Genetics apparently confirms what you can learn from almost any history of Spain.
My wife, who is Cuban and of Spanish ancestry, was raised a Catholic. But she and her family have little doubt that they have a Sephardic /Jewish bloodline. In fact she “appears” more Jewish than many Jews I know.
My point remains unaffected by your interesting remarks. The Basques were isolated from the mainstream Spaniards even during the 700 year Moorish occupation. Selecting them as representative of the original Spanish genotype, prior to intermingling with Moors, Jews, and others after 1492 is an unproven assumption, thus the confound.
This melting pot probably occurred after centuries of coexistence and tolerance among Muslims, Jews and Christians ended in 1492
This is a Liberal/Black Legend lie. The persecutions in the summer of 1391 expelled much of the Jewish population from the big cities, were their quarters could be easily stormed, sacked and burnt. The survivors moved to smaller towns, living in smaller numbers, so they could usually seek protection in the feudal lord's castle (to whom they lent money).
The Catholic kings acted against such disruptions of internal order in the same way the English and French have done before them. They were creating a State, and a State is defined by the monopoly of violence. They could not tolerate rioting and they could not tolerate attacks against Jews, because, according to Feudal laws, Jews were the property of the King: each time this happened, the power of the King was eroded.
Sephardic Jews, whose Iberian roots extend to the first century AD, received much the same treatment.
The moriscos -Muslims said to be converted- were expelled in 1609, after one century trying to absorb them. Cryptojews -Jews said to be converted- could not move out of Spain until around 1590. They went then preferably to the Low countries. However, they no longer lived segregated, as during the Middle Ages: they went in smaller numbers and fully integrated in the society. (Segregation was one of the causes of rioting.)
Some authors estimated the Jew population converted during the century of persecutions (1391-1492) and the expulsion in 100,000 people, in a population of 6 million Spaniards: many of us must have Jewish ancestry.
Other 100,000 Jews moved out of Spain in 1492 (estimated figures).
The expulsion effectively terminated the ferocious popular Spanish antisemitism until modern times (the foundation of the State of Israel and the Arab wars). It can only be traced back in the use of some words.
Sefardic Jews can seek the Spanish citizenship since 1924, by a law approved by General Primo de Rivera. This allowed diplomat
Sanz Briz to save 5,000 Jews from Budapest during the WWII. Some came from Greece (if the Nazi forces let them reach the Spanish embassy in Athens to apply for it). Unfortunately, for many Sefardic Jews this law was unknown (it was never publized).
The Black Legend itself, used by Protestant nations to somewhat justify their actions, was founded in Italy during the wars between Spain and France (1490-1510) on grounds that the people from the new nation created by the Catholic Kings have too much Jewish ancestry (they were
marranos, pigs).
PIGS still define the peoples of Portugal, Italy, Greece and Spain in some Northern European press' articles.