Population genetics of the hispid cotton rat (Sigmodon hispidus): patternsof genetic diversity at the major histocompatibility complex

The hispid cotton rat, Sigmodon hispidus, is a common rodent widely distrib uted across the southern USA and south into South America. To characterize major histocompatibility complex WHO diversity in this species and to eluci date large-scale patterns of genetic partitioning, we examined MHC genetic variability within and among 13 localities, including a disjunct population in Arizona and a population from Costa Rica that may represent an undescri bed species. We also tested the hypothesis that populations within the USA are at equilibrium with regard to gene flow and genetic drift, resulting in isolation-by-distance. Using single-strand conformation polymorphism (SSCP ) analysis we identified 25 alleles from 246 individuals. Gene diversity wi thin populations ranged from 0.000 to 0.908. Analysis of molecular variance (AMOVA) revealed that 83.7% of observed variation was accounted for by wit hin-population diversity and 16.3% was accounted for by among-population di vergence. The disjunct population in Arizona was fixed for a single allele. The Costa Rican population was quite divergent based on allelic compositio n and was the only population with unique alleles. Within the main portion of the geographical distribution of S. hispidus in the USA there was consid erable divergence among some populations; however, there was no significant pattern of isolation-by-distance overall (P = 0.090). Based on the signifi cant divergence of the only sampled population to its east, the Mississippi River appears to represent a substantial barrier to gene flow.