That its there isn't shocking to me, I simply stated that the frequency of E3a doesn't correspond to the frequencies of haplotype IV found in Lucotte et al's study If you think otherwise you need to produce evidence for it.
Makes no sense. You say that E3a doesn‘t correspond to the frequencies of haplotype 4, even though an extract from a study was cited *explicitly* stating that the former does associate with the latter.
Reiteration of evidence that you proclaim isn't there:
Lucotte et al.'s data, Keita, and your own citation of Luis et al. are all provided evidence. You simply deny them - but denial of evidence is not "evidence to the contrary", nor does it diminish the weight of evidence provided.
- What evidence do you have that states, that IV doesn't correspond to M2-associated lineages? That‘s right, you have produced none so far; you only have a 'suspicion' to fall back on.
-Not that it really matters, but since you made qualms about it, Luis et al.'s frequencies for E3a does tie in well with that shown in Lucotte et al.'s, as far as Lower Egypt is concerned.
quote:Originally posted by Charlie Bass:
You got me totally wrong, and what about the virtual absence of E3a in Sudan
Who said it is absent, i.e. if by Sudan, you are referring to "lower Nubia"? Not according to data used by Lucotte et al. or Keita, that is for sure; in fact, that data says otherwise.
quote:Originally posted by Charlie Bass:
yet Lucotte et al says higher frequencies of haplotype IV is supposed to be there?
It makes sense for higher frequencies to be in the region straddling Egypt and northern Sudan, since it is naturally closer to sub-Saharan Africa than the coastal north regions. But this is just a distraction; if you have evidence that haplotype IV doesn't correspond to M2 bearing chromosomes as already cited, then produce it.
quote:Originally posted by Charlie Bass:
I have perfectly good reasons for having some suspicion about the correlation between haplotype IV and E3a.
But you produce no substantive merit to back it up.
In the meantime…
A piece of this was already cited here earlier, but for a broader read, we have:
Haplotype IV, designating the M2/PN1 subclade, as noted, is found in high frequency in west, central, and sub-equatorial Africa in speakers of Niger-Congo—which may have a special relationship with Nilosaharan—spoken by Nubians; together they might form a superphylum called Kongo-Saharan or Niger-Saharan (see Gregersen 1972, Blench 1995), but this is not fully supported. The spatial distribution of p49a,f TaqI haplotypes in the geographically-widespread speakers of Nilosaharan languages has not been fully characterized, but the notable presence of haplotype IV in Nubians speaking the Eastern Sudanic branch is interesting in that this subgroup is in the Sahelian branch of speakers, whose ancestors may have participated in the domestication of cattle in the eastern Sahara (Ehret 2000, Wendorf and Schild 2001). Sometimes haplotype IV (and the M2 lineage) is seen as being associated with the “Bantu expansion” (2000-3000 bp), but this does not mean that it is not much older, since expansion and origin times cannot be conflated. Haplotype IV has substantial frequencies in upper Egypt and Nubia, greater than VII and VIII, and even V. Bantu languages were never spoken in these regions or Senegal, where M2 is greater than 90 percent in some studies. - Keita, 2005.
1 - Lucotte and Mercier (2003a) 2 - Lucotte and Mercier (2003b) 3 - Al-Zahery et al. (2003); *haplotype XI here is documented from two biallelic lineages 4 - Lucotte et al. (2000) 5 - Lucotte and Smets (1999)
6 - Lucotte et al. (1996) References 2, 4, 5, as in Table 2A. *Haplotype XI in groups admixed with northern Europeans is usually affiliated with haplogroup R1; in Africa it is usually associated with haplogroup E (al-Zahery 2003).
These distributions of haplotype 4 make perfect sense, if they were strongly associated with E3a chromosomes.
^Tables courtesy Keita, 2005.
But if you think Keita is alone in his observation, then consider this:
A total of 21 different 49a,f haplotypes were found and are illustrated in Fig. 4 as a sub-classification of the Iraqi Y-chromosome haplogroups. The most represented haplotype of haplogroup E is haplotype 5 (A 2 C 0 D 0 F 1 I 1 ). This is followed by haplotype 11 (A 3 C 0 D 0 F 1 I 1 ) at a much lower frequency. Haplotypes 5 and 11 were observed both in Africa (Lucotte et al., 2001; Passarino et al., 1998; Persichetti et al., 1992; Santachiara-Benerecetti and Semino, 1996; Spurdle and Jenkins, 1992; Torroni et al., 1990) and Eurasia (Passarino et al., 2001; Semino et al., 2000b) but in Africa they belong to haplogroup E, whereas in Eurasia, particularly in *Northeastern Eurasia*, they belong mainly to the haplogroup R-M17. Interestingly, the proportion of haplotypes 5 and 11 in haplogroups E and R-M17 is reversed, with haplotype 5 prevalent in haplogroup E and haplotype 11 in haplogroup R-M17. By considering that the two haplotypes differ by a single band change and their different proportion in the two lineages, it is likely that haplotype 11 is a derivative of haplotype 5 in haplogroup E and just the opposite in haplogroup R-M17.
And...
It is worth mentioning that in haplogroup E two subjects belong to the African specific E-M2 clade, which is very frequent in the Western and Southern part of the continent (Cruciani et al., 2002; Passarino et al., 1998; Scozzari et al., 1999; Seielstad et al., 1994; Semino et al., 2002; Underhill et al., 2000) and has been related to the Bantu expansion. These two Y chromosomes **harbor haplotype 4** (A 1 C 0 D 0 F 1 I 1 ) which is also African- specific and **shows the same geographic distribution** (Excoffier et al., 1987; Passarino et al., 1998; Spurdle and Jenkins, 1992; Torroni et al., 1990). Within haplogroup J, haplotypes 7 (A 2 C 0 D 1 F 1 I 0 ) and 8 (A 2 C 0 D 1 F 1 I 1 ) are the most represented, but haplotype 7 is observed only in the J-M172 sub-set. This suggests that the 49a,f haplotype 7 arose on a 12f2-8Kb/M172 Y chromosome. - N. Al Zahery et al. 2003, Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations
^More reason for Charles to present evidence to the contrary; Keita is joined by more authors in backing up his observation about the close association between haplotype 4 and E3a, but who is backing you up to the contrary?
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posted
Difficult issue to resolve matching TAqI to Y chromosome Polymorphism.
What is most striking to me is the absense of Haplotype IV in Ethiopian populations which is concordant with the absense of E3a in Ethiopia.
In other words - there is the same pattern of IV being predominent in West Africa, present to lesser degree in NorthWest Africa and SouthWest Asia, but absent in Ethiopia that can be found with E3a.
However this is based on the assumption that TaqI can be reliably mapped to Y chromosome.
I don't understand the relationship well enough to comment on that.
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However this is based on the assumption that TaqI can be reliably mapped to Y chromosome.
I don't understand the relationship well enough to comment on that.
To understand how Al Zahery et al. were able to link RFLP haplotypes to SNP markers on the chromosomes under study, they identified the former by using TaqI restriction enzyme digests and the latter with the likes of PCR and DHPLC analysis; essentially this sort of approach to testing for both RFLP markers and binary markers has been exemplified in the following link - we discussed the methods utilized in relative detail, in the sorting out of RFLP markers into respective sub-clades: Haplotype V revisitedPosts: 1947 | Registered: Sep 2005
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posted
Supercar, please post a study that shows substantial frequencies of E3a in Sudan and Upper Egypt that correspond to the frequencies of haplotype IV in Lucotte et al's study.
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Supercar, please post a study that shows substantial frequencies of E3a in Sudan and Upper Egypt that correspond to the frequencies of haplotype IV in Lucotte et al's study.
Already provided. Please cater to my outstanding requests.
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quote:Originally posted by Mystery Solver: [QUOTE]Haplotype IV, designating the M2/PN1 subclade, as noted, is found in high frequency in west, central, and sub-equatorial Africa in speakers of Niger-Congo—which may have a special relationship with Nilosaharan—spoken by Nubians; together they might form a superphylum called Kongo-Saharan or Niger-Saharan (see Gregersen 1972, Blench 1995), but this is not fully supported.
Evergreen Writes:
Key takeaways -
A. The research community investigating the phylogenetic history of haplogroup E has a history of working with patterns of conscious and subconscious bias.
B. Little research on haplogroup E3a has been conducted.
C. Sample sizes and samples of a wide variety of populations in Chad, Sudan, Egypt, Niger, etc have not been conducted.
D. When samples are taken inappropriate models based upon stereotype and bias have been constructed.
E. Wide samples of Nilo-Saharan have not been taken.
F. Archaeology and linguistics indicate Nilo-Saharan inputs into Neolithic and Pre-Dynastic Egypt (Southern Egypt and Northern Sudan).
G. Nilo-Saharan and Niger-Congo languages seem to have a deep time-depth relationship and this is congruent with a shared pre-LGM heritage. This would indicate a common E3a ancestry for these populations. This is consistent with what we know of haplogroup E distributions among Senegalese populations.
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posted
A few of trhe studies I've saw that have tested Nilo-Saharans don't show a high frequency of E3a. The Maasai and datoga both show high frequencies of M35 and A3b2 and relatively lower frequencies of E3a which *COULD* be due to recent mixture with Bantu speakers.
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E3a isn't as high in some bantu speakers as one may think though it will vary from population to population. Same for haplotype IV, its absent in the Central African Republic and in Pygmies according to one study I read.
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quote:Originally posted by Charlie Bass: A few of trhe studies I've saw that have tested Nilo-Saharans don't show a high frequency of E3a. The Maasai and datoga both show high frequencies of M35 and A3b2 and relatively lower frequencies of E3a which *COULD* be due to recent mixture with Bantu speakers.
Evergreen Writes:
Key word is "the few studies". To better understand the early Holocene y-chromosome lineage of Nilo-Saharan speakers we need broad sampling and well refined modeling.
Posts: 2007 | From: Washington State | Registered: Oct 2006
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A. The research community investigating the phylogenetic history of haplogroup E has a history of working with patterns of conscious and subconscious bias.
B. Little research on haplogroup E3a has been conducted.
C. Sample sizes and samples of a wide variety of populations in Chad, Sudan, Egypt, Niger, etc have not been conducted.
D. When samples are taken inappropriate models based upon stereotype and bias have been constructed.
E. Wide samples of Nilo-Saharan have not been taken.
F. Archaeology and linguistics indicate Nilo-Saharan inputs into Neolithic and Pre-Dynastic Egypt (Southern Egypt and Northern Sudan).
G. Nilo-Saharan and Niger-Congo languages seem to have a deep time-depth relationship and this is congruent with a shared pre-LGM heritage. This would indicate a common E3a ancestry for these populations. This is consistent with what we know of haplogroup E distributions among Senegalese populations.
Yes to all, and I'll like to add that each study has to be carefully reviewed on its methodological merits, which includes regions sampled, sample size, *target* markers of the authors and actual markers found, regional and ethnic diversity of samples.
quote:Originally posted by Charlie Bass:
Same for haplotype IV, its absent in the Central African Republic and in Pygmies according to one study I read.
You do realize what RFLP haplotype IV corresponds to, right?
Given that haplotype 4 = (A1, C0, D0, F1, I1)
Which study are you referring to that mentions the absence of the above in Central African Republic and in Pygmies?
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Changed Ethiopia. It had 0/47 E3a from Wood (2005), now I added 3/88 E3a from Underhill (2000), making the final Ethiopia figure 3/135 = 2% E3a. The Wood samples are new (not from Underhill).
Extended the blue colored range from Lake Chad up to east Niger. Cruciani (2004) found 14/22 E(xE3b) in "Tuareg from Niger". Later, Wood (2005) showed a map of Africa with the populations sampled in previous studies, and the map showed 3 previous samples for Niger, 2 of them obviously from Cruciani (2004), the Fulbe and Hausa, and the 3rd was the Kanuri, whom are a nomadic people historically linked with a Berber migration, so it's very likely this was the "Tuareg from Niger" sample from Cruciani (2004). I don't know what part of their E(xE3b) is E3a, but comparing with neighbors in north Cameroon in which E3a is about 2/3 of their overall E(xE3b), the Kanuri E3a is perhaps around 40%. I put the number with a question mark. By the way, the Kanuri people also had 10% E3b1b (2/22), while none was found in the 200+ samples from the nearby north Cameroon region of Lake Chad.
Extended the blue colored range into north Mali, because Underhill (2000) found 9/44 E3a in "Mali", and judging from the Wood (2005) map showing samples from previous studies, the only possible candidate are the Tuareg in north Mali. Also, the fact that they have 30% E3b1b and 20% E3a makes it very unlikely they would be from south Mali, since its neighbors in Burkina Faso and elsewhere are 80%+ E3a and 0% E3b1b.
Corrected the percentage for the region around south Mali and Burkina Faso after relocating the Mali sample to north Mali. It used to say 30% and 80%, now it says 70%. This makes West Africa more uniformly E3a, ranging from 70% to 90%.
The extended blue zone looks almost as big as West Africa but has less than 1% of its population. It's mostly Sahara desert, and a part of the Sahel.
I think I'm going to redo the map completely so that it shows the country borders. It sucks trying to figure things out without them.
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This map shows the distribution of E3a and the population density.
Evergreen Writes:
Your map needs work. Does it not strike you as odd that E3a approaches frequencies near 10% in Palestine and 0% in Upper Egypt according to your graphic.
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posted
The Palestinian figure is from a study in 2005 by Carlos Flores and Ana Gonzalez, on the y-dna of Jordan. From what I could make out of the graph (I didn't read the actual study), they found 9% of 147 Palestinians belonged to E-P2 (E3), and didn't belong to M78, M81, or M123. So it's possible that they could belong to E3*, E3a, or E3b1*; but it's most likely that all these samples are E3a.
The low percentage for Egypt is verified in almost half a dozen y-dna studies.
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Your map needs work. Does it not strike you as odd that E3a approaches frequencies near 10% in Palestine and 0% in Upper Egypt according to your graphic.
You're probably wasting your time in pointing out any shortcomings; I've tried, and it proved to be futile.
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The length of the Y chromosome in Nubian males and its location in metaphase spreads.
Nasjleti et. al.
A total of 242 metaphase plates from the peripheral blood of Nubian males living near Aswan, Egypt were studied with respect to the length of the Y chromosome and its location in metaphase spreads. The length of the Y was similar to that found in American Negroes, and the Y chromosome was peripherally located in 79 of the 242 cells.
-------------------- Black Roots. Posts: 2007 | From: Washington State | Registered: Oct 2006
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^ But is not E3a also found among the Lower Nile Valley populations of Sudan and Egypt?
Yes, but in extremely low frequencies.
Evergreen Writes:
What study are you using as a basis to this claim?
^A necessary question. Other studies like the following [a recap btw], have suggested otherwise, if we are to acknowledge IV as the haplotype associated with the M2 mutation:
Of note are the frequencies of the aforementioned haplotypes; V, XI, and IV:
Lower Egypt (n=162); V=51.9%, XI=11.7%, and IV=1.2%.
Upper Egypt (n=66); V=24.2%, XI=28.8%, and IV=27.3%.
Lower Nubia (n=46); V=17.4%, XI=30.4%, and IV=39.1%.
The primary haplotypes found in Europe, XII and XV, according to Keita, could have likely entered into the country via Greco-Roman invasions, are found in Lower Egypt at 3.7% and 6.8% respectively. Not surprising, the frequencies of these two are lower in Upper egypt, with XII not represented, while XV is at 6.1%. They are absent in Lower Nubia. These results are according to Lucotte and Mercier's findings, 2003
** Lower Egypt may be an outlier due to the infiltration of large numbers of non-indigenous Africans post-Late Kingdom Dynastic era.
Haplogroup E3a may have spread from the Central Sahara to the Nile Valley during the pre-early Neolithic phase. There is further evidence of the spread of Saharan cultural elements such as bi-facial arrowheads and pottery into the early neolithic Faiyum and southern Levant. Further itterations of immigration may have followed with the early Dynastic and Middle Bronze Age Egyptian colonial activity in "Canaan".
West Africa and the Central Sahara in turn may be connected via the movement of early holocene, pottery and bi-facial arrowhead (Ounan points) using populations from West African regions such as Ounjougou Mali into the Central Sahara. Hence, West Africa is a likely population source of the early Holocene Central Sahara and by default early neolithic base population of ancient Egypt.
Evergreen Posts:
A Y-chromosome portrait of the population of Jerba (Tunisia) to elucidate its complex demographic history Manni et. Al.
The Jewish population
The genetic profile of the Jewish sample is related to populations in the Middle East where Hg E3a has its highest frequencies. Moreover, the Middle Eastern origin of the Jewish group is confirmed by preliminary results on Y-chromosome microsatellites of 15 individuals sampled in Tlamim; 13 of them carried for the Cohen Modal Haplotype (CMH). This haplotype is frequent in the Jewish diaspora and it has been suggested that it might be particularly frequent in families which trace patrilineal ancestry to the Jewish priesthood (Thomas et al. 2000). While the CMH is not specific of Jews, being widespread in several Middle Eastern populations (Brinkmann et al. 1999, Zoosman-Diskin 2000), such a datum seems to support two different scenarios for the Jewish colonization of Jerba: a) a founding group that migrated to Jerba in an early dispersal of Jewish population from the Middle East or b) a recent migration of families of ancient Jewish ancestry. The first scenario seems unrealistic because microsatellite markers are rapidly evolving, therefore we would expect more variable microsatellite haplotypes in the case of an ancient founding event, unless some bottlenecks occurred in the male lineage of Jerban Jews.
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** Lower Egypt may be an outlier due to the infiltration of large numbers of non-indigenous Africans post-Late Kingdom Dynastic era.
Haplogroup E3a may have spread from the Central Sahara to the Nile Valley during the pre-early Neolithic phase. There is further evidence of the spread of Saharan cultural elements such as bi-facial arrowheads and pottery into the early neolithic Faiyum and southern Levant. Further itterations of immigration may have followed with the early Dynastic and Middle Bronze Age Egyptian colonial activity in "Canaan".
West Africa and the Central Sahara in turn may be connected via the movement of early holocene, pottery and bi-facial arrowhead (Ounan points) using populations from West African regions such as Ounjougou Mali into the Central Sahara. Hence, West Africa is a likely population source of the early Holocene Central Sahara and by default early neolithic base population of ancient Egypt.
Evergreen Writes:
The semi-sedentary cultures found in early Holocene West Africa would lead to population increases and expansion across the Sahel and into the Central Sahara. What’s needed now is a reassessment of haplogroup E3a sub-lineages in North Africa and around the Mediterranean basin to better understand the phylogenetics.
quote:Originally posted by Evergreen: [QUOTE]
Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs.
Sims et. al.
Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y-SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub-clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi-allelic markers described here are expected to find application in human evolutionary studies and forensic genetics.
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