Joined: 30 Mar 2005 {Posts: 1053 } Location: New Jersey
Posted: Fri 28 Apr 2006 20:10 Post subject: Refuting "Racial Reality" re Italians and Sicilians
[M1 section corrected -- 4/25/'07]
Disclaimer: The purpose of this posting is not to "prove" Italians are "really Black" because of a few drops of sub-Saharan blood, or any such nonsense. African DNA has been found in most populations in Europe, as has Asiatic DNA. The purpose of the post is to show that sub-Saharan genes have entered the Italian population, contrary to the drivel one may read on "Medocentric" message boards, where every study illustrating this (and there are many) is somehow deemed "wrong" or "outdated" or "refuted" or some such malarkey by those with an idealogical interest in the (non-existent, of course) "White purity" of various Mediterraneans. All of the studies are valid. We here at ODR have no axe to grind, and are simply stating the facts and citing all sources. Iberians are over-studied in this regard, and other countries should also be examined genetically.
Mainland Italians (particularly southern Italians), Sardinians, and Sicilians all have sub-Saharan admixture. There is a veritable closet-full of information on this. The Hbs found in Sicilians is predominantly the Benin strain, known as #19. This strain originated in Benin or nearby regions of Central West Africa. Most of the following are studies that can be found in our Admixture Index.
Incidentally, "Racial Reality" has a habit of pooling information from various parts of Italy together into a single Italian sample. While there is nothing intrinsically wrong with this, as it creats an average, it utterly confounds the large local differences. That is precisely his reason for doing it. For example, in most samples from northern Italy, sub-Saharan mtDNA markers tend to be found at very low levels (but the samples have been small, and future studies will likely show higher sub-Saharan mtDNA and other DNA levels due to Venice and Genoa being involved in the slave trade, etc.). In the Rome province, such DNA is higher (roughy 4%) in the samples taken. In Apulia, it is similar. In another sample of southern Italy, it reaches over 8%. Of course, different samples will yield different results, and "Racial Reality" tends to ignore those which have a higher sub-Saharan content. Even Sicily varies, with no sub-Saharan mtDNA found in one sample of 49 from a single Sicilian village (which shouldn't surprise); to other one or few village samples which show around 1-2%; to an island-wide sample which shows about 10% in Sciacca, about 4% in Castelammare, and about 2% in Ragusa; to another island-wide sample which shows 4.4% overall. In another Sciacca sample, sub-Saharan mtDNA reaches over 13%. So, the Italian mtDNA results are comparable to the Iberian mtDNA results. Some studies show lower percentages, and others show higher ones. Another important point is that most studies don't test for all markers, as evidenced below. Some rely only on mtDNA, others on Y-chromosomes, others on autosomal DNA, etc. Some only test for certain mtDNA markers (like L1 and L2, but not equally-African L3 and M1) or Y markers, etc.
Blood proteins (HbS, etc.) (there are a few more on HbS in the post below)
Acta Haematol. 1978;60(6):350-7. Related Articles, Links
Blood group phenotypes and the origin of sickle cell hemoglobin in Sicilians.
Sandler SG, Schiliro G, Russo A, Musumeci S, Rachmilewitz EA.
As an approach to investigating the origin of sickle cell hemoglobin (hemoglobin S) in white persons of Sicilian ancestry, two groups of native Sicilians were tested for blood group evidence of African admixture. Among 100 unrelated Sicilians, the phenotypes cDe(Rho) and Fy(a-b-), and the antigens V(hrv) and Jsa, which are considered to be African genetic markers, were detected in 12 individuals. Among 64 individuals from 21 families with at least one known hemoglobin S carrier, African blood group markers were detected in 7 (11%). These findings indicate that hemoglobin S is only one of multiple African genes present in contemporary Sicilian populations. The occurrence of hemoglobin S in white persons of Sicilian ancestry is considered to be a manifestation of the continuing dissemination of the original African mutation.
Hemoglobin. 1992;16(6):469-80. Related Articles, Links
Clinical, hematological, and molecular features in Sicilians with sickle cell disease.
Schiliro G, Samperi P, Consalvo C, Gangarossa S, Testa R, Miraglia V, Lo Nigro L.
Department of Pediatric Hematology, University of Catania, Sicily, Italy.
We report the clinical, hematological, and molecular findings observed in 32 Sicilian patients with sickle cell disease. None of our patients received regular blood transfusions and careful infectious disease prophylaxis was carried out for all. Haplotyping of beta S chromosomes was performed in all patients; all were homozygous for haplotype #19 (Benin). Gene mapping excluded the presence of an alpha-thalassemia in 13 of our patients; none of the relatives showed any evidence of the presence of alpha-thalassemia. Hb F levels were 11.8 +/- 5.9% with G gamma representing 39.6 +/- 3.6% of total gamma chain. Hb F levels were higher in females than in males (12.5 +/- 5.9% versus 9.7 +/- 6.5%) but the difference was not statistically significant. All patients, regardless of age and sex, were anemic with normal mean corpuscular hemoglobin concentration, high mean corpuscular volume and mean corpuscular hemoglobin, and mild reticulocytosis. Analysis of clinical manifestations suggests that our patients have a disease of moderate severity.
: J Med Genet. 1980 Feb;17(1):34-8. Related Articles, Links
Sickle cell disease in Sicily.
Roth EF Jr, Schiliro G, Russo A, Musumeci S, Rachmilewitz E, Neske V, Nagel R.
The chemical and physical properties of haemoglobin S derived from homozygotes for this haemoglobin in Sicily were examined, as well as some erythrocytic characteristics. Sicilian Hb S was identical to that found in USA black patients in electrophoretic mobility on both starch and citrate agar media, solubility, mechanical precipitation rate of oxyhaemoglobins, and minimum gelling concentration, as well as by peptide mapping and amino-acid analysis of all beta-chain peptides. Taken together with the presence in Sicily of African blood group markers and certain historical considerations, it seems clear that the source of Hb S in Sicily is Africa. While the clinical severity in nine Sicilian children did not seem remarkably different from the disease in the USA, the most severe and fatal complications were not seen. Mean Hb F Was 10.5% and 2,3-diphosphoglycerate (2,3-DPG) values were higher in Sicilian homozygotes than in black USA counterparts (21.79 mumol/g Hb vs 15.16). Red cell AT values were also slightly higher in Sicilian patients. The presence of concomitant thalassaemia was excluded by both family studies and globin chain synthetic ratios. In conclusion, haemoglobin S in Sicilian homozygotes is identical to Hb S found in USA blacks. Although the severity of the disease seems quite similar in both groups of patients, other erythrocytic properties were found to be different. Whether these factors influence severity remains to be elucidated.
Am J Hematol. 1988 Feb;27(2):139-41. Related Articles, Links
Beta S gene in Sicily is in linkage disequilibrium with the Benin haplotype: implications for gene flow.
Ragusa A, Lombardo M, Sortino G, Lombardo T, Nagel RL, Labie D.
INSERM Unite 15, Paris, France.
Hemoglobin beta-like gene cluster haplotypes defined by restriction enzyme polymorphic sites are useful in determining the origin of the beta S gene found in several human populations. We present here evidence that the beta S gene found among Sicilians is associated with the same haplotype observed among sickle cell anemia patients from Central West Africa. In addition, this haplotype is either nonexistent or very rare among normal Sicilian individuals. We conclude that the beta S gene was introduced to Sicily from North Africa and that the gene flow originated in Central West Africa and traveled north through historically well-defined trans-Saharan commercial routes.
Am J Hematol. 1992 Jan;39(1):5-8. Related Articles, Links
Molecular characterization of hemoglobin C in Sicily.
Travi M, Cremonesi L, Primignani P, Di Benedetto S, Testa R, Schiliro G, Ferrari M.
Istituti Clinici di Perfezionamento, Laboratorio di Ricerche Cliniche, Milan, Italy.
Analysis of polymorphisms of the beta-globin gene cluster was performed on 12 families and on one unrelated individual of Sicilian origin who carried hemoglobin C (Hb C). Two different haplotypes were found in association with beta c Sicilian alleles, corresponding to haplotypes I and II previously described in American blacks. In our population, the more frequent one (haplotype I) was linked to the lack of a polymorphic HpaI site 3' to the beta gene (13.0-kb fragment), similarly to haplotype I in blacks, while the less frequent one was linked to a 7.0-kb HpaI fragment attributable to a site that had never been previously described in linkage with beta c alleles. In Italy, these two haplotypes have been found in rare cases in association with beta A alleles. These findings provide new insights into the origin of Hb C present in Sicily, suggesting that (1) the beta c mutation detected in Sicily derived from African black chromosomes and does not represent a new mutation; and (2) Hb C may have originated either by multiple mutational events on separate chromosomes or by mutation in the HpaI site 3' to the beta gene in a pre-existing beta c chromosome.
Am J Hematol. 1992 Aug;40(4):313-5. Related Articles, Links
Presence of an African beta-globin gene cluster haplotype in normal chromosomes in Sicily.
Ragusa A, Frontini V, Lombardo M, Amata S, Lombardo T, Labie D, Krishnamoorthy R, Nagel RL.
I.R.C.C.S., OASI, Troina, Italy.
African admixture in Sicily has been long suspected because of the presence of the sickle gene. Nevertheless, the degree of African admixture cannot be derived from the study of HbS frequency, since this gene was most likely expanded by the selective pressure of malaria, for a long time endemic to the region. We have examined 142 individuals from the Sicilian town of Butera (12% sickle trait) to search for other markers of the globin gene cluster less likely to be selected for by malaria. The TaqI polymorphism in the intervening sequences between the two gamma genes is informative. We have found only two instances of this African marker (TaqI(-)) among 267 normal chromosomes, demonstrating that the admixture occurred at a much lower level than previously thought.
Hum Genet. 1992 Jul;89(5):553-6. Related Articles, Links
Alpha I/65 hereditary elliptocytosis in southern Italy: evidence for an African origin.
del Giudice EM, Ducluzeau MT, Alloisio N, Wilmotte R, Delaunay J, Perrotta S, Cutillo S, Iolascon A.
Department of Pediatrics, University of Naples, Italy.
alpha I/65 Hereditary elliptocytosis (HE) is due to the duplication of TTG codon 154 (leucine) of alpha-spectrin and is associated with a constant haplotype. It was encountered exclusively in African and American Blacks, and in North Africans. We assumed that it diffused from the Benin-Togo area to Northern Africa. We now report two South Italian families with alpha I/65 HE. The phenotype fully conformed to previous descriptions. The mode of transmission was dominant; however, the manifestations were more pronounced when the common, low expression level alpha V/41 allele occurred in trans to the alpha I/65 allele, also conforming to previous records. The mutation underlying alpha I/65 HE turned out to be, again, the duplication of TTG codon 154 and the associated haplotype was the same as that encountered previously (+-+; XbaI, PvuII, MspI). Thus, the alpha I/65 allele found in Italy must have been introduced from North Africa across the Sicilian channel and would ultimately have originated from the Benin-Togo area. It would witness the same migratory stream as that followed by the Benin type haemoglobin S allele, which is also present in Southern Italy.
Immunogenetics. 2004 Jan;55(10):674-81. Epub 2003 Dec 2. Related Articles, Links
Gm and Km immunoglobulin allotypes in Sicily.
Cerutti N, Dugoujon JM, Guitard E, Rabino Massa E.
Department of Animal and Human Biology, University of Turin, Via Accademia Albertina 17, 10123, Turin, Italy.
The aim of this study was to evaluate the intra- and inter-population variability of the Gm/Km system in the Madonie Mountains, one of the main geographical barriers in north-central Sicily. We analysed 392 samples: 145 from Alia, 128 from Valledolmo, 25 from Cerda and 94 from Palermo. Serum samples were tested for G1m (1,2,3,17), G2m (23), G3m (5,6,10,11,13,14,15,16,21,24,28 ) and Km (1) allotypes by the standard agglutination-inhibition method. We found the typical genetic patterns of populations in peripheral areas of the Mediterranean basin, with a high frequency of haplotypes Gm5*;3;23 and Gm5*;3;. The frequency of Gm21,28;1,17;. (about 16%) is rather high compared with other southern areas. Of great importance is the presence of the common African haplotype Gm 5*;1,17;., ranging in frequency from 1.56% at Valledolmo to 5.5% at Alia. The presence of this haplotype suggests past contacts with peoples from North Africa. The introduction of African markers could be due to the Phoenician colonization at the end of the 2nd millennium b.c. or to the more recent Arab conquest (8th-9th centuries a.d.).
Publication Types:
Historical Article
PMID: 14652700 [PubMed - indexed for MEDLINE]
Note: Although the reader might suppose that the Gm 5*;1,17;... morph is specific to North Africa, due to the mentioning in the study that the haplotype could suggest contact with North Africans, it appears to indeed be sub-Saharan. This is supported by usage of the phrases "common African haplotype" and (below) "typical African marker". If it were a specifically North African marker, that would have been mentioned. Sub-Saharan haplotypes were certainly introduced into Sicily by both sub-Saharans themselves and North Africans, who often carry sub-Saharan markers. In fact, North Africa is mentioned only in the abstract, and this is because it is through North Africans the authors feel the sub-Saharan marker became established in Sicily.
Inside the study itself, the following is stated:
Quote:
The presence of a typical African marker (haplotype Gm 5*;1,17;...), especially in the genetic structure of Alia and Palermo, highlights the possibility of past contacts with peoples from Africa. [...] Therefore, the introduction of an African polymorphism could have been due to the Phoenician colonization or to the more recent Arab conquest of the territory (9th century A.D.). A study (Semino et al. 1989) carried out with restriction enzymes on mtDNA indicated the presence of African haplotypes (4.4%) in a sample of Sicilians. The authors hypothesized an input of genes from Africa to Sicily (estimated at about 10%) brought by Phoenician migrations.
The mentioning of Semino's study solidifies the Gm marker's being sub-Saharan, since Semino's African findings at a rate of 4.4% were sub-Saharan L1/L2 markers.
Hum Genet. 1990 Nov;86(1):49-53. Links
Genetic heterogeneity at the glucose-6-phosphate dehydrogenase locus in southern Italy: a study on a population from the Matera district.Calabro V, Giacobbe A, Vallone D, Montanaro V, Cascone A, Filosa S, Battistuzzi G.
Dipartimento di Genetica, Biologia Generale e Molecolare, Naples, Italy.
Glucose-6-phosphate dehydrogenase (G6PD) has been analyzed by gel electrophoresis and by quantitative assay in an unselected sample of 1524 schoolboys from the province of Matera (Lucania) in southern Italy. We have identified 43 subjects with a G6PD variant. Of these, 31 had severe G6PD deficiency, nine had mild to moderate deficiency, and three had a non-deficient electrophoretic variant. The overall rate of G6PD deficiency was 2.6%. The frequency of G6PD deficiency, ranging from 7.2% on the Ionian Coast to zero on the eastern side of the Lucanian Apennines, appears to be inversely related to the distance of each town examined from the Ionian Coast, suggesting that this geographic distribution may reflect, at least in part, gene flow from Greek settlers. Biochemical characterization has shown that most of the G6PD deficiency in this population is accounted for by G6PD Mediterranean. In addition, we have found several examples of two other known polymorphic variants (G6PD Cagliari and G6PD A-); three new polymorphic variants, G6PD Metaponto (class III), G6PD Montalbano (class III), and G6PD Pisticci (class IV); and two sporadic variants, G6PD Tursi (class III) and G6PD Ferrandina (class II). These data provide further evidence for the marked genetic heterogeneity of G6PD deficiency within a relatively narrow geographic area and they prove the presence in the Italian peninsula of a gene (GdA-) regarded as characteristically African.
PMID: 2253938 [PubMed - indexed for MEDLINE]
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The following 3 studies don't have abstracts available, but by their very titles, they tell us what we need to know:
Note: The claim on Internet message boards (by those with idealogical investments in the non-existent "purity" of Sicilians, started by Racial Reality, of course) that this 1989 study has been "refuted" by a quote from another study (Vona, 2001) is fraudulent and utterly ridiculous, and clearly illustrates what one may find on message boards and sites with a political or idealogical slant. This 1989 study definitely found 4 sub-Saharan lineages in the 90 Sicilians (from all over the island) tested. There is no way this can be "refuted" by anything. It is perfectly valid. The 2001 Vona study (which finds no sub-Saharan L lineages because it tests just 49 people from only one Sicilian village) cites this 1989 study in that misrepresented quote for comparison purposes, only, and doesn't attempt to, and, more importantly, can't, "refute" anything regarding the 1989 Semino study. For detailed explanation, see our admixture index. It should be noted that the Black African HpaI-3/AvaII-3 complex described in the 1989 study (abstract below) is equivalent to sub-Saharan haplogroups L1 or L2, as learned by corresponding directly with Dr. Semino. The HpaI-3 is equivalent to +3592HpaI coding region mutation that defines haplogroups L1/L2.
[Incidentally, the use of restriction enzymes is just as valid as sequencing the section of DNA in question; it is not "outdated" or "invalid" or "unreliable" or any such drivel, and is still frequently used because it is relatively inexpensive and accurate. (Even the Vona study cited above recommends this method for further studying the relationship between Sicilians and other peoples.) Indels (insertion/deletion polymorphisms) are easy to spot using this method, and the method saves the cost of sequencing the section in question. In fact, when sequencing the HVR does not give satisfactory results, or if the two HVR's don't match, often restriction enzymes will be applied to the coding region to determine the mutation, and then haplotype can be ascertained.]
Quote:
Ann Hum Genet. 1989 May;53 ( Pt 2):193-202. Related Articles, Links
Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry.
Semino O, Torroni A, Scozzari R, Brega A, De Benedictis G, Santachiara Benerecetti AS.
Dipartimento di Genetica e Microbiologia 'A. Buzzati-Traverso', Universita di Pavia, Italy.
mtDNA polymorphisms were studied in a sample of 90 individuals of the Sicilian population using six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII and HincII. (1) Three new patterns, for MspI, AvaII and HincII, have been detected. (2) At least two different mutations were found to account for both the AvaII morph 3 and the AvaII morph 9 as in many other Caucasian groups so far examined. (3) Seventeen types were found; of these six are new. The frequency (54.5%) of type 1-2 (2.1.1.1.1.2) is lower than in the rest of Italy whereas those of type 6-2 (2.1.2.1.1.2) (10.0%) and type 18-2 (2.3.1.4.9*.2) (12.2%) lie at the upper level of the Italian range. The 18-derivative, type 57-2 (2.3.1.4.13*.2), which is consistently found in all Italian samples, is present also among Sicilians with an incidence of 2.2%. (4) Of particular interest is that the HpaI-3/AvaII-3 complex, which is unique to groups of African ancestry, was found in Sicily at a frequency of 4.4%. For the first time an estimate of the amount of gene flow from Blacks to the Sicilian gene pool could be obtained.
Data not available in abstract, and study not available online, but according to Dr. Ornella Semino, with whom I corresponded, sub-Saharan haplogroup L1/L2 (HpaI-3/AvaII-3 complex, see comments to above study) was found in the 87 subjects studied at a rate of 3.4% (3 out of 87).
Two haplogroups not common in Europe are present: haplogroup M, separated from Eastern Africa to Western Asia and Eurasia about 50,000 years ago (Quintana-Murci et al. 1999) has been found in Sciacca (8%), Castellammare (3%) and Ragusa (2%); and haplogroup L1/L2 originating from Africa (Watson et al. 1997) has been found in Sciacca (2%) and Castellammare (less than 1%).
It should be noted that the M haplotypes found in Sicily are nearly always M1, which is concentrated in eastern Africa, and radiates out from there, appearing sporadically in Mediterraneans. It is not found in India, or indeed east of the Caucasus (where it appears at very low levels). Therefore, it simply must be a reliable marker of sub-Saharan eastern African ancestry, despite claims to the contrary. More on this below.
It should also be noted that this study (and Semino, 1989 above) did not test for any L3 markers, which Sicilians have more of than L1 and L2. This brings us to another point. Racial Reality likes to claim L3 may not be sub-Saharan. This is flatly incorrect. All L's, including all L3's, are indeed sub-Saharan in origin. The confusion on his part, if it is not an outright lie, is due to one (or both) of two points:
Firstly, all non-African mtDNA haplogroups and paragroups branch off of African L3. In fact, it is possible those Africans who left to colonize the world all carried L3. But this would have morphed into what we now call M and N, which are not African originating, and hence, not African specific (except for M1, which, in this scenario, would have evolved independently from L3 in Africa; see above and at the end of post. Some claim M* -- the ancestor of all M's -- originated in East Africa before the Diaspora, and that those Africans who colonized the planet carried this marker, with the Asian-specific M's developing from this in Asia. The M* remaining in East Africa subsequently morphed into M1.) At any rate, no L3's survived outside of Africa, and the presence of L3 markers in non-African populations is due to admixture/gene flow.
The other source for the confusion is due to this Pereira, et al. study. In this study, it is mentioned that some L3*'s (with an asterisk, which means the aboriginal form of L3 that didn't form clades) may not have an African origin. However, Pereira admitted the category they labeled "L3*" was a default category. What actually occurred here is that L3* was not properly distinguished from non-African M and N. According to this study, sub-Saharan L3* is distinguished from M and N at nucleotide positions 10400 and 10873, respectively. (Incidentally, Plaza, 2003 used the Pereira sample; they re-examined the motifs, and made some adjustments. Some of the Portuguese motifs assigned to L3* that may not have actually been so were not listed as L3's in the Plaza study.) So, true L3* is indeed sub-Saharan African, and, as mentioned above, so are all other L3's. In other studies where researchers were not able to differentiate L3* from M and N, the default group is labeled as "L3/M/N," which is a little less confusing.
Finds one sub-Saharan haplogroup L (L2a) in a sample of 106 Sicilians from Castellammare (data not in abstract, only in full study, available for fee).
Full study shows one definite sub-Saharan L3b sequence in 49 individuals from Tuscany. Haplogroups are not given in study, but the motifs have been examined by a geneticist acquaintance for haplogroup assignment. Plaza, 2003 also examined the motifs and found that one falls into L3. There is an additional ambiguous sequence that may or may not be an L3; it has been classified variously as L3b and L3* (with uncertainty) with regard to one of the HVR's, while the other HVR doesn't match and probably falls into W. Therefore it may be best to leave it unclassified. So, to summarize, the study definitely found one L3b sequence, and possibly there is another L3.
Full study (not available through Pubmed) shows that out of 80 Sicilians from Sciacca, three have L2a, one has L3*, two have L3e, and five have M1 (13.8% maternal sub-Saharan contribution). Haplogroups are not given in this forensics study, but the motifs have been examined by a geneticist acquaintance for haplogroup assignment. The other published samples from Agrigento Province (Sicily) and Greece are being examined presently.
An examination by a geneticist acquaintance (who is familiar with all these studies) reveals sub-Saharan (East African) M1 in Greeks. Also found are one sub-Saharan L3e and one sub-Saharan M1 in a sample of 90 Sicilians from Troina (n.=42) and Trapani (n.=48 ). In 48 Romans there are one L2a and one L3b sequences. In 69 Sardinians, there are one L1a and one L2a (from Di Rienzo & Wilson, 1991).
Study examines, in addition to Croation minority in Molise, Croatians from Croatia and ethnic Italians in Molise, Abruzzo, Campania, Lazio, and Puglia. Finds one L1b in a sample of 26 Puglians (Apulians) and one M1 in 52 individuals from Lazio (both of these samples were of ethnic Italians). (Also, incidentally, finds one L1c in 98 Croatians from Korcula and one M1 in 41 Croatian-Italians.) A slightly earlier, unpublished/unused set of 88 sequences from this study labeled as "Molise/Abruzzo, Campania, Puglia" has one L1b and one L2a.
L haplogroups are relatively infrequent in Italians (with a maximum of 8.1% in South Italians) and Iberians (with a maximum of 6.1% in Central Portuguese). On the contrary, L haplogroups are distributed in all North African populations at high frequencies (from 26% in South Berbers to 43.5% in Mauritanians) with the exception of Mozabites (12.9%) and Moroccan Berbers (3.2%). In fact, the frequency of the L haplogroups in Moroccan Berbers is similar to that found in Iberians and Italians. The frequency of the L haplogroups might represent the sub-Saharan genetic flow into the populations analysed, which has shown to be substantial in NW Africa but very limited in European populations.
[. . .]
This may be even clearer in Italy, where the frequency of U6 is much lower than in Iberia (one out of 411 individuals), and where none of the eight L sequences has been found in NW Africa. Three Italian L sequences have been described throughout Africa, and the remaining five are not found in >1,000 sub-Saharan individuals. Thus, the presence of L sequences cannot be attributed to migration from NW Africa, and may instead represent gene flow from other sources, such as the Neolithic expansion or the Roman slave trade.
Data from tables show L sequences as follows in Italy:
Central Italy: 1.2 (From Tagliabracci, 2001) (L3*)
Sardinia: 2.8 (From DiRienzo & Wilson, 1991, and unpublished Rickards data) (L1a & L2a)
Sicily: 0.6 (From Cali, 2001, with additional sample from unpublished Rickards data and Rickards, 2000 added) (L2a)
South Italy: 8.1 (From unpublished Rickards and Rickards, 2000 data, not available online) (L1 and L3 haplogroups)
Tuscany: 2.0 (Tuscan data from Francalacci, 1996, listed above.) (L3b) As stated above, there may or may not be an additional sequence that falls into L3 (not counted here).
This is the Di Rienzo & Wilson study mentioned above, which finds one L1a, one L2a, and one M1 in 69 Sardinians. Haplogroups (determined by examining motifs) supplied by a geneticist acquaintance.
Tagliabracci study mentioned above, which finds one sub-Saharan L3* out of 83 Central Italians. Also found is one Asiatic M*. Full list of haplogroups supplied privately by a geneticist acquaintance.
Full study (available for fee) shows one sub-Saharan Y-haplogroup A in a sample of 81 Sardinians (as well as sub-Saharan markers in Maltese and Cypriots). Also shows various forms of E3b, which ultimately traces its way back to eastern sub-Saharan Africa (since it originated there) in various Mediterraneans, including Sicilians, Sardinians, and mainland Italians.
Two sequences, from Sardinia and Portugal, are members of RFLP haplogroup L2 (confirmed by testing for the HpaI site at position 3592 characterizing L1 and L2 in Africans: Chen et al. 1995). One, from Iberia, is a one-step derivative of the most frequent and widespread member of L3b. An individual from North Germany, one from Britain and one from Sardinia are members of L1, and the 6209±16223±16311 sequence is a member of an African subcluster of L3a, and ndeed is found in a Portuguese subject with Angolan ancestry.
Study's data table shows sub-Saharan E-M35* as follows in Italians:
Sardinians (1.1%)
And sub-saharan E(xE3b):
Sardinians (1.6%)
Note on E-M35*: The last 2 studies above show E-M35*, the ancestral form of E-M35 that didn't form clades, to be present at high frequencies only in Ethiopians and southern Africans. It is only found sporadically at low rates in Europeans (and North Africans). This shows it is a useful marker of sub-Saharan admixture. E-M78, versions of which are found in Greeks and other Mediterraneans, arrived there many thousands of years ago from sub-Saharan eastern Africa, and a distinct "trail" can be seen leading from eastern Africa to the Mediterranean. E-M35* doesn't have such a trail into Europe, and, as mentioned above, its presence in Europe (Iberia, Sicily, Italy, Sardinia) is sporadic and sparse. This would suggest it arrived there more recently, perhaps during the Saracen/Moorish era with sub-Saharan slaves.
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Note on M1: Haplogroup M as found in the Mediterranean is mostly the East African version (M1), as shown by Quintana-Murci (1999), and not the eastern/southern Asian versions, except in a few cases. The origin of M1 (indeed M in general) is hotly debated. Some believe M1 must have originated in southern or eastern Asia, because all the other branches of haplogroup M are restricted to South Asia, East Asia, and Australasia, and because the diversity of M is greater in Asia than in Africa. They explain that M1's absense there now is because it died out. This scenario doesn't make much sense.
Others say M1 must have originated in East Africa because it is not present in any southern or eastern Asian samples, it reaches its highest frequency by far in East Africa, and it is found at considerably lesser rates in nearby North African and Middle Eastern populations. Support for the second theory is obtained by the calculation of RFLP data, which shows the age of East African M1 to be compatible with Asian M, suggesting aboriginal M* arose just prior to our species' expansion out of Africa, with Asian-specific M's developing in Asia, and haplogroup M remaining in East Africa then becoming M1. The lack of diversity in East Africa is explained by the fact that a small localized population cannot develop the diversity in a marker that can develop when it exists in a population that spreads throughout a much larger area. Again, see Quintana-Murci. (Alternatively, one could suggest that L3 carriers left Africa, with M* and its descendants, except M1, developing in Asia. Some L3's remaining in East Africa then morphed into M1 independently. But M1 would still be African-originating.) The scenario of M1 originating in East Africa is the only one that makes any sense.
At any rate, since M1 isn't found further east than western Asia, and it reaches its highest frequency in East Africa, we can conclude that less frequent occurrences of this marker in neighboring regions of North Africa and the Middle East, and the sporadic occurrences in the northern Mediterranean area, are due to expansion from East Africa. Richards (2003) aren't sure of its origin, but mention its concentration in East Africa. They don't seem to dispute that the presence of the marker in the Near East is due to expansion from East Africa, but claim that they can't be certain that any given M1 there was from recent immigration. (For that matter, it isn't 100% certain that L markers here, which are clearly sub-Saharan, are from recent immigration, either; they could have been introduced much earlier. But this isn't too likely for L's or M1's there -- except in a few cases -- because of a lack of a "trail"; see below). Richards (2000) definitely take M1 to be an indicator of sub-Saharan introgression (along with haplogroup L) in the Near East. There are a few studies on Iberians where M1 is definitely taken to be a marker of sub-saharan ancestry (links will be provided soon).
So, it is virtually certain that M1 found sporadically in Mediterranean Europe (Iberia, Sicily, Greece, etc.) is due to sub-Saharan admixture/gene flow. Furthermore, this is indeed likely from the time of the trans-Saharan slave trade, and not from a very ancient movement, (except for a few sub-clades that aren't found in Africa, suggesting their ancestors arrived in Europe from sub-Saharan East Africa much earlier, with the mutations developing in Europe). This is because its presence there is sparse, and because there is no "trail" suggesting an ancient movement out of East Africa, as with Y-marker E-M78. Also, Quintana-Murci (1999) say it is virtually absent in the Levant, where it would certainly be present had it been carried into Europe in a mass movement, say with E-M78. Also possible is that M1 was carried into Mediterranean Europe by relatively recent M1-carrying North African or western Asian immigrants or slaves. But even here, it ultimately traces its way back to eastern sub-Saharan Africa, since this is where it is concentrated. There doesn't seem to be any way to avoid this conclusion.
----------
Here is an additional study, on Parkinson's Disease in Mediterraneans, that mentions Sardinians have some Negroid features:
Neurology. 1980 Mar;30(3):250-5. Related Articles, Links
The risk of Parkinson disease in Mediterranean people.
Rosati G, Granieri E, Pinna L, Aiello I, Tola R, De Bastiani P, Pirisi A, Devoto MC.
On the basis of previous epidemiologic studies, Parkinson disease was thought to be evenly distributed throughout the world. These studies, however, were conducted only on North European populations. The position with regard to the Mediterranean peoples was still unknown, and we therefore studied the frequency of Parkinson disease on the island of Sardinia, where some ethnic groups of the Mediterranean stock are represented. Based on 967 accepted cases, the prevalence 100,000 population on January 1, 1972, was 65.6; the average annual incidence for the period 1961 through 1971 was 4.9. These figures are one-half of the figures established for North Europeans. Our findings suggest racial differences in predisposition to Parkinson disease. Some Negroid features are present in Sardinians. If, as seems likely, Africans prove to be relatively unsusceptible to the disease, the risk for Sardinians and other Mediterranean ethnic groups might be intermediate between North Europeans and Africans.
PMID: 6965773 [PubMed - indexed for MEDLINE]
Last edited by William on Tue 15 Apr 2008 19:24; edited 56 times in total
Joined: 30 Mar 2005 {Posts: 1053 } Location: New Jersey
Posted: Fri 28 Apr 2006 20:19 Post subject:
It would be wise to clear a few things up, some of which have been addressed already elsewhere; but they have validity here, in light of what was posted above.
An individual (with one hell of an idealogical investment in the non-existent purity of southern Italians, Sicilians, and Greeks) known as "Racial Reality" likes to claim on various Internet message boards that blood group markers are "useless" for studying population relationships, and so he dismisses studies using them that find sub-Saharan markers in his "pet" populations. He cites a quote from one David Goldstein, Professor of Genetics at Duke University, as "evidence" of this:
Quote:
...blood groups are not now considered a good marker for population relationships, and they provide very little information about individual ancestry.
It is true that blood proteins and antigens don't provide much information on individual ancestry. (Then again, neither do mtDNA and Y-chromosome markers.) It is also true that some of them (but not all) can undergo selection, and these shouldn't be used to quantify any given admixture. But the claim that they're "useless" for determining population relationships is not accurate. First of all, if Dr. Goldstein had truly meant that they're "useless," one can clearly see that the idea that a single quote can erase decades of research is patently ridiculous. Blood group markers were the subject of study for decades, so researchers know where they originated, or at least where they concentrated. This is why all population-specific blood proteins are perfectly valid for simply determining that admixture occurred, whether they're under selection or not.
For example, one can see that Sicilians have sub-Saharan admixture by the presence of the Benin strain of HbS. In this case, the marker wouldn't be used for quantification, because malaria can cause artificial expansion, since those with HbS tend to be somewhat resistant to the disease. But selection can only cause an already present marker to expand; it can't "create" the marker. Therefore, its mere presence isn't caused by malaria; it can only have gotten there by admixture, whether direct (the importation of and mixing with sub-Saharan slaves) or indirect (through admixture North Africans, who had mixed with sub-Saharans). So, if (hypothetically) HbS is found at a rate of 12% in Sicilians, one could not necessarily say that sub-Saharan admixture occurred at that rate. But one can correctly say that sub-Saharan admixture occurred; this can't be disputed, since the Benin strain of HbS definitely originated in Central West Africa. One can also correctly say that 12% of the sample studied definitely have sub-Saharan ancestors. Other markers that aren't as likely to undergo selection, like TaqI(-), can be used for quantification; but the quantification applies only to the marker studied, and doesn't necessarily equal the true rate of admixture, which may be higher, since not all of the "admixing" peoples would have carried the same marker.
But if one knows a little about the subject, one can easily see that what Professor Goldstein is saying is not that blood group markers are totally useless for determining admixture, but rather that since the decoding of the human genome, it is no longer necessary to use blood proteins, which were for a long time considered the best genetic markers. Looking directly at the DNA provides far more detail than examing proteins. Therefore, DNA analysis is much better than protein analysis; but this does not suggest by any stretch of the imagination that protein analysis is useless. Consider this analogy: In 1880, a horse-and-buggy was the best form of personal transportation. Now that we all drive very reliable cars, we can honestly say that the horse-and-buggy is not now considered a good form of personal transportation. What has changed? The horse-and-buggy's ability? Certainly not. Only our perception. The car is now a much better form of personal transportation, but the horse-and-buggy will still get us to most destinations a car will...eventually! Indeed, it is still used by some populations, like the Amish. Likewise, blood group markers can still tell us about the existence of foreign admixture in a population. And, despite the fact that they have fallen out of favor, studies using them are still being conducted, as is evidenced by this 2002 study on Sicilians (see above for a 2004 Sicilian study using the Gm/Km system):
Am J Hum Biol. 2002 May-Jun;14(3):289-99. Related Articles, Links
New data on the genetic structure of the population of Sicily: analysis of the Alia population (Palermo, Italy).
Ghiani ME, Calo MC, Autuori L, Mameli GE, Succa V, Vacca L, Cerutti N, Rabino Massa E, Vona G.
Department of Experimental Biology, University of Cagliari, Italy.
The distribution of 13 genetic markers (AB0, Rh, ACP, ADA, AK, ESD, GLO, PGD, PGMl, SOD, GC, TF, and PI) were studied in a sample from the Alia population of Sicily, Italy. A total of 34 alleles were detected. In comparison with other Sicilian populations, Alia always appeared genetically distinctive, either in terms of overall genetic diversity or for the number of unique alleles present. The results are consistent with previous studies that show no genetic uniformity within the island. More specifically, the data support the genetic divergence of the eastern and western halves of the island and highlight genetic boundaries that run through Sicily and divide it into three distinct areas. Copyright 2002 Wiley-Liss, Inc.
PMID: 12001085 [PubMed - indexed for MEDLINE]
Also, the same individual, "Racial Reality," likes to dismiss the cDe marker as "useless" because of a quote from Dobzhansky, 1962:
Quote:
But note that the cDe gene is nevertheless present in a fraction of the gene pool almost everywhere in the world. [...] Does it follow that once upon a time everybody in sub-Saharan Africa was homozygous for cDe, and in the rest of the world nobody had this gene? Should Europeans, Asiatics, and Americans who carry the cDe gene be presumed to have some Negro ancestry? There is no basis whatsoever to think so. The gene cDe is almost cosmopolitan in distribution, though for some unknown reason it reaches its highest frequency in Africa.
Also quoted are cDe frequencies from Mourant in 1954:
Quote:
EUROPE
Spaniards ..... 3.7%
English ....... 2.8%
Germans ....... 2.6%
Danes ......... 1.8%
Italians ...... 1.6%
Basques ....... 0.5%
It is true that cDe is found in many populations of the world, some with no apparent recent connection to sub-Saharans. However, it seems as though a little more has been learned since 1954 and 1962. In fact, the Sandler study quoting it in the post above was done in 1978, and the scientists performing the study consider it to be a marker of sub-Saharan origin in Sicilians. There are others from that time and later that also do. This is because it reaches its highest frequency by far in sub-Saharan Africa.
A quote from this 1999 study, specifically mentions that cDe is a "predominantly Black African allele":
Quote:
The predominantly Black African allele cDe displayed a unique set of microsatellite alleles, providing a method of identifying individuals carrying this haplotype.
This 1975 study clearly considers it to be an African genetic marker (quote):
Quote:
Genetic markers in people of African ancestry and tables comparing Africans and Europeans are compiled to illustrate the blood differences. The existence of the African genetic characters, R0 (cDe), D-u and Ee (e-s, ce-s) in an Rh-Hr system are discussed. The high incidence of R0 (81.9%) in Africans is evident.
The presence of the cDe allele and the Gm1,5,13,14,17 haplotype in low frequencies indicates black admixture.
In Mourant AE, Kopéc AC, Domaniewska-Sobczak K. The distribution of the human blood groups and other polymorphisms. London, Oxford University Press, 1976, p. 73, we find support:
Quote:
As usual in the Mediterranean area CDe is high, and cDe, presumably from African admixture, reaches about 6 per cent.
[. . .]
. . . the presence of over 5 per cent cDe [in Cyprus] suggests African immigration.
According to Luigi Luca Cavalli-Sforza, Paolo Menozzi, and Alberto Piazza, in The History and Geography of Human Genes [trans. Sarah Thorne (Princeton: Princeton University, 1994) pages 132-133], as far as anyone can tell, our ancestors before the great African diaspora of 60 kya all had "cDe." This was the original haplotype. Hence, it is more common in sub-Saharan Africa than anywhere else, because it originated there. The others, CDe, cde, etc., arose later.
So, since it originated in sub-Saharan Africa, it is definitely a marker of sub-Saharan ancestry. But do we know if the marker as found in other populations is left over from the Great Diaspora, or from later sub-Saharan admixture? No, not really, but we can conclude that in most cases, it is indicative of later sub-Saharan admixture. Also, geography and history can be of assistance. In Eskimos, the marker might be (although this is not by any stretch of the imagination certain, for later admixture may have occurred) a lingering trace of the Diaspora. In Pacific Islanders, other post-Diasporic sub-Saharan markers have been found, so cDe could very well be of later sub-Saharan admixture. In the Navajo, it almost certainly is of more recent (trans-Atlantic slave trade) origin, since American Indians are known to have mixed with African slaves. In the cases of Sicily and Greece (where it has also been found), we can also conclude that cDe almost certainly is not residual Diasporic material, but evidence of later admixture, perhaps during the time of the trans-Saharan slave trade. Why? This is because of these lands' locations in the Mediterranean near Africa, the fact that history mentions the presence of sub-Saharans (and northern Africans, who have some sub-Saharan admixture) in these areas, and the fact that several other sub-Saharan markers are present in these populations. All of this lends support to a more recent origin for cDe in these areas.
Fy(a-b-), or Duffy null, is perfectly valid for determining if admixture of sub-Saharans into a European population occurred, since it is the predominant phenotype of those originating in sub-Saharan Africa, particularly West Africa, and is rare among Europeans and Asians. The claim that it may be under selection due to malaria (like Hbs) is peripheral to the point, as that may cause problems with quantification, but does not change the fact that the marker originated in sub-Saharan Africa, and does not change the fact that the presence of the marker in Europeans is due to admixture (the only way it could have arrived there). See above HbS section for more about this point.
Quote:
.0002 DUFFY NULL; Fy(a-b-) [FY, -46T-C]
FY*O
The Fy(a-b-) phenotype is rare among white and Asian populations, whereas it is the predominant phenotype among populations of black people, especially those originating in West Africa. Tournamille et al. (1995) demonstrated that the molecular basis of the Fy(a-b-) phenotype is a T-to-C transition in the GATA box of the FY*B promoter. This mutation disrupts the binding site for the GATA1 erythroid transcription factor, results in a silent FY*B allele in erythroid cells, and is considered to be responsible for most cases of Fy(a-b-) erythrocytes in black populations. The GATA mutation generates a StyI restriction site, allowing the identification of this mutation by RFLP.
The Duffy blood group system consists of two principal antigens, Fya and Fyb produced by FY*A and FY*B co-dominant alleles. Antisera, anti-Fya and anti-Fyb, define four phenotypes: Fy(a+b-), Fy(a-b+), Fy(a+b+) and Fy(a-b-). Neither antiserum agglutinates Fy(a-b-) cells, the predominant phenotype in Blacks. Outside the Black population, Fy(a-b-) phenotype is very rare.
As can be seen when viewing Sandler (1978), Fy(a-b-) is used by those doing serological analysis. It is also used by those doing autosomal research, like DNAPrint. This shows a link between blood group markers and DNA, and makes nonsense of the claim that blood group markers aren't valid for determining population relationships. As Frank W. Sweet has stated, the Duffy blood-group types have been known for many decades, as has their usefulness in identifying continent or region of ancestry. But it has been only within the past decade [since the decoding of the human genome] that we have known that a person's Duffy blood-group type is encoded on the long arm of his/her chromosome #1, about 23.2 centimorgans out from the chromosome's centromere. In general, you can measure the end-result of a person's genetic makeup by serological analysis, or you can measure the actual genetic makeup itself in the DNA. The latter is more precise since some proteins are produced (or not) only in homozygotes and so some of the corresponding alleles would be invisible to serological analysis but visible in the DNA.
Finally, and this shouldn't require mentioning because it was touched upon a few paragraphs up and is obvious when reading the related studies above, the HbS in Sicilians (and Greeks) definitely originated in sub-Saharan Africa. By far the most common strain is the Benin haplotype (#19). It is called the Benin haplotype because it originated in Benin or a neighboring region of Central West Africa. This genetic marker can only have entered Greek and Sicilian populations by admixture, whether direct (importation of sub-Saharan slaves) or indirect (sub-Saharans mixing with North Africans, and North Africans mixing with southern Europeans). Either way, the end result is the same: irrefutable sub-Saharan ancestry. Here is yet another quote on this from The Geography of Sickle-Cell Disease, an excellent article that summarizes and explains the origins of this disease (and marker) in various populations by analyzing the available studies, some of which have been quoted above:
Quote:
The Benin haplotype accounts for HbS associated chromosomes in Sicily, Northern Greece, Southern Turkey, and South West Saudi Arabia, suggesting that these genes had their origin in West Africa.
Baillieres Clin Haematol. 1992 Apr;5(2):331-65. Related Articles, Links
Genetic epidemiology of the beta s gene.
Nagel RL, Fleming AF.
The beta s gene arose at least four times in Africa, with three of these mutations expanding through diverse ethnic groups, but limited to definite geographical areas: Atlantic west Africa for the Senegal haplotype linked beta s; central west Africa for the Benin haplotype; and equatorial, eastern and southern Africa for the Bantu haplotype. The fourth mutation (linked to the Cameroon haplotype) is restricted to a single ethnic group, the Eton of central Cameroon. The Benin haplotype linked beta s gene was spread by gene flow to the Mediterranean (north, south and east) and to the western portions of Saudi Arabia. An independent mutation linked to a fifth haplotype, Arab-India, is found among the tribals of India (independent from their geographical origin) and in the eastern oases of Saudi Arabia. It is also suspected of being associated with the beta s gene found in Afghanistan, Iran, Transcaucasia and central Asia. The selective force involved in the expansion of the gene was most likely P. falciparum malaria, and the time of the gene frequency increase was likely to have been during the expansion of agriculture about 4000 or more years ago in India and about 3000 years ago in Africa. The partial protection against severe and life-threatening malaria is through the limitation of P. falciparum parasitaemia. This is a complex process which involves at least two mechanisms: early intraerythrocyte parasite forms are in a suicidal position through increasing the tendency of HbAS cell to sickle and then be destroyed by the spleen; intraerythrocyte growth is inhibited during deep vascular schizogony. Although there is evidence that P. falciparum (and P. malariae) parasitaemias are limited in HbSS red cells, malaria is a major trigger to haemolytic and infarctive crises in sickle-cell disease, and a common cause of morbidity and mortality.
Hum Biol. 1991 Jun;63(3):241-52. Related Articles, Links
Origin and spread of beta-globin gene mutations in India, Africa, and Mediterranea: analysis of the 5' flanking and intragenic sequences of beta S and beta C genes.
Laboratoire de Biologie Cellulaire, CNRS UMR 106, Universite Claude Bernard Lyon I, Villeurbanne, France.
Nucleotide polymorphisms of both the 5' flanking and intragenic regions of the human beta-globin gene were investigated by directly sequencing genomic DNA after amplification by the polymerase chain reaction in 47 subjects homozygous for the beta S or the beta C mutation. The sickle-cell mutation was found in the context of five different haplotypes defined by eight nucleotide substitutions and various structures of a region of the simple repeated sequence (AT) chi Ty. All subjects from the same geographic origin bear an identical chromosomal structure, defining the Senegal-, Bantu-, Benin-, Cameroon-, and Indian-type chromosomes. These results strengthen our previous conclusions about the multiple occurrence of the sickle-cell mutation. The Benin-type chromosome was also found among Algerian and Sicilian sickle-cell patients, whereas the Indian-type chromosome was observed in two geographically distant tribes, illustrating the spread of these sickle-cell genes. We also found that the intragenic sequence polymorphisms (frameworks) are not always in linkage disequilibrium with the BamH I polymorphism downstream from the beta-globin gene, as had been previously observed. Finally, we present a tentative phylogenetic tree of the different alleles at this locus. Some polymorphisms of this sequence might be contemporary with our last common ancestor, the great apes, that is, about 4-6 millions years old.
PMID: 1676014 [PubMed - indexed for MEDLINE]
Incidentally, the comments formerly below this have been moved here, as I want to keep this thread as clean as possible.
Last edited by William on Thu 25 Jan 2007 18:05; edited 12 times in total
Impressive layout of counter arguments to "Racial Reality's" interpretations, and I pretty much agree with much of it. "Racial Reality" is out of touch with genetics to the point of invoking pale-skin women as ideal models of E3b-bearing groups. Now of course, I've pointed out to him that this undertaking ridicules him, for the simple fact that "normal" females don't carry Y chromosomes. So, although refutation of his claims is necessary for the sake of spreading fact, particularly to those who might not least be familiar with molecular genetics, I sometimes get the impression that the act of doing so, may well give "Racial Reality" a false sense of being well-informed when it comes to population genetics.
Anyway, not to ramble on unnecessarily, a few pieces caught my attention:
William wrote:
[Incidentally, the use of restriction enzymes is just as valid as sequencing the section of DNA in question; it is not "outdated" or "invalid" or "unreliable" or any such drivel, and is still frequently used because it is relatively inexpensive and accurate. (Even the Vona study cited above recommends this method for further studying the relationship between Sicilians and other peoples.) Indels (insertion/deletion polymorphisms) are easy to spot using this method, and the method saves the cost of sequencing the section in question. In fact, when sequencing the HVR does not give satisfactory results, or if the two HVR's don't match, often restriction enzymes will be applied to the coding region to determine the mutation, and then haplotype can be ascertained.]
True. If there is any shortcoming here, it will be the exclusive reliance on RFLP sequencing of the control region or HVR segment. The reason being that these markers may not be exclusive to a particular macrohaplogroup or clade, mainly due to random parallel mutations that can occur in HVR segment across different monophyletic phylums of mtDNA. On the other hand, narrow selection of restriction enzyme markers can also result in a good deal of information being left out. Just to demonstrate this, take the following C. Fox and Krings et al. pieces:
C. Fox, 1997:
mtDNA analysis in ancient Nubians supports the existence of gene flow between sub-Sahara and North Africa in the Nile valley
Abstract:
The Hpal (np3,592) mitochondrial DNA marker is a selectively neutral mutation that is very common in sub-Saharan Africa and is almost absent in North African and European populations. It has been screened in a Meroitic sample from ancient Nubia through PCR amplification and posterior enzyme digestion, to evaluate the sub-Saharan genetic influences in this population. From 29 individuals analysed, only 15 yield positive amplifications, four of them (26·7%) displaying the sub-Saharan African marker. Hpa I (np3,592) marker is present in the sub-Saharan populations at a frequency of 68·7 on average. Thus, the frequency of genes from this area in the Merotic Nubian population can be estimated at around 39% (with a confidence interval from 22% to 55%). The frequency obtained fits in a south-north decreasing gradient of Hpa I (np3,592) along the African continent. Results suggest that morphological changes observed historically in the Nubian populations are more likely to be due to the existence of south-north gene flow through the Nile Valley than to in-situ evolution.
Krings et al study, 1999:
mtDNA Analysis of Nile River Valley Populations: A Genetic Corridor or a
Barrier to Migration?
To assess the extent to which the Nile River Valley has been a corridor for human migrations between Egypt and sub-Saharan Africa, we analyzed mtDNA variation in 224 individuals from various locations along the river. Sequences of the first hypervariable segment (HV1) of the mtDNA control region and a polymorphic HpaI site at position 3592 allowed us to designate each mtDNA as being of "northern" or "southern" affiliation. Proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the southern Sudan. At slowly evolving sites within HV1, northern-mtDNA diversity was highest in Egypt and lowest in the southern Sudan, and southern-mtDNA diversity was highest in the southern Sudan and lowest in Egypt, indicating that migrations had occurred bidirectionally along the Nile River Valley. Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia. Spatial autocorrelation analysis demonstrates a smooth gradient of decreasing genetic similarity of mtDNA types as geographic distance between sampling localities increases, strongly suggesting gene flow along the Nile, with no evident barriers. We conclude that these migrations probably occurred within the past few hundred to few thousand years and that the migration from north to south was either earlier or lesser in the extent of gene flow than the migration from south to north.
The authors indeed rely on just the hypervariable region, which as they acknowledge is known to be limited on the very probable potential of harboring "parallel mutations", and the absence or presence of the restriction enzyme identified site of the said HapI marker. They say:
Utilizing three sites in this manner should minimize incorrect classification of mtDNA types; however, because the two sites in HV1 are subject to repeated mutations (Hasegawa et al. 1993), we were concerned that some incorrect classification might nevertheless occur....
Approximately one-third of the Nile River Valley mtDNA types could be unambiguously classified on the basis of this database comparison; the results were nearly completely concordant with the classification based on the three sites, with the single discrepancy involving an Egyptian mtDNA that, on the basis of the three sites, was classified as northern but, on the basis of the database comparison, was classified as southern because it was identical to sequences found in two Songhai from Mali and two Kikuyu from Kenya (Watson et al. 1996). Because alteration of the classification of this one sequence does not significantly change any of the results that follow, this Egyptian mtDNA was still classified as northern, in accordance with the results from use of the three sites.
I see the method used herein, almost akin to using RFLP in Y chromosomes and microsatellite motifs, without having details on binary markers that could clearly define the monophyletic units themselves, thereby pooling otherwise different lineages based on absence or presence of certain restriction sites. We've seen this in the case of Y chromosomes, wherein E-M78, E-M81 and some other yet-to-be identified lineage were pooled together based on certain RFLP sequences, but when binary markers were tested, these related but distinct lineages came to the fore. Relying heavily on three hypervariable segment sites for analysis, along with the testing for just a single restriction enzyme marker, has definitely got to be one of the weakest aspects of this study.
The mere assignment of "sub-Saharan" reference to only certain mtDNA which tested positive for the said marker, might mislead one into thinking that the others which tested negative for the said marker were not necessarily of African origin or African specific as well. This is because the testing for a restrictive enzyme marker at a single site made it impossible to learn about the unique characteristic or identifying markers of other mtDNA lineages. L3 is obviously as African as L1 and L2 superclades in origin, but this clade lacks the said HapI marker. M1 which is largely prevalent amongst east Africans, as an L3 derivative, naturally also lacks this marker.
To demonstrate the basic point above, we have the following from Clemencia Rodas et al.:
The main sub-Saharan African haplotypes, thus, are characterized by a combination of 10394DdeI(+)/10397AluI(-)/3592HpaI(+) markers (haplogroup L, comprising the LI and L2 lineages) (Chen et al. 1995, 2000). A less frequent group of haplotypes lacks the African-specific 3592 HpaI marker [10394DdeI(+)/ 10397AluI(-)/3592HpaI(-)] (Chen et al. 1995, 2000) and has been designated as haplogroup L3 (Watson et al. 1997). A minority of African haplotypes (2.3% of Africans) lack all three of these mutations [10394DdeI(-)/10397AluI(-)/ 3592HpalI(-)]. Some align with the European lineage U (Chen et al. 2000), but a number of the mtDNAs belong to branches of the African haplogroup L3, itself derived from African haplogroup L1 (Watson et al 1997). - Clemencia Rodas et al., Mitochondrial DNA studies show asymmetrical Amerindian admixture in Afro-Colombian and Mestizo populations, 2003.
Ps - Note that even in the above piece, even though restriction enzyme markers allow for grouping into superphyletic units [in the case of those which were deemed to belong to the L3 supergroup, it isn't even that clearcut, as there are those which lack all the restriction markers tested, and then there are those which harbor 10394DdeI(+). L1 and L2 lineages on the other hand, seemed to have been pooled under that which tested positive for 3592HpalI - as such, without further information, we are hardly told about which ones specifically fall into L1 and L2 respectively], these alone don't tell us much about the specific designated haplogroups or else subclades actually involved. *Distinct* subclades would have just been pooled under specific restriction enzyme identified sites, pending more information on subclade-specific characteristic or definitive markers.
William wrote:
He cites a quote from one David Goldstein, Professor of Genetics at Duke University, as "evidence" of this:
Quote:
...blood groups are not now considered a good marker for population relationships, and they provide very little information about individual ancestry.
It is true that blood proteins and antigens don't provide much information on individual ancestry. (Then again, neither do mtDNA and Y-chromosome markers.) It is also true that some of them (but not all) can undergo selection, and these shouldn't be used to quantify any given admixture.
Can you elaborate on the highlighted piece; I take it you mean that it doesn't inform us about *every* ancestor of an individual - which would be the case.
I agree that blood protein and antigen markers have their limitations when it comes to reconstructing chronologically-invoked human bio-history, because of the fact that they are more often than not, under selective pressure, which makes it difficult, if not impossible, to date mutation events. As you already know, Y chromosomes and mtDNA markers on the other hand, do allow us to do just that; reconstruct chronologically-invoked human bio-history via TMRCAs mainly along our immediate paternal and maternal lines, made possible by not only the accumulation of new unique event single nucleotide polymorphisms and associated clusters, but also tendency of these markers to be preserved for a great amount of time.
William wrote:
But if one knows a little about the subject, one can easily see that what Professor Goldstein is saying is not that blood group markers are totally useless for determining admixture, but rather that since the decoding of the human genome, it is no longer necessary to use blood proteins, which were for a long time considered the best genetic markers. Looking directly at the DNA provides far more detail than examing proteins. Therefore, DNA analysis is much better than protein analysis; but this does not suggest by any stretch of the imagination that protein analysis is useless.
...because after all, we are talking about *genes* or *alleles* in all cases here, i.e. including the blood group systems so-mentioned, but I know what you mean. All of these markers can generally be located on certain chromosomes at designated sites. Folks just have to know how to use different marker types as "supplementary' material to other types, i.e. if we are to add precision to our understanding of state of affairs.
Good presentation; please keep it coming, if there is any more that is pertinent to this topic!
HbS is more of a 'disease marker' than a historical bio-marker (DNA/genome) though they can mimic each other. Interestingly, when describing the individuals showing the marker, they refer to said as 'white person of Sicilian ancestry' as opposed to what? A black person of Sicilian ancestry!
It can show show a shared historical root context regarding, in this case, hbS and its presenece in Southern Europe/Mediterranean, India, Arabian peninsula and the Americas and of course, the origin of the marker!
It can show show a shared historical root context regarding, in this case, hbS and its presenece in Southern Europe/Mediterranean, India, Arabian peninsula and the Americas and of course, the origin of the marker!
Right; HbS is a "disease marker", but since it is obviously deemed to have geographical origin, it does invoke shared ancestry as well. William is right about the Benin haplotype denoting African ancestry in those European and "Near Eastern" populations which bear this type. Thus, while selective pressure bearing on the expansion of the haplotype makes it inadequate for reconstructing biohistorical timeline indices, the fact that it is assigned geographical origin, makes it a reliable designator of shared ancestry from the assigned geographical origin. For instance, we know that of those regions you mentioned, HbS in the regions hugging the Mediterranean sea on its either side [Southern Europe and North Africa], are of African extraction - mainly the Benin haplotype. This haplotype goes as far as Asian Minor. HbS in India is of the Asian-Arabian haplotype. Perhaps the Arabian peninsula best represents the "intermediate" location, wherein both the Benin and the Arabian-Asian haplotypes are prevalent; unsurprisingly, the Benin haplotype is predominant in western Arabia, while the Asian haplotype is prevalent in eastern Arabia. In Americas, the HbS types will be represented according to the make up of populations based on the geographical origins from where they trace their most recent common ancestors, e.g.; if there is any representation of HbS in populations of Indian descent in the Americas, it will very likely be of the Asian haplotype, and likewise, African-American and Carribean populations of recent common African descent will very likely represent a mosaic of African HbS haplotypes from the Benin haplotype, the Senegalese to the Bantu haplotype.
Joined: 30 Mar 2005 {Posts: 1053 } Location: New Jersey
Posted: Thu 20 Mar 2008 17:43 Post subject:
Dr. Semino, who was involved in studies of Italians and Sicilians, mentioned long ago that she would send me the full studies that contained data on sub-Saharan admixture. I now have the full studies, and they have been uploaded. The URL's in our Admixture Index will be updated accoringly.
Most Europeans have Sub-Saharan genes? How can one explain this?
I can find nowhere (in this site or anywhere else) where such a claim is made. Sirius2008 should please explain why he/she asks such a bizarre question on this site.
sirius2008 wrote:
Do most Sub-Saharan Africans have European genes?
Not to my knowledge. Again, I would like to know what prompts such a strange question?
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