The study uses amplified fragment analysis, finding evidence for parapatric speciation occurring in populations of the intertidal snail Littorina saxatilis (rough periwinkle) living on rocky shores. Non-allopatric speciation hypotheses often lead to debate and controversy. Rice and Hostert (1993) demonstrated simple models where genetic divergence can occur in circumstances of strong disruptive selection, without any period of isolation between populations. In the study’s L. saxatilis example, populations are distributed across a vertical gradient. Gene flow is limited between the populations according to position along the cline. Strong selection and either pleiotropy or linkage is necessary between genes responsible for the adaptive polymorphism and genes affecting probability of gene exchange between sympatrically diverging populations. Initial differentiation can be amplified to increase isolation by the accumulation of different alleles between diverging populations. Allopatric speciation shows uniform divergence across the genome. A signature of non-allopatric speciation occurring can be inferred when some loci show allele frequency differentiation and others not, suggesting genetic exchange is variably restricted across the genome. The study compares FST values of 306 AFLP loci with a FST predicted value distribution derived from a model using mutation and migration data. 15 loci of the 306 loci (5%) showed greater differentiation than expected from the model, compared to the majority remainder where differentiation was weak. Inferred is that 95% of experimental loci are in an equilibrium of mutation, drift and dispersal. At loci where differentiation exceeded predictions of the model, selection on the loci (or closely linked loci) is suggested as maintaining divergence. An alternative hypothesis described in the paper explains the pattern of divergence as differential introgression after an instance of secondary contact. Uniformly divergent populations resulting from allopatric speciation mechanisms may later differentially introgress, producing homogenisation of allele frequencies at all loci other than those under selection or those linked to other loci under selection. The possibility of in situ divergence is also discussed, where strong selection pressure can produce a similar pattern of divergence despite gene flow. The collected specimens were two morphs of Littorina saxatilis, a periwinkle, found in five locations in Yorkshire. These two morphs were parapatric populations with an observable cline. Using head-foot tissue samples, their DNA was isolated and amplified fragment length polymorphism analysis (AFLP analysis) was conducted. Gels with the primer-treated product were used to expose a film and the products were scored by band presence. Analysis assumed banded individual dominance and Hardy-Weinberg genotype frequencies. A simulation was run to compare its FST values to that of the real population. Ten loci of the experiment population had higher values. These were removed, and further comparisons of the morphs were run. Fifteen loci were eventually identified that showed variation between the H and M morph. These loci were theorised to be either under selection themselves or linked to loci that were selected upon. This only occurred between morphs from different locations. This variation did not occur within morphs. FST values, even with removal of these loci, show that there is a small barrier between populations to prevent gene exchange. There was also evidence of a distance barrier, but this was not entirely responsible for mating prevention between morphs. This barrier grows larger when the fifteen identified loci remain. Therefore they, or linked loci, are the reason for selection, and are being maintained by it. It was not determined if this was due to primary or secondary differentiation.