The Basques have more or less the same genetic 'mix' as most other Spanish/Southern French peoples . It is their Language which is unique as it did not come under the influence of Roman ,nor Celtic , nor Arab invasions .
Basque women have difficulty having more than one child with the surrounding peoples, because of the Rh-negative blood with its very high concentration in the Baques, and not-very-high concentration in the other peoples. Where Rh negative blood is found in any concentration, it's part of the Basque diaspora (County Munster in Ireland, Chile).
The blood difference, which leads to "blue baby" syndrome, is a key physiological differential between the Basques and other people, and is probably THE key biological reason that the Basques preserved more of their ancient identity. Conquerors and invaders of the Basque country were always at a reproductive disadvantage when they took Basque women as wives or concubines, because an Rh negative woman can generally only produce one child with a double Rh+ male (her body will reject the second baby and thereafter), but she can produce many children with Rh - males (which, of course, meant either other Basques, or mixed-blood children of Basques).
Now, one might say that the genetic difference between people with Rh negative and Rh positive blood is trivial, and that may even be true on a simple mathematical comparison of gene similarities. But the fertility differential that blood issues makes has been a steep cliff that has favored the preservation of the Basques as distinct throughout the ages.
Given that blood type is a genetic issue, and given that the demographic cliff between Basque/Basque fertility and Basque/Non-Basque fertility has been caused throughout history by that difference, I would have to say that all genes are not created equal. Any "genetic similarity" study that doesn't pick up that key blood typing difference, which is almost certainly the reason for the unique preservation of Basque culture and civilization as a unique thing apart, is too simplistic to be of any real use.
The Basques ARE different from the people around them, on a physiological level. Throughout history, and without modern medical intervention even today, the characteristic Rh negative blood of the Basques makes the Basques only partially interfertile will all of the surrounding humans. That's WHY the Basques have been preserved unique - invaders could have one baby with Basque women; Basques could have many with each other. And whether the baby grew up to be interfertile depended on that blood type allele. The Rh negative Basques breed easily with the Rh negative Basques and Rh negative people of the Basque diaspora. Rh positive alleles produce blue baby syndrome in the second child, and cut off the interfertility, causing the Basque population, over the generations, to skew back to the Basques.
They really are different, and it's at a genetic level. Specifically right there. It makes a difference, a non-trivial one.
Lots of misery has been caused to couples over the centuries because of blue baby deaths. In my own family it produced three miscarriages in my mother, and 7 in her twin sister. Only the Rh negative babies made it. Ten dead babies in a generation, multiplied by 500 generations - if the "genetic tests" don't pick that up (and apparently they don't), then the "genetic similarity" claim is simply not specific enough.
