A genetic analysis of northern Portuguese crypto-Jews recently yielded a mysterious discovery: It exposed an isolated Jewish community that has somehow retained its genetic identity for centuries - while avoiding the inbreeding that usually occurs in such situations.

Now scientists are trying to understand how these Jews managed to bypass a condition which worries most small, closed Jewish communities in the world.

The new study by researchers from Porto and Coimbra Universities showed that Jews from the Braganca area are genetically closer to Middle Eastern Jews than to the surrounding Portuguese - even after living there for 500 years. This emerged from an analysis of the Y chromosome, which is passed exclusively from father to son with negligent recombination.

This genetic match was observed also in the Jews of Belmonte, a small town situated some 200 kilometers south of Braganca. However, the genetic analysis of Belmonte Jews showed a dramatic drop in genetic diversity, indicative of inbreeding. This is normal for isolated communities, simply because less genetic material is introduced each generation.

"All small-sized gene pools tend to lose diversity, but the communities from the Braganca area have succeeded in maintaining a very high diversity, with a relatively small non-Jewish introgression," said Professor Antonio Amorim, a geneticist from the University of Porto who performed the research.

The recently published research by Amorim's team of scientists characterized examined the paternal lineages of 57 unrelated males of established Jewish origins from around Braganca. The community there is estimated at a few hundred people at most.

A high lineage diversity was found, at both haplotype and haplogroup levels (98.74 and 82.83%, respectively), demonstrating the absence of a strong genetic drift, the research said. It was the first time that the genetic makeup of northern Portuguese Jews had been analyzed.

"The results of surprised me," Amorim told Haaretz of his team's study, which appeared a few weeks ago in the American Journal of Physical Anthropology. "My surprise is two-fold," he added, referring to both the low level of inbreeding and to the retention of Jewish genes.

"These results can only be explained assuming that the effective size of the population is much greater that it would seem at the first sight," Amorim concluded, "and/or that there is a reproductive strategy minimizing the loss of male lineages but not avoiding totally the input of non-Jewish males."

The team of researchers said that "a deeper and more detailed investigation is required to clarify how these communities avoided the expected inbreeding caused by over four centuries of religious repression." They are still waiting for the analyses on the maternal lineages, Amorim said.

Jews have resided in the rugged and isolated towns around Braganca since 1187, but most settled there after the 1492 Decree of Expulsion from Spain during the Spanish Inquisition. Jews were allowed to stay in Portugal if they converted to Christianity, but whole communities continued to practice in secret, becoming crypto-Jews. The people studied in the research belonged to such families.

Portugal is currently seeing the turning toward Judaism of thousands of Portuguese who believe they are descended from crypto-Jews. They are assisted by the Jerusalem-based organization Shavei Israel, headed by the U.S.-born Michael Freund.

"This study demonstrates the extent to which the Jews of Portugal who were forcibly converted more than five centuries ago sought to preserve their Jewishness down through the generations," he said. "They made heroic efforts to sustain their Jewish identity in secret, and many only married among themselves, as the findings of this study indicate," he said.