I am somewhat skeptical of the Y-chromosome results included in this paper:
For one thing, the extreme paucity of haplogroup J contradicts previous reports on the Iranian population and seems hardly consistent with the geographical position of Iran. On the other hand, the excess of Y* chromosomes (the two best candidates for what they represent are G and H) is also difficult to understand. 0/51 J in Shiraz Muslims and 1/37 in Zoroastrians seems difficult to believe. The low frequency of J in Assyrians (11%) also seems to contradict the results of the public information on that population; the admin of the Aramaic DNA project estimates a 33% occurrence of that haplogroup for Assyrians based on 23andMe, FTDNA, and SMGF samples, and this seems easier to reconcile than the 11% value.
The authors also cite Yonan et al. (2009), which, as far as I can tell, does not appear to be published anywhere (let me know if it is) except as an abstract in the linked site.
Ann Hum Biol. 2011 Feb 18. [Epub ahead of print]
Y chromosome diversity among the Iranian religious groups: A reservoir of genetic variation.
Lashgary Z, Khodadadi A, Singh Y, Houshmand SM, Mahjoubi F, Sharma P, Singh S, Seyedin M, Srivastava A, Ataee M, Mohammadi ZS, Rezaei N, Bamezai RN, Sanati MH.
Background: Iran is ethnically, linguistically and religiously diverse. However, little is known about the population genetics of Iranian religious communities. Aim: This study was performed in order to define the different paternal components of the Iranian gene pool. Subjects and methods: Fourteen Y chromosome bi-allelic markers were analysed in 130 male subjects from Assyrian, Armenian and Zoroastrian groups in comparison with 208 male subjects from three Iranian Muslim groups. Results: Among the three Iranian Muslim groups, the Uromian people possessed a particularly close genetic relationship to the Armenian, whereas the Zoroastrian group was different from the Uromian, but had a close genetic relationship to the two other Muslim groups (Kermanian and Shirazian). The genetic results indicate a relationship between Armenian and Assyrian groups in Iran and a clear distinction of the former from the Zoroastrian group. However, Assyrians had elevated frequency (40%) of R*(xR1a) and low frequency (11%) of J. Conclusion: The results of this study may suggest that the Assyrian population either experienced Eurasian gene flow (possibly from Armenia) or that enforced relocations and expulsion of conquered people with different origin led to the integration of descendants with R haplogroup. This could also be due to genetic drift due to small population size and endogamy resulting from religious barriers.