Multilocus sequence analysis of Penicillium and Eupenicillium species

Taxonomy of Hyphomycetes has always been a challenging problem, with experts viewing species in different ways and modifying the taxonomy of groups to reflect their best evaluation of species limits and concepts. The advent of phylogenetic analysis, relatively easy DNA sequencing techniques and PCR has provided an opportunity for mycology to move from a strictly morphological analysis of species to phylogenetic analysis of DNA sequences. Phylogenetic theory dictates that data from different loci will produce congruent or at least non-contradictory evolutionary histories of a clonal lineage. Tests of tree ongruence such as the index of association can show whether lineages are clonal, and has revealed that some species long thought to be clonal are cryptically recombining. Genealogical concordance phylogenetic species recognition allows unambiguous identification of species boundaries.