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Sub-Saharan DNA admixture in Europe refers to the way in which Sub-Saharan African DNA is lightly scattered throughout the European continent.

Between 1500 and up to 1900, about four million African slaves were transported to island plantations in the Indian Ocean; eleven million were taken by the Atlantic slave trade to the Caribbean, North America, Central America, and, above all, South America—mainly to Brazil; an estimated eight million were transported north across the Sahara to North Africa by the Arab slave trade.<ref>Pier M. Larson, Reconsidering Trauma, Identity, and the African Diaspora: Enslavement and Historical Memory in Nineteenth-Century Highland Madagascar, William and Mary Quarterly 56, no. 2 (1999): 335-62.</ref> Of the vast majority shipped by the Atlantic trade, most were sent directly to the Americas as part of an Atlantic triangular trade, and so never saw Europe. Most of the trans-Saharan trade ended at markets in North Africa and the Middle East.

In the same period about 200,000 Africans were sold into Europe via the Atlantic slave trade<ref>Hugh Thomas, The Slave Trade: The Story of the Atlantic Slave Trade: 1440-1870 (New York: Simon and Schuster, 1997), 804</ref>, and these seem to have "vanished" without a trace. However, they can account for much of the presence of Sub-Saharan African DNA markers in the modern European gene pool, although it is not clear how much (in opposition to traces from pre-historic and medieval migrations). It also must be noted that levels of Sub-Saharan African DNA from these relatively recent arrivals are too low to have had an appreciable effect on phenotypes.

Approaches to detecting admixture[edit]

There are three main approaches to detecting continent-of-ancestry admixture: gender-specific markers (Mitochondrial DNA and Y-chromosome DNA), neutral autosomal markers, and adaptive autosomal markers.

Each approach has strengths and weaknesses in distinguishing ancient sub-Saharan markers (from our species' common origin in Africa) from more recent ones. Some approaches are more quantifiable than others.

It should be noted that differences among the major population groups of the world constitute only 3% to 5% of genetic variation, while within-population differences among individuals account for 93% to 95% of such variation. <ref>Genetic structure of human populations. Rosenberg NA, et al., Dec 2002</ref>

Gender-specific markers[edit]

Mitochondrial DNA (mtDNA) and Y-chromosome DNA trace individual lineages, matrilineal and patrilineal, respectively.

They do not mix or recombine at each generation. Hence, they can identify different population migrations. The descendants of the sub-Saharan Africans who first began the Great Diaspora about 70 millennia ago can be distinguished from the sub-Saharan groups who helped to re-colonize Europe after the glaciers melted 16 millennia ago, and from sub-Saharan people who crossed or went around the Mediterranean in Ancient Egyptian or Roman times or thereafter as slaves, soldiers, settlers, or traders.

Because mtDNA and Y-DNA haplogroups are inherited as single loci and are subject to genetic drift and stochastic errors, they can only provide a rough estimate of a modern population's overall admixture, and the approach cannot measure an individual's genealogy. A person born around the year 2000 would have had about slightly more than half a million ancestors alive in the year 1500 alone<ref>If one calculates 20 generations in 500 years, that would make a total of 524,288 individual genealogical positions (without pedigree collapse) in the 20th generation alone; plus an exactly equal number, minus 1, in all the preceding generations (1 to 19th generations). Notice that the number doubles with each generation, thus, in the 21st generation one has 1,048,576 individual genealogical positions in that generation alone.</ref>, if there were no pedigree collapse, but only two of them would have carried that person's mtDNA and Y-DNA. Differences between the patterns of mtDNA and Y-DNA can suggest why populations migrated: military conquest tends to propagate Y lineages but leave mtDNA lineages in place (men tend to be mobile, women stay in place), mass migrations in search of a new homeland tend to propagate mtDNA and Y lineages equally, and a slave trade tends to propagate mtDNA lineages but leave Y lineages in place (female slaves are encouraged to propagate, males are not).


In a study by Pereira et al. 2005,<ref>Pereira et al. (2005) African female heritage in Iberia: a reassessment of mtDNA lineage distribution in present times</ref> sub-Saharan mtDNA L haplogroups were reported at rates of 5.85% in the Portuguese (including 11.38% in Southern Portugal), 2.86% in Sardinians, 2.38% in Albanians, 2% in Finns, 1.61% in Spaniards (including 3.26% in Galicia), 1% in the British, 0.94% in Sicilians and 0.62% in a German-Danish sample.

Gonzalez et al. 2003<ref>Gonzalez et al. (2003)</ref> found L markers at rates of 8.6% in Southern Portugal (Alentejo and Algarve), 4.3% in Central Portugal, 2.9% in Spain (Galicia), 2.2% in Northern Portugal, 1.4% in France, 0.7% in Northern Germany, 0.4% in England and 0.1% in Scotland.

Achilli et al. 2007<ref>Achilli et al. 2007</ref> used generally large samples of numerous populations to come up with the following frequencies: 10.84% in the Southern Portuguese, 6.4% in the Central Portuguese, 3.7% in Northwestern Spaniards (Galicians), 3.19% in the Northern Portuguese, 2.9% in Central Italians from Latium, 1.9% in Central Italians from Tuscany, 1.9% in Southern Italians from Sicily, 1.68% in Northeastern Spaniards, 0.99% in Greeks from Crete, 0.98% in Central Italians from Marche, 0.83% in Finns, 0.71% in Bulgarians, 0.69% in Bosnians, 0.68% in Central Spaniards, 0.64% in Basques, 0.6% in the English, 0.54% in Italians from Sardinia, 0.44% in the Swiss, 0.32% in Southern Italians from Campania, 0.3% in Frenchmen, 0.3% in Germans and 0.18% in Poles. No admixture was detected in Northern Italians from Lombardy and Piedmont, Southern Italians from Apulia and Calabria, Greeks from Lemnos, Rhodes and elsewhere, Germans from Bavaria, Austrians, Russians, Romanians, Czechs, Estonians, Latvians, Slovakians, Slovenians, Swedes, Danes, Norwegians, Irishmen, Welshmen or Scots.

Malyarchuk et al. identified 8 African haplogroups in Russians, Czechs, Slovaks and Polish populations. These haplogroups included L1b, L2a, L3b, and L3d, of which some appeared to be of West African origin. Haplogroup L2a1a was identified as most likely having entered Europe about 10,000 years ago, possibly through the Iberian Peninsula. <ref>Template:Cite journal</ref>


For the reasons outlined above, sub-Saharan Y-DNA markers are much less common in Europe. The small presence of the Haplogroups E(xE3b) (i.e. clades of E other than E3b) and Haplogroup A in Europe is almost exclusively attributable to the slave trade, as these haplogroups are characteristic of western, central and southern Africans and are barely observed elsewhere.<ref>Sanchez et al. (2005). "High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males". European Journal of Human Genetics; 13:856–866</ref> The haplotypes have been detected in Portugal (less than 3%), the Arbëreshë (2.9%), France (2.5% - in a very small sample), Germany (2%), Sardinia (1.6%), Calabria (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).<ref>Cruciani et al. 2004,
Flores et al. 2004,
Brion et al. 2005,
Brion et al. 2004,
Rosser et al. 2000,
Semino et al. 2004,
DiGiacomo et al. 2003.</ref> Other studies show the frequency in France as being much lower (0%)<ref>The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective</ref>.

Neutral autosomal markers[edit]

Neutral autosomal markers are odd fragments of DNA that do not affect a person's physical traits. Because they are autosomal (within the nuclear DNA that is subject to meiosis), such markers reflect the recombination of paternal and maternal DNA with each generation. Hence, they are less useful than mtDNA or Y-DNA in tracking migrations and they are less precise as to time. This makes it hard to tell if any particular marker dates from the 1500-1800 slave trade, or from the post-glacial re-colonization of Europe, or from some time in between. On the other hand, neutral autosomal markers are useful for individual genealogies since they reflect just how much of an individual's genome came from which population group.

Two studies by Rosenberg et al. 2002<ref>Rosenberg et al. 2002</ref> and Wilson et al. 2001<ref>Wilson et al. 2001</ref> failed to detect any sub-Saharan admixture in Scots (from Orkney), Russians, Basques, Frenchmen or Italians (from Lombardy, Tuscany and Sardinia), while 1% was observed in Norwegians. More recently, Bauchet et al. 2007<ref>Bauchet et al. 2007</ref> tested several European groups for black admixture, and while cluster membership coefficients are not provided, the chart of Bayesian cluster results shows admixture levels to be equally low in Greeks, Spaniards (from Valencia), Basques, Frenchmen, Southern Italians, East English, West Irish, Poles, Germans (from Hanover) and Finns.

A similar study by Auton et al. 2009<ref>Auton et al. 2009</ref>, which also contains an admixture analysis chart but no cluster membership coefficients, shows little to no sub-Saharan African influence in a wide array of European samples, i.e. Albanians, Austrians, Belgians, Bosnians, Bulgarians, Croatians, Cypriots, Czechs, Danes, Finns, Frenchmen, Germans, Greeks, Hungarians, Irish, Italians, Kosovars, Latvians, Macedonians, Netherlanders, Norwegians, Poles, Portuguese, Romanians, Russians, Scots, Serbians, Slovakians, Slovenians, Spaniards, Swedes, Swiss (German, French and Italian), Ukrainians, United Kingdom and Yugoslavians.

Results like these using the STRUCTURE program are considered to be highly accurate quantifications of admixture.<ref>Pritchard et al. 2000</ref>

Adaptive autosomal markers[edit]

Adaptive autosomal markers are those that have evolved and spread because they enhance survivability. Several such markers of sub-Saharan African origin are present in Europeans, most notably HbS (sickle cell), Fy(a-b-) (Duffy-null), and GM and KM immunoglobulin allotypes, all of which confer immunity to malaria and are thus selected for in environments where this disease still poses a threat.<ref>Ragusa et al. 1992</ref><ref>[1]</ref><ref>Pandey et al. 2007</ref>

Traits such as these have two main advantages for population studies: First, they have been well-studied for centuries, so different strains are easily identified and tracked. Second, because their adaptive advantages are known, their dates of origin and spread are also known to reasonable precision. Their big disadvantage, however, is that they cannot tell what fraction of a population came from which ancestry. That HbS is found in, say, ten percent of some European populations does not mean that these populations have ten percent sub-Saharan ancestry; it may simply be that many individuals lacking the trait in the past died without progeny due to malaria.

Though widely used in the early days of population genetics, adaptive autosomal markers are today largely avoided because of their unreliability. Recently, the genetic testing company AncestryByDNA was criticized for providing information about ancestry based in part on loci that have undergone strong selection and may reflect similar environmental exposures rather than shared ancestry.<ref>Bolnick et al. 2007</ref>

The Arnaiz-Villena controversy[edit]

An often-cited study from 2001 by Antonio Arnaiz-Villena et al.<ref>Arnaiz-Villena et al.</ref> which maps 28 world population based on the HLA DRB1 locus, concluded that "the reason why Greeks did not show a close relatedness with all the other Mediterraneans analyzed was their genetic relationship with sub-Saharan ethnic groups now residing in Ethiopia, Sudan, and West Africa (Burkina Faso)." Later that year, the same data was used in another study by the same author published in a different journal.<ref>Abstract</ref> This second paper dealt specifically with the relatedness of Palestinians and Israelis and was subsequently "deleted from the scientific literature" because, according to the editor-in-chief Nicole Suciu-Foca, it "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".<ref>Human Immunology, Vol: 62, Issue: 10, October, 2001, pp1063</ref>

Erica Klarreich's report on the controversy further quotes Suciu-Foca as saying that the reaction against the paper was so severe that "We would have had mass resignations and the journal would have been destroyed if this paper were allowed to remain."<ref>Nature</ref> The controversy was further reported on in numerous locations including The Observer.<ref>The Observer</ref>

Shortly after this, three respected geneticists, Luca Cavalli-Sforza, Alberto Piazza and Neil Risch, argued that the scientific limitations of Arnaiz-Villena's methodology.<ref>Nature</ref> They stated that "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.", making specific allusion to the findings on Greeks (among others) as "anomalous results, which contradict history, geography, anthropology and all prior population-genetic studies of these groups."

No multiple-marker analysis has ever duplicated Arnaiz-Villena's results. In The History and Geography of Human Genes (Princeton, 1994), Cavalli-Sforza, Menozzi and Piazza grouped Greeks with other European and Mediterranean populations based on 120 loci (view MDS plot<ref>MDS plot</ref>). Then, Ayub et al. 2003<ref>Ayub et al. 2003</ref> did the same thing using 182 loci (view dendrogram<ref>dendrogram</ref>).

Another study was conducted in 2004 at Skopje's University of Ss. Kiril and Metodij, using high-resolution typing of HLA-DRB1 according to Arnaiz-Villena's methodology. Contrary to his earlier conclusion, no sub-Saharan admixture was detected in the Greek sample.<ref>High-resolution typing of HLA-DRB1 locus in the Macedonian population</ref>

A 2006 study by Tunisian scientists again asserted the relatedness of the Greeks to sub-Saharans by calculating genetic distances at the DRB1 locus,<ref name="ncbi.nlm.nih.gov">HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans.</ref> the same marker used in the controversial Arnaiz-Villena paper. Both papers interpreted those results as suggesting an admixture occurred due to the displacement of Egyptian-Ethiopic people during the Pharaonic period. However, the Tunisian scientists failed to analyze any new Greek genetic material, relying solely on the data contained in the earlier Arnaiz-Villena paper, and no Greek laboratory contributed to their research.<ref name="ncbi.nlm.nih.gov"/>

The credibility of Arnaiz-Villena was seriously damaged after he was suspended without pay from the Hospital Doce de Octubre in Madrid, where he heads the department of immunology and molecular biology, after being charged with embezzlement of funds.<ref>[ http://www.bmj.com/cgi/content/full/324/7339/695 Controversial immunologist faces court case]</ref> In addition to this charge, Dr Arnaiz-Villena is facing allegations of "moral harassment" at the Universidad Complutense de Madrid, where he chairs a research and teaching immunology unit.


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