Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L-(Brassicaceae): haplotype relationships and population structure

Chloroplast DNA (cpDNA) sequence variation is currently the most widely use d tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than c oding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many o f these studies is that intraspecific cpDNA variation is either absent or l ow and therefore will not interfere with the reconstruction of interspecifi c relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspe cific cpDNA sequence variation. These levels were compared to levels of int erspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoi des, and intraspecific differences were often larger than interspecific dif ferences. cpDNA haplotype relationships were explored using a maximum parsi mony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the p resumed evolutionary history of cpDNA haplotypes. A combined effect of cpDN A introgression and complex lineage sorting was inferred to explain the pat tern of cpDNA variation found in D. aizoides. Our results suggest that intr aspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships a mong closely related taxa.