tag:blogger.com,1999:blog-6886680068187530519.post7839957537639163896..comments2024-02-07T23:25:07.429-06:00Comments on Bell Beaker Blogger: 10% of Bronze Age Europeans Lactase Persistentbellbeakerbloggerhttp://www.blogger.com/profile/01848982163843593127noreply@blogger.comBlogger56125tag:blogger.com,1999:blog-6886680068187530519.post-37799233653648126772015-06-29T00:04:29.615-05:002015-06-29T00:04:29.615-05:00Can't help you. I only did some of those long ...Can't help you. I only did some of those <a href="http://leherensuge.blogspot.com.es/2009/03/european-and-anatolian-r1b-structure.html" rel="nofollow">long ago</a> and all by hand, when trying to understand R1b structure in Europe with the limited data we had prior to 2010. There's probably some sort of software but I do not know that much.<br /><br />Maybe you could ask Palisto of <a href="kurdishdna.blogspot.com" rel="nofollow">Kurdish DNA blog</a>. He has made some of those for the blue eyes allele that were very informative. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-3430625134373747852015-06-28T06:51:00.337-05:002015-06-28T06:51:00.337-05:00Ok I have to confess I have not produced a haploty...Ok I have to confess I have not produced a haplotype tree before (I am an 'armchair geneticist'); however I am more than willing to have a go at it.<br /><br />Any tips for me? Would a median-joining network be best? And which software should one use?<br /><br />If you have created one before, let me know how you went about doing it.Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-12653607800407457912015-06-27T13:44:19.034-05:002015-06-27T13:44:19.034-05:00Now you're providing very interesting informat...Now you're providing very interesting information, thanks. I don't have time to double-check but, following your analysis, there is some chance indeed that the 13910-T haplotype could have an African origin (but migrated to Europe via West Asia, what is in itself intriguing). I'd like to see all that in tree-like image for better clarity though. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-27667554625595223282015-06-27T09:43:56.420-05:002015-06-27T09:43:56.420-05:00My own analysis of the supplemental data from the ...My own analysis of the supplemental data from the 2008 paper was very interesting.<br /><br />*Derived at 1 position [from ancestral haplotype]:- Iranians [x2]; Ob-Ugrics [x2];<br />*Derived at 2 positions:- Sudan Mahas [x1]; Sudan Gali [x2]; Utah Whites[x1]; Levant Arabs [x2]; Ob-Ugrics [x1];<br />*Derived at 3 positions:- Saudi Arabia [x1]; Fulani Sudanese [x1]; Baluch [x1]; Morocco [x1]; Levant Arbs [x3]; Kalash [x2]; South Korea [x1];<br />*Derived at 4 positions:- Sudan Mahas [x3]; Levant Arabs [x1]; Iranians [x1]; Kalash [x1]; South Korea [x2];<br />*Derived at 5 positions:- Saudi Arabia [x1]; Sudan Mahas [x1]; Morocco [x1]; Iranians [x3]; South Korea [x2];<br /><br />*Derived at 6 positions - FIRST HAPLOTYPE CONTAINING 13910*T:- Fulani Sudanese [x1];<br />*Derived at 7 positions - SECOND HAPLOTYPE CONTAINING 13910*T:- Baluch [x1];<br />*Derived at 10 positions - THIRD HAPLOTYPE CONTAINING 13910*T:- Morocco [x1];<br /><br />[The skipping others]<br /><br />*Derived at 16 positions - FIRST HAPLOTYPE FOUND TO CONTAIN BOTH 13910*T & 22018*A IN LINKAGE DISEQUILIBRIUM [THE HALLMARK OF THE 'EUROPEAN' LP HAPLOTYPE]:- Iranians [x1];<br /><br />*Derived at 17 positions - MORE HAPLOTYPES CONTAINING BOTH 13910*T & 22018*A IN LINKAGE DISEQUILIBRIUM:- Levant Arabs [x1]; Morocco [x1]; Utah [x1];<br /><br />*Derived at 18 positions - MORE HAPLOTYPES CONTAINING 13910*T & 22018*A IN LD:- Ob-Ugrics [x1]; Levant Arabs [x1]; Saharawi [x2]; Baluch [x1]; Fulani Sudanese [x3]; Utah [x1];<br /><br />*Derived at 18 positions - ONE HAPLOTYPE CONTAINING 13910*T BUT NOT CONTAINING 22018*A:- Fulani Sudanese [x1];<br /><br />[Many more omitted]<br /><br /><br />We also know from Tishkoff et al. (2014) that the 'European' haplotype containing 13910*T and 22018*A together in linkage disequilibrium was also found in Cameroon Fulani and Chad Bulala [number of dervied positions unknown].Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-24196350111620475512015-06-27T08:52:59.627-05:002015-06-27T08:52:59.627-05:00Ok there is a much more recent paper than the one ...Ok there is a much more recent paper than the one I mentioned above [which is from back in 2008].<br /><br />The other paper, which I am sure you have seen, is:-<br /><br />"Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa"<br />[Tishkoff et al, 2014]<br /><br />http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980415/<br /><br />Scroll down to the 'supplemental data' section at the bottom of that paper.<br /><br />Then click to view 'Document S1. Figures S1–S12:'<br /><br />On this pdf, go to page 2, and you will see:-<br /><br />Figure S1: Haplotype network.<br />"Haplotype network analysis based on 97 SNPs, identi ed in the three sequenced regions, and four fast-evolving microsatellites spanning a total of 197.88 kb for 509 individuals (Figure 1). Haplotypes are shown as circles and the size of each circle is proportional to the number of individuals with a given haplotype. We assigned the same weight to SNPs and STRs." Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-1641173373168429902015-06-25T15:22:25.848-05:002015-06-25T15:22:25.848-05:00Thanks for your comments Maju.
I will have a go a...Thanks for your comments Maju.<br /><br />I will have a go at building a haplotype tree over the weekend as I have some spare time available.<br /><br />With so many papers and so much supplementary data to read it's sometimes hard to find the time, what with work and other commitments.<br />Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-70731238068122975012015-06-25T13:53:00.431-05:002015-06-25T13:53:00.431-05:00Erratum: it's not Mahra Arabs, but Mahas from ...Erratum: it's not Mahra Arabs, but Mahas from Sudan. Also the Gaali are another population from Sudan, as are the sampled Fulani (who therefore may well be unrelated or only partly related to Fulani in general). Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-31352844709003243692015-06-25T13:49:44.839-05:002015-06-25T13:49:44.839-05:00But that's age estimate based on each populati...But that's age estimate based on each population's internal diversity of the haplotypes, not a real phylogeny. It just means that the haplotypes of the populations scoring older ages are more varied. It may be a hint but I'm a bit disappointed at the evidence. I was hoping for a haplotype network of some sort, possibly even phylogenetically sorted. <br /><br />For example it's possible that Europeans together have a greater diversity and hence an older joint age estimate than Africans (even if those are only Fulani), and, IF that would be the case, then your conclusion would just be wrong on the very same dataset and the very same logic. Your conclusion would only be partly right in cases in which haplotype diversity in Basque and Finns would be a subset of the haplotype diversity in Utahans (~British+Danish), and even then the age estimate of these and Fulani is close enough to each other than they rather seem both sets derived from a common ancestor rather than one descending from the other. <br /><br />Sadly, without any sort of haplotype network it's impossible to judge this issue properly. <br /><br />Note: there's a haplotype network but the populations at each node are not detailed. Maybe in the supp. materials? Hmm, there is a haplotype data for some of the populations but it's not organized... it'd need some work but so far the LCT+ haplotype closest to the ancestral state I could spot is Utahan (#97, derived at 2 positions), not Fulani (#27 is derived at 3 positions). <br /><br />If you're very interested on the matter (and you seem to be), Chris, I'd suggest that you build a haplotype tree with some patience using that supp. material data. It should be very revealing.<br /><br />"I know that they share the whole haplotype with Bulala and Saharawi."<br /><br />That would be interesting if true. However my impression from the supp. material is that the Sudanese Fulani and Sahrawi haplotypes do not look particularly related. In many cases the Sahrawi haplotype seems to share markers with Saudi and Mahra Arabs, while there is a characteristic sequence in intron 13 among many Fulani and Gali that is not shared by anybody else. Where are those Gali from? Sudan?, Ethiopia?<br /><br />"ADMIXTURE runs which I have seen seem to suggest that Fulani are related to West Africans, Saharawi or Mozabites, and Chadic &/or Sudanic in some combination or other".<br /><br />I agree re. Sahrawis + West Africans, can't say about the rest.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-19521792577460514322015-06-25T08:13:12.570-05:002015-06-25T08:13:12.570-05:00http://www.ncbi.nlm.nih.gov/pmc/articles/PMC225396...http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253962/<br /><br />Scroll all the way down the article and look for 'Table 5'.<br /><br />Open table 5.<br />http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253962/table/tbl5/<br /><br />POPULATION ALLELE AGES OF THE ALLELE [GENERATIONS] <br /><br />Fulani T-13910 245<br />Finns, East T-13910 217<br />Finns, West T-13910 208<br />Basques T-13910 208<br />Saharawi T-13910 149<br />Moroccans T-13910 82<br />'Arabs' T-13910 39<br /><br />Ok, I remembered it ever so slightly wrong - 'Finns, East' are in second place behind the Fulani in first place. And Basques and 'Finns,West' are tied for third place.<br /><br />"I'd also like to know if other African populations have been considered, because, you know, Fulani do not exist nor have existed (paleo-)historically in a vacuum."<br /><br />I know that they share the whole haplotype with Bulala and Saharawi. The Saharawi have harbored the whole haplotype for far fewer generations than Fulani according to my data. But I don't have data for Bulala.<br /><br />ADMIXTURE runs which I have seen seem to suggest that Fulani are related to West Africans, Saharawi or Mozabites, and Chadic &/or Sudanic in some combination or other.<br /><br />http://www.unzcloud.com/wp-content/uploads/2012/01/fula1.png<br />http://blogs.discovermagazine.com/gnxp/files/2012/01/fula1.png<br />http://img690.imageshack.us/img690/1290/k6allaf001af080.png<br />https://forwhattheywereweare.files.wordpress.com/2012/01/admixture.png ---> THIS ONE IS YOURS MAJU!<br /> <br /><br /><br /><br />Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-33689535567629430512015-06-25T05:14:54.091-05:002015-06-25T05:14:54.091-05:00@Chris: Alright, thank you. It's R1b-M343 (i.e...@Chris: Alright, thank you. It's R1b-M343 (i.e. unclear what subclade), so most probably is V-88 borrowed from Chadic populations from Cameroon, via the Fulani realm of Adamawa and in general pastoralist mobility and shared lifestyle. It is not a lineage that define the Fulani and, excepted two localities (Zinder and Diffa) it is very minor. <br /><br />What you say about following the haplotypes' phylogeny is correct, at least in the outline, however I'd like to know how can you conclude that the Fulani have the oldest or most upstream known haplotype in this set. I'd also like to know if other African populations have been considered, because, you know, Fulani do not exist nor have existed (paleo-)historically in a vacuum. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-30362421039271132072015-06-25T04:12:27.263-05:002015-06-25T04:12:27.263-05:00@ Bell Beaker Blogger -
It does appear [at least...@ Bell Beaker Blogger - <br /><br />It does appear [at least superficially] that there is some correlation between R1b distribution and 13910*T distribution, I must agree.<br /><br />"The question isn't when or where T-13910 originated, because it is not relevant and it happened a long time ago."<br /><br />Yes, but we have to consider the long, extended haplotype of which 13910*T is a part. <br /><br />Assuming that 13910*T as an allele existed long prior to dairy consumption, and was found in random individuals in many different populations around the world at low frequencies, it would have likely been included in a wide variety of random haplotypes containing various different random alleles. <br /><br />Yet at some point in time, in some individuals in some population in some part of the world, dairy farming was starting to be practiced and one of the many possible random haplotypes containing 13910*T was the one which ended up being selected for and came to prominence as the so-called 'European' LCT haplotype.<br /><br />A haplotype is like a unique 'fingerprint' - the chances that the whole, entire 11 allele-long haplotype got selected for in exactly the same format in Fulani, Basques, British, Finns, and Udmurts in my opinion are slim.<br /><br />I believe that it originated in one population and then spread through asymmetric migration, with subsequent selection.<br /><br />13910*T is generally prominent only in those populations which contain the same long haplotype where selection has acted. For all I know the Andaman Islanders could harbor 13910*T as an allele, but is has never been selected for, and they certainly don't harbor the 'European' LCT 11-allele-long extended haplotype.<br /><br />So out of those prominent populations containing the unique extended haplotype, we can refer to a paper which has determined the TMRCA for 13910*T in those populations and therefore determine where the haplotype was likely to have been selected for first and subsequently migrated from. And it happens to be the case that the highest TMRCA is in the Fulani, with Basques and Finns/Udmurts tied for second place. And the date is early Neolithic.<br /><br />Interestingly, African GM immunoglobulin allotypes are also found in Iberians/Basques plus Volga Urals/Central Asia - this is something I need to look into. And I've already mentioned the HLA haplotypes.<br /><br />I also need to dig out that old 'Saami & Berbers - An Unexpected mtDNA Link' paper. <br />Guinean Fulani, Algerian Berbers, Italians, Spanish, Yakut, and Saami all possess the same mtDNA marker.<br />Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-75720726236883276272015-06-25T03:13:05.904-05:002015-06-25T03:13:05.904-05:00http://dienekes.blogspot.co.uk/2013/03/y-chromosom...http://dienekes.blogspot.co.uk/2013/03/y-chromosomes-of-pastoralists-and.html<br /><br />Y chromosomes of pastoralists and farmers from the Sahel<br /><br />Am J Phys Anthropol DOI: 10.1002/ajpa.22236<br /><br />Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel<br /><br />Jana Bučková et al.<br /><br />The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. MOREOVER, THE R1b-M343 IS REPRESENTED IN OUR DATASET EXCLUSIVELY IN THE FULANI GROUP and our analyses infer a north-to-south African migration route during a recent past. Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-918326678484598632015-06-24T16:44:08.204-05:002015-06-24T16:44:08.204-05:00Well, excuse my ignorance but I'm not aware of...Well, excuse my ignorance but I'm not aware of any Fulani population or individual that are R1b. Could you illustrate me?Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-5420233650793792262015-06-24T13:53:02.607-05:002015-06-24T13:53:02.607-05:00@Anonymous
Lactase persistence will appear at a l...@Anonymous<br /><br />Lactase persistence will appear at a low frequency in any mammal species that is lactose intolerant. A large portion of domesticated cats, for example, are lactase persistent. Because house cats were probably domesticated in the Middle East, it may be a sign of convergent selection given the culture of their diariest owners. BTW, populations with strong T-13910 allelic frequency and dairying tradition generally have strong Rhesus D deletion. (the Basque as one example)<br /><br />But regardless, the native state in mammals occurs naturally as it did in Paleolithic humans and as it does randomly from Tibet (three additional haplotypes) to Peru (others) at whatever frequency.<br /><br />The question isn't when or where T-13910 originated, because it is not relevant and it happened a long time ago. The question is how did this trait reach the frequency in the populations that have it at such high rates. Maciamo's map of the worldwide distribution of R1b and T-13910 nearly correlates to the "T" (no pun intended) and this is because of specific population movements beginning in the 4th millennium and I would suppose that the two are roughly ancestry proportioned. It's a reasonable hypothesis, so yes.<br /><br />"That might explain Ireland 98% or Scotland, but how is Sweden a non R1b majority country listed at 99% or the Danes at 96%.?""<br /><br />One thing to keep in mind is that most maps are interpolations of small test groups and Sweden straddles a cline so the data is kind of shaky in my opinion. You may well have a high phenotype in Southern Sweden with ethnic Swedes and then dropping off quickly after that. Some of the data may not exclude non-ethnic Swedes either.<br />The allelic and phenotype frequency I've seen for Sweden has been all over the place so it's hard to make a quick judgement. <br /><br />@Maju<br /><br />I meant the percentage of ethnic Fula that are R1b which various among Fulani of different nationalities. I would say that they roughly correlate.<br /><br />bellbeakerbloggerhttps://www.blogger.com/profile/01848982163843593127noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-44910169572177769552015-06-24T04:11:06.977-05:002015-06-24T04:11:06.977-05:00I missed this one earlier but mind you: Fulani are...I missed this one earlier but mind you: Fulani are not high in R1b-V88, that's preposterous! R1b-V88 is high among some Chadic peoples and ill-researched R1b (which could well be largely V88 but uncertain) is high in Sudan. Fulani are not Chadic, nor (with a lesser exception) Sudanese: they are West African by geography (extreme West African by origin: from Senegal) and Nigher-Congo by language. They do however sport some West Eurasian admixture of the NW African kind (Sahrawi-like) but the 13910-T allele is rare in NW Africa (Sahrawis have not yet been studied though). Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-70714885367251786992015-06-24T00:02:44.755-05:002015-06-24T00:02:44.755-05:00"And why would T13910 and other appear with R..."And why would T13910 and other appear with R1b V88 high Fulani in Northern Sudan, Niger and Cameroon but not their neighbors? And why in M73/M269 Western China or in Baluchi but not their neighbors?"<br /><br />Are you suggesting, as does Maciamo Hay, that lactase persistence spread with R1b? That might explain Ireland 98% or Scotland, but how is Sweden a non R1b majority country listed at 99% or the Danes at 96%.?<br /><br />"If R1b stemmed from near the steppe and spread during the copper age then V88 people would have had quite a journey: to Egypt then down to Sudan, across that pastoralist strip south of the Sahara to the gold fields of West Africa then up north again to hook up with BB / Atlantic Megalith in NW Africa.<br /><br />People will go a long way for gold."<br /><br />R U Serious? Obviously R1b is old and the V88 branch broke off well before the chalcolithic. R1b only spread into west Europe in the late neolithic to chalcolithic.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-7384431201708443832015-06-17T04:05:13.611-05:002015-06-17T04:05:13.611-05:00@ Marnie:
I'll start with the HLA haplotypes....@ Marnie:<br /><br />I'll start with the HLA haplotypes.<br /><br />Those that have been in European populations a long time are highly equilibrated; those that are more more recent are highly dis-equilibrated.<br /><br />HLA haplotype: A29-Cw16-B44 [shorthand].<br /><br />= A*29:02-B*44:03-C*16:01-DRB1*07:01-DQB1*02:01 [longhand].<br /><br />Peak European frequencies:-<br />*Gipuzkoa Basque 10.00% [#1 haplotype in Basques]<br />*Spain Catalonia Girona 7.50%<br />*Spain Ibiza 6.10%<br />*Arratia Valley Basque 5.30%<br />*Spain Murcia 5.10%<br />*Spain Majorca & Minorca 4.40%<br />*Spain Minorca 3.90%<br />*Northern Ireland 2.90%<br />*Spanish migrants in Germany [N=1107] 2.78%<br />etc. etc.<br />[Eastern Europe = 0%]<br /><br />The haplotype and versions of it are found in Maghreb, Cameroon, Zambia, South Africa Zulu, etc. [probably many others, but Africa needs better sampling - we have plenty of data from Eurasia alredy].<br /><br />The haplotype and its allelic components are found at their greatest frequency and diversity of recombinants in tropical African populations.<br /><br />Let's look at the alleles contained within this haplotype [class I alleles] - peak world frequencies:-<br /><br />A*29:02<br />*South Africa Natal Zulu 11.00%<br />*Cameroon Yaounde 10.40%<br />*Zimbabwe Harare Shona 9.60%<br />*Cameroon Bamileke 8.40%<br />*Cameroon Sawa 7.70%<br />*Morocco Chaouya 6.80%<br />*Tunisia 6.70%<br />*Cameroon Beti 6.30%<br />*Zambia Lusaka 5.80%<br />*Kenya Luo 5.30%<br />*Uganda Kampala pop.2 5.10%<br />etc. etc.<br /><br />B*44:03<br />*Cameroon Beti 10.90%<br />*South Africa Natal Zulu 10.50%<br />*Cameroon Bakola Pygmy 9.44%<br />*Ghana Ga-Adangbe 8.78%<br />*Cameroon Bamileke 8.40%<br />*Central African Republic Mbenzele Pygmy 7.26%<br />*Zimbabwe Harare Shona 5.80%<br />*Uganda Kampala 4.70%<br />etc. etc.<br /><br />C*16:01<br />*Mali Bandiagara 28.30%<br />*Burkina Faso Fulani 21.40%<br />*Burkina Faso Mossi 17.90%<br />*Ghana Ga-Adangbe 17.18%<br />*Senegal Niokholo Mandenka 16.80%<br />*Burkina Faso Rimaibe 16.00%<br />*Equatorial Guinea Bioko Island Bubi 10.50%<br />*Zambia Lusaka 10.00%<br />*Kenya 8.40%<br />*Zimbabwe Harare Shona 8.00%<br />*Tunisia 7.20%<br />*Morocco Chaouya 7.10%<br />*South Africa Black 6.60%<br />*Cameroon Beti 6.00%<br />*Sudan Mixed 5.00%<br />*Uganda Kampala 4.90%<br />*Cameroon Bamileke 4.50%<br />*Kenya Luo 4.50%<br />*Kenya Nandi 4.40%<br />etc. etc.<br /><br />[Source: www.allelefrequencies.net]<br /><br />So my reasoning was, if HLA haplotypes have moved northward, eg. from Fulani or proximal populations towards Basque Country, and Basques happen to share the exact same lactase persistence haplotype with Fulani, then why could the LCT haplotype not also have moved northwards rather than southwards.<br /><br />Moreover, another paper which I presented a link to recently demonstrated that the TMRCA for the active allele contained within the LCT haplotype, 13910*T, is greater in Fulani than in Basque [though both give a Neolithic time frame].Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-67316964364406151952015-06-16T23:26:42.045-05:002015-06-16T23:26:42.045-05:00Thanks Chris. I look forward to reading this.Thanks Chris. I look forward to reading this.Marniehttps://www.blogger.com/profile/10850856778953207810noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-87114578170510043812015-06-16T23:22:47.995-05:002015-06-16T23:22:47.995-05:00@Chris Davies
"I think that this suggests ge...@Chris Davies<br /><br />"I think that this suggests gene-flow northward to the Basque region and not vice-versa" <br /><br />Just wondering why you think northward and not southward.Marniehttps://www.blogger.com/profile/10850856778953207810noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-54145913297044550322015-06-16T15:36:54.981-05:002015-06-16T15:36:54.981-05:00NW Africans have only low frequencies of the Europ...NW Africans have only low frequencies of the European LCT allele. I wonder if Sahrawis or Mauritanians have it (seems that Tuareg do not). That would simplify the process of transmission a lot. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-50644579101498314232015-06-16T15:24:10.972-05:002015-06-16T15:24:10.972-05:00Never mind: I found the reference myself: http://w...Never mind: I found the reference myself: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031279/ (see table 1).<br /><br />That is fascinating because it seems to imply (my opinion) that somehow they have inherited the trait from the Paleolithic flows into NW Africa at the Oranian genesis (Fulani have like 1/3 of NW African "Eurasian" ancestry, most similar to Sahrawis specifically). In other words: there is a good chance that the T allele originated in Paleolithic populations of Europe (however it has yet to be found among them, I reckon, but also among the much better sampled Neolithic farmers), otherwise it is nearly impossible to explain its presence among the Fulani.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-57952572112297739042015-06-16T15:14:16.485-05:002015-06-16T15:14:16.485-05:00Can you document the presence of the European LCT ...Can you document the presence of the European LCT allele in Fulani? My data does not report it so far.<br /><br />Anyhow, IF there was a selection for the West European LCT allele, it must have happened before 3000 BCE. I must insist on the Upper Ebro sites issue (never mind Gokhem): http://forwhattheywereweare.blogspot.com/2012/01/caught-in-act-lactose-intolerant-and.html<br /><br />What we see in San Juan Ante Porta Latinam and Longar (military cemeteries dated to c. 3000 and 2500 BCE) are two distinct populations: one with the T allele fixated and another one with the C allele fixated (almost no CT individuals, underlining a clear segregation of both populations before death). The latter is dominant and fits well with all other Neolithic findings (save Gokhem) in being lactose intolerant (apparently), the former however has the T allele fixated and that is super-important: it means that selection (if that's the cause) had already acted in them driving the T allele to fixation (alternatively it's a random founder effect or fluke fixation by mere drift, fixated T in any case). <br /><br />So there is no need to appeal to selection after those dates but a realistic scenario can well be that of expansion of the T-fixated population from (I believe) Atlantic Europe eastwards. <br /><br />This scenario would also explain other genetic traits that are most concentrated in the Western coastal region of Europe, including haploid structure, be it Y-DNA R1b or mtDNA H1 and H3. <br /><br />Another piece of evidence in favor of an early Atlantic fixation for the T allele is the massive consumption of dairies in Neolithic Britain (and its persistence up to the Danelaw, which is when love for fish is reintroduced in the island). See: http://forwhattheywereweare.blogspot.com/2014/02/neolithic-peoples-from-britain-and.htmlMajuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-78335177683688845322015-06-16T14:52:04.105-05:002015-06-16T14:52:04.105-05:00"If there had been so much selection on light..."If there had been so much selection on light eyes and skin plus lactose persistence it would show up in linkage disequilibrium, but it doesn't so it didn't happen."<br /><br />The lactase persistence haplotype found in Europeans is very extended and very disequilibrated, and given its frequencies I don't doubt that it was selected for. The thing which I have been quibbling over is the geographic origin of the haplotype. I don't think that it necessarily originated in Europe. Same haplotype shared between Fulani and Basques, but Fulani have a higher TMRCA for the active allele contained within the haplotype [13910*T]; plus there seems to be another variant of the haplotype in Africa which contains the 13907*G derived allele [no such diversity in Europe].<br />Given that Basques also share a disequilibrated HLA haplotype with tropical western Africans, and this haplotype has diverse recombinants in Africa but not in Basques, Iberians, or French, I think that this suggests gene-flow northward to the Basque region and not vice-versa, and I also believe that the lactase persistence haplotype did the same.<br />People are saying that the presence of the so-called European LCT haplotype in Fulani must be due to the Romans or the Vandals in North Africa; I am totally not convinced.<br /><br />"But I think they know that, they have zero interest to find the truth, just to make some lame political statements."<br /><br />Agree with this statement. Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-1418818314847650062015-06-16T11:51:48.561-05:002015-06-16T11:51:48.561-05:00If there had been so much selection on light eyes ...If there had been so much selection on light eyes and skin plus lactose persistence it would show up in linkage disequilibrium, but it doesn't so it didn't happen.<br /><br />You can keep sampling eastern and central europe neolithic a million years and won't find where NW european people came from because they were already there/ Even if there was some megamigrations, certainly r1b DNA was where it is now by then.<br /><br />But I think they know that, they have zero interest to find the truth, just to make some lame political statements.Fiend of 9 worldshttps://www.blogger.com/profile/17712083368615685458noreply@blogger.comtag:blogger.com,1999:blog-6886680068187530519.post-73903585981717870482015-06-15T06:54:07.786-05:002015-06-15T06:54:07.786-05:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.com