Gene genealogies, cryptic species, and molecular evolution in the human pathogen Coccidioides immitis and relatives (Ascomycota, Onygenales)

Previous genealogical analyses of population structure in Coccidioides immi tis revealed the presence of two cryptic and sexual species in this pathoge nic fungus but did not clarify their origin and relationships with respect to other taxa. By combining the C. immitis data with those of two of its cl osest relatives, the free-living saprophytes Auxarthron zuffianum and Uncin ocarpus reesii, we show that the C. immitis species complex is monophyletic , indicating a single origin of pathogenicity. Cryptic species also were fo und in both A. zuffianum and U. reesii, indicating that they can be found i n both pathogenic and free-living fungi. Our study, together with a few oth ers, indicates that the current list of known fungal species might be augme nted by a factor of at least two. However, at least in the C: immitis, A. z uffianum, and U. reesii complexes, cryptic species represent subdivisions a t the tips of deep: monophyletic clades and thus well within the existing f ramework of generic classification. An analysis of silent and expressed div ergence and polymorphism values between and within the taxa identified by g enealogical concordance did not reveal faster evolution in C. immitis as a consequence of adaptation to the pathogenic habit, nor did it show positive Darwinian evolution in a region of a dioxygenase gene (tcrP gene coding fo r 4-HPPD) known to cause antigenic responses in humans. Instead, the data s uggested relative stasis, indicative of purifying selection against mostly deleterious mutations. Two introns in the same gene fragment were considera bly more divergent than exons and were unalignable between species complexe s but had very low polymorphism within taxa.