Coccidioides immitis, cause of a recent epidemic of "Valley fever" in California, is typical of many eukaryotic microbes in that mating and meiosis have yet to be reported, but it is not clear whether sex is truly absent or just cryptic. To find out, we have undertaken a population genetic study using PCR amplification, screening for single-strand conformation polymorphisms, and direct DNA sequencing to find molecular markers with nucleotide-level resolution. Both population genetic and phylogenetic analyses indicate that C. immitis is almost completely recombining. To our knowledge, this study is the first to find molecular evidence for recombination in a fungus for which no sexual stage has yet been described. These results motivate a directed search for mating and meiosis and illustrate the utility of single-strand conformation polymorphism and sequencing with arbitrary primer pairs in molecular population genetics.Unlike most plants and animals, the vast majority of eukaryotic microorganisms can reproduce asexually, and this together with their small size can make it very difficult to determine the relative importance of sexual reproduction in nature by direct observation alone. Rather, molecular markers must be used to test for the clonal population structure expected if sex is absent and the recombinant genotypes expected if sex is present (1-3). It is important in such studies that marker identity reflect common descent and that identities due to convergences, parallelisms, and reversals be minimized; in this respect, the most informative markers are DNA sequences (4,5). However, most studies of human pathogens have used allozymes or random amplified polymorphic DNAs (RAPDs) (1-3, 6). Neither approach is completely satisfactory, as allozyme patterns can be misleading because of natural selection (7), and RAPD patterns can be difficult both to repeat and to interpret in terms of Mendelian loci (8)(9)(10) (coccidioidomycosis) in California, with case reports 10 times more frequent than normal (13,14). Like some 20% of fungi (15), no sexual stage has ever been reported in C. immitis (16). Unfortunately, the inability to cross strains has hindered basic and applied research on this species.The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. MATERIALS AND METHODSFor our study we have analyzed 30 clinical isolates from 25 patients at a single hospital in Tucson, Arizona. Three patients contributed multiple samples, collected up to 3 weeks, 16 months, and 8 years apart, respectively (Table 1). ¶ All isolates were collected in [1979][1980][1981][1982][1983][1984][1985][1986][1987][1988][1989][1990], before the epidemic.Our strategy for finding molecular markers begins with low-stringency PCR amplification from genomic DNA using arbitrary primers (-20-mers) in various pairwise combinations (11). Genomic DNA was isolated following heat treatment to k...

Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein-coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein-coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.

Long-distance population dispersal leaves its characteristic signature in genomes, namely, reduced diversity and increased linkage between genetic markers. This signature enables historical patterns of range expansion to be traced. Herein, we use microsatellite loci from the human pathogen Coccidioides immitis to show that genetic diversity in this fungus is geographically partitioned throughout North America. In contrast, analyses of South American C. immitis show that this population is genetically depauperate and was founded from a single North American population centered in Texas. Variances of allele distributions show that South American C. immitis have undergone rapid population growth, consistent with an epidemic increase in postcolonization population size. Herein, we estimate the introduction into South America to have occurred within the last 9,000 -140,000 years. This range increase parallels that of Homo sapiens. Because of known associations between Amerindians and this fungus, we suggest that the colonization of South America by C. immitis represents a relatively recent and rapid codispersal of a host and its pathogen.

Abstract:Coccidioides posadasii sp. nov., formerly known as non-California (non-CA) Coccidioides immitis, is described. Phylogenetic analyses using single nucleotide polymorphisms, genes, and microsatellites show that C. posadasii represents a divergent, genetically recombining monophyletic clade. Coccidioides posadasii can be distinguished from C. immitis by numerous DNA polymorphisms, and we show how either of two microsatellite loci may be used as diagnostic markers for this species. Growth experiments show that C. posadasii has significantly slower growth rates on high-salt media when compared with C. immitis, suggesting that other phenotypic characters may exist.

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