Molecular population genetics of Arabidopsis species

Traits that have functional effects on survival and fitness in the wild often exhibit widespread phenotypic and molecular variation. I demonstrate that functionally important genetic variation can be influenced by a variety of ecological and demographic factors, including natural selection, genetic drift, mating system, population dynamics, and possibly species hybridization events.; The pattern of variation at a candidate plant defense gene, the myrosinase-encoding locus, TGG1A, was investigated in multiple individuals from two populations of Arabidopsis lyrata for evidence of natural selection. The observed variation in A. lyrata appeared to be neutral, and the two populations were highly diverged. The lack of genetic exchange between the two populations will permit the populations to evolve independently, through the processes of genetic drift and natural selection. I observed a different pattern of nucleotide variation at the myrosinase-encoding locus (TGG1) in a worldwide sample of Arabidopsis thaliana ecotypes. The estimate of nucleotide variation at this locus was low for this species, and there was an excess of high frequency derived sites relative to neutral expectations. A single ecotype shared many bases with the ancestor, and had lower myrosinase activity than all others. The data suggested the action of positive selection to increase physiological activity of a plant defensive enzyme.; I investigated the origins and divergence of Arabidopsis thaliana and close relatives A. halleri, A. lyrata ssp. petraea, and A. lyrata ssp. lyrata. I report polymorphism levels within species and divergence among species for three nuclear loci. In general, patterns of nucleotide variation support theoretical predictions that outcrossing species have higher genetic variability than inbreeding species. Outcrossing Arabidopsis lyrata was the least variable of all taxa examined, and A. lyrata alleles were a subset of A. petraea alleles. I hypothesize that A. lyrata experienced a population bottleneck during its colonization of North America. I confirm that A. thaliana diverged from the other species approximately 5 million years ago, with the other taxa diverging more recently. At one locus, A. halleri and A. petraea segregate identical polymorphisms. I hypothesize that some combination of geographic substructure, selection, and/or gene flow between species caused the observed pattern.