Phylogenetic Analysis Reveals a Cryptic Species Blastomyces gilchristii, sp. nov. within the Human Pathogenic Fungus Blastomyces dermatitidis

Elizabeth M Brown,Lisa R Mctaggart,Sean X Zhang,David A Stevens,Susan E Richardson,Donald E Low,Anastasia P Litvintseva

doi:10.1371/journal.pone.0059237

Abstract

BackgroundAnalysis of the population genetic structure of microbial species is of fundamental importance to many scientific disciplines because it can identify cryptic species, reveal reproductive mode, and elucidate processes that contribute to pathogen evolution. Here, we examined the population genetic structure and geographic differentiation of the sexual, dimorphic fungus Blastomyces dermatitidis, the causative agent of blastomycosis.Methodology/Principal FindingsCriteria for Genealogical Concordance Phylogenetic Species Recognition (GCPSR) applied to seven nuclear loci (arf6, chs2, drk1, fads, pyrF, tub1, and its-2) from 78 clinical and environmental isolates identified two previously unrecognized phylogenetic species. Four of seven single gene phylogenies examined (chs2, drk1, pyrF, and its-2) supported the separation of Phylogenetic Species 1 (PS1) and Phylogenetic Species 2 (PS2) which were also well differentiated in the concatenated chs2-drk1-fads-pyrF-tub1-arf6-its2 genealogy with all isolates falling into one of two evolutionarily independent lineages. Phylogenetic species were genetically distinct with interspecific divergence 4-fold greater than intraspecific divergence and a high Fst value (0.772, P<0.001) indicative of restricted gene flow between PS1 and PS2. Whereas panmixia expected of a single freely recombining population was not observed, recombination was detected when PS1 and PS2 were assessed separately, suggesting reproductive isolation. Random mating among PS1 isolates, which were distributed across North America, was only detected after partitioning isolates into six geographic regions. The PS2 population, found predominantly in the hyper-endemic regions of northwestern Ontario, Wisconsin, and Minnesota, contained a substantial clonal component with random mating detected only among unique genotypes in the population.Conclusions/SignificanceThese analyses provide evidence for a genetically divergent clade within Blastomyces dermatitidis, which we use to describe a novel species, Blastomyces gilchristii sp. nov. In addition, we discuss the value of population genetic and phylogenetic analyses as a foundation for disease surveillance, understanding pathogen evolution, and discerning phenotypic differences between phylogenetic species.

Highlights

Microorganisms are the most abundant life forms on earth in terms of protoplasmic biomass [1,2] and second only to insects in estimated species diversity [3]
Sequencing and advancement of phylogenetic analysis has provided a powerful way to study the differentiation of fungal species at a more fundamental level by examining evolutionary processes such as population-level gene flow and genetic isolation that lead to the evolution of differential phenotypic characteristics
After reducing the dataset to 7 unique genotypes by removing clones [46] the Index of Association (IA) and rd values (Table 2) declined but remained significant (P = 0.020) signifying a deviation from panmixia. These findings indicate that a considerable portion of the association between alleles was contained within the population structure separating Phylogenetic Species 1 (PS1) from Phylogenetic Species 2 (PS2)

Summary

Introduction

Microorganisms are the most abundant life forms on earth in terms of protoplasmic biomass [1,2] and second only to insects in estimated species diversity [3]. Applying GCPSR together with other measures of genetic recombination and gene flow, cryptic species and sexual recombination have been identified among the human pathogens Histoplasma [10], Coccidioides [9,11,12,13], Paracoccidioides [14,15], and Absidia [16], the filamentious fungi Neurospora [5], Aspergillus [17,18], and Penicillium [19], and the mycorrhizal fungus Cenococcum [20]. We examined the population genetic structure and geographic differentiation of the sexual, dimorphic fungus Blastomyces dermatitidis, the causative agent of blastomycosis

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Conclusion