Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.)

Levels of genetic diversity within and among populations and species are sh aped by both external (population-level) and internal (genomic and genic) e volutionary forces. To address the effect of internal pressures, we estimat ed nucleotide diversity for a pair of homoeologous Adh loci in an allotetra ploid species, Gossypium hirsutum. These data represent the first such esti mates for a pair of homoeologous nuclear loci in plants. Estimates of nucle otide diversity for AdhA in Gossypium are lower than those for any plant nu clear gene yet described. This low diversity appears to reflect primarily a history of repeated, severe genetic bottlenecks associated with both speci ation and recent domestication, supplemented by an unusually slow nucleotid e substitution rate and an autogamous breeding system. While not statistica lly supportable, the sum of the observations also suggest differential evol utionary dynamics at each of the homoeologous loci.