UPDATE: The paper uses the wrong Zhivotovsky et al. "evolutionary" mutation rate, hence their age estimates are inflated 3-fold. Hence, their conclusion that religion differences were superimposed on an already structured population is also wrong, in my opinion.
The write, for example that:
The Christian–Muslim split dated to 3475 (2000–6025) ybp for pooled Muslims and 3325 (1875–4225) ybp for pooled Christians.Divide these by 3 and you get about 1.2ky which is quite close (given the huge confidence intervals, of course) to the arrival of Islam to the country. Once again, the genealogical mutation rate conforms with history, while the "evolutionary" one suggests a speculative scenario about the supposed long-term maintenance of structure on which the Islam-Christian distinction was superimposed.
European Journal of Human Genetics advance online publication 1 December 2010; doi: 10.1038/ejhg.2010.177
Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon
Marc Haber et al.
Cultural expansions, including of religions, frequently leave genetic traces of differentiation and in-migration. These expansions may be driven by complex doctrinal differentiation, together with major population migrations and gene flow. The aim of this study was to explore the genetic signature of the establishment of religious communities in a region where some of the most influential religions originated, using the Y chromosome as an informative male-lineage marker. A total of 3139 samples were analyzed, including 647 Lebanese and Iranian samples newly genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified by geography and religion across Lebanon in the context of surrounding populations important in the expansions of the major sects of Lebanon, including Italy, Turkey, the Balkans, Syria, and Iran by employing principal component analysis, multidimensional scaling, and AMOVA. Timing of population differentiations was estimated using BATWING, in comparison with dates of historical religious events to determine if these differentiations could be caused by religious conversion, or rather, whether religious conversion was facilitated within already differentiated populations. Our analysis shows that the great religions in Lebanon were adopted within already distinguishable communities. Once religious affiliations were established, subsequent genetic signatures of the older differentiations were reinforced. Post-establishment differentiations are most plausibly explained by migrations of peoples seeking refuge to avoid the turmoil of major historical events.