Genetics Studies in the Greek Population
vs
Pseudoscience

 

 

What counts is not what sounds plausible, not what we would like to believe, not what one or two witnesses claim, but only what is supported by hard evidence rigorously and skeptically examined. Extraordinary claims require extraordinary evidence.

Carl Sagan

 

 

January 10, 2011.

 

 

Christos Karatzios¹, Stephen G. Miller², Costas D. Triantaphyllidis*³.

 

1- McGill University Health Centre, Division of Infectious Diseases, Montreal Children's Hospital, Montreal, Quebec, Canada.

2- University of California, Berkeley, California, USA.

3- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece.

 

Christos Karatzios MD, Assistant Professor of Paediatrics and Costas Triantaphyllidis, Professor Emeritus of Genetics and Human Genetics co-wrote the genetics part, while Stephen Miller, Professor Emeritus of Classical Archaeology wrote the history part of the article. Christos Karatzios participated in the design of the article.

 

*Corresponding author: C. Triantaphyllidis, e-mail: triant@bio.auth.gr

 

Cosigner and author of the editorial:

George P. Patrinos

Assistant Professor of Pharmacogenomics, University of Patras,

School of Health Sciences, Department of Pharmacy, Patras, Greece;

Communicating editor, Human Mutation.

 

 

 

Abstract: Arnaiz-Villena et al. published five papers making the claim of a Sub-Saharan African origin for Greeks. Hajjej et al. essentially published copies of Arnaiz-Villena's studies using the same methods, and data sets. World leading geneticists have rejected Arnaiz-Villena's methodology (the primary defect is that they relied on too few genetic markers to reliably compare populations). Numerous studies using proper methodology and multiple genetic markers are presented, showing that Greeks cluster genetically with the rest of the Europeans, disproving Arnaiz-Villena's claims. History, as well as genetics, have been misused by Arnaiz-Villena's (and by extension Hajjej's) unprofessional statements and by their omissions and misquotations of scientific and historical citations. The abuse of scientific methods has earned Arnaiz-Villena's research a citation in a genetics textbook as an example of arbitrary interpretation and a deletion of one of his papers from the scientific literature. In order to protect science from misuse, the related papers of Arnaiz-Villena et al. and Hajjej et al. should also be retracted from the scientific literature.

 

 

  Table of Contents

  I. INTRODUCTION

        The Arnaiz-Villena Studies

  II. GENETICS

        Studies that Claim the Opposite

        Arnaiz-Villena Contradicts his Conclusions

        The Studies that Copied Arnaiz-Villena

        Arnaiz-Villena's Faulty Methodology

                i. Single Locus Gene Studies are Inappropriate for Population Genetics

                ii. The Congolese Cluster with the Basques and Icelanders?

        Arnaiz-Villena's Confusing Charts

        Criticism and Rejection by the Scientific Community

                i. The Textbook that Calls it "Arbitrary Interpretation":

                ii. The three Geneticists that Call it "Unreliable and Unacceptable":

                iii. The Retraction

        The Article that Calls it "Scientific Hubris"

        Proper Methodology

        Faulty Methodology, Faulty Studies

        The Curious Omissions

                i. The Japanese appear to cluster with Sub-Saharans

                ii. The Japanese appear to cluster with Africans and Italians

                iii. African genes are present in numerous non-African populations

                iv. Misquoted Data

        Dörk does not support Arnaiz-Villena

        Greeks Cluster Genetically with other Europeans

        The African Origins of all Humans

        Arnaiz-Villena's Answer to his Critics

        Proposed Retractions

  III. HISTORY

        Arnaiz-Villena's Misquotations of Ancient Sources

        Citations of Modern Sources in Support of Inaccuracies

        Inaccurate Statements Without Ancient Documentation

        Contradictory Statements on History

  IV. CONCLUSIONS

  References

 

 

 

 

---

 

 

I. INTRODUCTION

 

The Arnaiz-Villena Studies

 

 

There are five human populations genetic studies from A. Arnaiz-Villena et al. whose authors make the claim of a Sub-Saharan African origin for Greeks.

 

1) Arnaiz-Villena et al. (2001a) [1] (Universidad Complutense in Madrid and Tissue Typing Laboratory in Skopje) analysed the HLA genes' (HLA-A, -B, -DR, -DQ) variability and haplotypes [2] in individuals from the FYROM (Vardar Slavs [3]). However, using results from the analysis of only a single locus (the HLA-DRB1) they constructed a genealogical tree and map of 26 populations from Europe, the Middle East and Africa (FIG. 1). They then claimed that:

• Vardar Slavs show the closest genetic relatedness with Cretan Greeks, and are closely related to other Mediterraneans but not to mainland Greeks, who are geographically closer.
• Greeks do not belong to the "older" Mediterranean peoples, and are genetically related more to Sub-Saharan (Ethiopian and western African) people. Arnaiz-Villena offers a historical hypothesis that some Sub-Saharans had migrated to Greece during antiquity, but not to Crete.

 

 

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FIG. 1 - Arnaiz-Villena et al. (2001a) [1], figure 1. Dendogram constructed on the basis of genetic distances based on HLA-DRB1 allele frequencies.

 

 

2) Arnaiz-Villena et al. (2001b) [4] examined the genetic relationships of Palestinians with other Mediterranean populations. They made exactly the same claims about the relatedness of Vardar Slavs to Cretan Greeks, and they showed that the Greeks and Japanese cluster with various Sub-Saharan Africans. Additionally, they claimed that Jews and Palestinians share a very similar HLA genetic pool. Thus, they claimed that Jewish – Palestinian rivalry is based on cultural and religious, but not genetic, differences. (This paper was subsequently retracted)

 

3) Arnaiz-Villena et al. (2002) [5] used the results from the previous two papers and made an effort to explain the conclusions about the relatedness of Greeks with Sub-Saharans by proposing a revision of history as a means to understand the above results. Furthermore, they show the Italians, Egyptians, San (Bushmen) and Japanese to cluster together.

 

4) Arnaiz-Villena et al. (2001c) [6] published their conclusions on the genetic relatedness of Turks, Kurds and Armenians to each other and to other Mediterranean populations. Despite the study's intended focus on the Kurds, Turks, and Armenians, Arnaiz-Villena et al. curiously spend a few paragraphs discussing the purported Greek and Sub-Saharan relatedness. They refer to Arnaiz-Villena's original study [1] and discuss the "substantial" Sub-Saharan DNA that Greeks carry.

 

5) Arnaiz-Villena et al. (2001d) [7] published a study about the Usko-Mediterranean peoples. Again they showed the Greeks to cluster with Sub-Saharan Africans and the Italians, Egyptians, San (Bushmen) and Japanese to cluster together.

 

All of the above studies used the same methodology [8] and the same data samples [1,4,5,6,7].

 

 

II. GENETICS

 

Studies that Claim the Opposite

 

The following two studies claim that Vardar Slavs and Greeks are closely related. They both used a methodology similar to Arnaiz-Villena's, and analyzed the same genetic marker: i.e. HLA-DRB1.

 

1) Ivanova M. et al. (2002) [9] from the Medical University of Sofia claim that Bulgarians, Vardar Slavs and Greeks are very close genetically, with respect to other European populations and Middle Eastern people living near the Mediterranean (FIG. 2, FIG. 3).

 

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FIG. 2 - From Ivanova M. et al. (2002) [9], figure 1. Dendrogram based on HLA-DRB1 allele frequencies. The Bulgarians appear to be closer to Vardar Slavs and Greeks.

 

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FIG. 3 - From Ivanova M. et al. (2002) [9], figure 2. Correspondence analysis showing the relationships between Bulgarians and other populations according to HLA-DRB1 allele frequencies. The Bulgarians appear to be closer to Vardar Slavs, Greeks and Romanians.

 

2) Petlichkovski A et al. (2004) [10] from the University of "Ss. Kiril and Metodij" in Skopje conclude that the samples from FYROM, Greece and Croatia cluster in the same group, while North African populations grouped on the opposite side of the phylogenetic tree [11]. Cretan Greeks group closest with Bulgarians (FIG. 4).

 

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FIG. 4 - From Petlichkovski A et al. (2004) [10], figure 1. Phylogenetic tree constructed on the basis of genetic distances based on HLA-DRB1 allele frequencies. Samples from FYROM, Greece and Croatia cluster together.

 

The results from the above two studies are contrary to Arnaiz-Villena's. If all these studies are correct, then are Vardar Slavs and Greeks related [9,10] or not [1,4,5,6,7] ? If all those people are closely related (from FYROM, Greece, Bulgaria, Croatia and Romania) [9,10], then they must be related to Sub-Saharan people as well [1,4,5,6,7].

 

 

Arnaiz-Villena Contradicts his Conclusions

 

 

I. Arnaiz-Villena et al. (2001c) [6], constructed a dendrogram (FIG. 5) by using results from four genetic markers (HLA-A, -B, -DR and -DQ), showing the Greeks to cluster with the Italians. This contradicts Arnaiz-Villena's conclusion that the Greeks cluster with Sub-Saharans and not with Mediterraneans [1,4,5,6,7].

 

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FIG. 5 - From Arnaiz-Villena et al. (2001c) [6], figure 2. Dendrogram constructed on the basis of genetic distances based on HLA-A, - B, -DRB1 and DQ allele frequencies. The Greeks are shown to be close to the Italians. Please note this dendrogram yields low confidence limits (bootstrap values) in most cases.

 

II. Arnaiz-Villena et al. (2003) [12], again using two genetic markers (HLA-DR, and -DQ), constructed a dendrogram (FIG. 6) showing the Vardar Slavs to have the closest genetic distance with Bulgarians, while the Cretan Greeks are placed genetically very far away. This contradicts Arnaiz-Villena's conclusion that the Vardar Slavs are genetically very close to Cretan Greeks [1,4,5,7].

 

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FIG. 6 - From Arnaiz-Villena et al. (2003) [12], figure 4. Here the Vardar Slavs are shown to have the closest genetic distance with Bulgarians. (The red arrows are added by the editor). Please note this dendrogram yields low confidence limits (bootstrap values) in most cases.

 

Still however, none of those studies' dendrograms or correspondence analysis are acceptable from the population genetics perspective because they use faulty methodology.

 

The Studies that Copied Arnaiz-Villena

 

The following studies repeated what Arnaiz-Villena had already done: Same data and same methodology; therefore, the same results were obtained.

 

Hajjej A. et al. (2006a) [13], Hajjej A. et al. (2006b) [14] and Hajjej A. et al. (2011) [72] claimed that their studies confirm the relatedness of Greeks to various Sub-Saharan African populations.

 

Same Data : These studies used the same sample data as Arnaiz-Villena et al. (2001a) [1], and Arnaiz-Villena et al. (2001b) [4], for Vardar Slavs, Greeks and Sub-Saharan Africans [1,4,13,14,72].

 

Hajjej A. et al. actually reported that they examined a subset of the Greeks and Sub-Saharans, which makes these studies slightly less powered to detect differences when compared to Arnaiz-Villena's studies. They reported examining 85 samples from "Greeks (Attica / Aegean)" [13,14] or "Greeks" [72], taken from J. Clayton and C. Lonjou [15]. On the other hand Arnaiz-Villena et al. reported 85 samples from "Greeks (Aegean)" and 96 samples from "Greeks (Attica)" [1,4], taken from the same source. Hajjej A. et al. either examined subsets as mentioned above, or simply they made a mistake in reporting the data they examined.

 

However, if the original source of the sample data (J. Clayton and C. Lonjou [15]) is examined, it is unclear from what population of Greeks Hajjej et al. have used samples. The original data is divided by J. Clayton and C. Lonjou [15] into the following groups:

• Greeks (Attica): 100 samples of which 96 are reported in the concluding anthropology tables in J. Clayton and C. Lonjou [15] (also see FIG. 17 - FIG. 20).
  
• Greeks (mainland, islands; "all over"): 104 of which 98 are reported in the concluding anthropology tables in J. Clayton and C. Lonjou [15] (also see FIG. 17 - FIG. 20).

 

Assuming that Arnaiz-Villena et al. (and by extension Hajjej et al.) did not include the Greek Pontii, Greek Pomaki, and Greek Cypriot samples from J. Clayton and C. Lonjou [15] (66, 100, and 105 samples respectively) in their analyses, we are to surmise that each investigating group worked with a subset of the available samples from the original data archive of "Attica" and "mainland/island" Greeks [15]. However, without proper explanation, there is a lack of transparency in the selection method and the potential for a selection bias can not be ignored.

 

Same Methodology [8] : All dendrograms and correspondence analysis graphs in the three Hajjej A. et al. studies that claimed to confirm the relatedness of Greeks to various Sub-Saharan African populations, used a single gene marker (the HLA-DRB1). These analyses had previously been done by Arnaiz-Villena et al. (2001a) [1] and Arnaiz-Villena et al. (2001b) [4] :

 

Table 1 - Comparison between Hajjej A. et al. and Arnaiz-Villena et al. strudies.

 

 

The genetic similarities detected between Greeks and Sub-Saharan Africans in these studies can be explained by the fact that anybody who uses the same data samples and same methodology/analysis will reproduce the same results. Therefore the above findings in addition to Arnaiz-Villena's are of low scientific merit.

 

There is actually a single dendrogram from Hajjej A. et al. (2006b) [14], where they analysed Greeks using slightly different methodology from Arnaiz-Villena: they used 3 genes (HLA-A, -B and -DRB1), (FIG. 7). However, in this dendrogram the Greeks appear to cluster with the Cretan Greeks, Vardar Slavs and Rimaibe (Sub-Saharans).

 

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FIG. 7 - From Hajjej A. et al. (2006b) [14], figure 1. Here the Greeks appear to cluster with the Cretan Greeks, Vardar Slavs and Rimaibe (Sub-Saharans). Please note this dendrogram yields low confidence limits (bootstrap values) in most cases.

 

Still, none of those studies are acceptable from the population genetics perspective because they use faulty methodology.

 

 

Arnaiz-Villena's Faulty Methodology

 

i. Single Locus Gene Studies are Inappropriate for Population Genetics

 

Theoretical work suggests that data from multiple loci provide better estimates of population genetic parameters, than do single loci.

 

Single locus gene studies are inappropriate for population genetics. This has been attested to many times by many geneticists, that these are "insufficient for evolutionary analyses" (Cavalli-Sforza and Feldman [16], Cavalli-Sforza et al. [27]). Consequently, the primary defect of Arnaiz-Villena's studies is that they relied mostly on one and in some cases two genetic markers. Furthermore, they analyzed the HLA gene, which is under strong selection. This methodology often leads to large errors and arbitrary results [17,18,19].

 

 

ii. The Congolese Cluster with the Basques and Icelanders?

 

Here is another erroneous result produced by the HLA system: Piazza and Viganotti conducted a worldwide anthropological genetics study, published in 1972 [20]. A part of this study that used HLA genes, found the Basques and the Icelanders to have the closest relation with the Congolese (FIG. 8). According to Piazza and Viganotti, the anomalous results were due to the low amount of gene markers examined for the Congolese.

 

Similarly, Arnaiz-Villena et al., and Hajjej et al. use too few HLA gene markers to come to reliable conclusions. Therefore one can only conclude that the clustering of Greeks with Sub-Saharans is wrong.

 

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FIG. 8 - From Piazza and Viganotti [20], page 735, figure 2a. Dendrogram based on HLA polymorphism. The Congolese appear to have the closest relation with the Basques and the Icelanders. (The red arrow is added by the editor).

 

According to Mourant et al. (1976) [21], the HLA system was the most powerful single genetical system for population genetics at that time (in 1976). They did recognize though its shortcomings and the possible erroneous results and gave as example the worldwide study conducted by Piazza and Viganotti [20] that classified the Congolese with the Basques and the Icelanders (FIG. 8).

 

Currently population genetics studies are considered reliable only if they follow the guidelines of proper methodology.

 

 

 

Arnaiz-Villena's Confusing Charts

 

 

The arbitrary groupings of the Senegalese:

 

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FIG. 9 - From Arnaiz-Villena et al. (2001a) [1], figure 2. Correspondence analysis showing the relationship between Mediterranean, and Sub-Saharan and Black African populations according to HLA-DRB1 allele frequencies.

 

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FIG. 10 - From Arnaiz-Villena et al. (2001b) [4], figure 5. Note: This is the correspondence analysis chart based on HLA-DRB1 allele frequency data that criticized by the genetics textbook "Human Evolutionary Genetics: Origins, Peoples & Disease" [22] for arbitrary selection of the groupings.

 

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FIG. 11 - From Arnaiz-Villena et al. (2001b) [4], figure 6. Correspondence analysis showing the relationship among Palestinians, West Mediterraneans, East Mediterraneans, Greeks and Sub-Saharan populations and Blacks according to to HLA-DR and DQ allele frequencies

 

The Senegalese: In FIG. 9 and FIG. 11, the San (Bushmen), South-African Blacks and Senegalese are grouped together yet in FIG. 10 they are separate. The following question arises from this: Are the Senegalese genetically related to San (Bushmen) and South-African Blacks? Yes [1,4] or No [4]?

 

It is very interesting that although graphs FIG. 10 and FIG. 11 are taken from the same study (Arnaiz-Villena et al. (2001b) [4]), they contradict each other.

 

 

The arbitrary grouping of the Japanese:

 

In FIG. 10, the Japanese are plotted very close to the San (Bushmen) and South-African Blacks group. In FIG. 11, the Japanese are plotted very close to the San (Bushmen) and the rest of the Africans group. However the Japanese are grouped separate from those populations. The criteria for this separate grouping are not obvious and Arnaiz-Villena et al. (2001b) [4], fail to discuss them.

 

 

The arbitrary groupings of the Oromo and Amhara (Sub-Saharan populations):

 

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FIG. 12 - From Arnaiz-Villena et al. (2001a) [1], figure 3. Correspondence analysis showing the relationship among West Mediterraneans (green), East Mediterraneans (orange), Greeks and Sub-Saharan populations (red) and Blacks (grey) according to HLA-DR and DQ allele frequencies. The same chart appears in Arnaiz-Villena et al. (2002) [5], figure 4 (where all groups are colored white).

 

In FIG. 9 and FIG. 10, the Greeks and Sub-Saharans (Oromo, Amhara, Fulani, Mossi and Rimaibe) are grouped together. Yet in FIG. 11 and FIG. 12 the Oromo and Amhara are very far away from the rest, therefore they need to be grouped separately. Arnaiz-Villena et al. accordingly, place them in a different circle. However in FIG. 12 they use the same colour (red) for all the populations on the right side of the analysis figure, in an attempt to link them together.

 

So again a question arises: Are the Oromo and Amhara (Sub-Saharans) genetically related to Greeks, Fulani, Mossi and Rimaibe? Yes [1,4] or No [1,4,5] ?

It is very revealing that although graphs FIG. 9 and FIG. 12 are taken from the same study (Arnaiz-Villena et al. (2001a) [1]), they contradict each other.

 

 

The Greeks, San (Bushmen) and Japanese are grouped together:

 

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FIG. 13 - From Arnaiz-Villena et al. (2001c) [6], figure 4. Correspondence analysis showing the relationship between Turkish and other populations according to HLA-DR and DQ allele frequencies.

 

Arnaiz-Villena et al. (2001c) [6] constructed a correspondence analysis graph (FIG. 13) where the Greeks, San (Bushmen) and Japanese are grouped together. In the same graph, the Cretan Greeks and Italians are placed very far away, in two different groups. In the very same study they constructed a dendrogram (FIG. 5) showing the Greeks to cluster with the Cretan Greeks and Italians. However they fail to give satisfactory explanation for these extraordinary and contradictory results.

 

 

 

Criticism and Rejection by the Scientific Community

 

 

i. The Textbook that Calls it "Arbitrary Interpretation":

 

In the genetics textbook "Human Evolutionary Genetics: Origins, Peoples & Disease" (chapter 1, page 12), Arnaiz-Villena's work on the alleged "Sub-Saharan" origin of the Greeks is used as an example of arbitrary interpretation [22] :

The grouping chosen by Arnaiz-Villena et al. (2001) is (d) (adduced as support for a Sub-Saharan origin for the Greeks) but is essentially arbitrary. Why is it preferred to alternative groupings shown in (b) and (c)? If the population origins were unknown when the groupings were made, would it affect the outcome? Note that this locus is generally regarded as being under strong selection. *

 

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FIG. 14 - From the textbook "Human Evolutionary Genetics: Origins, Peoples & Disease" [22], chapter 1, page 12, figure 1.5.

 

In the upper left corner (a) you can see the populations according to Arnaiz-Villena et al. (2001b) [4]. These populations can be grouped in many different ways and three of them are displayed here (b,c,d). Arnaiz-Villena et al. (2001b) chose (d), however they gave no justification for their selection.

 

 

ii. The three Geneticists that Call it "Unreliable and Unacceptable":

 

This is what the distinguished geneticists Neil Risch, Alberto Piazza and L. L. Cavalli-Sforza had to say about the Jews/Palestinians study [4] and Arnaiz-Villena's methods [17]:

 

Dropped Genetics Paper Lacked Scientific Merit

Sir – Even though the controversial withdrawal of a paper on the genetic relatedness of Palestinians and Jews by the journal Human Immunology (see Nature 414, 382; 2001) is a minor episode compared with the tragedies caused by ethnic/religious conflicts over past decades, the issues involved are worth revisiting.

The stated purpose of the paper by Antonio Arnaiz-Villena et al. was to "examine the genetic relationships between the Palestinians and their neighbors (particularly the Jews) in order to: (1) discover the Palestinian origins, and (2) explain the historic basis of the present ... conflict between Palestinians and other Muslim countries with Israelite Jews".

They conclude: "Jews and Palestinians share a very similar HLA genetic pool that supports a common ancient Canaanite origin. Therefore, the origin of the long-lasting Jewish–Palestinian hostility is the fight for land in ancient times."

It is difficult to believe that knowledge of genes may help to explain the present conflict. Although population genetics can address issues of relatedness of populations, mating patterns, migrations and so on, obviously it cannot provide evidence about reasons for conflicts between people.

Our primary concern, however, is that the authors might be perceived to have been discriminated against for political, as opposed to legitimate scientific, reasons.

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. *

 

Neil Risch and L. Luca Cavalli-Sforza
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

Alberto Piazza
Department of Genetics, Biology and Biochemistry, University of Torino, Via Santena 19, 10126 Torino, Italy

 

 

iii. The Retraction

 

The Jews/Palestinians paper raised such a wave of criticism in the scientific community, that it was retracted from the scientific literature.

 

The Editor in chief of the Human Immunology Journal issued a retraction of the Arnaiz-Villena et al. (2001b) [4] paper whose editors also happened to be its authors (Arnaiz-Villena and Martinez-Laso). Below is the text of the editorial excerpted verbatim [23].

In the past it has been the tradition of the Editorial office to leave the editorial judgment for special volume to the guest editors. This has also been the case with the issue on Anthropology and Genetic Markers edited by Antonio Arnaiz-Villena with the assistance of Luis Allende and Jordge Martinez-Laso. As Editor-in-Chief, I did not read Dr. Antonio Arnaiz-Villena's own paper in Human Immunology in depth until the issue was published.

I regret deeply that the authors have confounded the elegant analysis of the historic basis of the people of the Mediterranean Basin with a political viewpoint representing only one side of a complex political and historical issue. While the authors have the right to their political opinion, they have no special expertise in this area and their views have no place in a scientific journal. The Editors deplore the inappropriate use of a scientific journal for a political agenda and apologize to the readers. This paper has been deleted from the scientific literature.

 

Since Antonio Arnaiz-Villena was a guest editor for Human Immunology when his paper on the population genetics of Jews/Palestinians [4] was accepted for publication in Human Immunology [24], the potential for an editing bias cannot be ignored.

 

 

 

The Article that Calls it "Scientific Hubris"

 

According to "The Gene Wars" article [25]:

• The Neil Risch, Alberto Piazza and L. L. Cavalli-Sforza critique [17] applies equally to Arnaiz-Villena's Greeks/Sub-Saharans [1] and his Jews/Palestinians [4] studies, since both papers were based on the same data set and used the same techniques.
• The conclusions of the Greeks/Sub-Saharans study are "scientific hubris".
• The reliance on a single genetic marker (the HLA DRB1 gene) is what makes the study inaccurate.

• Experts suggest that 60 genetic markers would be needed for 90% accuracy and 100-160 genetic markers for 99% accuracy, as stated by Bamshad et al. [26].

 

 

 

Proper Methodology

 

When studying the long term evolution and phylogeny of populations, the following guidelines should be observed:

• When analyzing genes that are subject to strong natural selection and frequent mutation, then a minimum of 20 and upwards of 100 – 160 unlinked [27,28] genes should be used (for 99% accuracy) [17,18,19,26,29,30,31]. If this is not done, the risk of large errors and arbitrary results is high [18]. HLA genes fall into this category.

• When analyzing autosomal genes [32] that are not under strong natural selection (have neutral properties under natural selection), then a smaller number of genes may suffice [33,34,35,36,37,38]. Likewise many scientists also presume that the Y-chromosome and the mtDNA genetic loci are not affected by natural selection, and that the major process responsible for changes in these genes has been random individual mutation. This does not affect the process of evolution of the Y and mtDNA genes on a major scale. As a result, Y-chromosomal and mtDNA genes can be used reliably to ascertain the genetic origins of populations [16,34,39].

 

 

Multiple Autosomal Gene Markers

 

In the study of population genetics and phylogeny, the generally accepted rule according to most experts is the use of multiple gene markers. Before the year 2000, ten loci was the minimum requirement for a population analysis. Ever since, some experts suggest a minimum of 20 genes [18,19,27,30,31] whereas others suggest 60 genetic markers would be needed for 90% accuracy and 100-160 genetic markers for 99% accuracy [26].

By using HLA blood leukocyte genes as markers for genetic relatedness (especially only one or two genes), one cannot make assumptions about whole populations being more or less related to one another. Unfortunately, this is what happens with the Arnaiz-Villena and Hajjej studies. In a December 2000 perspective manuscript, Evolution (The International Journal of Organic Evolution belonging to The Society for the Study of Evolution) published this statement: "a move away from single-locus studies to multilocus, multispecies studies should increasingly dominate comparative phylogeography." [19].

 

 

Y-chromosomal and Mitochondrial Multiple DNA Gene Markers

 

The genes contained on the Y chromosome and in mitochondrial DNA (mtDNA) can be used to trace one's origins through lineages [16,34,39]. The varieties of genes are classified into groups called haplogroups [40]. The Y chromosome is transmitted from fathers to sons and a patrilineal lineage can be determined using this. The mitochondria are small structures that provide energy to all cells and they contain their own DNA. They are transmitted in a matrilineal manner and therefore matrilineal tracing can be done using their DNA. The Y chromosomal haplogroups can be especially used as gene markers to determine a person's ethnic origins [33,34,39].

 

MtDNA is widely accepted as a marker for tracing the evolution of humans out of Africa and into Europe and the rest of the World using a matrilineal line – the original mtDNA being termed "the mitochondrial Eve" [16,38]. Various studies have been performed using mtDNA to establish genetic relationships between populations [41,42,43,44]. Like Y chromosomal DNA, it too is classified into haplogroups with various peoples having certain haplogroups. There are also African and non-African haplogroups that have been identified. Examples include haplogroup H (non-African European) and L (Sub-Saharan African).

 

Faulty Methodology, Faulty Studies

 

 

Based on the defined current proper methodology and the analysis presented above, it can be concluded that none of the following human population genetic studies are accurate enough to warrant extraordinary claims about the origin and relationship of populations:

• Arnaiz-Villena et al. (2001a) [1].
• Arnaiz-Villena et al. (2001b) [4].
• Arnaiz-Villena et al. (2001c) [6].
• Arnaiz-Villena et al. (2001d) [7].
• Arnaiz-Villena et al. (2002) [5].
• Ivanova M. et al. (2002) [9].
• Petlichkovski A. et al. (2004) [10,11].
• Hajjej A. et al. (2006a) [13].
• Hajjej A. et al. (2006b) [14].
• Hajjej A. et al. (2011) [72].

 

 

The Curious Omissions

 

i. The Japanese appear to cluster with Sub-Saharans

 

Arnaiz-Villena et al. (2001b) [4], present a dendrogram (FIG. 15) where the Japanese appear to cluster with Sub-Saharan Africans (the Senegalese, South-African Blacks and San). Therefore those Sub-Saharans appear to be genetically closer to the Japanese, than to the rest of the Sub-Saharan Africans (Oromo, Amhara, Fulani, Rimaibe and Mossi) who appear to cluster with the Greeks. However, there is no explanation for this extraordinary finding anywhere in their manuscript.

Note: this is exactly the argument made by the three geneticists in their critique to Arnaiz-Villena.

 

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FIG. 15 - From Arnaiz-Villena et al. (2001b) [4], figure 4. Genetic distances were calculated by using HLA-DRB1 allele frequencies (high resolution). In the dendrogram, the Japanese appear to cluster with the Senegalese, South-African Blacks and San.

 

 

ii. The Japanese appear to cluster with Africans and Italians

 

Furthermore, Arnaiz-Villena et al. (2002) [5], present a dendrogram (FIG. 16) where the Italians, Egyptians, San and Japanese appear to cluster together. However, there is still no explanation for this extraordinary finding anywhere in their manuscript.

 

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FIG. 16 - From Arnaiz-Villena et al. (2002) [5], figure 3. Genetic distances were calculated by using HLA-DR and - DQ (generic typing). Please note this dendrogram yields low confidence limits (bootstrap values) in most cases. In the dendrogram, the Italians, Egyptians, San and Japanese appear to cluster together.

 

The following questions arise from the above:

• Since all serious scientific researchers provide explanations for all their findings, why did they not provide any on this?
• Both the Greeks/Sub-Saharans, and the Italians/Africans/Japanese relatedness are extraordinary findings. Why did Arnaiz-Villena allocate so much of their papers to explain the first finding while ignoring the second?
• The only implication is that this is an arbitrary finding. If so, then why can't the finding of Greek/Sub-Saharan relatedness also be arbitrary?

• In population genetics research it is common practice to use data from previously published large populations. Why didn't they also use a previously existing and extensive Greek HLA databank (246 samples) published by Papassavas E. et al. [45]?

 

 

iii. African genes are present in numerous non-African populations

 

Arnaiz-Villena et al. curiously omit to mention or adequately discuss that there are many alleles that are shared by Sub-Saharan people and distant native populations in Europe, America and Pacific islands.

 

 

Arnaiz-Villena et al. [1,4] cite J. Clayton and C. Lonjou [15] as the source of their data for the sharing of HLA gene alleles between Greeks and Sub-Saharan people. The same source [15] reports many more African genes present in non-African populations, but not shared by Greeks (see the following Table 2, as well as FIG. 17, FIG. 18, FIG. 19, FIG. 20 and Table 3). However Arnaiz-Villena et al. [1,4] fail to mention them.

 

 

Table 2 - African genes present in non-African populations (but not shared by Greeks) reported by Clayton and Lonjou [15].

HLA DRB Allele	African populations	non African populations
DRB1*0306	Rimaibe (0.8%) Fulani (0.2%) Mossi (0.8%)	Myanmar Hoton (Asia, 0.8%) Hungarians (0.4%) Latin American Mestizos (4.1%)
DRB1*0309	Fulani (0.4%) Mossi (0.5%)	Myanmar Hoton (Asia, 6.1%) Hungarians (0.3%)
DRB1*08042	Rimaibe (0.9%) Fulani (0.9%) Mossi (0.6%)	Latin American Mestizos (2%)
DRB1*1103	Rimaibe (0.3%)	Hvar Island (Croatia, 0.4%) Orcadians (United Kingdom, 1.1%)
DRB1*1113	Rimaibe (0.3%)	Hvar Island (Croatia, 0.4%)
DRB1*1120	Noba (Sudan, 2.2%) Oromo (0.5%) Rimaibe (2.1%) Fulani (2.2%) Mossi (2%)	Island of KRK (Eastern Europe, 0.2%) Hvar Island (Croatia, 0.1%)
DRB1*1121	Rimaibe (2.1%) Fulani (2.2%) Mossi (2%)	Latin American Mestizos (2%)
DRB1*1202	Mossi (0.3%)	Myanmar Hoton (Asia, 1.6%) Thai-Chinese (1.4%) Romanian (0.5%) Hungarians (1.8%)
DRB1*1306	Rimaibe (0.8%) Fulani (0.2%) Mossi (0.8%)	Hvar Island (Croatia, 0.4%) Hungarians (0.4%)
DRB1*1316	Amhara (0.8%) Rimaibe (1.9%) Fulani (4.9%) Mossi (3.1%)	Hungarians (1.6%) Spanish (0.7%)
DRB1*1317	Noba (Sudan, 1.6%)	Hungarians (0.9%)
DRB1*1321	Fulani (0.4%) Mossi (0.5%)	Hvar Island (Croatia, 1%) Hungarians (0.6%)
DRB1*1324	Fulani (0.4%) Mossi (0.5%)	Latin American Mestizos (2.4%)
DRB1*1326	Rimaibe (0.8%) Fulani (0.2%) Mossi (0.8%)	Hvar Island (Croatia, 0.4%) Hungarians (0.7%)
DRB1*1408	Noba (Sudan, 1.8%)	Hungarians (0.7%)
DRB1*1413	Fulani (0.3%)	Hungarians (0.9%)
DRB1*1423	Noba (Sudan, 4%)	Hungarians (0.4%)
DRB5*0101	Noba (Sudan, 0.9%) Oromo (3.1%) Fulani (0.1%) Cameroonians (3.3%)	Myanmar Hoton (Asia, 4.5%) Turkish (5.5%) Orcadians (United Kingdom, 19.9%)

 

 

Examples of HLA-DRB1 alleles that are shared by Sub-Saharan and other populations reported in Arnaiz-Villena et al. (2001a) [1]:

• Some of the common HLA-DRB1 alleles between Greeks and Sub-Saharan Africans, are also present in Hungarians, Lebanese, Croatians from Hvar Island, Amerindians, and some Pacific peoples (see footnote to Table 5 in [1]) (FIG. 21). It is interesting that the only discussion by Arnaiz-Villena et al. (2001a) [1] for those populations is: "Some of these alleles are sporadically present in other populations without any relationships among them".
• The HLA extended gene haplotype A*01-B*52-DRB1*1502-DQB1*0601 is found in Cretan Greeks, Vardar Slavs, Spaniards and Italians and they state their possible origin is North African-Mediterranean (see Table 4 in [1]).

 

 

The question then remains: Why are the genes that are shared among Greeks and Sub-Saharans "quasi-specific" and are the basis for an anthropology hypothesis yet the genes shared among Sub-Saharans and Hungarians, Croatians, Latin American Mestizos or Orcadians of the United Kingdom are inadequately discussed or not mentioned at all?

 

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FIG. 17 - From Clayton and Lonjou [15], page 676. HLA-DRB1 allele frequencies in different populations.

 

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FIG. 18 - From Clayton and Lonjou [15], page 677. HLA-DRB1 allele frequencies in different populations.

 

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FIG. 19 - From Clayton and Lonjou [15], page 678. HLA-DRB1 allele frequencies in different populations.

 

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FIG. 20 - From Clayton and Lonjou [15], page 679. HLA-DRB5 allele frequencies in different populations.

 

Table 3 - Legend to the populations from Clayton and Lonjou [15] tables (FIG. 17 - FIG. 20).

Code	Region	Population Name
112-hot	Asia	Hoton
85-tha	Asia	Thai-Chinese
67-rom	Eastern Europe	Romanian
19-krk	Eastern Europe	Island of KRK
20-hva	Eastern Europe	Island of Hvar
36-hun	Eastern Europe	Hungarian
165-gre	Mediterranean	Greeks
34-gre	Mediterranean	Greek
166-gre	Mediterranean	Greek Cypriots
84-nob	North Africa	Noba Sudan
185-yuk	South and Central America	Yukpa
199-mes	South and Central America	Latin American Mestizos
154-oro	Sub-Saharan Africa	Oromo
155-amh	Sub-Saharan Africa	Amhara
231-rim	Sub-Saharan Africa	Rimaibe
233-ful	Sub-Saharan Africa	Fulani
232-mos	Sub-Saharan Africa	Mossi
145-lib	South-West Asia	Lebanese
82-spa	Western Europe	Spanish
62-ork	Western Europe	Orcadian

 

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FIG. 21 - From Arnaiz-Villena et al. (2001a) [1], table 5.

 

 

iv. Misquoted Data

 

Arnaiz-Villena et al. (2001a) [1] on table 5 present common HLA-DRB1 alleles between Greeks and Sub-Saharan Africans (FIG. 21) and cite J. Clayton and C. Lonjou [15] as the source of their data. In the footnote of table 5, Arnaiz-Villena et al. (2001a) [1] report other populations that also share those alleles. However there are discrepancies (Table 4) between the footnote of table 5 and the cited source:

 

Table 4 - Discrepancies between Arnaiz-Villena et al. (2001a) [1] and their cited source J. Clayton and C. Lonjou [15].

HLA DRB Allele	Arnaiz-Villena et al. (2001a) [1] report (footnote of Table 5) (FIG. 21):	J. Clayton and C. Lonjou [15] report (FIG. 17, FIG. 18, FIG. 19, FIG. 20):
DRB1*0305	"Not found in other populations"	Also present in: Hungarians (0.3 %)
DRB1*0411	"Found in Amerindians and some Pacific peoples"	Apart from: Amerindian Yukpa (64.6%) Also present in: Hvar Island (Croatia) (0.4%) Latin American Mestizos (2.0%)
DRB1*0413	"Not found in other populations"	Also present in: Latin American Mestizos (4.6%)
DRB1*1310	"Also present in Hva Island (Croatia, 1.0%)"	Apart from: Hvar Island (Croatia, 1.0%) Also present in: Hungarians (0.4 %)

 

From Table 4, we conclude:

• There are five more instances where non-African populations share some of the common alleles between Greeks and Sub-Saharans, and Arnaiz-Villena et al. (2001a) [1] fail to report.
• Arnaiz-Villena et al. (2001a) [1] report that three alleles (DRB1-0305, DRB1-0413 and DRB1-1304) are shared only between Greeks and Sub-Saharans. However, according to their cited source, DRB1-0305 and DRB1-0413 are shared by other non-African populations too.

 

 

Dörk does not support Arnaiz-Villena

 

Arnaiz-Villena uses Dörk as supporting evidence, although Dörk's findings and conclusions do not support him.

 

Arnaiz-Villena et al. (2002) [5] state:

"Other Negroid genes have also been found in Greeks. They are the only Causasoid population who bears cystic fibrosis mutations typical of Black Africans (Chromosome 7). See Dork, et al. In Am. J. Hum. Genet, 1998: 63: 656–682 [sic]." [5]

 

Arnaiz-Villena et al. (2002) [5], however, do not tell the whole story: In Am. J. Hum. Genet. 1998, 63: 656-662 [46], Dörk's conclusions do not support Arnaiz-Villena's conclusions:

 

Arnaiz-Villena claims:

1. There is a "substantial" African contribution to Greek DNA (but not Greek Cretan DNA), therefore the Greeks are genetically different and do not cluster with other Mediterraneans [1,4,5,6,7].
2. The explanation for the above (African contribution to Greek DNA) is that some Sub-Saharans had migrated to Greece during antiquity, while they claim that the supposedly strong Minoan sea empire may have hindered foreigners' establishment in Crete, if the alleged African invasion occurred in Minoan times [1,4,5,7].

 

However Dörk states that:

1. There is an African-type of cystic fibrosis mutation found in Greeks, but it is so rare that it was detected only in three Greek families [46].
2. "Historical contacts-for example, under Alexander the Great or during the ancient Minoan civilization-may provide an explanation for the common ancestry of disease mutations in these ethnically diverse populations."[46]

 

An African gene detected in only three greek families does not support a "substantial African contribution to Greek DNA".

 

 

 

Greeks Cluster Genetically with other Europeans

 

No multiple gene-marker, Y chromosomal, or mtDNA analysis has ever duplicated Arnaiz-Villena's results. Contrary to his conclusion, Greeks cluster genetically with other Europeans and Japanese cluster with other Southeast Asian groups.

 

We have selected a number of publications and studies based on the accuracy of their methodology. These studies fulfill at least two of the following criteria:

• At least 20 and upwards of 100 autosomal gene markers.
• Many Y chromosomal genes as markers.
• Many mtDNA genes as markers.

 

 

Multiple Autosomal Gene Markers

 

In the "The History and Geography of Human Genes" Cavalli-Sforza, Menozzi and Piazza [47] studied the relatedness of Greeks with other European and Mediterranean populations based on 88 to 120 loci (FIG. 22, FIG. 23, FIG. 24).

 

Ayub et al. [48] used 182 autosomal gene markers and 168 individuals representing 19 different human populations (FIG. 25).

 

Auton et al. [49] used 443,434 autosomal single-nucleotide polymorphisms (SNPs) [50] and 3,845 individuals representing four continental regions.

Bauchet et al. [51] studied the genetic relationship of European (including 8 Greeks), North and Sub-Saharan African, Armenian, Middle Eastern, Indian and Central Asian populations using 9,724 autosomal single-nucleotide polymorphisms (SNPs). They repeated the statistical analysis using two different approaches (principal coordinate analysis/PCoA, and the Structure software program).

 

Oscar Lao et al. [52] documented the genetic relatedness of 2,514 Europeans (including 51 Greeks from Macedonia (northern Greece)). They used 309,790 autosomal single-nucleotide polymorphisms (SNPs) for the construction of the genetic map.

 

Novembre et al. [53] documented the genetic relatedness of 1,387 Europeans (including 8 Greeks from Macedonia (Northern Greece)). They used 197,146 autosomal single-nucleotide polymorphism for the construction of the map (FIG. 26).

 

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FIG. 22 - From Cavalli-Sforza et al. (1994) "The History and Geography of Human Genes" [47], page 82, Figure 2.3.5. Principal-component map of the 42 populations. Greeks cluster with the Europeans (upper right corner).

 

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FIG. 23 - From Cavalli-Sforza et al. "The History and Geography of Human Genes" [47], page 268, figure 5.5.1. Genetic tree of 26 European populations. Greeks grouped with other European and Mediterranean populations. Fst distances are based on an average of 88 genes. [Fixation index (Fst) is a measure of population differentiation, genetic distance, based on genetic polymorphism data, such as single-nucleotide polymorphisms (SNPs) or microsatellites.]

 

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FIG. 24 - From Cavalli-Sforza et al. "The History and Geography of Human Genes" [47], page 269, figure 5.5.2. Principal component map of Caucasoids: N, C, and S denote Northern, Central, and Southern Europeans. All European populations are related to Greeks, Basques, and Finns, which form the borders of the genetic structure in Europe.

 

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FIG. 25 - From Ayub et al. [48], figure 2. Neighbor-joining tree, representing relationship between 19 modern human populations. Tree is based on Das genetic distances for 182 tri- and tetranucleotide microsatellite repeats. Bootstrap resampling values are provided at each fork. Greeks cluster with the Europeans.

 

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FIG. 26 - From Novembre et al. [53], figure 1a. Population structure within Europe. The authors used 1,387 Europeans (for whom they have high confidence of individual origins) and 197,146 autosomal single-nucleotide polymorphisms (SNPs) for the construction of this graph showing their genetic pattern. It resembles very much the geographic map of Europe. Neighboring populations cluster close to each other, while being distinguishable. The Iberian peninsula, the Italian peninsula, southeastern Europe, Cyprus and Turkey can be recognized on the graph.

 

 

Conclusions from the studies using multiple autosomal gene markers

• Greeks cluster genetically with 41 other Europeans populations tested [49].
• Greeks cluster with other South European (like Italians) and
  North-European populations and are close to the Basques [48] (FIG. 25).
• Greeks grouped with other European and Mediterranean populations [47,51], (FIG. 22, FIG. 23).
• Greeks are some of the earliest contributors of genetic material to the rest of the Europeans as they are one of the oldest populations in Europe [54].
• Greeks are closest to Italians, Romanians (small sample size) and Former Yugoslavians [52], and to Albanians, southern Balkan Slavs, Romanians, Bulgarians, and Italians [53] (FIG. 26).
• Vardar Slavs cluster very close to Bulgarians [53] (FIG. 26).

 

 

Y Chromosomal DNA Gene Markers

 

Various studies have been performed using Y chromosomal DNA to establish the genetic relationship of Greeks and other Europeans [33,55,56,57,58,59,60,61] (FIG. 27). One study also looked at the Y chromosomes of Japanese men [34].

 

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FIG. 27 - From King et al. [55], figure 3. Principal component factor analysis of Middle Eastern and South East European population affinities from the gene pool of Y-chromosome haplogroup frequencies. Greeks cluster with Middle Eastern and South East European populations. (G1-G3 data points indicate three geographic regions in Greece. T1-T9 data points indicate nine geographic regions in Turkey). Egypt, Oman and the Bedouin samples from the Negev tend to form an isolated cluster, distinct from the Greek data.

 

 

Conclusions from the studies using Y chromosomal DNA

• Greeks carry some of the oldest Y haplogroups in Europe [the J2 haplogroup (and other J subhaplogroups) and E haplogroups] [33,58,59,61].
• Greeks carry signature haplogroups that are rarely seen in other populations (the J2 haplogroup and other J subhaplogroups) [33,58,59,61].
• The Greek regional samples from the mainland cluster with those from the Balkans while Cretan Greeks cluster with the Central Mediterranean and Eastern Mediterranean Samples [55]. Egypt, Oman and the Bedouin samples from the Negev tend to form an isolated cluster, distinct from the Greek data (FIG. 27).
• Greek signature DNA influence can be seen in Southern Italy and the Southern Balkans [58,59].
• Classical sub Saharan Y chromosomal haplogroups are not seen in the Greek population. The African type E haplogroups seen in the Oromo and Amhara peoples of Ethiopia are virtually not existent among Europeans although some E subhaplogroups are shared by sub Saharans and Europeans [58].
• Contrary to Arnaiz-Villena's and Hajjej's conclusions, Greeks and sub Saharan people do not cluster together genetically in modern times [55,58], (FIG. 27).
• Greeks cluster with other Europeans [33,55,56,57,58].
• Vardar Slavs are similar to other Slavs in that they carry a higher percentage of the R1a haplogroup than other peoples [33,61].
• The Japanese do not cluster with Africans but rather with other Southeast Asian peoples [34].

 

 

Mitochondrial DNA Gene Markers

 

Various studies have been performed using mtDNA to establish the genetic relationship of Greeks and other Europeans [41,42,43,44].

 

Conclusions from the studies using mtDNA

• Greeks (from the islands and the mainland) group with other Mediterranean European populations [42,43,44].
• African mtDNA haplogroups can be seen in most European populations [42,43]. The Greeks do not carry more Sub-Saharan mtDNA haplogroups than the rest of their European counterparts [41,44].

 

 

For a more detailed analysis of the genetic results, please click here.

 

 

 

The African Origins of all Humans

 

Humanity's prehistoric origin in Sub-Saharan Africa is widely accepted in anthropology and genetics [16,37,48,62,64,65,66,67].

 

A comprehensive article published in 2001 in the Journal of The American Institute of Biological Sciences concluded that:

 

For the moment, the majority of anatomical, archaeological and genetic evidence gives credence to the view that fully modern humans are a relatively recent evolutionary phenomenon. The current best explanation for the beginning of modern humans is the Out of Africa Model that postulates a single, African origin for Homo sapiens. The major neurological and cultural innovations that characterized the appearance of fully modern humans has proven to be remarkably successful, culminating in our dominance of the planet at the expense of all earlier hominid populations.[66]

 

 

 

Arnaiz-Villena's Answer to his Critics

 

Arnaiz-Villena made an attempt to defend his work, but his arguments were weak

 

In 2002, Arnaiz-Villena made an attempt to defend his use of a single gene marker for population genetics. In that article he used the following arguments [68]:

1. Although he admitted that "single-locus markers can lead to misleading results", he claimed that other genetics studies follow similar methodology.
2. These "anomalous" results have to be interpreted "in the light of other types of data" like history, anthropology and linguistics.
3. These "anomalous" results have to be tested using other genetic markers. Here he referred to Dörk et al. [46] and also stated that they were currently investigating the populations reported in their paper using other markers.

 

However, the previous three arguments from Arnaiz-Villena's are not valid, because:

1. There do exist genetics studies that follow a similar methodology (single locus gene markers), however these are not studies which link populations in terms of genetic relatedness in the way Arnaiz-Villena et al. [1,4,5,6,7], Hajjej et al. [13,14,72], and Ivanova et al. [9] do. If any population genetics study follows this methodology, then it is subject to inaccurate or faulty results [16,18]. Arnaiz-Villena is not excused for using a methodology that is inaccurate simply because others do it as well. More importantly, he cannot use this faulty methodology, have "anomalous" results, and then make extraordinary claims based on them.
2. Arnaiz-Villena is contradicting himself. Instead of using history to explain his "anomalous" findings, he has revised history to make it fit his findings about Greeks/Sub-Saharans. It becomes even more curious that he did not even attempt to use history, anthropology or linguistics to explain the Sub-Saharans/Japanese and Italians/Africans/Japanese findings.

3. Arnaiz-Villena cannot use Dörk et al. [46] as supporting evidence because Dörk et al. do not support Arnaiz-Villena's theory (as stated above). Also, up to this day, Arnaiz-Villena has not produced another study, with different gene markers, that can verify his previous findings.

 

Arnaiz-Villena's case is further undermined since he contradicts his own conclusions regarding the genetic clustering of Greeks, Cretans and Vardar Slavs. Finally, no multiple gene-marker analysis has ever duplicated Arnaiz-Villena's results. Contrary to Arnaiz-Villena's explanations and conclusions, Greeks cluster genetically with other Europeans.

 

 

 

Proposed Retractions

 

 

In the Faulty Methodology, Faulty Studies section we listed several studies from Arnaiz-Villena and Hajjej that make extraordinary claims based on bad science. However, only Arnaiz-Villena's paper on the Jews/Palestinians [4] was retracted. The question arises: Why didn't the scientific community protest with the same strength against the other papers too?

 

There are many faulty studies published in scientific journals but only rarely are they retracted [69]. There are claims that politics played a big role in the retraction of the Jews/Palestinians paper [17,23,70]. There is a long lasting conflict between the Jews and Palestinians that could justify an increased political sensitivity. Despite this, the retraction was indeed scientifically justified, as shown in the sections Arnaiz-Villena's Faulty Methodology and Proper Methodology.

 

With this in mind, following the above mentioned retraction and the publication of the present article, the Editors in chief of the scientific journals of Tissue Antigens, Human Immunology, Ann. Human Biology and of the European Journal of Medical Genetics should immediately investigate whether the following papers, claiming a Sub-Saharan African origin for Greeks, should also be retracted from the scientific literature:

• Arnaiz-Villena et al. (2001a) [1]
• Arnaiz-Villena et al. (2001b) [4]
• Arnaiz-Villena et al. (2001c) [6]
• Arnaiz-Villena et al. (2001d) [7]
• Arnaiz-Villena et al. (2002) [5]
• Hajjej A. et al. (2006a) [13]
• Hajjej A. et al. (2006b) [14]
• Hajjej A. et al. (2011) [72]

 

 

 

III. HISTORY

 

 

Arnaiz-Villena's statements on history are completely unprofessional and contradictory. He makes false statements without providing specific citations for ancient sources, or he misquotes them badly.

 

Arnaiz-Villena's Misquotations of Ancient Sources

 

 

"Herodotus wrote that 'Macedonians' were 'Dorians' and were never admitted to the Greek community." [1]

 

In fact, Herodotus (1.58) states that "the chief peoples (of Greece) were the Spartans among the Dorians and the Athenians among the Ionians. These races, Ionian and Dorian, were the foremost in ancient time, the first a Pelasgian and the second a Hellenic people." It should be noted that, according to Arnaiz-Villena, the other Doric peoples of Greece who "were never admitted to the Greek community" must have included Corinthians, Argives, Epidaurians, Eleans, Therans, Cretans, Rhodians, Syracusans, and many more. Arnaiz-Villena will soon strip Greece of all the Greeks.

 

 

"Herodotus states that the daughters of Danaus (who were black) came from Egypt in great numbers to establish a presence in Greece." [5]

 

Herodotus mentions the daughters of Danaus twice (2.171 and 182) but makes no statement about their color or their number. Arnaiz-Villena fails to mention that, according to Aeschylus, Suppliants 276-330, the daughters of Danaus traced their ancestry back to Io, a native of Argos, and that they were thereof of Greek stock.

 

 

"Herodotus wrote that Macedonians came from the Pindus mountains, now in central Greece . . . ". [5]

 

In fact, Herodotus (8.137) states that the Temenids, who founded the royal house of Macedonia, came as exiles from Argos. Their wanderings took them through Illyria (roughly modern Albania) before they arrived and settled in Macedonia. In other words, Herodotus actually disproves Arnaiz-Villena's claim of an ethnic distinction between Greeks and Macedonians.

 

 

Citations of Modern Sources in Support of Inaccuracies

 

 

"Ancient Macedonians were...considered by the classical Greeks as 'non-Greek barbarians' that would not participate in the Greek Olympic Games." [1]

 

His source is, he says, Villar F., Los indoeuropeos y los origenes de Europa Madrid: Gredos, 1996. In fact, however, the Macedonians could and did compete in the Olympic Games. Herodotus (5.22) tells us that Alexander I of Macedon, around 500 B.C., was certified as Greek at Olympia and did compete. His descendants also competed and Philip II won several times at Olympia, as well as at Delphi (another center of Hellenism; see Plutarch, Alexander 3.9 and 4.9; Moralia 105A).

 

 

"Indeed, ancient Greeks believed that their religion and culture came from Egypt."[5]

 

Here Arnaiz-Villena cites Herodotus, without specific references, and Bernal, Black Athena. He thereby fails to acknowledge that Herodotus describes older Egyptian practices that the Greeks had borrowed, and many other practices that were completely different from the Greek ones (2. 35-91). This is not the same as believing that Greek culture and religion were Egyptian. More reprehensible, however, is to cite Bernal without acknowledging that his work has been thoroughly discredited by the scientific community [71].

 

 

"The Macedonian empire extended from the Balkan Peninsula to the Himalayas and to North Africa during the reign of Philip's son, Alexander the Great." [1]

 

Arnaiz-Villena documents this statement by reference to R. Morkott Historical Atlas of ancient Greece. London: Penguin books, 1996. He does not explain why a non-Greek Macedonian empire should be shown in an atlas of ancient Greece.

 

 

Inaccurate Statements Without Ancient Documentation

 

 

"The fact that classical Greeks recognized Macedonians as barbarians speaking other languages . . ." [5]

 

It is very clear that the Macedonians spoke and read and wrote Greek, exclusively. See M. Hatzopoulos, "The speech of ancient Macedonians, in the light of recent epigraphic discoveries," Ancient Macedonia VI (1999). The "barbarian" appellation for the Macedonians comes only from the Philip-hater Demosthenes who calls other opponents of his barbarians, even though they were Athenians like him (21.150). Moreover, there is much positive evidence for Greek on Macedonian tongues. To give just one example, Euripides – who died and was buried in Macedonia– wrote his play Archelaos in honor of the great-uncle of Alexander, and in Greek. While in Macedonia, Euripides also wrote the Bacchai, again in Greek. Presumably the Macedonian audience could understand what he wrote and what they heard. See Thucydides apud Pal. Anth. 7.45; Pausanias 1.2.2; Diodorus Siculus 13.103.

 

 

"Macedonians fought against the Greeks between 357-336 B.C. under King Philip II." [1]

 

In fact, Macedonians fought with other Greeks against other Greeks. One of many examples of the Greekness of Macedonian conflicts during this period is the so-called Battle of the Crocus Plain in 352 B.C. where Phocians and allied mercenaries were defeated by Macedonians and Thessalians and Thebans who wore crowns of laurel into battle as a sign of their presence as agents of Apollo at Delphi (Justin 8.2.3).

 

 

"They defeated the Greeks at the Battle of Chaironea (338 B.C.)." [1]

 

Arnaiz-Villena again wants to make a distinction between Macedonians and Greeks. In fact, however, the two sides in the battle were totally Greek. One side (the ultimate losers) was led by Athens and Thebes that together supplied more than 60% of the forces. Corinth, Megara, Akarnania, Phokis, Achaia, Euboia, Leukas, and Kerkyra joined them (Demosthenes, De Corona 18.237) but note those who were missing: Sparta, Elis, Aigina, Epidauros, and many more.

 

The Macedonians dominated the other side, but there were substantial numbers of Thessalians as well as Argives and Arkadians (Demosthenes, Letters 4.8). In other words, as throughout so much of their history, the Battle of Chaironeia was Greek vs. Greek.

 

 

Contradictory Statements on History

 

 

"Kurds remained as 'the Mountains People' through Persian, Greek and Roman Anatolian rule." [6,7].

 

This statement is a self-contradiction of their theory that the Macedonians were not Greek [1,5]. Historically, the only time that the Kurds were ruled by Greeks was during Alexander the Great's Greek empire and the subsequent Hellenistic Age.

 

 

 

IV. CONCLUSIONS

 

• The above Arnaiz-Villena's and Hajjej's studies in population genetics are totally unreliable. No genetics study using multiple and/or highly conserved gene markers ever reproduced Arnaiz-Villena's and Hajjej's findings.
• Arnaiz-Villena's methodology is rejected by the scientific community to the point that his studies are used in a genetics textbook as an example of arbitrary interpretation and deleted from the scientific literature.
• Arnaiz-Villena' statements about ancient Greek history are inaccurate.
• Greeks cluster genetically with other Europeans.
• Greeks are amongst the earliest contributors of genetic material to the rest of the Europeans.
• African genes are present in most European populations, and Greeks do carry them in similar quantities.
• All humans have African alleles, since Homo sapiens sapiens originated in Africa.

 

 

 

The present article is by no means a diatribe against any population (white or black), and is not meant to negate or belittle any black African genetic contribution to humanity's genes. This article distances itself from any connotation or implication of racial superiority, and rejects any form of racism. Rather it is a commentary on the misuse of science and the use of pseudohistorical claims for political gain that have no basis in the advancement of responsible science and history.

 

 

(*) Words in bold type are the emphasis of the editor.

 

 

 

 

 

 

References

 

 

[1] Arnaiz-Villena A., Dimitroski K., Pacho A., et al. (2001a). HLA genes in Macedonians and the Sub-Saharan origin of the Greeks. Tissue Antigens 57: 118-127.

 

Table 5 - From Arnaiz-Villena et al. (2001a) [1], Table 1. Populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Present study [1].
Greeks (Aegean)	85	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Attica)	96	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Cyprus)	101	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Rimaibe	39	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Amhara	98	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Oromo	83	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Mossi	42	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Fulani	38	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

[2] Haplotype: A set of alleles of a group of linked genes on a chromosome which are usually inherited as a unit.

 

[3] Vardar Slavs: Is the largest ethnic group (according to individuals' declaration) in the Former Yugoslav Republic of Macedonia (FYROM), having a Slavic background (approximately 64% of the total population). They are also known as Slav Macedonians. They would like to be called simply Macedonians but this has raised protests with Greeks living in neighbouring Macedonia, Greece who also call themselves Macedonians. The Greek region of Macedonia practically superimposes the same territory as the ancient Hellenic kingdom of Macedonia. Pending a settlement on the name issue between Greece and the FYROM, and to avoid confusion, we have elected to call the dominant ethnic group of the FYROM by the appellation Vardar Slavs. In antiquity, most of the territory of the FYROM was included in the kingdom of Paionia. Additionally the FYROM includes small parts of ancient Illyria, Dardania, Lyncestis and Pelagonia. Present day Stip (Astibus) was the capital of Paionia, Veles (Vylazora) was a trading center of Paionia, and Skopje (Skupi) was a trading center of Dardania. In modern times, it was a province of the Kingdom of Serbs, Croats, and Slovenes (Yugoslavia) known as "Vardar Banovina" after the Vardar River that flows through it. After 1944, it was known as the "Socialist Republic of Macedonia" which was part of the Federal Socialist Republic of Yugoslavia.

 

Further reading :

State Statistical Office of the FYROM, 2002 census. Available at: http://www.stat.gov.mk/publikacii/knigaX.pdf . Accessed February 1, 2010.

 

Bennett Linda A., ed. Encyclopedia of World Cultures; iv - Europe. G.K. Hall & Co 1992. pp 238-242.  Available at http://www.encyclopedia.com/doc/1G2-3458000707.html. Accessed February 1, 2010.

 

Herodotus 5.17, 7.128, et alibi.

 

United Nations General Assembly Resolution A/RES/47/225, 27 April 1993. Available at http://www.un.org/documents/ga/res/47/a47r225.htm. Accessed May 29, 2010.

 

Wilkes John: The Illyrians, Wiley-Blackwell, 1996, ISBN 0631198075, p. 49; also Sealey, Raphael, A history of the Greek city states, ca. 700-338 B.C., University of California Press, 1976 ISBN 0520031776, p. 442.

 

Evans Thammy: Macedonia, Bradt Travel Guides, 2007, ISBN 1841621862, p. 13.

 

The Cambridge Ancient History Volume 3, Part 3: The Expansion of the Greek World, Eighth to Sixth Centuries BC by John Boardman and N. G. L. Hammond,1982,ISBN 0521234476, page 284.

 

Bauer Susan Wise: The History of the Ancient World: From the Earliest Accounts to the Fall of Rome (2007), ISBN 039305974X, page 518.

 

[4] Arnaiz-Villena A., Elaiwa N., Silvera C., et al. (2001b). The origin of Palestinians and their genetic relatedness with other Mediterranean populations. Hum. Immunol. 62:889-900. (This paper was subsequently retracted)

 

Table 6 - From Arnaiz-Villena et al. (2001b) [4], Table 1. Populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Greeks (Aegean)	85	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Attica)	96	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Cyprus)	101	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Japanese	493	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.
Rimaibe	39	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Amhara	98	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Oromo	83	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Mossi	42	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Fulani	38	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

[5] Arnaiz-Villena A., Gomez-Casado E., Martinez-Laso J. (2002). Population genetic relationships between Mediterranean populations determined by HLA allele distribution and a historic perspective. Tissue Antigens 60: 111-121.

 

[6] Arnaiz-Villena A., Karin M., Bendikuze N., et al. (2001c). HLA alleles and haplotypes in the Turkish population: relatedness to Kurds, Armenians, and other Mediterraneans. Tissue Antigens 57:308-317.

 

Table 7 - From Arnaiz-Villena et al. (2001c) [6], Table 1. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Greeks (Attica)	96	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Japanese	493	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

[7] Arnaiz-Villena A., Martińez-Laso J., Alonso-Garciá J. (2001d). The correlation between languages and genes: The Usko-Mediterranean peoples. Hum Immunol. 62:1051-1061.

 

[8] The following studies that claim Greeks cluster with Sub-Saharan populations, are based on the "same methodology":

• All Dendrograms and Correspondence Analysis graphs used one to two genetic markers.
• They only used gene markers form the HLA-A, -B, -DR, -DQ group.

 

Table 8. Indicates some studies that compared Greek population samples with other population samples using HLA markers, as well as the figures or tables where the statistical analysis is presented.

 

[9] Ivanova M., Rozemuller E., Tyufekchiev N., et al. (2002). HLA polymorphism in Bulgarians defined by high-resolution typing methods in comparison with other populations. Tissue Antigens 60: 496-504.

 

Table 9 - From Ivanova et al. (2002) [9]. Indicates the Greek and Vardar Slav populations used, the number of individuals analysed and the source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Greeks	246	Papassavas E, Spyropoulou-Vlachou M, Papassavas R, Schipper A, Doxiadis I, Stavropoulos-Giokas C. (2000). MHC class I and class II phenotype, gene and haplotype frequencies in Greeks using molecular typing data. Human Immunology 61: 615-623.[45]

 

[10] Petlichkovski A., Efinska-Mladenovska O., Trajkov D., et al. (2004). High-resolution typing of HLA-DRB1 locus in the Macedonian population. Tissue Antigens 64: 486-491.

 

Table 10 - From Petrichkovski et al. (2004) [10], Table 2. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	158	Present study [10].
Vardar Slavs	172	Arnaiz-Villena et al. (2001a)[1]
Vardar Slavs	80	Hristova-Dimceva A, Verduijn W, Schipper RF,Schreuder GMTh. (2000). HLA DRB and DQB1 polymorphism in the Macedonian population. Tissue Antigens 55: 53–6.
Greeks	246	Papassavas E, Spyropoulou-Vlachou M, Papassavas R, Schipper A, Doxiadis I, Stavropoulos-Giokas C. (2000). MHC class I and class II phenotype, gene and haplotype frequencies in Greeks using molecular typing data. Human Immunology 61: 615-623.[45]

 

[11] Petlichkovski et al. (2004) [10] examine the relatedness of populations for the purpose of bone marrow compatibility. This article does not criticize those findings. It just happens that they use the same methodology as Arnaiz-Villena and do not agree with his results. We therefore stress the inappropriateness of this methodology in population genetics for anthropological purposes.

 

[12] Arnaiz-Villena A., Martińez-Laso J., Moscoso J., et al. (2003). HLA genes in the Chuvashian population from European Russia: Admixture of Central European and Mediterranean populations. Hum Biol. 75(3):375-392.

 

Table 11 - From Arnaiz-Villena et al. (2003) [12], Table 1. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Bulgarians	116	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Japanese	493	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

[13] Hajjej A., Hmida S., Kaabi H., Dridi A., Jridi A., El Gaaled A., et al. (2006a). HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans. European Journal of Medical Genetics 49:43-56.

 

Table 12 - From Hajjej et al. (2006a) [13], Table 1. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Greeks (Cyprus)	101	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Attica / Aegean)	85	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Japanese	493	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.
Rimaibe	39	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Amhara	98	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Oromo	83	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

[14] Hajjej A., Kâabi H., Sellami M.H., et al. (2006b). The contribution of HLA class I and II alleles and haplotypes to the investigation of the evolutionary history of Tunisians. Tissue Antigens 68 (2): 153–62.

 

Table 13 - From Hajjej et al. (2006b) [14], Table 1. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Greeks (Cyprus)	101	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks (Attica / Aegean)	85	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Rimaibe	39	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Amhara	98	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Oromo	83	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.

 

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[49] Auton A., Katarzyna B., Boyko A.R., et al. (2009). Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Research 19: 795-803.

 

[50] Single-nucleotide polymorphisms (SNP; pronounced "snip"): a single base pair within a DNA sequence that can vary among individuals. An example of a SNP is the change from A to T in the sequences AATGCT and ATTGCT.

 

[51] Bauchet M., McEvoy B., Pearson L.N., et al. (2007). Measuring European population stratification with microarray genotype data. Am. J. Hum. Genet. 80:948-956.

 

[52] Lao O., Lu T.T., Nothnagel M., et al. (2008). Correlation between genetic and geographic structure in Europe. Current Biology 18: 1241-1248.

 

[53] Novembre J., Johnson T., Bryc K., et al. (2008). Genes mirror geography within Europe. Nature 456: 98-101.

 

[54] Cavalli-Sforza L.L., Menozzi P., Piazza A. (1994). "The History and Geography of Human Genes". Princeton, NJ: Princeton University Press, (pp 255-301).

 

[55] King R., Ozcan S.S., Carter T., Kalfoglou E., Atasoy S., Triantaphyllidis C., Kouvatsi A., Lin A., Chow C., Zhivotovsky L., Michalodimitrakis M. and  Underhill P. (2007). Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic. Annals of Human Genetics 72: 205-214.

 

[56] Rosser Z.H., Zerjal T., Hurles M.E., et al. (2000). Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language, Am. J. Hum. Genet. 67(6):1526-1543.

 

[57] Semino O., Passarino G., Oetner P.J., et al. (2000). The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective. Science 290:1155-1159.

 

[58] Semino O., Magri C., Benuzzi G., et al. (2004). Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: Inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am. J. Hum. Genet. 74:1023-1034.

 

[59] Di Gaetano C.D., Cerutti N., Crobu F., et al. (2009). Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome. Eur. J. Hum. Genet. 17:91-99.

 

[60] Di Giacomo F., Luca F., Anagnou N., et al. (2003). Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects. Mol. Phylogenet. Evol. 28:387-395.

 

[61] Barać L., Peričić M., Klarić I.M., et al. (2003). Y chromosomal heritage of Croatian population and its island isolates. Eur. J. Hum. Genet. 11:535-542.

 

[62] Li J.Z., Absher D.M., Tang H., et al. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science (New York, N.Y.). 319:1100-1104.

 

[63] Zerjal T., Wells R.S., Yuldasheva N., et al. (2002). A genetic landscape reshaped by recent events: Y-chromosomal insights into Central Asia. Am. J. Hum. Genet. 71(3):466-482.

 

[64] Wilson A.C. and Cann R.L. (1992). The recent African genesis of Humans. Scientific American 266: 68-73.

 

[65] Fitzpatrick T. (2006). "New analysis shows three human migrations out of Africa". Washington University in St. Louis. February 2, 2006.

 

[66] Johanson D. (2001). "Origins of modern humans: Multiregional or out of Africa?" http://www.actionbioscience.org/evolution/johanson.html.

 

[67] Ramachandran S., Deshpande O., Roseman C.C., Rosenberg N.A., Feldman M. W. and Cavalli-Sforza L.L. (2005). Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America 102:15942-15947.

 

[68] Arnaiz-Villena A., Gomez-Casado E., Martinez-Laso J. (2002). Single-locus studies. Nature 416:677.

 

[69] Faulty scientific studies are usually subjected to scholarly critique and very rarely retracted. An example is the controversial study published in The Lancet in 1998 by British gastroenterologist Andrew J. Wakefield and colleagues. Wakefield et al.'s findings that the combined measles, mumps, and rubella vaccine (MMR) may have been associated to autism caused a worldwide controversy and raised fear that a vaccine which prevented serious infectious diseases was in fact harming children beyond repair. This led to a decrease in the use of the MMR vaccine and contributed to an outbreak of 200.000 cases of measles in late 1999 to early 2000 leading to 111 vaccine preventable hospitalizations and 3 vaccine preventable deaths. It was later argued that Andrew J. Wakefield had received funding for his study by various anti-vaccination lobby groups and that the data was manipulated to imply a link between MMR and autism.

Eventually, the editors of The Lancet commented on the controversy and blamed Wakefield for failure to disclose any bias in his research. Following that, Andrew J. Wakefield's colleagues wrote a letter to The Lancet asking to be publically distanced and to be officially retracted from Wakefield's implied results.

Wakefield's results have never been reproduced by any further study on MMR and autism. The controversy kept on for 12 years and eventually the manuscript was fully retracted by The Lancet from the published literature on February 2, 2010. This was a decision based on a judgement by the UK General Medical Council's Fitness to Practice Panel which concluded that the results presented by Wakefield were based on faulty and biased methods.

 

Further reading :

Pepys M.B. (2007). Science and serendipity. Clinical Medicine 7:562-578.

Wakefield AJ, Murch S.H., Anthony A., et al. (1998). Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet 351: 637-641.

 

McBrien J., Murphy J., Gill D., et al. (2000). Measles outbreak in Dublin. Ped. Infect. Dis. J., 22:580-584.

 

Deer B. Revealed: MMR research scandal. Times Online. February 22, 2004. Available at: http://www.timesonline.co.uk/tol/news/uk/health/article1027603.ece. Accessed December 10, 2009.

 

Deer B. MMR doctor Andrew Wakefield fixed data on autism. The Sunday Times. February 8, 2009. Available at: http://www.timesonline.co.uk/tol/life_and_style/health/article5683671.ece. Accessed December 10, 2009.

 

Wakefield A.J. (1999). MMR vaccination and autism. Lancet 354:949-950. See comment by Taylor B., Miller E., and Farrington P. on page 950.

Horton R. (2004). A statement by the editors of The Lancet. Lancet 363:820-821.

 

Murch S.H., Anthony A., Casson D.H., et al. (2004). Commentary. Retraction of an Interpretation. Lancet 363:750.

 

The Editors of The Lancet. Retraction—Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet. 2 February 2010. Available at: http://www.lancet.com/journals/lancet/article/PIIS0140-6736%2810%2960175-7/fulltext. Accessed February 3, 2010.

 

[70] McKie R. (2001). Journal axes gene research on Jews and Palestinians. Guardian. November 25, 2001. Available at: http://www.guardian.co.uk/Archive/Article/0,4273,4307083,00.html. Accessed October 5, 2009.

 

[71] In "Black Athena" Bernal argues that western philosophical and scientific thought came from Africa in ancient times and there was a conspiracy to hide this fact. His work was discredited by, first, M. R. Lefkowitz, Not Out of Africa (1996) and continued by 20 other scholars in M.R. Lefkowitz and G. M. Rogers (eds.) Black Athena Revisited (1996). See especially the article by Edith Hall, "When Is a Myth Not a Myth; Bernal's 'Ancient Model'"; pp. 342-343. In 2003, the Intercollegiate Studies Institute (a non-profit US educational organization) listed Black Athena as one of the worst books of the twentieth century (http://www.isi.org/journals/ir/50best_worst/50worst.html).

 

Further reading :

Kagan D., "Stealing History," The New Criterion, March 1996. Available at: http://www.newcriterion.com/articles.cfm/stealing-history-3624. Accessed April 8th, 2010.

 

[72] Hajjej A., Sellami M.H., Kaabi H., et al. (2011). HLA class I and class II polymorphisms in Tunisian Berbers. Annals of human biology 38:156-164.

 

Table 14 - From Hajjej et al. (2011) [72], Table 1. Some of the populations used, number of individuals and source of the sample data.

Population	Number	Source of the Sample Data
Vardar Slavs	172	Arnaiz-Villena et al. (2001a) [1].
Greeks (Cretans)	135	Arnaiz-Villena A, Iliakis P, González-Hevilla M, et al. (1999). The origin of Cretan populations as determined by characterization of HLA alleles. Tissue Antigens 53: 213–26.
Greeks (Cyprus)	101	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Greeks	85	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Rimaibe	39	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Amhara	98	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Oromo	83	Clayton J, Lonjou C. Allele and haplotype frequencies for HLA loci in various ethnic groups. In: Charron D, editor. Genetic diversity of HLA: Functional and medical implication. Vol. 1. Paris: EDK, 1997: 665–820.
Bushmen (San)	77	Imanishi T, Akaza T, Kimura A, Tokunaga K, Gojobori T: Allele and haplotype frequencies for HLA and complement loci in various ethnic groups. In: Tsuji K, Aizawa M, Sasazuki T (eds): HLA 1991. Vol 1. Oxford: Oxford University Press, 1992: 1065-220.