Study Clarification V

This study claims Sub-Saharan African affinities in a Byzantine population from southwest Turkey, excavated at the archeological site of Sagalassos, and ridiculously extrapolates from that similar affinities in Mesolithic and Neolithic populations throughout North Africa, West Asia and Europe. The problem is, none of it is supported either by the present data or the other sources cited.

[NB: The study is much more noteworthy for demonstrating once again the Caucasoid affinities of Ancient Egyptians and Nubians, which the Afrocentrists who quote it selectively always fail to notice.]

Study:

Cranial Discrete Traits in a Byzantine Population and Eastern
Mediterranean Population Movements

Ricaut and Waelkens (2008)
Human Biology

Link to Abstract

Misused Quotes:

Finally, as noted previously, intriguing affinity patterns of the Sagalassos population have been detected without obvious explanations: on the one hand, with two populations from northern and central Europe (Scandinavia and Germany); and on the other hand, with two sub-Saharan populations (Somalia and Gabon).

[...]

From the Mesolithic to the early Neolithic period different lines of evidence support an out-of-Africa Mesolithic migration to the Levant by northeastern African groups that had biological affinities with sub-Saharan populations.

Clarification:

Affinities with Somalis are easy enough to explain, owing to that population's Caucasoid ancestry. Affinities with Gabon not so much. But it turns out that these are tenuous at best and not manifested in all of the data:

Finally, a detailed review of the different statistical tests (MMD_st; MDS and Ward clustering) shows that the unexpected biological proximity of some northern and central European and sub-Saharan populations to the Sagalassos population is not supported to the same significance. Indeed, as seen by the MMD_st values displayed in Table 3, Scandinavians and Germans (MMD_st of 0.72 and 1.02, respectively) present stronger affinity to Sagalassos than populations from Somalia and Gabon, which have nearly significant MMD_st values (1.68 and 1.93, respectively). In addition, only the biological affinity between the Sagalassos and Scandinavian populations suggested by the MMD_st values is preserved when all the comparative populations are considered (see Figures 2 and 3).

Indeed, Figures 2 and 3 demonstrate that the true affinities of the Sagalassos population (and also the Ancient Egyptians and Nubians) are with Western Eurasians/Caucasoids:

The MDS representation of the global data set of 28 populations (Figure 2) shows roughly three main population clusters: (1) Central, Northeast, and East Eurasian populations, which are found in the top left; (2) West Eurasian and ancient Egyptian and Sudanese populations in the lower part; and (3) recent sub-Saharan populations in the top right. The Sagalassos population clusters with the second group and is most closely related to Greek, Cypriot/Turkish, and Scandinavian populations.

The dendrogram produced by Ward's clustering procedure for the global data set is shown in Figure 3 and provides a relatively similar representation of the MMD_st distance matrix than that provide by the MDS analysis. The populations clearly fall into two groups. The first main group can be broken down into two subgroups: (1) all the recent sub-Saharan populations and (2) mainly Central, East, and Northeast Eurasians. West Eurasians form the second main group, which is also subdivided into two subgroups. One of these subgroups includes all the eastern Mediterranean populations (three ancient Egyptian/Sudanese populations from Naqada, Gizeh, and Kerma as well as the Cypriot/Turkish, Greek, and Sagalassian populations) and the Scandinavian sample; the second subgroup includes the other West Eurasian populations.

Yet even with this admitted lack of support for their main claim, the authors go on to speculate at length about how these non-existent "Sub-Saharan morphological elements" could have entered the Sagalassos population, which leads them to cite all sorts of dubious conclusions about Nazlet Khater Man, Mesolithic Nubians, Natufians and Neolithic Farmers, all tied together with the genetic "evidence" of adaptive sickle cell and North African haplogroup E-M78.

Another perfectly good study marred by poor analysis that unfortunately plays right into the hands of people with an Afrocentric racial agenda.

Study Clarification IV

Here's the latest paper being paraded around by Nordicists and Afrocentrists, who, as usual, haven't bothered to look beyond a couple of passages they find favorable.

Study:

Genetic analysis of a Sicilian population using 15 short tandem repeats

Calo et al. (2003)
Hum Biol

Link to Full Text

Misused Quotes:

Other authors, studying classical markers (Piazza et al. 1988; Cavalli-Sforza and Edwards 1969) and surnames (Guglielmino et al. 1991), have stressed the existence of genetic differentiation between the eastern and western areas of Sicily and, in general, a remarkable internal variation. In addition, the boundaries found within the Palermo district have been stressed as a sort of economic boundary in a study focusing on surnames (Zei et al. 1993). The variability that has been found could be a consequence of the various dominations that Sicily has undergone: Sycanians, Siculi, and Elymians to begin with (Piazza et al. 1988), followed by Greeks, Romans, Normans, and Arabs (Sandier et al. 1978; Beretta et al. 1986). Among these, Arab domination seems to have had a very strong genetic impact.

[...]

Further analysis shows within the same cluster a certain degree of affinity between Egypt and the populations of Sicily. The relationship between Sicilian and North African populations is controversial in population genetics (Piazza et al. 1988; Rickards et al. 1992; Rickards et al. 1998). Our data seem to confirm the hypothesis of Sandler et al. (1978) that underlines the African contribution to the Sicilian gene pool, because of the high frequencies of Hbs, cDe, and Fy (a-b-). In a paper on mtDNA, Semino et al. (1989) found support for this hypothesis, dating back to the introduction of black slaves by Phoenicians and Romans and to the later influxes of Arab immigrants.

[...]

A genetic boundary, in fact, clearly divides Sicily from north-central Italy and from northern European populations, besides the other populations from the western Mediterranean basin.

Clarification:

To begin with, most of the research cited in parentheses is from the 60s, 70s, 80s and early 90s, and based on antiquated methods of analyzing blood groups that are now known to be under selective pressure, like HbS, Fy(a-b-) and cDe. A problematic Semino paper is also cited, and two references are even surname analyses pertaining to "economic boundaries," which have nothing to do with genetics at all. Needless to say, none of this is reliable evidence for anything.

Despite the claims of Arab and black admixture being detected in the present data, no Middle Eastern or sub-Saharan African populations are sampled in the study — only two North African populations and other Europeans were tested. The neighbor joining tree (unfortunately not reproduced) is said to group the Sicilian samples on one side with Egyptians among them, and the western/central European samples on the other side with Moroccans among them. The best explanation for this arrangement is the known divide between the eastern and western Mediterranean in terms of Neolithic ancestry, which affects both the European and African coasts and runs vertically through Italy, dividing north from south.

However, the authors use this inconclusive Sicilian-Egyptian connection anyway, and for double duty. First they imply that it serves as evidence of Arab admixture, which is problematic in itself because Egyptians are not particularly good representatives of Arabs. Then in the very next paragraph, they say it confirms the earlier findings of Semino and Sandler alleging African admixture. But Egyptians are North African Caucasoids, while both of those studies deal with markers prevalent in Negroids from sub-Saharan Africa. So in the span of two paragraphs, the authors jump from "Arabs" to "Egyptians" to "North Africans" to "Africans" to "black slaves" and then back to "Arab immigrants," as if these were all synonymous. Very sloppy.

Finally, all of these supposed foreign influences in Sicily are only referred to vaguely using qualifiers and indefinite language like "seems" and "a certain degree." The adjective "strong" is used once, but we know from past experience how a word like that can be an exaggeration that actually amounts to very little admixture. So even if we were to accept the authors' outdated references and ludicrous interpretations, they would have to be taken with a grain of salt for that reason alone.

Study Clarification III

Here's an old paper from the 80s that "estimates" between 10% and 34% Negroid gene flow into Sicily based on what essentially amounts to 4 African L mtDNA markers found in a single sample of 90 people.

Study:

Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry

Semino et al. (1989)
Ann Hum Genet

Link to Abstract

Misused Quotes:

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. [...] Using the weighted mean of the frequencies of the HpaI-3/AvaII-3 marker in Senegalese and in Bantu as representative of the parental African population, the total amount of gene migration (M) from Blacks into the Sicilians was estimated according to the method of Bernstein (1931) and a value of 0.108 ± 0.053 was obtained.

[...]

The Negroid component could have been transmitted directly through the introduction of groups of Negro slaves into the island by Phoenicians and Romans and/or indirectly through Arabic migrations. [...] The only Arabs for which data on mtDNA polymorphisms are available, are from Israel (Bonnk-Tamir et al. 1986). These show an incidence of the combination of interest of 12.8%, a frequency which is compatible with a Negro contribution in the Arabic gene pool of about 30%. [...] If one assumes that Negro genes arrived in Sicily only through Arabs, a 0.344 ± 0.049 value would be obtained for the amount of Arab gene migration (M).

Although the actual genetic contribution from African populations could only be estimated as lying in between the two M values we calculated, this work shows that, whichever way these genes arrived, a substantial Negro component is present in the Sicilian gene pool.

Clarification:

This is an old study and the marker being used is not an actual haplogroup but a restriction enzyme. And the way that admixture is being "estimated" isn't very common practice in population genetics. Not only is it imprecise and unreliable, as the authors freely admit, but in this case it's based on an unusually high frequency (4.4%) of African mtDNA in Sicily, as we'll see below.

But even disregarding all that, the lower limit estimated has a margin of error of ± 5.3, so it could be as little as 5.5% (i.e. 2.75% total admixture), and the upper limit assumes huge levels of Arab admixture that are not born out by any research. Moreover, the Arab reference sample is composed of Palestinians, whom the authors "estimate" have received 30% African gene flow. Yet when Palestinians were tested with the STRUCTURE admixture program using 377 autosomal microsatellite loci, they only had 2% total African admixture (Rosenberg et al. 2002; Table 2 in the Supplementary Information), and when the same sample was typed at 642,690 SNPs, they showed no African admixture at all (Li et al. 2008; Table S1). That's a powerful example of the limitations of this study's outdated estimates.

Another study from more than a decade later, Vona et al. (2001), addressed some of these issues and the old Semino paper directly, showing that with a different sample and method, different results are obtained:

In work carried out with restriction enzymes on mtDNA in a sample of Sicilians, Semino et al. (1989) indicated the presence (4.4%) of the African complex HpaI-3/AvaII-3 (40% in Senegal and in the Bantu of South Africa). The authors hypothesized a migration of genes from Africa to Sicily, estimated at about 10%, which was introduced into the Sicilian gene pool by Black slaves brought by the Phoenicians and the Romans and/or by Arab migrations. Results at the mtDNA sequencing level, however, show no Black African influence in the Sicilian population.

Two years after that, a definitive analysis of Sicilian mtDNA was conducted by Romano et al. (2003), using a much larger sample and seven different locations. Unlike Vona et al., this study did find some Negroid maternal DNA in Sicily, but at a rate of only 0.65% (3 sequences in the sample of 465).

If we pool all of the above data — which is always a good idea — we get 7 sequences in a sample of 604, which is 1.16% maternal admixture (or 0.58% total admixture), a figure that's extremely low and comparable to admixture levels elsewhere in Europe.

This result, together with the absence of Negroid Y-chromosomes in Sicily, discredits claims that Sicilians have a Black African racial component.

Updated 11/13/2009

Study Clarification II

Dienekes Pontikos already wrote a complete deconstruction and exposé of the following study and its politically motivated authors on his old blog (also available on his website), yet the study continues to be cited regularly by Nordicists, Afrocentrists and Macedonian Nationalists in support of their racial and political agendas. So it's worth revisiting this disputed paper to summarize its scientific inaccuracies, and compare it to later, more reliable research.

Study:

HLA genes in Macedonians and the sub-Saharan origin of the Greeks

Arnaiz-Villena et al. (2001)
Tissue Antigens

Link to Full Text

Misused Quote:

Greeks are found to have a substantial relatedness to sub-Saharan (Ethiopian) people, which separate them from other Mediterranean groups. Both Greeks and Ethiopians share quasi-specific DRB1 alleles, such as *0305, *0307, *0411, *0413, *0416, *0417, *0420, *1110, *1112, *1304 and *1310. Genetic distances are closer between Greeks and Ethiopian/sub-Saharan groups than to any other Mediterranean group and finally Greeks cluster with Ethiopians/sub-Saharans in both neighbour joining dendrograms and correspondence analyses. The time period when these relationships might have occurred was ancient but uncertain and might be related to the displacement of Egyptian-Ethiopian people living in pharaonic Egypt.

Clarification:

At about the same time this study was published, its main author, Antonio Arnaiz-Villena, had a similar HLA study published in Nature, which was later dropped following criticism by three top men in the field of population genetics (Risch, Piazza and Cavalli-Sforza 2002). They rejected the conclusions Arnaiz-Villena drew based on the HLA DRB1 allele — the same marker analyzed in the present study:

Even a cursory look at the paper's diagrams and trees immediately indicates that the authors make some extraordinary claims. They used a single genetic marker, HLA DRB1, for their analysis to construct a genealogical tree and map of 28 populations from Europe, the Middle East, Africa and Japan. Using results from the analysis of a single marker, particularly one likely to have undergone selection, for the purpose of reconstructing genealogies is unreliable and unacceptable practice in population genetics.

The limitations are made evident by the authors' extraordinary observations that Greeks are very similar to Ethiopians and east Africans but very distant from other south Europeans; and that the Japanese are nearly identical to west and south Africans. It is surprising that the authors were not puzzled by these anomalous results, which contradict history, geography, anthropology and all prior population-genetic studies of these groups. Surely the ordinary process of refereeing would have saved the field from this dispute.

We believe that the paper should have been refused for publication on the simple grounds that it lacked scientific merit.

Note, however, that when analyzed properly even HLA genes, while not ideal markers for tracing ancestral relationships, demonstrate the affinity of Greeks to other Balkan and European peoples, as shown by two recent studies:

In the present study we analyzed for the first time HLA class I and class II polymorphisms defined by high-resolution typing methods.... Phylogenetic and correspondence analyses showed that Bulgarians are more closely related to Macedonians, Greeks, and Romanians than to other European populations and Middle Eastern people living near the Mediterranean.

Ivanova et al. 2002

The present study is the first to be performed in Macedonia using high-resolution sequence-based method for direct HLA typing. ... A phylogenetic tree constructed on the basis of the high-resolution data deriving from other populations revealed the clustering of Macedonians together with other Balkan populations (Greeks, Croats, Turks and Romanians) and Sardinians, close to another "European" cluster consisting of the Italian, French, Danish, Polish and Spanish populations. The included African populations grouped on the opposite side of the tree.

Petlichkovski et al. 2004

More importantly, this obvious affinity has been confirmed with the most up-do-date research on autosomal microsatellites. For example, Ayub et al. 2003 used 182 loci (as opposed to Arnaiz-Villena's one) to group several world populations based on genetic distance. Their results reveal Greeks' distance from Africans, and closeness to Basques and other Europeans:


Update 10/26/04: A new textbook written by geneticist Mark Jobling uses this very Arnaiz-Villena study as an example of shoddy research based on arbitrary interpretations. You can access relevant passages at Dienekes' blog.

Update 04/27/11: A group of academics have put together a website containing a lengthy article that addresses and thoroughly refutes this study and others like it, calling for them all to be retracted. Read more.

Study Clarification I

I see the same misunderstood studies turn up in discussions everywhere — usually posted by people who haven't bothered to read beyond the Abstract — and I get tired of having to clarify them over and over again. So occasionally I'll be using this blog to create handy clarifications for easy linking. I'll start with a study that was cited in a recent discussion.

Study:

Y-chromosome 10 locus short tandem repeat haplotypes in a population sample from Sicily Italy

Ghiani et al. (2004)
Legal Medicine

Link to Abstract

Misused Quote:

Overall, results indicate Sicily is closest genetically to the mainland Italian population but also with evidence of a significant African component in the male gene pool.

Clarification:

That's from the Abstract and, as is often the case, greatly exaggerated and somewhat misleading. The body of the study reveals that the "African component" is specifically North African, and puts the use of the adjective "significant" into perspective:

Sicily and North West Africa share five of the seven-locus haplotypes.... Furthermore, these five haplotypes are not present in any other Italian population [20–23]. The shared five haplotypes represent 5% of the total Sicilian haplotypes [that's just 2.5% admixture]. These African haplotypes most probably were introduced into Sicily sometime between the 7th and 8th century, during the island’s domination by the Arab Empire.

[...]

The UPGMA tree (Fig. 2) visualizes the relationship of the populations of the Mediterranean Basin, Europe and North West Africa using pairwise distances. The North West African and Spanish (Spain and Basques) populations occupy an outgroup position within the tree, located some distance away with respect to the other European groups, which includes Sicily. Within the European cluster there is a tight grouping containing Sicily (South Italy), Italy (from all mainland), Germany, Holland, Hungary, Lombardy (North Italy) and Tuscany (Centre Italy). Sardinia lies in a separate branch at the edge of the cluster, and well way from Sicily.

Misused Quote:

An African contribution to the Sicilian gene pool gains support from several lines of evidence. ... Bernstein [29], Ragusa [30], Barrai [31]...agreed upon the fact that there has been a low but significant level of admixture with Africa. Using mtDNA haplotype frequency, Semino et al. [32] estimated that African gene flow into Sicily ranged between 10 and 34%.

Clarification:

The authors are a bit behind the times in terms of the research they've chosen to cite. The first three studies are based on the adaptive sickle cell gene, while the mtDNA study by Semino is from the 80s and problematic. Its results have not been duplicated by subsequent studies using more contemporary mtDNA sequencing methods. For example, Simoni et al. 2000 sampled a variety of Europeans, including Sicilians, and came to this contradictory conclusion:

Note that the analysis of molecular variance failed to identify any significant differences between northern and southern Europe; allele frequencies are roughly the same in the two regions.

Other studies like Vona et al. 2001 (TREE) and McEvoy et al. 2004 (PLOT) show a similar separation between Sicilian and North African/Middle Eastern mtDNA pools. And this, as well as the above Y-chromosome data, is reinforced by superior autosomal DNA testing. See, e.g., Kandil et al. 1999 (PLOT).

[NB: Excerpts from some of the cited studies and others can be viewed on this page.]