We introduce a spatially explicit model of natural hybrid zones that allows
us to consider how patterns of allele frequencies and linkage disequilibri
a change over time. We examine the influence of hybrid zone origins on patt
erns of variation at two loci, a locus under selection in a two-patch envir
onment, and a linked neutral locus. We consider several possible starting c
onditions that represent explicit realizations of two alternative scenarios
for hybrid zone origins: primary intergradation and secondary contact. Our
results indicate that in some circumstances, differences in hybrid zone or
igins will result in substantially different patterns of variation that may
persist for thousands of generations. Our conclusions are generally simila
r to those previously derived from partial differential equations, but ther
e are also some important differences.