posted
Below is the same PC graph differing only in removal of Palestinians and Japanese (why?) from one of them.
Well that's not the only difference. In one the San, South African Blacks, and the Senegalese form a single cluster. In the other the Japanese who should fall within that cluster do not do so and the Senegalese are also taken out of that cluster.
Although the PC is for the same populations' HLA-DRB1 allele frequencies the coordinates for Rimaibe, Fulani, Algerians, Spaniards and Moroccans vary.
Fig. 2. Correspondence analysis showing a global view of the relationship between Mediterraneans and sub-Saharan and Black African populations according to the HLA allele frequencies in three dimensions (bidimensional representation). HLA-DRBI allele frequencies data.
FIGURE 5 Correspondence analysis depicting a global view of the relationship between Mediterraneans and Palestinians according to HLA allele frequencies in three dimensions (bidimensional representation). HLA-DRB1 allele frequencies data.
Anyway, how significant is this one gene for assuming an overall HLA relationship?
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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quote:Originally posted by africurious: Zarahan, thanks for posting that study and excerpts. However, i perused the study and it seems to have some questionable (to be nice) ideas. For example, in the HLA dendogram in Fig.4 "japanese" are listed as close to "senegalese", "south-african blacks" and "san". Then the "fulani" and "mossi" are listed as less close to those aforementioned africans, but close to "greeks" from "aegean" and "cyprus". Wth? Esp with "fulani" not grouping with "senegalese".
Indeed. With the sloppy plotting and whimsical clustering on top of it being for just one single HLA gene (DRB1) instead of using several such its very support for overall genetic similarity of Greeks and Africans is worthless, but see the other CA, the dendrograph and tables in A. Arnaiz-Villena HLA genes in Macedonians and the sub-Saharan origin of the Greeks Tissue Antigens 2001: 57: 118–127
Discussion Greeks are genetically related to sub-Saharans
Much to our surprise, the reason why Greeks did not show a close relatedness with all the other Mediterraneans analyzed (Tables 5, 6 and Figs 1–3) was their genetic relationship with sub-Saharan ethnic groups now residing in Ethiopia, Sudan and West Africa (Burkina-Fasso). Although some Greek DRB1 alleles are not completely specific of the Greek/sub-Saharan sharing, the list of alleles (Table 5) is self-explanatory. The conclusion is that part of the Greek genetic pool may be sub-Saharan and that the admixture has occurred at an uncertain but ancient time.
The origin of the West African Black ethnic groups (Fulani, Mossi and Rimaibe sampled in Burkina-Fasso) is probably Ethiopian (26, 27) (Fig. 4). The Fulani are semi-nomadic hunters and gatherers and one of the few people in the area to use cows’ milk and its byproducts to feed themselves and to trade; their facial parameters show a Caucasian admixture. The Rimaibe Blacks have been slaves belonging to the Fulani and have frequently mixed with them (27).
The Nuba people are now widespread all over Sudan, but are descendants of the ancient Nubians that ruled Egypt between 8th–7th centuries B.C. (28) and later established their kingdom at Meroe, North Khartoum. Two kinds of Nubians were described in ancient times: Reds and Blacks, probably reflecting the degree of Caucasian admixture. Both the Oromo and Amharic peoples live in the Ethiopian mountains (27). They obviously have in common a genetic background with the west-African groups mentioned above. Linguistic, social, traditional and historical evidence supports an east-to-west migration of peoples through the Sahel (southern Sahara strip), although this is still debated (26, 27).
Thus, it is hypothesized that there could have been a migration from southern Sahara which mixed with ancient Greeks to give rise to a part of the present day Greek genetic background. The admixture must have occurred in the Aegean Islands and Athens area at least (Figs 1 and 2). The reason why this admixture is not seen in Crete is unclear but may be related to the influential and strong Minoan empire which hindered foreigners establishment (10).
Also, the time when admixture occurred could be after the overthrow of some of the Negroid Egyptian dynasties (Nubian or from other periods) or after undetermined natural catastrophes (i.e.: dryness). Indeed, ancient Greeks believed that their religion and culture came from Egypt (4, 25).
26. McEvedy C. The Penguin atlas of African history. London: Penguin Books Ltd, 1980.
27. Gonem A. The encyclopedia of the peoples of the world. Jesuralem: Jesuralem Publishing House Ltd., 1996: 143–5.
28. Manley B. Historical Atlas of ancient Egypt. London: Penguin Books, 1996.
10. Arnaiz-Villena A, Iliakis P, Gonza´lez- Hevilla M et al. The origin of Cretan population as determined by characterization of HLA alleles. Tissue Antigens 1999: 53: 213–26.
4. Herodotus. History. Madrid: Gredos, 1989.
25. Bernal M. Black Athena: The Afroasiatic roots of classical civilization. London: Free Association Books, New Brunswick, Rutger University Press, 1987.
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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posted
Africurious: For example, in the HLA dendogram in Fig.4 "japanese" are listed as close to "senegalese", "south-african blacks" and "san".
^^Keep in mind that the data being used is highly variable HLA genes. However the presence of Japanese clustering with south Africans is not as far fetched as it seems. HLA genes are useful in analyzing certain arthritis conditions. There is hard medical data in various HLA studies that indeed show Japanese and south African blacks in a broad, general grouping together in relation to certain arthritis conditions. See the data below.
but see the other CA, the dendrograph and tables in
A. Arnaiz-Villena HLA genes in Macedonians and the sub-Saharan origin of the Greeks Tissue Antigens 2001: 57: 118–127
^^Indeed. That study DIRECTLY bears on Greeks and Africans and is not tied into the Jew - Palestinian "controversy". Numerous attempts to confuse the two by "biodiversity" types are completely bogus. You are right to point out the limitations of HLA, but few have been able to shake Arnaiz-Villena's findings on the Greek data. It should be noted that medical studies on arthritis do indeed somewhat cluster Greeks with blacks, along with other populations. Recap of the Greek study, which excludes the Japanese outliers:
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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I don't see where the study shows relationship by descent as in origin. It's skewed to emphasize HLA-DRB1. What makes HLA-DRB1 so revelatory? Table 5 clearly shows that the HLA-DBR1 alleles shared by Greeks and Arnaiz-Villena's caucasoid Africans has much higher frequencies in Greeks. Off-handedly, that seemingly indicates flow from Greeks to the caucasoid Africans more so than the other way around.
The sloppy plotting and contradictory clustering of the two PC graphs computed from the self-same raw data raises doubt in confidence and questions as to why the Japanese were left out. Was it because if Greeks cluster with Africans is supposed to mean African origins then Japanese clustering with Africans must likewise mean African origins and that is just a little too much to take seriously. Then there's the Crete issue. If HLA-DBR1 shows origins then no way can Crete have such alleles not related to Africans. There is too much artistic evidence of Africans in Crete to even assume they left no genetic imprints despite Arnaiz-Villena's attestation that "the influential and strong Minoan empire [] hindered foreign[] establishment."
We know the high frequency of African derived nrY chromosomes in Greeks and that stands on solid ground for proclaiming partial African origins of Greeks. There is no doubt about that. What is in doubt is any usefulness of Fig 2 PC graph as valid support of that fact. If anything it weakens the point for all the preceding reasons.
I would like to compare the study with another one A. Petlichkovski High-resolution typing of HLA-DRB1 locus in the Macedonian population Tissue Antigens 2004: 64: 486–491.
EDIT: AV uses many more and various African samples than P who's dendrogram only included an Algerian, an Egyptian, two Moroccan sites, and Mandenka. I suspect P's intentions since they avoided each and every inner African population in AV.
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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quote:Originally posted by zarahan- aka Enrique Cardova: Recap of the Greek study, which excludes the Japanese outliers:
What Japanese outliers? No such thing as this dendrogram shows.
quote: FIGURE 4 Neighbor-Joining dendrogram demonstrating relatedness between Palestinians and other populations. Genetic distances between populations (DA) were calculated by using HLA-DRB1 (high resolution). Data from other populations were from references detailed in Table 1. Bootstrap values from 1000 replicates are illustrated
Both dendrograms come from the same raw data. Shrink them down and examine them side by side. There are serious discrepancies.
Posts: 8014 | From: the Tekrur in the Western Sahel | Registered: Feb 2006
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quote:Originally posted by alTakruri: We know the high frequency of African derived nrY chromosomes in Greeks and that stands on solid ground for proclaiming partial African origins of Greeks. There is no doubt about that. What is in doubt is any usefulness of Fig 2 PC graph as valid support of that fact. If anything it weakens the point for all the preceding reasons.
Yea, i was thinking the same.
Posts: 214 | Registered: Oct 2011
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The sloppy plotting and contradictory clustering of the two PC graphs computed from the self-same raw data raises doubt in confidence and questions as to why the Japanese were left out. Was it because if Greeks cluster with Africans is supposed to mean African origins then Japanese clustering with Africans must likewise mean African origins and that is just a little too much to take seriously. Then there's the Crete issue. If HLA-DBR1 shows origins then no way can Crete have such alleles not related to Africans. There is too much artistic evidence of Africans in Crete to even assume they left no genetic imprints despite Arnaiz-Villena's attestation that "the influential and strong Minoan empire [] hindered foreign[] establishment."
^Agreed. There are a number of questionable, sweeping statements not to mention his outmoded terminology.
On the matter of Crete, Villena does not totally rule out African admixture, holding that admixture could have occurred after the ascenion of more Middle Eastern influence in Egypt after the 25th Dynasty. Note that he says: "hindered foreigners establishment if the African invasion occurred in Minoan times."
But what if the African movement occurred in PRE Minoan times, and is just not being picked up in his sampling? He does not rule out the African elements being in place as far as I can see.
The skeletal data showing definite tropical African traces in the Aegean is also dated before the Cretan Bronze. Is it possible that the sub-Saharan elements were so diluted that they are not picked up in today's analyses, but artistic and cultural influence remains behind? In other words, the Sub-Saharan influence is there- but it is just not picked up by one particular analysis. Villena, does not totally discount it, but notes a time factor. WHat would you say to this possibility? ------------
HEre is the skeketal data for the Aegean, courtesy of the conservative Encyclopedia Britannica:
"The inhabitants of the Aegean area in the Bronze Age may have been much like many people in the Mediterranean basin today, short and slight of build with dark hair and eyes and sallow complexions. Skeletons show that the population of the Aegean was already mixed by Neolithic times, and various facial types, some with delicate features and pointed noses, others pug-nosed, almost negroid, are depicted in wall paintings from the 16th century BC. But men and women are always represented with black hair, and the presence of fair-haired people is not attested in the Aegean until later Greek times. Some very tall men buried in the Mycenaean shaft graves may be descendants of invaders who entered the mainland at the end of the 3rd millennium. A few skeletons from the single graves that appear on the mainland at the very end of the Bronze Age suggest the presence of new people from the north." --- Sinclair Hood, The Home of the Heroes: The Aegean Before the Greeks (1967) also found in Encyclopedia Britannica 1990 ed. Macropedia Article, Vol 20: Greek and Roman Civilizations -----------------------
We know the high frequency of African derived nrY chromosomes in Greeks and that stands on solid ground for proclaiming partial African origins of Greeks.
Fair enough. Can you recap some of that nrY data with citations? Just so readers can lock in a clear chain of evidence and put HLA weaknesses in proper perspective. SO far in the chain of GReek - African links we have:
--HLA (with the weaknesses noted) --SKeletal (Macedonian and Aegean ancients per Angel 72) --Benin Sickle Cell (per Ricaut and others) --What else can be added?
What Japanese outliers? No such thing as this dendrogram shows.
^The Japanese outliers were in the Palestinian study but do not show up in the Macedonian/Greek/African study. The presence of the Japanese in terms of any origin issue is a definite weak spot.
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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This thread has a focus. It is directed to the use of HLA-DBR1 alleles to specify genetic origins of a population in regards to parent child. Bringing up other non-HLA parameters does not alter the fact that the measure Arnaiz-Villena uses to propose an African origin for Greeks holds no water. Genetic relation does not mean a parent child relationship. In fact genetic relation in itself means little pending which genetic material is considered. After all there is a genetic relation between human and ape yet one does not descend from the other. There is even a genetic relationship between animals and plants.
I posted the dendrogram from the Palestinian study and it shows Japanese are not an outlier. If anything, it shows Senegalese as the outlier to two south African populations and the Japanese. There is no avoiding this. Out of all the populations in A-V's 2001 HLA reports only the Japanese were intentionally left off the Greek study version of the CA and dendrogram because they show how ridiculous it is to assume sharing of a few alleles of one loci is evidence of a parental genetic relationship. It was dishonest of A-V to strip the Japanese from the Greek study in order to make a single west and south African cluster whereas previously he has seperate south African, Japanese and Senegalese clusters. It's not hard to see. The Japanese are no outlier in A-V's tree. They are entrenched between Senegalese and south Africans who altogether form one branch.
A-V is quite adamant in Crete not having HLA in common with Africans. His historical conjectures are totally haphazard. The leaps of credulity include time warps and disparate populations all jumbled up to build a matchstick house.
There are fine sources to show parental genetic relationships between Africans and Greeks but A-V's HLA studies are worse than poor in this regard. Close examination of Table 5 along with the in comparison sloppy CAs and dendros makes A-V an overstated and detrimental "support" of partial African ancestry for Greeks. A-V's CAs and dendros hinder confirmation of African - Greek parental genetic relationship and should not be used as any, leave alone a scientifically valid confirmation of that fact.
The idea is to employ the strongest evidence in confirmation of African inclusion in all our studies whether historical, linguistic, literary, archaeological, cultural, physical anthropology, or genetics. Flimsy evidence actual makes a case against what we are finding out about the role of Africans in all these things in EurAsia and the Americas.
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See Negroid affinities in ancient Greece??? thread or search the archive for Cruciani for nrY evidence.
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The Arnaiz-Villena study has considerable merit. Other researchers have cobfirmed his findings of a close relationship between Greeks and sub-Saharan Africans.
quote:
HLA class I and class II polymorphisms in Tunisian Berbers March 2011, Vol. 38, No. 2 , Pages 156-164 (doi:10.3109/03014460.2010.504195)
A. Hajjej1, M. H. Sellami1, H. Kaabi1, G. Hajjej2, A. El-Gaaied3, K. Boukef1, W. Y. Almawi4, S. Hmida1 1National Blood Transfusion Center, Tunis, Tunisia 2Faculty of Sciences of Sfax, Tunisia 3Laboratory of Immunogenetics, Department of Biology, University of Tunis-El-Manar, Tunis, Tunisia 4College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain Correspondence: Professor Slama Hmida, Centre National de Transfusion Sanguine, Rue Djebel Lakhdhar, Bab Saadoun, 1006 Tunis, Tunisie. E-mail: hajjej2@yahoo.fr
Background: The HLA polymorphism is a powerful genetic tool to study population origins. By analysing allele frequencies and haplotypes in different populations, it is possible to identify ethnic groups and establish the genetic relationships among them. Aim: The Berber (endogenous Tunisians) HLA class I and class II genotypes were analysed and compared with those of Mediterranean and Sub-Saharan African communities using genetic distances, Neighbour-Joining dendrograms, correspondence and haplotype analysis. Subjects and methods: One hundred and five unrelated Berbers were typed for HLA class I (A, B) and class II (DRB1, DQB1) gene alleles using reverse dot-blot hybridization. Results: High frequencies of A*0201 (24.76%), A*3402 (22.38%) and B*44 (32.85%) alleles were recorded for Berbers, the highest recorded for Mediterranean and North African populations. This study shows a close relatedness of Tunisian Berbers to other Tunisians, North Africans and Iberians. Conclusion: The apparent relatedness of Tunisian Berbers to present-day (North African) Tunisians, Algerians and Moroccans suggests that the Arab invasion of North Africa (7th–11th centuries AD) did not significantly impact the genetic makeup of North Africans. Furthermore, Tunisian Berbers appear to be closely related to Iberians (Spaniards and Basques), indicating that the 7th century AD gene flow of invaders was low in Iberians and that the main part of their genetic pool came after the Northward Saharan migration, when hyper-arid conditions were established in Sahara (before 6000 BC). Other studied populations belong to the old Mediterranean substratum, which has been present in the area since pre-Neolithic times. This study indicates a higher proportion of Iberian than Arab ancestry in Tunisian Berbers, which is of value in evaluating the evolutionary history of present-day Tunisians. Greeks seem to share genetic HLA features (Chr 6) with Sub-Saharans. The relatedness of Greeks to Sub-Saharans has been confirmed by other studies based on chromosome 7 genetic markers. Keywords
quote: Eur J Med Genet. 2006 Jan-Feb;49(1):43-56. Epub 2005 Feb 10.
HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans. Hajjej A, Hmida S, Kaabi H, Dridi A, Jridi A, El Gaa l ed A, Boukef K. SourceNational Blood Transfusion Centre, Tunis, Tunisia.
Abstract South Tunisian HLA gene profile has studied for the first time. HLA-A, -B, -DRB1 and -DQB1 allele frequencies of Ghannouch have been compared with those of neighboring populations, other Mediterraneans and Sub-Saharans. Their relatedness has been tested by genetic distances, Neighbor-Joining dendrograms and correspondence analyses. Our HLA data show that both southern from Ghannouch and northern Tunisians are of a Berber substratum in spite of the successive incursions (particularly, the 7th-8th century A.D. Arab invasion) occurred in Tunisia. It is also the case of other North Africans and Iberians. This present study confirms the relatedness of Greeks to Sub-Saharan populations. This suggests that there was an admixture between the Greeks and Sub-Saharans probably during Pharaonic period or after natural catastrophes (dryness) occurred in Sahara.
PMID:16473309[PubMed - indexed for MEDLINE]
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