Molecular population genetics of floral homeotic loci: Departures from theequilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana

Molecular variation in genes that regulate development provides insights in to the evolutionary processes that shape the diversification of morphogenet ic pathways. Intraspecific sequence variation at the APETALA3 and PISTILLAT A floral homeotic genes of Arabidopsis thaliana was analyzed to infer the e xtent and nature of diversity at these regulatory loci. Comparison of AP3 a nd Pl diversity with three previously studied genes revealed several featur es in the patterning of nucleotide polymorphisms common between Arabidopsis nuclear loci, including an excess of low-frequency nucleotide polymorphism s and significantly elevated levels of intraspecific replacement variation. This pattern suggests that ii. thaliana has undergone recent, rapid popula tion expansion and now exists in small, inbred subpopulations. The elevated intraspecific replacement levels may thus represent slightly deleterious p olymorphisms that differentiate distinct ecotypes. The distribution of repl acement and synonymous changes in AP3 and PI core and noncore functional do mains also indicates differences in the patterns of molecular evolution bet ween these interacting floral regulatory genes.