Topic: Haplogroup E and A are probably West African
Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Here's something Beyoku proposed and I think worth more expansion for clarity and precision. There're many facets inside that declaration. An excellent Africana topic for our fresh board.
quote: Its quite obvious that Haplogroup E and A are probably West African......why do we call them East African? Are we appealing to authority? ....
I have to add an appeal to authority fallacy only exists if the appealed to authority is not trained in the discussed field. Like appealing to an electrical engineer for an anthropology conclusion.
Posters on here who are familiar with geographic assignments WITHIN Africa can help out for A1b1b2 and mtDNA L0d2c1, L0d2a1, L0d2 , L0d2a1a, L3e3b1, L3e1b2, L3e2b1a2
Are these Bantu’s? I think not. No mtDNA L2a1* and no E1b1a. So I would say , no, yDNA E is definitely not West African. I predicted this a long time ago. yDNA E1b1a will NOT be found in aDNA in West Africa beyond 2000BC. Hell it looks like it is not part of the supposed Bantu Expansion.
It is absurd and ridiculous to think E is West African
quote:Originally posted by Elmaestro: I'm certain that this will be addressed in Xyymans thread, if it comes off the ground, we have ancient African DNA that is changing the game.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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Though you might be right about what it is you are saying, might I ask... who said anything about E1b1a??? you know where basal DE can be found? Ish?
Posts: 1781 | From: New York | Registered: Jul 2016
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The Oldest Haplogroup A lineages are found in West Africa and North West Africa. These would be A00 and A1. East African A-M13 and South African A-M51 are united by an old but not as old A-M32. South African A-M6(A2) is old, but again not as old as West African A00/A1. I am using the old nomenclature but the data is still the same.
In relation to Haplogroup E....West Africa has a few things that the East doesn't have. THe East does have a new lineage(s) found in Trombetta: V-44. BUt Both regions have underived E*, both regions have what was once sampled as Pn2* The West has a large successful Early branch E1a. The Trump card is the west having the precursor, DE*.....the Double Ace is the West carrying those D* lineages found in Benin. Source
I think the evidence as far as Phylogeny point to the West African origin of A and E. Probably B too. People say the origin is East Africa simply for convenience...and it being somewhat status quo.
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007
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I remember I use to always talk about haplogroup A1 and how SOME Moroccans still carried it. To me I think that was the clade the Aterian culture were carrying. Also wasn't there a big thing with an African-American man carrying Haplogroup A00?
But man... Just man... If its confirmed that E came from West Africa then I see a bunch of...
from EVERYONE. **** like that would be big. What Beyoku told me about DE opened up my eyes...
@Tukuler and @Beyoku correct me if I am wrong but is it true that West Africa has the older L lineages too?
Posts: 1891 | From: NY | Registered: Sep 2014
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'Oldest' L is pretty much Southern African - L0 is most basal branch of L, L0d and L0k are most basal branches of L0. Other L0 in East Africa, West Africa has only downstream L0a. L1 is second branch off and has West/Central African origin AFAIK.
All this stuff (and the A branches) is well over 100 000 years ago though, so modern distribution could be totally misleading.
quote:Originally posted by beyoku: The Trump card is the west having the precursor, DE*.....the Double Ace is the West carrying those D* lineages found in Benin. Source
The D is a typo; check the ref, it's DE(xE), from Nigeria. Though I agree that West is just as diverse as East at the basal level of E if not more so. E2a-M41, E3-V44 in East, E2b-M98, E1a-M33 in West. DE* in West, D in, uh, far northeast Africa. Even barely existent E1b2-P75: Canary Islands, Palestine.
Posts: 660 | From: Canada | Registered: Mar 2017
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Have yall seen this study. It has Nigerians carrying DE. Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria
Can somebody save me a lil time and put up Fig. S2. b on hg A, please.
Also, for clarity's sake, please use mutation instead of phylogeny. Phylogenies change. Defining mutations remain and append.
Per Chiaroni's map today's E hi-freq • M33 -- only in W Afr • PN2 -- concentrated from Gulf of Guinea to Gibraltar are pieces of evidence favoring W Afr origin of E.
Frequency isn't as important as μ-sat diversity mutation ages but they can't be ignored either.
What other evidences favor W Afr? What speaks against it? Both pans of the scale athwart the balance.
quote:Originally posted by beyoku: The Oldest Haplogroup A lineages are found in West Africa and North West Africa. These would be A00 and A1. East African A-M13 and South African A-M51 are united by an old but not as old A-M32. South African A-M6(A2) is old, but again not as old as West African A00/A1. I am using the old nomenclature but the data is still the same.
In relation to Haplogroup E....West Africa has a few things that the East doesn't have. THe East does have a new lineage(s) found in Trombetta: V-44. BUt Both regions have underived E*, both regions have what was once sampled as Pn2* The West has a large successful Early branch E1a. The Trump card is the west having the precursor, DE*.....the Double Ace is the West carrying those D* lineages found in Benin. Source
I think the evidence as far as Phylogeny point to the West African origin of A and E. Probably B too. People say the origin is East Africa simply for convenience...and it being somewhat status quo.
Damn, I learned something new
Posts: 2595 | From: Vicksburg | Registered: Feb 2006
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More on Haplogroup DE being found in Nigerians.
quote:The new haplogroup, labeled DE* according to the nomenclature of the Y CHROMOSOME CONSORTIUM 2002 Down, has been found in 5 Nigerians (from different villages, languages, ethnic backgrounds, and paternal birthplaces) from a data set of >8000 men worldwide, including 1247 Nigerians. The position of these 5 Nigerians on the Y chromosome tree has been confirmed by repeated typing for all the known UEP markers immediately above and below node a in Fig 1 (YAP, M145, M203, M174, M96, P29, and SRY4064) as well as for five additional UEP markers (92R7, M9, M20, 12f2, and SRY10831) as shown in Fig 1. The asterisk in DE* indicates that it is potentially, but not definitely, paraphyletic relative to one or both of groups D and E (Fig 2). The term "paragroup" has been applied to such haplogroups (Y CHROMOSOME CONSORTIUM 2002 Down). To help resolve the issue of paraphyletic status, we typed YAP-derived individuals in our data set for six microsatellites: DYS19, DYS388, DYS390, DYS391, DYS392, and DYS393. Of the five DE* individuals, three had a microsatellite haplotype consisting of repeat sizes 13-13-22-11-11-13 (loci arranged in same order as listed above) while the other two had a haplotype differing by one step at DYS391 only (13-13-22-10-11-13). This high level of similarity in such a rapidly evolving system strongly suggests that these five individuals share a private common ancestor (as in Fig 2C, Fig D, or e). We note that of the three possible branching patterns, two (Fig 2C and Fig D) would imply an African origin for YAP, while the third (Fig 2E) would leave the question of origins open. However, it is not easy to assess the relative probabilities of these three patterns.
quote:The B-M60 variant observed in almost all sub-Saharan collections [28] was only found in Nalú. One other Nalú individual belongs to the rare and deep-rooting DE* paragroup described in five Nigerians [37] and thus representing a coalescent "missing link", paraphyletic to haplogroups D and E. The two Western European R1b-P25 lineages in Fulbe and Bijagós are best explained by recent European influence, at the time of the slave trade. A partial introduction through North African pastoral immigrants can not be rejected, where the 3–12% of R1b-P25 are due to the geographic proximity and the long reported contacts with Europe and Middle-East [33]. The European source seems nevertheless more likely: firstly, Y chromosome signatures of European presence have a reported great expression in the nearby Cape Verdians [38] and secondly, highly frequent North African haplogroups that would have been equally carried by the migrants (e.g. E3b2-M81) are absent in Guineans. The M173 and P25 derived states in both our samples rule out a relationship to the R1*-M173 lineage previously found in Cameroon, Oman, Egypt and Rwanda, and adduced to support the "Back-to-Africa" theory [3,28].
quote:Further refinement awaits the finding of new markers especially within paragroup E3a*-M2. The microsatellite profile of the DE* individual is one mutational step away from the allelic state described for Nigerians (DYS390*21, DYS388 not tested; [37], therefore suggesting a common ancestry but not elucidating the phylogenetics.
quote:Originally posted by BlessedbyHorus: Have yall seen this study. It has Nigerians carrying DE. Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria
I notice that the branch is located nearby Cameroon. Yep, once again Cameroon. The oldest A0 branch also has been found there. And it's the same place where R-V88 has been found which relates to non-CpG sites. It could be all coincidence.
I recall Beyoku saying in that live conversation, how sometimes certain data sits there waiting to be published.
I think the following is going to give us the necessary answers in the near future, as aDNA will be researched on African fossils. The closer we get, the more I start to love and appreciate Cruciani's work.
The deepest branching separates A1b from a monophyletic clade whose members (1a A2, A3, B, C, and R) all share seven mutually reinforcing derived mutations (five transitions and two transversions, all at non-CpG sites).
--Fulvio Cruciani
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:Originally posted by beyoku: The Oldest Haplogroup A lineages are found in West Africa and North West Africa. These would be A00 and A1. East African A-M13 and South African A-M51 are united by an old but not as old A-M32. South African A-M6(A2) is old, but again not as old as West African A00/A1. I am using the old nomenclature but the data is still the same.
In relation to Haplogroup E....West Africa has a few things that the East doesn't have. THe East does have a new lineage(s) found in Trombetta: V-44. BUt Both regions have underived E*, both regions have what was once sampled as Pn2* The West has a large successful Early branch E1a. The Trump card is the west having the precursor, DE*.....the Double Ace is the West carrying those D* lineages found in Benin. Source
I think the evidence as far as Phylogeny point to the West African origin of A and E. Probably B too. People say the origin is East Africa simply for convenience...and it being somewhat status quo.
As per Fulvio Cruciani.
Third, contrary to previous phylogeny-based conclusions,15,16 the deepest clades of the revised MSY phylogeny are currently found in central and northwest Africa. Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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E is West Eurasian in terms of origin. There's also R1b V88 haplogroup in Northern Cameroon which sugges West Eurasian like admixture in West Africa during the Neolithic or even before. So my guess is that an ancient African population and a West Eurasian population did mix which created modern West Africans, while East Africans are a result of mix between West African/Eastern Bantu and Natufian like populations.
If we get access to find proto African skeletons from West and Central Africa then we can have a more clear access to estimate the archaic Eurasian like ancestry in modern West Africans which can be seen if we compare West Africans to even more Archaic African populations such as Khoisan people. As long as Yoruba people are being used to estimate Sub Saharan ancestry we can't have a more proper estimate to measure other influences in modern African populations.
Posts: 10 | From: Europe | Registered: Jul 2017
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quote:Originally posted by francesco01: E is West Eurasian in terms of origin. There's also R1b V88 haplogroup in Northern Cameroon which sugges West Eurasian like admixture in West Africa during the Neolithic or even before. So my guess is that an ancient African population and a West Eurasian population did mix which created modern West Africans, while East Africans are a result of mix between West African/Eastern Bantu and Natufian like populations.
If we get access to find proto African skeletons from West and Central Africa then we can have a more clear access to estimate the archaic Eurasian like ancestry in modern West Africans which can be seen if we compare West Africans to even more Archaic African populations such as Khoisan people. As long as Yoruba people are being used to estimate Sub Saharan ancestry we can't have a more proper estimate to measure other influences in modern African populations.
In terms of what origin?
Your whole theory makes no sense with this mythical eurasia hype.
quote: According to the current data East Africa is home to nearly 2/3 of the world genetic diversity independent of sampling effect. Similar figure have been suggested for sub-Saharan Africa populations [1]. The antiquity of the east African gene pool could be viewed not only from the perspective of the amount of genetic diversity endowed within it but also by signals of uni-modal distribution in their mitochondrial DNA (Hassan et al., unpublished) usually taken as an indication of populations that have passed through ‘‘recent’’ demographic expansion [33], although in this case, may in fact be considered a sign of extended shared history of in situ evolution where alleles are exchanged between neighboring demes [34].
Figure S1 Neighbor joining (NJ). NJ tree of the world populations based on MT-CO2 sequences. The evolutionary relationship of 171 sequences and evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 0.20401570 is shown. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 543 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4. Red dots: east Africa, Blue: Africa, Green: Asia, Yellow: Australia, Pink: Europe and gray: America. (TIF)
Figure S2 Multidimensional Scaling Plot (MDS). The 2nd and 3rd coordinates of an MDS plot of 848 nuclear microsatellite loci from 469 individuals of 24 world populations. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The figure, besides a separate clustering of east Africans, indicates the substantial contribution of Africans and east Africans to the founding of populations of Europe and Asia. (TIF)
Figure S3 Multidimensional Scaling Plot (MDS). The 3rd and 4th coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. The central position of east Africans and some other Africans emphasizes the founding role of east African gene pool and the disparate alignment on coordinates along which the world populations were founded including populations of Aftica aligning along the 4th dimension. (TIF)
Figure 4. Multidimensional Scaling Plot (MDS). A. First and second coordinates of an MDS plot of 848 Microsatellite Marshfield data set across the human genome for 24 populations from Africa, Asia and Europe. MDS plot was constructed from pairwise differences FST generated by Arlequin program (Table S3). B. First and second coordinates of an MDS plot of 848 Microsatellite loci, across the human genome in 469 individuals from 24 populations from Africa, Asia and Europe. MDS uses pairwise IBS data based on the 848 loci generated by PLINK software and plotted using R version 2.15.0. East Africans cluster to the left of the plot, while Beja (red cluster in the middle), assumes intermediate position. doi:10.1371/journal.pone.0097674.g004
Figure S4 Multidimensional Scaling Plot (MDS). First and second coordinates of an MDS plot based on MT-CO2 data set constructed from pairwise differences FST generated by Arlequin v3.11. Population code as follows: Nara: Nar, Kunama (Kun), Hidarb (Hid), Afar (Afa), Saho (Sah), Bilen (Bil), Tigre (Tgr), Tigrigna (Tig), Rashaida (Rsh), Nilotics (Nil), Beja (Bej), Ethiopians(Eth), Egyptians (Egy), Moroccans (Mor), Southern Africans (Sth), Pygmy (Pyg), Saudi Arabia (Sdi), Asia (Asi), Europe (Eur), Native Americans (NA), Australians (Ast), Nubians (Nub), Nuba (Nba) (TIF)
--Jibril Hirbo, Sara Tishkoff et al.
The Episode of Genetic Drift Defining the Migration of Humans out of Africa Is Derived from a Large East African Population Size
quote:Originally posted by francesco01: E is West Eurasian in terms of origin. There's also R1b V88 haplogroup in Northern Cameroon which sugges West Eurasian like admixture in West Africa during the Neolithic or even before. So my guess is that an ancient African population and a West Eurasian population did mix which created modern West Africans, while East Africans are a result of mix between West African/Eastern Bantu and Natufian like populations.
If we get access to find proto African skeletons from West and Central Africa then we can have a more clear access to estimate the archaic Eurasian like ancestry in modern West Africans which can be seen if we compare West Africans to even more Archaic African populations such as Khoisan people. As long as Yoruba people are being used to estimate Sub Saharan ancestry we can't have a more proper estimate to measure other influences in modern African populations.
quote:The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.
[...]
Yet Khoisan populations have maintained the greatest nuclear-genetic diversity among all human populations3, 4, 5 and the most ancient Y-chromosome and mitochondrial DNA lineages6, 7, implying relatively larger effective population sizes for ancestral Khoisan populations.
--Hie Lim Kim, Aakrosh Ratan, George H. Perry, Alvaro Montenegro, Webb Miller & Stephan C. Schuster
Received 25 Apr 2014 | Accepted 29 Oct 2014 | Published 4 Dec 2014
posted
Are they even able to find out what region of Africa such deep basal clades arose?? I mean unless experts are able to find a good quantity of prehistoric skeletal material from different parts of Africa dating from the Pleistocene retrieve DNA from there I can't see any other way.
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