interesting analysis. I would just want to add that it is generally advised to remove samples with PI_HAT > 0.15 (essentially first and second cousins - the Maasai and Luhya contain many of them). If this isn't done it may lead to clusters which are just a product of recent inbreeding and not ancestral divergence.jes-rhttps://www.blogger.com/profile/13572668095214926909noreply@blogger.comtag:blogger.com,1999:blog-7606098424948502460.post-39487489550257563972012-02-29T13:07:25.763-05:002012-02-29T13:07:25.763-05:00I was oblivious to the Sikora paper, thanks for th...I was oblivious to the Sikora paper, thanks for the mention. In a sense, with such a huge Mozambican sample, I'm not surprised that the clustered apart but still it is consistent with the Patin paper and is something to be explored. <br /><br />"I would like to really add a Southern Sudan Nilotic dataset of at least 20-30 people, as that is very important for East African analysis".<br /><br />Indeed that would be nice but I can't help you with that. :/Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.com