Book excerpt: One of the most impressive examples of parallel divergence in nature is the repeated loss of armour in freshwater threespine stickleback, yet we have little evidence for the mechanisms driving this evolutionary change. I tested two ecological factors hypothesized to drive armour divergence between marine and freshwater populations and examined the mechanisms maintaining armour variation within a polymorphic population of stickleback. I demonstrate how differences in salinity between marine and freshwater habitats might indirectly drive the reduction of lateral plate number in freshwater. Offspring with a reduced number of armour plates grew much faster than offspring with many plates when raised in fresh water, but not salt water. Larger size is positively associated with two measures of fitness, survival and reproductive potential, suggesting that the parallel loss of plates in fresh water arose through a correlated response to selection for faster growth during plate development. I show that predation by freshwater aquatic insects favours armour reduction and larger body size. Using an F2 intercross between divergent marine and freshwater populations, I measured selection on body size, spine traits and Ectodysplasin, a gene linked to quantitative trait loci for plate number, spine length, and body shape. Insect predation, when compared to experimental controls, resulted in increased juvenile size, shorter dorsal spine and pelvic girdle length after accounting for size, and favoured the low armor Ectodysplasin allele. My work on an Ectodysplasin polymorphism in a freshwater population revealed a rare example of a stable polymorphism with heterozygote disadvantage. Genetic analysis revealed that selection rather than population subdivision or assortative mating accounts for the observed heterozygote deficiency. Differences in carbon isotope signature hint that niche separation exists between Ectodysplasin homozygotes, providing an ecological mechanism (frequency-dep.