¹Departments of Ecology and Environmental Science, Umeå Plant Science Centre, University of Umeå, Umeå, Sweden

Correspondence: Dr PK Ingvarsson, Departments of Ecology and Environmental Science, Umeå Plant Science Centre, University of Umeå, Fysiologihuset, Umeå SE-891 87, Sweden. E-mail: pelle@wallace.emg.umu.se

Received 10 October 2006; Revised 2 April 2007; Accepted 7 May 2007; Published online 6 June 2007.

Abstract

Here, we describe an unusually pronounced haplotype structure at the PtABI1B locus in the obligately outcrossing tree Populus tremula. Both nucleotide diversity and divergence at PtABI1B was low compared to other P. tremula genes suggesting that the gene is located in a region with a low mutation rate. Despite this, PtABI1B shows a very marked excess of nonsynonymous polymorphisms across the entire coding region and linkage disequilibrium (LD) extending across the entire PtABI1B region of approximately 2.6 kb. Such extensive LD is normally not seen in P. tremula. The extensive LD at PtABI1B 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 PtABI1B region, suggesting that the unusual haplotype structure could be actively maintained by balancing selection.