This article will be an invaluable resource for students of Iberian Y-chromosome diversity, due to the numerous 18-marker haplotypes from all regions contained in the supplement.
The authors modeled the Iberian population as a 3-way mix with "Basque", "Sephardic", and "North African". The main thesis is that the fairly substantial "Sephardic" and "North African" components identified are evidence of substantial religious conversion of Jews and Muslims.
The North African component may be roughly correct; it is similar to the 6% reported for Sicily, which was also occupied by Muslims. The Sephardic component is however suspect, as it may be of either Arabic or Italian origin, or indeed even earlier population movements from the Eastern Mediterranean.
Another point of contention is with the use of Basques as pre-Sephardic/Muslim Iberians. The Christian population of Iberia prior to the arrival of the Jews and Muslims, included non-Basque Celtiberians, Romance speakers, as well as a Visigoth/Germanic layer.
Nor is it clear that the North African component in Iberians stems from Muslim converts, since bidirectional movement of populations across Gibraltar may predate the occupation of Iberia.
To see the reliability of this type of study, consider that what this study terms "Sephardic", is what another recent study termed "Phoenician". In the previous study Ibiza was considered Phoenician-influenced and compared with Mallorca and Minorca. In this one, Ibiza is assigned a hefty 33% "Sephardic Jewish" influence, while Minorca only -7.5%. At least, one would think they'd pick an admixture method that didn't result in negative contributions...
Choose your parental populations carefully, mix, shake, and get whatever result you please: Neolithic, Phoenician, Jewish, there's something for every taste.
UPDATE II (Dec 9)
Figure of frequencies added at the top of the post.
From the paper:
To formally assess the impact of North African and Sephardic Jewish contributions on the indigenous population, we carried out admixture analysis, employing the mY estimator and treating the study populations as hybrids of three parental populations. We chose the Basques as the Iberian parental sample. This is justified on the basis of a relative absence of Muslim occupation of the Basque region and supported by the genetic distinctiveness of the Basque and neighboring Gascon samples (Figure 3).
In plain English, the authors could just as well have written: "Basques are distinct from other Iberians. This may be due to either (i) the fact that there were indeed differences between Basques and other Iberians even before the Muslim occupation/Jewish settlement: after all they occupy their own region, not Iberia-at-large, and speak a different language. Or, (ii) it could be that the rest of the Iberians have undergone substantial admixture with Muslims and Jews. We arbitrarily choose hypothesis (ii) as our premise, and ¡qué sorpresa! our data backs up our pre-supposed idea."
More from the paper:
An additional factor that could lead to overestimation of Sephardic Jewish ancestry proportions is the effect of other influences on the Iberian Peninsula from eastern Mediterranean populations that might have imported lineages such as G, K*, and J. These influences fall into two different time periods: the Neolithic era, beginning in 10 KYA, the demographic effects of which are a matter for heated debate;1 and the last three millennia, the time period of Greek and Phoenician colonization.65 Effects in the second case are expected to be most marked in the eastern part of our sample area, but despite this, the apparent Sephardic Jewish ancestry proportions remain substantial in the west (Figure 4). The confounding effects of earlier population movement are likely to be particularly strong for Ibiza, Majorca, and Minorca, whose island natures make them more susceptible to influence by immigration and subsequent drift than inland sites. For example, history records that Ibiza, found to have a high apparent Sephardic Jewish ancestry proportion in our study, had an insignificant Jewish population compared to its neighbors66 yet had previously been an important Phoenician colony. Likewise, Minorca is recorded as having a substantial Jewish population,66 yet here, it shows no Sephardic Jewish ancestry.
It is true that Greek or Phoenician influence would be concentrated in particular regions. Whether Y-chromosomes "stay put" for a period of 2.5 thousand years is a different question. But, Neolithic Y-chromosomes certainly would have had ample time to be fairly uniformly distributed across the peninsula. And, the most important single aspect of Iberian history, i.e., the Roman conquest, which would have introduced not only the dominant language, but also a fair amount of genes is totally ignored.
In fact this is the single reference to the Roman period in this paper:
The Jewish presence was very long-established, with some evidence that it predated the Christian era; many Jews, however, are thought to have arrived during the Roman periodBut, seriously, in the Roman period, not only Jews, but most importantly Romans settled in Iberia. And, by the way, they must have been numerous enough to change the language. But, let's ignore these pesky Romans and pretend that Iberians are a simple mix of Basques/Moroccan/Jews.
Bottom line: great data, subpar interpretation.
American Journal of Human Genetics doi:
The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula
Susan M. Adams et al.
Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics--North African Muslims and Sephardic Jews. To address this issue, we analyzed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal and is likely to result from later enforced population movement--more marked in some regions than in others--plus the effects of genetic drift.