Sub-Saharan DNA admixture in Europe
Sub-Saharan DNA admixture in Europe refers to the way in which Sub-Saharan African DNA is lightly scattered throughout the European continent.
Not every population has been studied yet, but enough have so that a picture is starting to emerge. The amount of Sub-Saharan African admixture in Europe today ranges from a few percent in the Iberian Peninsula to almost none around the Baltic. It seems to show a decreasing cline from the Southwest to the Northeast, which corresponds with the areas most affected by the Moorish (North Africa) expansion and the African slave trade.
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. 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., 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 African DNA from these relatively recent arrivals are too low to have had an appreciable effect on Phenotypes.

# Approaches to detecting admixture
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. .

## Gender-specific markers
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.
Although mtDNA and Y-DNA can quantifiably estimate a modern population's overall admixture, the approach cannot measure an individual's genealogy. You had about a million ancestors alive in the year 1500, but only two of them carried your 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 conquer, women get raped), 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).

### mtDNA
A study by Gonzalez et al. 2003 found L haplogroups at rates of 0.1% in Scotland, 0.4% in England, 0.7% in North Germany, 1.4% in France, 2.9% in Galicia, 2.2% in Northern Portugal, 4.3% in Central Portugal, and 8.6% in Southern Portugal (Alentejo and Algarve) (note that these figures do not count the L3 lineage, which may be of ancient introduction and so remains ambiguous). For comparison, sub-Saharan mtDNA runs 21.8% in North Africa.
According to another study by Pereira et al. 2005, sub-Saharan mtDNA L haplogroups were found at rates of 0.62% in a German-Danish sample, 0.94% in Sicilians, 1% in the British/irish, 2.38% in Albanians, 2.86% in Sardinians. 
This paper which provides a deeper and more global insight into the African female influence in Iberia shows that the mean frequency reaches 3.83% in Iberians. The frequency is clearly higher in Portugal (32 sequences in 549 individuals; 5.83% with a high frequency of 11% in southern Portugal) than in Spain (8 out of 496; 1.61% with a higher frequency of 3.26% in Galicia) and without parallel in the rest of Europe.

### Y-DNA
Sub-Saharan African Y-chromosomes are much less common in Europe, for the reasons discussed above. However,  Haplogroups E(xE3b) and Haplogroup A spread to Europe due to migrations from Northeast Africa, rather than the slave trade. The haplotypes have been detected in Portugal (3%), France (2.5% - in a very small sample), Germany (2%),  Sardinia (1.6%), Austria (0.78%),  Italy (0.45%),  Spain (0.42%) and Greece (0.27%). By contrast, North Africans have about 5% paternal black admixture.
In the UK Sub-Saharan African y chromosomal haplotypes have been found in a Yorkshire village.

## Neutral autosomal markers
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 and Wilson et al. 2001 failed to detect any sub-Saharan admixture in Scots, Russians, Basques, Frenchmen or Italians, while 1% was observed in Norwegians.
However DNAPrint Genomics, which has published its work in the scientific literature for many years (including Journal Human Genetics and Journal of Forensics Sciences), mentions in its test using autosomal markers that the average South Europeans type with approximately 5% sub-Saharan genetic material (European American = 3%, Northern Euro < 1%). Even though in some cases, for an individual, a low reading such as this may be negated by the confidence interval, in South Europeans low levels of sub-Saharan admixture are consistenly found, making them signature results for these populations. This means they are not stastical "noise," but true results.

## Adaptive autosomal markers
Adaptive autosomal markers are those that evolved and spread because they enhance survivability.
The best-known example is HbS, which produces the sickle-cell trait. This Allele emerged in Arabian Peninsula shortly after the invention of Agriculture and spread to Europe because it confers near immunity to the most lethal form of Malaria.
There are many other such traits and they 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.
The main disadvantage of adaptive autosomal markers is that they cannot tell what fraction of a population came from which ancestry. That HbS is found in, say, 10 percent of some European population does not mean that ten percent have sub-Saharan ancestry; it may simply be that many of those lacking the trait in the past died without progeny due to malaria.

## Gm and Km allotypes
Two very recent studies "New insights into the peopling of the Iberian Peninsula" (2007) and "Genetic Position of Andalusians from Huelva in Relation to Other European and North African Populations" (2007) showed a "relatively high incidence" of the GM*1,17 23' 5- haplotype in Spain with a peak of 4.5% in Galicia. This haplotype is considered a genetic marker of sub-Saharan Africa, where it shows frequencies of about 80% (Excoffier et al. 1991). According to this new studies, although some researchers have associated African traces in Iberia to Islamic invasions, the presence of this african haplotype in the Spanish population may in fact be due to more ancient processes. In Spain, the average figure for this African haplotype is 2.4%,  whereas  in  other  non-Mediterranean  European  populations  that  value  is  nearly  eight times  lower  (0.3%). A relatively moderate frequency (3.8%) of this haplotype, similar to that found in populations from Galicia (4.5%) and the Pyrenees (3.7%; Giraldo et al. 2001), was observed in Huelva. Although this haplotype's frequency ranges between 1 and 3% in most Spanish populations, it occurs at frequencies between 3 and 4% in the Mediterranean islands of Corsica (Blanc and Ducos 1986), Sardinia (Piazza et al. 1976; Steinberg and Cook 1981), and Sicily (Cerruti et al. 2004). For comparaison these frequencies are even higher in North African populations: In some Berber and Arab groups from Morocco, Algeria, and Tunisia, they reach values between 20 and 33% (Chaabani et al. 1984; Dugoujon et al. 2004; Coudray et al. 2006). 

# The Arnaiz-Villena controversy
An often-cited study from 2001 by Antonio Arnaiz-Villena et al. 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. 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".
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." The controversy was further reported on in numerous locations including The Observer.
Shortly after this, three respected geneticists, Luca Cavalli-Sforza, Alberto Piazza and Neil Risch, argued that the scientific limitations of Arnaiz-Villena's methodology. 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). Then, Ayub et al. 2003 did the same thing using 182 loci (view dendrogram).
However a very recent study (2006) done by other scientists HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans. confirms the relatedness of the Greeks to sub-Saharans by calculating genetic distances at the DRB1 locus (this study, incidentally, and the Petlichkovski (2004) study, show that the Greek study is indeed cited by other scientists, and not merely northern European White Nationalists and Afrocentrists).
Y-haplogroup E-M78 (a derivative of E3b) originated in northeastern Africa and is found at relatively high levels in Greeks (and some other Mediterraneans), which suggests, in addition to the more recent admixture, a very ancient northeastern African contribution to the Greek genepool (Semino, 2004 and Cruciani, 2004). The fact that the most prevalent form of E-M78 (E-V13) found in Greeks is a later, mainly local variation is irrelevant, since the parental E-M78 originated in eastern Africa, as did all of its ancestral markers.

# Footnotes
-  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.
-  Hugh Thomas, The Slave Trade: The Story of the Atlantic Slave Trade: 1440-1870 (New York: Simon and Schuster, 1997), 804
-   Genetic structure of human populations.
Rosenberg NA, et al, Dec 2002
-  Gonzalez et al. 2003
-  Pereira et al. 2005 African female heritage in Iberia: a reassessment of mtDNA lineage distribution in present times
-  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.
-  Yorkshireman's African warrior heritage revealed
-  Rosenberg et al. 2002
-  Wilson et al. 2001
-  Journal of Forensics Sciences
-   /], ancestrybydna.com
-  GM and KM immunoglobulin allotypes in the Galician population: new insights into the peopling of the Iberian Peninsula
-  Genetic Position of Andalusians from Huelva in Relation to Other European and North African Populations
-  Arnaiz-Villena et al.
-  Arnaiz-Villena et al full text
-  Abstract
-  Human Immunology, Vol: 62, Issue: 10, October, 2001, pp1063
-  Nature
-  The Observer
-  Nature
-  MDS plot
-  Ayub et al. 2003
-  dendrogram