"Within N1b, the N1b2 haplogroup is considered as a founding lineage in Ashkenazi Jews with a ‘Hebrew/Levantine' origin.61 However, an alternative European origin encompassing an assimilation of this lineage into the founding Ashkenazi population along the north Mediterranean coast has been recently proposed.52 Unexpectedly, we found no samples belonging to the N1b2 haplogroup among the Bragança Jews — all N1b samples fall inside the N1b1 sister-clade (N1b1a2 and N1b1a5) and the N1a1a1a2 sub-haplogroup. According to the most parsimonious tree for complete sequences (Supplementary Figure 4), within sub-haplogroup N1b1a2, a transition at position m.204T>C defines a cluster with three samples, one from this study along with one from Zamora and another with an unknown origin. To further investigate this cluster, a search for similar CR haplotypes was performed in the EMPOP database and only three sequences were found. Two of them were from the same geographical area, namely Zamora (the same sample from Supplementary Figures 3 and 4) and Miranda do Douro,41, 42 both places with a well-documented history of Jewish presence. The remaining one was interestingly also from a Jew, an Ashkenazi from Hungary,62 thus this transition could be identified as a Jewish, albeit not exclusively Sephardic founding lineage.

In the N1b1a5 sub-clade, the only matches found at EMPOP database, including the transition at position m.16311T>C, were with five samples from Miranda do Douro41 and one from Uzbekistan,63 about which no further information was available. As neither the Bragança Jews nor the Mirandese population share haplotypes with the Portuguese population, and given their geographic proximity in a rather remote and isolated area, as well as the fact that there was an organized Jewish community in Miranda, at least from the twelfth century on,4 these individuals could easily also be Jewish descendants who lost memory of their origins or have not been detected as such, as in Mairal et al41 sampling did not include ethnical criteria.

Regarding the N1a1a1a2 branch, the transitions at positions m.150C>T, m.4501C>T and m.11977C>T defines a cluster that includes the Bragança Jews (with no shared haplotypes with the Portuguese population). Lineages carrying the m.150C>T transition were not found in available databases and thus represent what could be a specific feature of the Sephardic Jews from NE Portugal.

Considering that haplogroup N1 is very rare in contemporary European populations, the low number of complete available sequences from the Near East, as well as the poor definition obtained so far for this haplogroup in the Iberian Neolithic samples60 (N*), it seems at the moment hazardous to conclude whether the lineages found here are relics brought from the Near East by the first Jewish diasporas or were assimilated into the ancestral Iberian Jewish population in Europe."
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402619/