North-African marker in Andalusia

We find the following percentages for the typcial north-african (Berber) paternal marker, the Y-DNA haplogroup E-M81, obtained from different sources :

Southern Spaniards  n=1/62    1.6%    Scozzari 2001.
Huelva, Andalusia   n=5/167   2.99%  Ambrosio 2010.
Huelva, Andalusia   n=1/22      4.5%   Flores et al.2004
Seville, Andalusia  n=7/155     4.5%    Flores et al.2004
Cadiz, Andalusia    n=0/28      0.0%    Flores et al.2004
Cordoba, Andalusia  n=2/27   7.4%    Flores et al.2004
Malaga, Andalusia   n=3/26    11.5%   Flores et al.2004
Andalusia East      n=2/95       2.1%    Adams et al.
Andalusia West      n=10/73   13.7%   Adams et al.
-------------------------
Total South Spain :  31/655 = 4.73%

It is a similar result to percentages found in  French  (3/73 = 4.1% , Scozzari et al. 2001) or in regions of France ( 5.6% in Auvergne (5/89) and Île-de-France 5/91 = 5.5% ). This suggests that the presence of Islamic rule, which was longer in the South of Spain than anywhere else in Iberia, had very limited or no impact in the genetic pool of the population. We can conclude that the moorish population in Andalusia was extremely minoritary, the place were Islamic rule was stronger and longer. We can't also rule out the possibily that the presence of this marker, or part of it, could have entered in much earlier times (Neolithic or earlier), which would make the presence of moors in Al-Andalus even more insignificant. So, in other words, we can safely say the Islamic rule was just that, a military and religious rule, with no impact on the demographics and genetics of the authoctonous populations.


Ambrosio et al. 


The distribution of E-M81 haplogroup, a Berber marker, was found at a frequency of 3% in our sample. The distribution of M81 frequencies in Iberia seems to be not concordant with the regions where Islamic rule was most intense and long-lasting. The study also showed that most of M78 derived allele (6.6%) led to the V13* subhaplogroup. We also found the most basal and rare paragroup M78* and others with V12 and V65 mutations. The lineage defined by M34 mutation, which is quite frequent in Jews, was detected as well. Conclusions: The haplogroup E among Western Andalusians revealed a complex admixture of genetic markers from the Mediterranean space, with interesting signatures of populations from the Middle East and the Balkan Peninsula and a surprisingly low influence by Berber populations compared to other areas of the Iberian Peninsula.

Sub-Saharan admixture in the Mediterranean basin

González-Pérez et al. (2010) have analyzed populations from the northern and southern shores of the Mediterranean, with Central Europeans and West Africans as external references. In the Discussion section, they admit that the inflated "Alu/STR estimate might be artefactual" and favor the estimate based on the Alu  loci set alone because it's consistent with previous mtDNA, Y-chromosome and 500,000-SNP structure data.
According to the more accurate latter method, Sub-Saharan African admixture is ~13% in North Africa and "imperceptible" or noise (~ 0.01%) in Southern Europe:

Pyrenean Y-DNA

In the pie charts, dark blue refers
to R1b1b2d, dark light to R1b1b2c, white to other R, orange
to I2a2, salmon to other I and pink to lineages that entered
Iberia from the Neolithic onwards. The light gray slice refers to
R plus I lineages.

From the study of  López-Parra et al. 2009 which analyses 5 pyrenean populations (25 males from Vall d'Arán (Lleida province), 34 from Alt Urgell (Lleida province), 37 from Cerdanya (Girona province), 31 from Jacetania (Huesca province) and 42 from Cinco Villas (Navarre province).


As expected, the vast majority by far of these populations belong to haplogroup R1b1b2-M269 (total 131/169 = 77.5%), especially the subhaplogroup R1b1b2*, and the second most common haplogroup among the total Pyrenean samples was haplogroup I which accounted for 12.4% (21/169) of paternal lineages, being I2a2 the most common clade. The rest of haplogroups are quite minoritary. Here are the distributions for each of the pyrenean populations sampled :

Cerdeña (n=37)
R1b: 75.7%  I: 16.2%  G : 2.7%  J: 2.7%  E: 0% 

Alt Urgell (n=34)
R1b: 76.5%  I: 8.8%  J: 8.8%  E: 2.9% 

Vall d'Arán (n=25)
R1b : 84%  I: 12%  E: 4%  J: 0%

Jacetania (N=31) :
R1b : 64.%  I: 16.1%   J: 9.7%  R1: 6.45%    G: 3.2%   E: 0%

Cinco Villas (n=42)
R1b: 85.7%  I:  14.3%

TOTAL (n=169) :  R1b (131/169) : 77.5%  I (21/169) : 12.4%  J (7/169) = 4.14%, G (3/169) = 1.78% E (3/169) = 1.78%,    R1 (2/169) = 1.18%  and  Other 2/169 = 1.18%.

Summary

The male-mediated genetic legacy of the Pyrenean population was assessed through the analysis of 12 Y-STR and 27 Y-SNP loci in a sample of 169 males from 5 main geographical areas in the Spanish Pyrenees: Cinco Villas (Western Pyrenees), Jacetania and Valle de Arán (Central Pyrenees) and Alto Urgel and Cerdaña (Eastern Pyrenees). In the Iberian context, the Pyrenean samples present some specificities, being characterizeded by a high proportion of chromosomes R1b1b2-M269 (including the usually uncommon R1b1b2d-SRY2627 and R1b1b2c-M153 types) or I2a2-M26 and low proportions of other haplogroups. Our results indicate that an old pre-Neolithic substrate is preponderant in populations of the whole Pyrenean fringe. However, AMOVA revealed a high level of substructure within Pyrenean populations, partially explained by drift effects as well as by the signature of an ancient genetic differentiation between Western and Eastern Pyrenees.

Other interesting extracts from the study : 

I2a2 is virtually absent east of the Italian Apennines and shows the highest incidences in north-eastern Iberia/southern France, with the exception of the isolated and dramatic peak of frequency (40.9%) in Sardinia (Rootsi et al. 2004).
This was well illustrated in the phylogram of I2a2 in Figure 1 from Rootsi et al. (2004) based upon the population data available at the moment, within which Basques (Spanish and French mixed) and Bearnais (in the French Atlantic Pyrenees) showed the highest continental frequencies (6% and 7.7% respectively). New data from Spanish Basques (Alonso et al. 2005) did not reproduce such elevated values; in Biscay I2a2 was not detected and its frequency was 1.3% in Gipuzkoa and 4.5% in Alava plus Navarra. From the new data presented here it seems that the Pyrenees might indeed have been the region where I2a2 arose and from which it initiated the spreading process after the LGM.

One of the signs comes from the concentration of high frequencies of I2a2 among populations from the entire Pyrenean range. Our data strongly reinforce previous evidence that I2a2 arose during Mesolithic times in a region close to or within the Pyrenees. The dispersal of I2a2 from its place of origin throughout the Pyrenees and beyond, implied not only gene exchange but also considerable movement of people. Very likely, the demographic event associated with the expansion of I2a2 was the Ice-age repopulation of
Europe from the Franco-Cantabrian refuge. A number of studies on human mtDNA diversity have already indicated that the Franco-Cantabrian glacial refuge was a major source for the European gene pool (Achilli et al. 2004), and our data on I2a2 seemingly lend support to the role of the region as a Mesolithic diffusion center of male lineages.