Stationary Distributions of Microsatellite Loci Between Divergent Population Groups of the European Rabbit (Oryctolagus cuniculus)

Previous analysis of mitochondrial DNA polymorphism in the nativerange of the European rabbit (Oryctolagus cuniculus) demonstratedthe occurrence of two highly divergent (2 Myr) maternal lineageswith a well-defined geographical distribution. Analysis of bothprotein and immunoglobulin polymorphisms are highly concordantwith this pattern of differentiation. However, the present analysisof nine polymorphic microsatellite loci (with a total of 169alleles) in 24 wild populations reveals severe allele-size homoplasywhich vastly underestimates divergence between the main groupsof populations in Iberia. Nonetheless, when applied to morerecent historical phenomena, this same data set not only confirmsthe occurrence of a strong bottleneck associated with the colonizationof Mediterranean France but also suggests a two-step dispersalscenario that began with gene flow from northern Spain throughthe Pyrenean barrier and subsequent range expansion into northernFrance. The strength and appropriateness of applying microsatellitesto more recent evolutionary questions is highlighted by thefact that both mtDNA and protein markers lacked the allelicdiversity necessary to properly evaluate the colonization ofFrance. The well-documented natural history of European rabbitpopulations provides an unusually comprehensive framework withinwhich one can appraise the advantages and limitations of microsatellitemarkers in revealing patterns of genetic differentiation thathave occurred across varying degrees of evolutionary time. Thedegree of size homoplasy presented in our data should serveas a warning to those drawing conclusions from microsatellitedata sets which lack a set of complementary comparative markers,or involve long periods of evolutionary history, even withina single species.