An excess of nonsynonymous polymorphism and extensive haplotype structure at the PtABI1B locus in European aspen (Populus tremula):: a case of balancing selection in an obligately outcrossing plant?

Here, we describe an unusually pronounced haplotype structure at the PtAB/1B locus in the obligately outcrossing tree Populus tremula. Both nucleotide diversity and divergence at PtAB/1B was low compared to other P. tremula genes suggesting that the gene is located in a region with a low mutation rate. Despite this, PtAB/1B shows a very marked excess of nonsynonymous polymorphisms across the entire coding region and linkage disequilibrium (LD) extending across the entire PtAB/1B region of approximately 2.6 kb. Such extensive LD is normally not seen in P. tremula. The extensive LD at PtAB/1B is caused by the presence of two distinct haplotypes. The haplotype structure is not caused by a lack of recombination in the region, because evidence of recombination can be detected. In addition, several statistical tests strongly reject neutrality for the PtAB/1B region, suggesting that the unusual haplotype structure could be actively maintained by balancing selection.