The population biology of coccidioides: epidemiologic implications for disease outbreaks.

Studies of field- and patient-derived isolates conducted over the past 75 years have provided a general picture of the population structure of Coccidioides, the cause of coccidioidomycosis. Premolecular studies provided a general outline of the geographical range, epidemiology and distribution of the fungus. Recent studies based on molecular markers have demonstrated that the genus is comprised of two genetically diverse, and genetically isolated, species: Coccidioides immitis and C. posadasii. Both species are composed of biogeographically distinct populations. Structure for two of these populations (C. immitis from central California, and C. posadasii from southern Arizona) indicates that frequent genetic recombination occurs within the entire geographic range of each population, even though sex has never been observed in the genus. Outbreaks of coccidioidomycosis are not the result of the spread of a single clonal isolate, but are caused by a diversity of genotypes. Although it is now possible to match patient isolates to populations, the lack of apparent structure within each population and the current paucity of environmental isolates limit map-based epidemiological approaches to understanding outbreaks. Therefore, a comprehensive database comprised of soil-derived isolates from across the biogeographic range of Coccidioides will improve the utility of this approach. Appropriate collection of environmental isolates will assist the investigation of remaining questions regarding the population biology of Coccidioides. The comparative genomics of representative genotypes from both species and all populations of Coccidioides will provide a thorough set of genetic markers in order to resolve the population genetics of this pathogenic fungus.

Outcrossing and recombination in the lichenized fungus Letharia.

We report evidence for recombination in lichenized fungi based on sequenced nuclear DNA markers, judging from the incongruence of their gene genealogies. Recombining population structures were found in two phylogenetic species of Letharia, one species that is observed in nature to produce abundant sexual structures (ascomata) and another species that produces abundant clonal reproductive structures (soredia) and only rarely produces ascomata. To determine whether sexual reproduction was the cause of recombination in both species, we compared several variable loci in the ascomata and maternal tissue for evidence of outcrossing. All ascomata of both species were heterozygous for at least one locus, as would be expected to result from outcrossing and not from selling. Therefore, it appears that even in the sorediate species, rare sexual reproduction results in recombination.

Phylogenetic species recognition and species concepts in fungi.

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.