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Originally posted by StTigray:
WTH now I really feel like a moron, what does all that mean.

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Posts: 4028 | From: NW USA | Registered: May 2005  |  IP: Logged | 

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Originally posted by osirion:
Recent reports supports an African origin of E:


Scientists reshape Y chromosome haplogroup tree gaining new insights into human ancestry
Wednesday, April 2, 2008 –The Y chromosome retains a remarkable record of human ancestry, since it is passed directly from father to son. In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.

Human cells contain 23 pairs of chromosomes: 22 pairs of autosomes, and one pair of sex chromosomes. Females carry a pair of X chromosomes that can swap, or recombine, similar regions of DNA during meiosis. However, males harbor one X chromosome and one Y chromosome, and significant recombination between these dissimilar sex chromosomes does not occur. Therefore, the non-recombining region of the Y chromosome (NRY) remains largely unchanged over many generations, directly passed from father to son, son to grandson, and so on, along with genetic variations in the NRY that may be present. Scientists can use genetic variations, such as single nucleotide polymorphisms (SNPs), on the Y chromosome as markers of human ancestry and migration.

In 2002, the Y Chromosome Consortium (YCC) constructed a tree of 153 haplogroups based upon 243 unique genetic markers. In this report, researchers led by Dr. Michael Hammer of the University of Arizona recognized the need to revisit the Y chromosome haplogroup tree and incorporate the latest data. “The YCC effort in 2002 was a landmark in mapping the then known 300 or so Y-linked SNPs on a single tree, and getting the community to use the same nomenclature system,” explains Hammer. “The rate of SNP discovery has continued to increase over the last several years, as are publications on Y chromosome origins and affinities. While this new information is useful, ironically it also brings with it the danger of introducing more chaos into the field.”

Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando Mendez, a co-author of the study.

In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”

“More SNPs are being discovered, and we anticipate the rate to increase with the 1000 Genomes Project,” says Hammer, referring to the wealth of human genetic variation data that will soon be available. While this report represents a significant advance in mapping ancestry by Y chromosome polymorphisms, it is certain that future discoveries will necessitate continual revisions to the Y chromosome haplogroup tree, helping to further elucidate the mystery of our origins.


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Scientists from the University of Arizona (Tuscon, AZ) and Stanford University (Stanford, CA) contributed to this study.

This work was supported by the Salus Mundi Foundation.

Media contacts:

Michael Hammer, Ph.D., has agreed to be contacted by email for more information (mfh@u.arizona.edu).

Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (calicchi@cshl.org; +1-516-422-4012).

About the article:

The manuscript will be published online ahead of print on April 2, 2008. Its full citation is as follows: Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.

About Genome Research:

Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched in 1995, it is one of the five most highly cited primary research journals in genetics and genomics.

About Cold Spring Harbor Laboratory Press:

Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.

Genome Research issues press releases to highlight significant research studies that are published in the journal.

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Posts: 5905 | From: The Hammer | Registered: Aug 2008  |  IP: Logged | 

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Originally posted by StTigray:
WTH now I really feel like a moron, what does all that mean.

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StTigray: basically it boils down to this.

Eurocentrics, neo-nazis, Aryanists, alleged Egyptian "nativists" (who on a number of forums are bogus ‘fronts’ of the 3 above), and other assorted "ists" all try to deny that Egypt has any significant connection to Africa at all. They are always trying to paint Egypt white. The labels vary- they say 'Mediterranean", "Hamitic" "Middle Eastern" “Oriental” or what have you, but their aim is clear- move Egypt as far as possible from those 'darker' types. Don't take my word for it. Consider the complaint below by conservative white Egyptologists Berry and Ucko in 1967, over the “racial” inconsistency and double standards in the field. At various time, assorted European writers were positing North American Indians from thousands of miles away populating ancient Egypt- this being more believable than black Sudanics or Saharans a few score miles away.

Berry and Ucko (Genetical Change in Ancient Egypt):

"This is attested by the tendency in the past (summarised by Chantre 1904) to postulate all sorts of improbable racial amalgams in Egypt: mixtures of peoples representing a singular variety of groups (viz. Libyan, Caucasian, Arab, Pelasgian, Negro, Bushman, Mongol, Hamitic, Hamito-Semitic- even Red Indian and Australian aboriginal) were alleged to have migrated into the Nile Valley." . Indeed Keith (1905:92) complained that the literature at that time included hopeless contradictions of three, six, one and two races."

Later work was sometimes marked by the same pattern with even Cro-Magnons being thrown into the mix.[6] Berry and Ucko also note most Egyptologists in earlier years – quote:

"are at pains to disclaim any Negro element in the Egyptian populations after the predynastic period except for the population of Sudanese Kerma.." while producing shifting definitions of exactly what 'negroid' was. Further quote:

".. the basic weakness of all claims to distinguish or decry Negro elements on the basis of metrical analyses is the absence of any rigorous population comparisons to isolate particular featurers which can be described as negroid. It is typical of this unsatisfactory situation that F.P [Petrie] 1928:68) although basing himself entirely on the original Stoessiger report, could sumarise the Badarian skull material in terms which denied any serious Negro element."


Some of these methods have shifted to DNA analysis, but the multitude of studies being done and the growing pattern data, plus the rise of scholars like Armelagos, Keita, Templeton etc.. willing to challenge the status quo mean that the “black get back” modelers no longer have a free hand. Assorted ‘Aryan’ posters appear from time to time to strenuously deny that Haplogroup E is African. They have to because Haplo E has the highest frequency in Africa and tie together numerous peoples, East, West, north and south. So a narrow nosed a cattle herder in the Sahara is related to a broad nosed farmer in Mozambique without the need for any white “race mix” to explain why. You can see now why they have to go all out to deny it. See the Tutsi example below. Here are narrow nosed, thin lipped Africans in East African. Surely they must be ‘Caucasoid” no? Wrong. Their DNA links mostly with West Africans. See what I mean?




You can also see the hypocritical double standards at play when they, or certain other scholars discuss these studies. Hapo “J” appears mostly in SW Asia, and they call it SW Asian (Turkey/Middle East etc). Another hapo appears mostly in Europe and they call it 'European'. No problem there. But when it comes to Africa, where hapo E is most prevalent, and the original people whose subsets populated the world, well then a number of scholars (note I don't say all white scholars- some call the data as it is) quickly find a way to NOT call Hapo E African. They will slice, dice and beat around the bush, and use other sub-labels. Assorted Eurocentrics have tried to shift Hapo “E” as having an “Asian” origin by tying it to the D group found in Asia. Alack and alas, they fail.

Generally the European academy will always tend to use the biggest possible label - like "Eurasian" to group the biggest blocs together of what they claim to be "cacasoid", but strangely, will carefully narrowly delimit 'true' African populations into a "sub Saharan" bloc. Notice the pattern- make the category as broad and expansive as possible when dealing with so-called 'caucasoid" peoples, but draw it as narrowly as possible when it comes to blacks.

The Human Geonome Project for example has as one huge category something called "North Eurasia' - conveniently grouping SW Asia, Europe and yeah, you guessed it North Africa, but then they also have a "sub-Saharan" category to deal with the rest of Africa. See the hypocrisy? The Sahara was once a fertile greenbelt extending across one-third of Africa. It was not the way it is now, and even as a barrier, it has been a transmission belt for the trade and the movements of peoples across vast distances of Africa. Why not treat the African continent as one whole? Why combine Europe and SW Asia, but carefully segregate out "sub-Saharan" Africa from the rest of the continent? If haplogroup E unites numerous peoples from South to North why the split?


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You can also see a lot of sampling bias in certain DNA studies. Some for example take samples in the far north of Egypt near Cairo, an era with a lot of gene flow from Arabs, Greeks, Romans etc etc over time, and then they use that as “representative” of all of Egypt, ignoring or downplaying the “darker” south. They did the same thing with cranial studies, carefully rigging the deck and loading the dice to “fade out” certain areas and peoples. Again, don't take my word for it. Here is mainstream scholar S. Keita:

"However, in some of the studies, only individuals from northern Egypt are sampled, and this could theoretically give a false impression of Egyptian variability (contrast Lucotte and Mercier 2003a with Manni et al. 2002), because this region has received more foreign settlers (and is nearer the Near East). Possible sample bias should be integrated into the discussion of results." (S.O.Y. Keita, A.J. Boyce, "Interpreting Geographical Patterns of Y Chromosome Variation1," History in Africa 32 (2005) 221-246 )


Here is Egyptologist Barry Kemp on the worldwide CRANID database that used northern skull samples near the Mediterranean as "representative" of the ancient Egyptians, and classifying them in a "European" direction, while excluding key historic sites further south..
"If, on the other hand, CRANID had used one of the Elephantine populations of the same period, the geographic association would be much more with the African groups to the south. It is dangerous to take one set of skeletons and use them to characterize the population of the whole of Egypt." (Barry Kemp, Ancient Egypt Anatomy of a Civilisation, Routledge: 2005, p. 55)
And here are 2 examples of the rigged cards and loaded dice at work, not only in the Nile Valley but in Ethiopia and other places as well:

the loaded dice..


the stacked deck…

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ES vets will be able to break down the DNA more for you but the bottom line is that haplogroup E is African and it has many mutations- not surprising since Africa is the most genetically diverse in the world. The PN2 transition- a “bridge” marker so to speak, ties together numerous African peoples with "E” however, regardless of how they look. So the standard “true negro” dodge, whereby “true” black people are only “supposed” to look a certain way is once again defeated. The Tutsi example again is a case in point. Narrow noses or thin lips are nothing special in Africa. They are routine, built in variations in how Africans look without needing any “race mix” or "wandering Caucasoids" to explain why.

Posts: 5905 | From: The Hammer | Registered: Aug 2008  |  IP: Logged | 

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Originally posted by zarahan:
If haplogroup E unites numerous peoples from South to North why the split?

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Posts: 368 | Registered: Sep 2009  |  IP: Logged | 

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Table 1 lists the reported YAP+ frequencies in worldwide populations (refer to table note for references). Africans have the highest frequency of YAP+, and all of them belong to the sub-haplogroup E-M40. In contrast, D-M174 is in general East Asian specific with sporadic occurrence in adjacent regions, i.e. Central Asia, Middle East and Northeast India. The average frequency of D-M174 in East Asians is 9.60% with high frequencies in Tibet (41.31%), Japan (35.08%) and Andaman Island (56.25%), but rare in other East Asian populations (< 5%).

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The results of these haplogrouping experiments indicated that one ( Table 1 ) of the 18 SNPs evaluated shared derived alleles in haplogroups C and F while being at an ancestral state in the other haplogroups. [Erratum] These results hold up the phylogenetic scenario shown in Figure 8d , which is consistent with two independent founder types, D and CF, evolving outside Africa, and thus weakens the other two possible interpretations discussed above. However, the common ancestry of C and F founder types is supported by a short branch, defined by a single mutation, implying the diversification of CF from DE was shortly followed by the split of C from F. Although extinction events within Africa offset by haplogroup survival of descendents in Asia cannot be empirically demonstrated, both the refutation of the option shown in Figure 8b and the apparent absence of deep-rooted haplogroups for either CF or D chromosomes in Africa bolsters the model that haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia

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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.

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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].

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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.

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Posts: 1502 | From: Dies Irae | Registered: Oct 2010  |  IP: Logged |