Geneticists are now estimating that the Spanish Inquisition led to large amounts of intermarriage between nominally converted Muslims and Jews with Catholics in Spain after 1492.
From that date, the Spanish state forbade all religions but orthodox Catholicism in Spain, making Jews and Christians who chose to remain convert.
A new study finds that 1 in 10 of Spanish men has haplotypes (genetic patterns) on the y chromosome identical with that of North Africans (i.e. Moroccans, Algerians, Tunisians). And this study suggests that 1 in 5 have haplotypes identical with Jewish males.
The evidence with regard to Spanish women is inconclusive. (This article doesn’t seem to realize it, but this is because only a minority of Jewish women have ‘Palestinian’ patterns in their mitochondrial DNA; male Jewish merchant communities established around the Mediterranean from about the 800s AD took local wives and converted them, so the majority of Jewish women don’t have distinctive genetic markers.)
I’m not so sure that the Inquisition can explain these results, since the numbers seem incommensurate with the result.
There were about 100,000 Marranos or forcibly-converted Jews in Spain after 1492 (many Iberian Jews fled to Holland, North Africa or Istanbul to retain their faith).
There were initially some 315,000 Moriscoes or forcibly-converted Muslims in the 1500s. But at the beginning of the 1600s, these were expelled, as well. By 1609 it is estimated that all but 10,000 to 15,000 of these Catholic secret Muslims had been expelled (France, Italy, and North Africa were the major destinations of the victims of this ethnic cleansing).
Spain’s population in the 1500s was about 8 million.
So I don’t see how 50,000 Marranos males could produce a situation where 1/5 of the present-day male population is descended from them. And, the huge Arab and Berber population of medieval Spain and even the 300,000 there in the 1500s, with whom there would have been intermarriage, should have left a larger genetic heritage in Spain than just 1/10. Moreover, I would challenge the idea that most of the mixing only came after the conversions post-1492. People sleep with each other across cultural boundaries and don’t tell the historians about it. And, people convert from Islam to Catholicism and pretend they’d always been Catholics, something that could have been going on surreptitiously all through the centuries of the Reconquista.
Anyway, the haplotypes distinctive to Sephardic Jews are indistinguishable from those of Palestinians and Lebanese. So my guess is that the geneticists are finding descendants from the Phoenicians and from Arab populations that invaded North Africa and then Spain, along with descendants of Jews.