The use of anonymous DNA markers in assessing worldwide relatedness in theyeast species Pichia kluyveri Bedford and Kudrjavzev

Pichia kluyveri, a sexual ascomycetous yeast from cactus necroses and acidi c fruit, is divided into three varieties. We used physiological, RAPD, and AFLP data to compare 46 P. kluyveri strains collected worldwide to investig ate relationships among varieties. Physiology did not place all strains int o described varieties. Although the combined AFLP and RAPD data produced a single most parsimonious tree, separate analysis of AFLP and RAPD data resu lted in significantly different trees (by the partition homogeneity test). We then compared the distribution of strains per band to an expected distri bution. This suggested we could separate both the AFLP and RAPD datasets in to bands from rapidly and slowly changing DNA regions. When only bands from slowly changing regions (from each dataset) were included in the analysis, both the RAPD and AFLP datasets supported a single tree. This second tree did not differ significantly from the cladogram based on all of the DNA dat a, which we accepted as the best estimate of the phylogeny of these yeast s trains. Based on this phylogeny, we were able to demonstrate the strong inf luence of geography on the population structure of this yeast, confirm the monophyly of one variety, question the utility of maintaining another varie ty, and demonstrate that the physiological differences used to separate the varieties did not do so in all cases.