This paper is based upon a presentation made at the International Association of Jewish Genealogical Societies (IAJGS) conference in Paris in July 2012. For a PDF version of this article with footnoting, visit here: https://avotaynuonline.com/wp-content/uploads/2026/03/Nogueiro-Gusmao-Amorim-1.pdf

Abstract

Crypto-Judaism is defined as the secret adherence to Judaism while publicly professing another faith. A general outcome of religious intolerance, it has been more specifically associated with the Iberian Inquisition, both in Europe and in Portuguese and Spanish colonies overseas. In Portugal, the scientific community was surprised to acknowledge the persistence of the phenomenon at the beginning of the 20th century in some small communities in the central and northeastern regions of the country (e.g., Belmonte, Bragança, Miranda, and Chaves). The strong sense of Jewish ancestry still is alive in these regions.

Due to a constellation of well-known historical events, Jewish populations are a paradigm of constantly migrating communities. In our work, we focus on a specific subset of these complex movements: the fate of the 16th-century Iberian Jewish communities and how the persistence of hidden religious practices and a strong sense of belonging to a community translate into genetic patterns. At the time of the Inquisition, Iberian Jews were a demographically non-negligible minority that was suddenly forced either to convert or to be expelled. We intend to use genetic markers typed in extant populations to infer the demographic history of the communities that stayed in Iberia (the so-called crypto-Jews) and of those that have migrated to Northern Europe and the New World.

Our initial results on paternal lineages as well as on the maternal side show that the communities that scattered over the Bragança district of Portugal have succeeded in maintaining a high level of genetic diversity and show a much closer genetic relation to Jewish populations of Europe and the Middle East, especially other Sephardic groups, than to the Portuguese host population.

Background

The arrival of Jewish people in Iberia is quite ancient and somewhat controversial. In May 2012, an archeological team, headed by Dr. Dennis Graen, found a tomb slab with a Hebrew name inscription in Silves in the south of Portugal, dating from before the year 390 CE. This provides what seems to be the oldest archaeological evidence of Jewish presence in Iberia known to date. Several historical documents for the period 1279–1325 attest to the presence of Jewish communities in the NE region of Portugal, but probably Jewish communities existed there from at least 1187. During the Middle Ages and later in the 15th century, Portuguese Jewish communities were spread all over the country, likely accounting for about 10 percent of the total Portuguese population.

The degree of political and religious (Roman Catholic) tolerance towards these communities varied considerably during the late Middle Ages, but it ended completely and abruptly in Spain in 1492, when its monarchs issued the infamous Decree of Expulsion. The decree prompted a massive emigration, with an estimated 100,000-plus going to Portugal. Only four years later, however, the Portuguese king also issued a decree of expulsion ordering the departure of all Jews and Muslims from the country. This edict, though, was far different from the one issued in Spain, as the Portuguese crown did not want its Jews to leave the country. Accordingly, in 1497, about 20,000 Jews from all over the country, preparing to go into exile, were forcibly baptized against their will and allowed to remain in the country.

This mandatory conversion turned these people into regular members of the Catholic Church, and they, therefore, were subject to its authority and faith conformity enforcement. The Crown envisioned the Holy Office of the Inquisition as a solution to the religious, socioeconomic, and political problems of the country, and in 1536, the Inquisition was established in Portugal. Although any deviation from Catholic faith orthodoxy fell under the attention of the Inquisition, its main target was crypto-Judaism, understood as the secret adherence to the Jewish faith despite an outward Catholic appearance.

One of the regions where crypto-Jewish communities established themselves after the inauguration of the Portuguese Inquisition in 1536 was Tras-os-Montes in northeastern Portugal, one of the most remote areas of the country. In 1582–83, the Inquisition arrived in the Tras-os-Montes region, reaching its peak of activity around 1599 and continuing its activities steadily over the next two centuries.

For example, in one of the villages with about 300 inhabitants at the time, more than 250 people were accused by the Inquisition of Judaizing—but it prosecuted only one person—for witchcraft, the difference demonstrates how intense the persecutions were for the New Christians. The activities of the Inquisition accounted for a significant exodus of New Christians from all over the country, especially of the intellectual and mercantile elite. The activities of the Inquisition, paradoxically, were also responsible for the strengthening and self-encroaching self-defense of the crypto-Jewish communities. The degree of true conversions among those forcibly baptized remains a matter of controversy. Portugal had three Inquisition courts—in Coimbra, Evora, and Lisbon; during their four centuries of activity, they produced almost 25,000 condemnations.

Both the Inquisition and the distinction between Old and New Christians were extinguished in 1821, with a resultant resurgence of the Jewish communities. A Jewish community was founded in Bragança in 1927 as well as a synagogue and a yeshiva, reopened 400 years after the closing of the initial one. Unfortunately, this period of relief for the Jews was brief, since the country was ruled by a right-wing dictatorship that later disclosed sympathy towards Nazi Germany. In 1934, the Jewish community gradually dissolved and resumed the previous clandestine traditions it had used for centuries. Nevertheless, even where rituals and traditions are lost, a strong sense of Jewish ancestry is still alive, and people from these villages and towns are self-aware and recognized as Jews by the host population.

In view of this historical background, and because no systematic study of the Portuguese Jewish communities has been conducted, particularly those of Tras-os-Montes, we undertook a study to answer the following major questions:

• To what extent have the crypto-Jews of Tras-os-Montes not only kept their cultural identity, but also their genetic make-up?
• Has the cultural isolation resulted in the impoverishment of genetic diversity?
• Does their genetic profile reveal the incorporation of host population contributions?

We sampled 56 unrelated self-designated Jewish males living in the Bragança district, considering a combination of historical, geographic and ethnographic/religious criteria; villages/towns in Bragança district were chosen according to references to the presence of Jewish communities in the past; individual sampling was preceded by a questionnaire, under strictly confidential circumstances in which Jewish ancestry was confirmed and genealogy was traced back at least three generations.

The study used two genetic systems, the Y chromosome and the mitochondrial DNA (mtDNA). Both systems possess several characteristics that make them useful for population genetics studies. A remarkable one is their exclusive paternal and maternal inheritance pattern, respectively. Both mtDNA and Y-chromosome DNA are uniparentally inherited markers. Another notable characteristic is the absence of recombination. As a consequence, the Y chromosome and the mtDNA are transmitted unaltered across generations with the exception of mutational events that will define lineages or haplogroups. These lineages have a particular geographical distribution pattern, allowing us to reconstruct human migrations.

Results

Our results on the paternal lineages were published in 2010. The signature of Middle East origin was detected, as shown by the high frequency of T and J haplogroups, much less common in the local Portuguese population. In addition, a relatively high frequency of the R1b1b2 haplogroup, rare in Jewish populations (although much lower than in Iberia as a whole) indicates a non-negligible admixture with non-Jewish Iberian populations. After quantifying genetic distances between populations using a statistic that measures the differences in genetic frequencies, and thus the divergence between different populations, we found that the northeastern Portuguese Jews display a much closer genetic relation to Jewish populations of Europe and the Middle East, especially other Sephardic groups, than to the general Portuguese host population.

As part of a broader ongoing strategy to sequence the whole mtDNA genome for all samples, a small fragment called the “control region” was studied in order to define the female lineages. Our first results on maternal lineages were published in 2011. As with the paternal counterpart, high frequencies of lineages of typical Near-Eastern origin (haplogroups HV0, N1, T2, and U2) were found. The maternally transmitted gene pool also displays a much closer genetic relation to Jewish populations, especially Sephardic, than to the general Portuguese population.

The high genetic diversity found is unexpected, since the effects of a small number of founders and random loss of genes over generations both act to diminish it. We infer, therefore, that there was neither a low number of founders nor a high level of homogenization, which can be explained by stable size within the community and/or by constant exchange of partners from different, geographically distant communities and, to a lesser extent, with other, non-Jewish populations. Thus, the cultural isolation of these communities has not implied the impoverishment of its genetic diversity, as is clear by the dissimilar lineages observed.

Future Research

All this new data represents just the first steps on a long road of research that eventually will bring to light, in much greater detail, the complex history of the Iberian Jewish Diaspora. Our research team is now setting out to analyze the dispersion of Jewish populations of Iberian origin to Northern Europe and America, as well as to elucidate the genetic impact (if any) of the forced migration of Jewish children to São Tomé and Príncipe around 1500. This research will require the active involvement of local communities, and their cooperation in sample collection is essential.

We are eager to answer any questions. Specific diffusion actions such as public addresses, media communications, and discussion sessions with the communities targeted with an explanation of project aims and background will be undertaken, allowing for effective, informed consent on an individual and collective basis.

Notes (see PDF of article above for embedded footnote references)

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