Phylogenetic analyses of DNA sequence and RAPD data compared in Fusarium oxysporum and related species from maize

Phylogenetic relationships of several strains within the Fusarium oxysporum species complex and two related species from maize were used to test wheth er phylogenies inferred from nuclear-encoded translation elongation factor EF-1 alpha. and mitochondrial small subunit (mtSSU) ribosomal RNA gene sequ ences are concordant with one derived from random amplified polymorphic DNA (RAPD) characters. Results of a partition-homogeneity test (PHT) indicated that the EF-1 alpha and the mtSSU rDNA data-sets are highly homogeneous (P greater than or equal to 0.99) and could be analysed as a combined data-se t. On the basis of the results of the PHT, the three RAPD partitions were a lso analysed as a combined data-set. However, the PHT revealed conflict bet ween the nucleotide and RAPD data (P = 0.001). In addition, results of a t- test showed that the consistency, retention and rescaled consistency indice s obtained with the nucleotide sequence data were significantly higher than those obtained with the RAPD data. The t-tests of the RAPD data also showe d that these indices were significantly higher when using the 15-mer M13 RA PD primer compared with the two 10-mer primers. Although homoplasy was much greater for the RAPD data than for the DNA sequence data, topologically si milar trees were inferred from both data-sets. However, the RAPD data appea rs to be flawed because it failed to resolve the two major clades of the F. oxysporum complex and trees constructed from the RAPD decamer primers comp letely failed to resolve the F. oxysporum complex. An unnamed phylogenetica lly distinct species (Fusarium sp.) intermediate between the F. oxysporum c omplex and Fusarium redolens was identified in trees inferred from the DNA sequence and RAPD data.