On the association of restriction fragment length polymorphisms across species boundaries

We study the expected values of gametic-phase disequilibrium in both nuclear and cytonuclear systems in a finite population composed of reproductively isolated subpopulations. Random drift alone within each subpopulation will generate permanent overall non-zero gametic-phase disequilibrium in both a two-locus nuclear system and a cytonuclear system unless the population has an overall initial disequilibrium of zero. We derive formulae for the expected overall disequilibrium when mutation is involved and demonstrate that these values decay to zero at an extremely slow rate compared with the decay of the expected disequilibria within each subpopulation.