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Background  A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied, and can provide indirect insights into historical selection dynamics. Here we use this approach to examine the demographic and selective dynamics acting of a candidate gene involved in plant-insect interactions. Previous work documents the macroevolutionary and historical ecological importance of the nitrile-specifier protein ( Nsp ), which facilitated the host shift of Pieridae butterflies onto Brassicales host plants ~80 Myr ago.    Results  Here we assess the microevolutionary dynamics of the  Nsp  gene by studying the within and among-population variation at  Nsp  and reference genes in the butterfly  Pieris rapae  (Small Cabbage White).  Nsp  exhibits unexpectedly high amounts of amino acid polymorphism, unequally distributed across the gene. The vast majority of genetic variation exists within populations, with little to no genetic differentiation among four populations on two continents. A comparison of synonymous and nonsynonymous substitutions in 70 randomly chosen genes among  P. rapae  and its close relative  Pieris brassicae  (Large Cabbage White) finds  Nsp  to have a significantly relaxed functional constraint compared to housekeeping genes. We find strong evidence for a recent population expansion and no role for strong purifying or directional selection upon the  Nsp  gene.    Conclusions  The microevolutionary dynamics of the  Nsp  gene in  P. rapae  are dominated by recent population expansion and variation in functional constraint across the repeated domains of the  Nsp  gene. While the high amounts of amino acid diversity suggest there may be significant functional differences among allelic variants segregating within populations, indirect tests of selection could not conclusively identify a signature of historical selection. The importance of using this information for planning future studies of potential performance and fitness consequences of the observed variation is discussed.

Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore