A comparison of population differentiation across four classes of gene marker in limber pine (Pinus flexilis James)

We examined genetic differentiation among seven populations of limber pine using four classes of gene marker. Among-population differentiation was much higher for maternally inherited mitochondrial DNA polymorphisms than for paternally inherited chloroplast DNA, indicating that wind-dispersed pollen is the main agent of gene flow. Chloroplast DNA differentiation is consistent with gene flow estimated in a prior paternity analysis. Using the estimates of seed and pollen flow derived from mtDNA and cpDNA differentiation, we predicted the value of Fst expected at nuclear loci. Allelic frequency differentiation at seven allozyme loci was relatively homogeneous across loci and consistent with the level of differentiation predicted from the organellar haplotypes. By contrast four of the nine randomly applied polymorphic DNA (RAPD) markers we examined were more strongly differentiated than this prediction, suggesting the action of diversifying selection. However, the differentiated RAPDs and mtDNA were concordant in dividing the populations into two groups, suggesting some historical division. Simulations show that such historical division can increase the interlocus variance in Fst, but neither a historical nor an equilibrium model could account for the joint distribution of Fst estimates across both allozyme and RAPD loci. Thus at least one group of loci appears to be experiencing natural selection.