Phylogenetic species recognition and species concepts in fungi

Evolution of antifungal-drug resistance: mechanisms and pathogen fitness

Like other microorganisms, fungi exist in populations that are adaptable. Under the selection imposed by antifungal drugs, drug-sensitive fungal pathogens frequently evolve resistance. Although the molecular mechanisms of resistance are well-characterized, there are few measurements of the impact of these mechanisms on pathogen fitness in different environments. To predict resistance before a new drug is prescribed in the clinic, the full spectrum of potential resistance mutations and the interactions among combinations of divergent mechanisms can be determined in evolution experiments. In the search for new strategies to manage drug resistance, measuring the limits of adaptation might reveal methods for trapping fungal pathogens in evolutionary dead ends.

Multiple genetically distinct groups revealed among clinical isolates identified as atypical Aspergillus fumigatus

To investigate whether genetic variants of A. fumigatus are found among clinical isolates, four isolates that were originally identified as poorly sporulating strains of Aspergillus fumigatus were subjected to molecular analysis. DNA sequence analysis of the alkaline protease genes of these isolates showed that each is genetically distinct and each shows substantial variation (7 to 11%) from the A. fumigatus nucleotide sequence. Subsequent morphological examination suggested that all of the isolates could be classified as Aspergillus viridinutans. To clarify the taxonomic status of these four clinical isolates and of two previously identified as atypical A. fumigatus isolates, partial beta-tubulin and 18S rRNA gene sequences were determined. Each of the six atypical strains had a unique beta-tubulin sequence, whereas the sequences of three standard isolates of A. fumigatus, which were included as controls, were identical to the published A. fumigatus beta-tubulin sequence. The very low level of DNA sequence variation detected in standard isolates of A. fumigatus compared with other isolates from members of Aspergillus section Fumigati suggests that it may be a relatively recently evolved species. The 18S rRNA gene of two of the atypical isolates differed from that of A. fumigatus at a single nucleotide position. Phylogenetic analyses do not support the classification of all of these isolates as A. viridinutans. Thus, some of these isolates represent new species which are potential opportunistic pathogens.

Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters?

Trichoderma/Hypocrea is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches.

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota)

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.

Phylogenetic divergence in a local population of the ectomycorrhizal fungus Cenococcum geophilum

Cenococcum geophilum is a widely distributed mycorrhizal species associated with diverse gymnosperm and angiosperm hosts. In previous studies, a significant amount of genetic and genotypic diversity has been detected in this species, despite the fact that C. geophilum is not thought to reproduce by meiotic or mitotic spores. We conducted a phylogenetic analysis of 103 C. geophilum isolates from a California oak woodland and seven non-California isolates using a glyceraldehyde 3-phosphate dehydrogenase gene. In addition, a subset of isolates was analyzed using sequences from ITS-rDNA, a Group I intron located in the 3' end of the SSU-rDNA and a portion of the mitochondrial SSU-rDNA. Phylogenetically distinct lineages, or cryptic species, of C. geophilum were detected at the scale of a single soil sample within our field site. As much genetic diversity was found within a soil sample as was found for isolates collected across the USA. Our results help explain the large amount of physiological, phenotypic, and genetic differences reported among isolates of C. geophilum from similar as well as diverse geographic regions. The ecological role that these sympatric cryptic species play remains to be determined.

Recurrent colonization of successively implanted tracheoesophageal vocal prostheses by a member of the Fusarium solani species complex

Tracheoesophageal vocal prostheses (TVP) in laryngectomized patients commonly deteriorate due to overgrowth by yeasts, particularly Candida species. We describe the first case of colonization of such devices by a member of the Fusarium solani species complex in a patient with a history of glottal carcinoma. Three isolates, from three prostheses, were found morphologically consistent with the traditional picture of F. solani. Ribosomal sequence analysis showed that the isolates belonged to a distinct, as yet apparently unnamed phylogenetic species within the F. solani species complex. This species, one of two distinct genetic types (genotype 2) traditionally considered part of the plant-pathogenic subtaxon Fusarium solani f. sp. radicicola, has not previously been identified as an agent of human or animal disease, although it is closely related to a known etiologic agent of mycetoma, an Acremonium-like species recently renamed Fusarium falciforme. Sequence and multisatellite M13 polymorphism analysis revealed no distinctions among the case isolates. Production of cyclosporine was detected for all three case isolates.

The life cycle of Henneguya nuesslini Schuberg & Schroder, 1905 (Myxozoa) involves a triactinomyxon-type actinospore

The life cycle of the histozoic myxozoan parasite Henneguya nuesslini was investigated in two salmonid host species. Naive brown trout, Salmo trutta, and brook trout, Salvelinus fontinalis, were experimentally infected in two trials by triactinomyxon type actinospores from naturally infected Tubifex tubifex. In exposed common carp, Cyprinus carpio, no myxospore production was detected. The parasite formed cysts with mature myxospores in the connective tissue of the fish 102 days post-exposure. The morphology of both actinosporean and myxosporean stages was described by light microscopy and a 1417-bp fragment of the 18S rDNA gene was sequenced. Sequence analysis confirmed the absolute congruence of the two developmental stages and assisted in determining species identity. Host range, tissue specificity and myxospore measurements provided sufficiently distinctive features to confirm species validity and were thus crucial for identification. The triactinomyxon spores had 16 secondary germ cells, unique dimensions, a very opaque sporoplasm matrix and three conspicuously protruding, pyriform polar capsules. This is the first record of a Henneguya sp. life cycle with a triactinomyxon-type actinospore, which suggests a close relationship with the Myxobolus group and a polyphyletic origin of the genus Henneguya.

Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations

For eukaryotic pathogens that have low levels of genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity. Here, we describe the application of an MLMT system to the emerging pathogenic fungus Penicillium marneffei. Isolates used for this study were those held in the culture collections of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and the Chiang Mai University Department of Microbiology, Chang Mai, Thailand. High genetic diversity and extensive spatial structure were observed among clinical isolates, with the geographical area of origin for each isolate strongly correlating with the occurrence of two deeply divided clades. Within each clade, multilocus linkage associations were highly significant and could be explained by genetically differentiated populations or by an exclusively clonal reproductive mode, or both. Our results show that southeast Asian penicilliosis is caused by a fungus with a complex population genetic structure. Furthermore, this MLMT system generates digital data that can be easily queried against a centrally held database via the internet (http://pmarneffei.multilocus.net/); this provides a powerful epidemiological tool for analyzing the underlying parameters that are responsible for the emergence of P. marneffei in human immunodeficiency virus-positive populations.

Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin

Fusarium oxysporum is a phylogenetically diverse monophyletic complex of filamentous ascomycetous fungi that are responsible for localized and disseminated life-threatening opportunistic infections in immunocompetent and severely neutropenic patients, respectively. Although members of this complex were isolated from patients during a pseudoepidemic in San Antonio, Tex., and from patients and the water system in a Houston, Tex., hospital during the 1990s, little is known about their genetic relatedness and population structure. This study was conducted to investigate the global genetic diversity and population biology of a comprehensive set of clinically important members of the F. oxysporum complex, focusing on the 33 isolates from patients at the San Antonio hospital and on strains isolated in the United States from the water systems of geographically distant hospitals in Texas, Maryland, and Washington, which were suspected as reservoirs of nosocomial fusariosis. In all, 18 environmental isolates and 88 isolates from patients spanning four continents were genotyped. The major finding of this study, based on concordant results from phylogenetic analyses of multilocus DNA sequence data and amplified fragment length polymorphisms, is that a recently dispersed, geographically widespread clonal lineage is responsible for over 70% of all clinical isolates investigated, including all of those associated with the pseudoepidemic in San Antonio. Moreover, strains of the clonal lineage recovered from patients were conclusively shown to genetically match those isolated from the hospital water systems of three U.S. hospitals, providing support for the hypothesis that hospitals may serve as a reservoir for nosocomial fusarial infections.

Mechanisms of fungal speciation

The objective of this review is to provide a synthesis of speciation theory, of what is known about mechanisms of speciation in fungi and from this, what is expected, and of ideas on how speciation can be elucidated in more fungal systems. The emphasis is on process rather than pattern. Phylogeographic studies in some groups, such as the agarics, demonstrate predominantly allopatric speciation, often through vicariance, as seen in many plants and animals. The variety of life history factors in fungi suggests, however, a diversity in speciation mechanisms that is borne out in comparison of some key examples. Life history features in fungi with a bearing on speciation include genetic mechanisms for intra- and interspecies interactions, haploidy as monokaryons, dikaryons, or coenocytes, distinctive types of propagules with distinctive modes of dispersal, as well as characteristic relationships to the substrate or host as specialized or generalist saprotrophs, parasites or mutualists with associated opportunities and selective pressures for hybridization. Approaches are proposed for both retrospective, phylogeographic determination of speciation mechanisms, and experimental studies with the potential for genomic applications, particularly in examining the relationship between adaptation and reproductive isolation.

Diagnosis and Population Analysis of Pythium Species Using AFLP Fingerprinting

Accurate identification of Pythium species, the causal agents of Pythium root rot and dampingoff of seedlings, and characterization of populations within the species would greatly assist in selecting and implementing control strategies for these pathogens. Several molecular techniques offer methods for accurate and rapid identification of species, but provide little information about their populations. In this study, amplified fragment length polymorphism (AFLP) fingerprinting was used to characterize plant-pathogenic Pythium species and intraspecific populations. Species-diagnostic AFLP fingerprints for Pythium aphanidermatum, P. irregulare, and P. ultimum, and tentative fingerprints for six other species, were identified. Intraspecific distance analyses of P. aphanidermatum, P. ultimum, and P. irregulare revealed distinct patterns of intraspecific variation among the three species. P. aphanidermatum showed the smallest mean distance among isolates (15%), followed by P. ultimum (37%). P. irregulare had the largest mean distance among isolates (64%), which were divided into two populations with great genetic differentiation (F_ST = 0.2), suggesting the presence of a cryptic species boundary within this species.

Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics

Filamentous fungi and yeast from the genera Saccharomyces, Penicillium, Aspergillus, and Fusarium are well known for their impact on our life as pathogens, involved in food spoilage by degradation or toxin contamination, and also for their wide use in biotechnology for the production of beverages, chemicals, pharmaceuticals, and enzymes. The genomes of these eukaryotic micro-organisms range from about 6000 genes in yeasts (S. cerevisiae) to more than 10,000 genes in filamentous fungi (Aspergillus sp.). Yeast and filamentous fungi are expected to share much of their primary metabolism; therefore much understanding of the central metabolism and regulation in less-studied filamentous fungi can be learned from comparative metabolite profiling and metabolomics of yeast and filamentous fungi. Filamentous fungi also have a very active and diverse secondary metabolism in which many of the additional genes present in fungi, compared with yeast, are likely to be involved. Although the 'blueprint' of a given organism is represented by the genome, its behaviour is expressed as its phenotype, i.e. growth characteristics, cell differentiation, response to the environment, the production of secondary metabolites and enzymes. Therefore the profile of (secondary) metabolites--fungal chemodiversity--is important for functional genomics and in the search for new compounds that may serve as biotechnology products. Fungal chemodiversity is, however, equally efficient for identification and classification of fungi, and hence a powerful tool in fungal taxonomy. In this paper, the use of metabolite profiling is discussed for the identification and classification of yeasts and filamentous fungi, functional analysis or discovery by integration of high performance analytical methodology, efficient data handling techniques and core concepts of species, and intelligent screening. One very efficient approach is direct infusion Mass Spectrometry (diMS) integrated with automated data handling, but a full metabolic picture requires the combination of several different analytical techniques.

Molecular phylogeny and taxonomy of the genus Pythium

The phylogeny of 116 species and varieties of Pythium was studied using parsimony and phenetic analysis of the ITS region of the nuclear ribosomal DNA. The D1, D2 and D3 regions of the adjacent large subunit nuclear ribosomal DNA of half the Pythium strains were also sequenced and gave a phylogeny congruent with the ITS data. All the 40 presently available ex-type strains were included in this study, as well as 20 sequences of recently described species from GenBank. Species for which no ex-type strains were available were represented by either authentic strains (6), strains used in the 1981 monograph of the genus by van der Plaats-Niterink (33), or strains selected on morphological criteria (17). Parsimony analysis generated two major clades representing the Pythium species with filamentous or globose sporangia. A small clade of species with contiguous sporangia was found in between the two main clades. A total number of 11 smaller clades was recognized, which often correlated with host-type or substrate and in several cases with a subset of morphological characters. Many characters used in species descriptions, such as antheridium position, did not correlate with phylogeny. A comparison of the ex-type and representative strains with all ITS sequences of Pythium in GenBank revealed limited infraspecific variation with the exception of P. rostratum, P. irregulare, P. heterothallicum, and P. ultimum. The total number of species examined was 116 (including 60 ex-type strains). Twenty-six species had ITS sequences identical or nearly identical to formerly described species, suggesting possible conspecificity. The importance of comparing ITS sequences of putative new species to the now available ITS database in order to avoid unwarranted new species names being introduced.

Heading for disaster: Fusarium graminearum on cereal crops

SUMMARY The rapid global re-emergence of Fusarium head blight disease of wheat and barley in the last decade along with contamination of grains with mycotoxins attributable to the disease have spurred basic research on the fungal causal agent. As a result, Fusarium graminearum quickly has become one of the most intensively studied fungal plant pathogens. This review briefly summarizes current knowledge on the pathogenicity, population genetics, evolution and genomics of Fusarium graminearum.

TAXONOMY

Based on the sexual state Gibberella zeae (Schwein.) Petch: Superkingdom Eukaryota; Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetidae; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Gibberella.

HOST RANGE

The pathogen is capable of causing head blight or 'scab' on wheat (Triticum), barley (Hordeum), rice (Oryza), oats (Avena) and Gibberella stalk and ear rot disease on maize (Zea). The fungus also may infect other plant species without causing disease symptoms. Other host genera cited for Gibberella zeae or F. graminearum sensu lato (see below) are Agropyron, Agrostis, Bromus, Calamagrostis, Cenchrus, Cortaderia, Cucumis, Echinochloa, Glycine, Hierochloe, Lolium, Lycopersicon, Medicago, Phleum, Poa, Schizachyrium, Secale, Setaria, Sorghum, Spartina and Trifolium. Disease symptoms and signs: For wheat, brown, dark purple to black necrotic lesions form on the exterior surface of the florets and glume (Fig. 1). Although these lesion symptoms sometimes are referred to as scab, they are not formally related to the hyperplasia and hypertrophic epidermal growth associated with other scab diseases such as apple scab. Peduncles immediately below the inflorescence may become discoloured brown/purple. With time, tissue of the inflorescence often becomes blighted, appearing bleached and tan, while the grain within atrophies. Awns often become deformed, twisted and curved downward. In barley, infections are not always readily apparent in the field. Infected spikelets may show a browning or water-soaked appearance. Infected barley kernels show a tan to dark brown discolouration that can be similar to that caused by other kernel blighting organisms. During prolonged wet periods, pink to salmon-orange spore masses of the fungus are often seen on infected spikelets, glumes and kernels in both wheat and barley. For maize ear rot, infection occurs by way of colonizing silk and thus symptoms first appear at the ear apex. White mycelium, turning pink to red with time, colonizes kernels and may progress basipetally, covering the entire ear.

USEFUL WEBSITES

http://www.broad.mit.edu/annotation/fungi/fusarium/mips.gsf.de/genre/proj/fusarium/ http://www.cdl.umn.edu/scab/gz-consort.html http://www.scabusa.org/

IGS–RFLP analysis and development of molecular markers for identification of Fusarium poae, Fusarium langsethiae, Fusarium sporotrichioides and Fusarium kyushuense

The intergenic spacer (IGS) regions of the rDNA of several Fusarium spp. strains obtained from the collaborative researchers (Int. J. Food Microbiol. (2003)) were amplified by polymerase chain reaction (PCR), and an IGS-RFLP analysis was performed. Restriction digestion with AluI, MspI and PstI allowed differentiation between the related Fusarium poae and Fusarium kyushuense species. Fusarium langsethiae was also separated from Fusarium sporotrichioides (including var. minus) on the basis of the banding patterns after MspI digestion, while specific XhoI, AluI and MspI restriction patterns were found in the IGS amplicons of F. sporotrichioides var. minus. According to the phylogenetic analysis of IGS-RFLP patterns, F. langsethiae (except for one strain), F. sporotrichioides, F. poae and F. kyushuense strains formed four well-supported clades with high-bootstrap values. Based on the sequence differences in the IGS region, species-specific primers were designed for the F. langsethiae/F. sporotrichioides group and for F. poae. The specificity and sensitivity of the primers were tested on various Fusarium species and isolates, and on several other important fungal genera associated with cereals. The F. poae-specific primers, designed in this study, showed the same specificity as primers Fp82f/Fp82r developed previously. The two phylogenetic subgroups of F. langsethiae, found by IGS sequencing analysis, were separated on the basis of size differences of the amplification products with primers CNL12/PulvIGSr specific for the F. langsethiae/F. sporotrichioides group. RFLP analysis of the amplified IGS region is a useful molecular assay for characterisation and a phylogenetic study of several related Fusarium species-F. langsethiae, F. sporotrichioides, F. sporotrichioides var. minus, F. poae and F. kyushuense. The primers designed in this study were highly specific and allowed identification of F. poae and the F. langsethiae/F. sporotrichioides group.

Phylogenetic analyses of the Fusarium poae, Fusarium sporotrichioides and Fusarium langsethiae species complex based on partial sequences of the translation elongation factor-1 alpha gene

Phylogenetic relationships between four Fusarium species were studied using parts of the nuclear translation elongation factor-1 alpha (EF-1alpha) gene as a phylogenetic marker. Sequences from 12 isolates of Fusarium poae, 10 isolates of Fusarium sporotrichioides and 12 isolates of Fusarium langsethiae yielded 4, 5 and 5 haplotypes, respectively. In addition, we included one isolate of Fusarium kyushuense. The aligned sequences were subjected to neighbor-joining (NJ), maximum parsimony and maximum likelihood (ML) analyses. The results from the different analyses were highly concordant. The EF-1alpha-based phylogenies support the classification of F. langsethiae as a separate taxon in the section Sporotrichiella of Fusarium, as the closest sister taxon to F. sporotrichioides, while F. kyushuense is the sister taxon to F. poae. This corresponds well with the ability of F. langsethiae and F. sporotrichioides to produce T-2 and HT-2 toxins. In contrast, morphological characters indicate a closer relationship between F. langsethiae and F. poae on the one hand, and between F. sporotrichioides and F. kyushuense on the other hand.

Metschnikowia chrysoperlae sp. nov., Candida picachoensis sp. nov. and Candida pimensis sp. nov., isolated from the green lacewings Chrysoperla comanche and Chrysoperla carnea (Neuroptera: Chrysopidae)

Fourteen yeast isolates comprising three taxa were cultured from digestive tracts of adult Chrysoperla species (Neuroptera: Chrysopidae) and their eggs. The yeast taxa were distinguished based on an estimated molecular phylogeny, DNA sequences and traditional taxonomic criteria. The new yeasts are closely related to Metschnikowia pulcherrima but are sufficiently distinguished by sequence comparison of rRNA gene sequences to consider them as novel species. Here, three novel species are described and their relationships with other taxa in the Saccharomycetes are discussed. Metschnikowia chrysoperlae sp. nov. (type strain, NRRL Y-27615T=CBS 9803T) produced needle-shaped ascospores and was the only teleomorph found. Large numbers of chlamydospores similar to those observed in M. pulcherrima were also produced. The other two novel species are asexual yeasts, Candida picachoensis sp. nov. (type strain, NRRL Y-27607T=CBS 9804T) and Candida pimensis sp. nov. (type strain, NRRL Y-27619T=CBS 9805T), sister taxa of M. chrysoperlae and M. pulcherrima. A specialized relationship between yeasts and lacewing hosts may exist, because the yeasts were isolated consistently from lacewings only. Although M. chrysoperlae was isolated from eggs and adult lacewings, suggesting the possibility of vertical transmission, no yeast was isolated from larvae.

Multigene phylogeny reveals new lineage for Stachybotrys chartarum, the indoor air fungus

Stachybotrys chartarum is an asexually reproducing fungus commonly isolated from soil and litter that is also known to occur in indoor environments and is implicated as the cause of serious illness and even death in humans. Despite its economic importance, higher level phylogenetic relationships of Stachybotrys have not been determined nor has a sexual state for S. chartarum been reported. DNA sequences from four nuclear and one mitochondrial gene were analyzed to determine the ordinal and familial placement of Stachybotrys within the Euascomycota. These data reveal that species of Stachybotrys including S. chartarum, S. albipes, for which the sexual state Melanopsamma pomiformis is reported, species of Myrothecium, and two other tropical hypocrealean species form a previously unknown monophyletic lineage within the Hypocreales. These results suggest that Stachybotrys and Myrothecium are closely related and share characteristics with other hypocrealean fungi. In addition, S. chartarum may have a sexual state in nature that consists of small, black, fleshy perithecia similar to Melanopsamma.

Evidence of sexual recombination among Cryptococcus neoformans serotype A isolates in sub-Saharan Africa

The most common cause of fungal meningitis in humans, Cryptococcus neoformans serotype A, is a basidiomycetous yeast with a bipolar mating system. However, the vast majority (>99.9%) of C. neoformans serotype A isolates possess only one of the two mating type alleles (MATalpha). Isolates with the other allele (MATa) were recently discovered and proven to mate in the laboratory. It has been a mystery whether and where C. neoformans strains undergo sexual reproduction. Here, we applied population genetic approaches to demonstrate that a population of C. neoformans serotype A clinical isolates from Botswana contains an unprecedented proportion of fertile MATa isolates and exhibits evidence of both clonal expansion and recombination within two partially genetically isolated subgroups. Our findings provide evidence for sexual recombination among some populations of C. neoformans serotype A from sub-Saharan Africa, which may have a direct impact on their evolution.

Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade

Species limits were investigated within the Fusarium graminearum clade (Fg clade) through phylogenetic analyses of DNA sequences from portions of 11 nuclear genes including the mating-type (MAT) locus. Nine phylogenetically distinct species were resolved within the Fg clade, and they all possess contiguous MAT1-1 and MAT1-2 idiomorphs consistent with a homothallic reproductive mode. In contrast, only one of the two MAT idiomorphs was found in five other species, four of which were putatively asexual, and the other was heterothallic. Molecular evolutionary analyses indicate the MAT genes are under strong purifying selection and that they are functionally constrained, even in species for which a sexual state is unknown. The phylogeny supports a monophyletic and apomorphic origin of homothallism within this clade. Morphological analyses demonstrate that a combination of conidial characters could be used to differentiate three species and three species pairs. Species rank is formally proposed for the eight unnamed species within the Fg clade using fixed nucleotide characters.

The Impact of Species Concept on Biodiversity Studies

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.

Genetic Constitution and Pathogenicity of Lolium Isolates of Magnaporthe oryzae in Comparison with Host Species-Specific Pathotypes of the Blast Fungus

ABSTRACT Fungal isolates from gray leaf spot on perennial ryegrass (prg isolates) were characterized by DNA analyses, mating tests, and pathogenicity assays. All of the prg isolates were interfertile with Triticum isolates and clustered into the crop isolate group (CC group) on a dendrogram constructed from rDNA-internal transcribed spacer 2 sequences. Since the CC group corresponded to a newly proposed species, Magnaporthe oryzae, all of the prg isolates were designated M. oryzae. However, DNA fingerprinting with MGR586, MGR583, and Pot2 showed that the prg isolates are divided into two distinct populations, i.e., TALF isolates and WK isolates. The TALF isolates were virulent only on Lolium species, whereas the WK isolates were less specific, suggesting that gray leaf spot can be caused not only by Lolium-specific isolates but also by less specific isolates. We designated the TALF isolates as Lolium pathotype. The TALF isolates showed diverse karyotypes in spite of being uniform in DNA fingerprints, suggesting that theyare unstable in genome organization.

Phylogenetic identification of Pneumocystis murina sp. nov., a new species in laboratory mice

Pneumocystisis a fungal genus that contains multiple species. One member of the genus that has not been formally analysed for its phylogenetic relationships and possible species status is thePneumocystisfound in laboratory mice,Pneumocystis murinasp. nov. (type strain ATCC PRA-111T=CBS 114898T), formerly known asPneumocystis cariniif. sp.muris. To advance research in this area, approximately 3000 bp of additional DNA sequence were obtained from the locus encoding rRNAs. This sequence and others were used to determine genetic distances betweenP. murinaand other members of the genus. These distances indicated thatP. murinaDNA is most similar to that of the species ofPneumocystisfound in laboratory rats. Nevertheless,P. murinais at least as diverged from these otherPneumocystisspecies as species in other fungal genera are from each other. The 18S rRNA gene sequence divergence exhibited byP. murinacould not be ascribed to accelerated evolution of this gene as similar levels of divergence were observed at seven other loci. When five genes were used to construct phylogenetic trees for fivePneumocystistaxa, includingP. murina, all the trees had the same topology, indicating that genes do not flow among these taxa. The gene trees were all strongly supported by statistical tests. When sequences from the rRNA-encoding locus were used to estimate the time of divergence ofP. murina, the results indicated thatP. murinais as old as the mouse. Taken together, these data support previous recognition of multiple species in the genus and indicate thatP. murinais a phylogenetic species as well.

Molecular phylogeny of the Leptosphaeria maculans-L. biglobosa species complex

Leptosphaeria maculans (anamorph Phoma lingam), the ascomycete causing stem canker of crucifers, is a species complex that can be separated into at least seven distinct subgroups using a combination of biochemical and molecular criteria. In the present study sequences of the entire ITS region, including the 5.8S rDNA, of 38 isolates representing the seven subgroups, along with specimens from culture collections, were analysed, compared to those of closely related Leptosphaperia species, and the phylogeny inferred using parsimony and distance analyses. A well-supported clade encompassed all isolates of the seven subgroups along with L. conferta, a known saprobe of dried crucifer stems. The L. maculans isolates were further separated into two well-supported clades corresponding to L. maculans s. str. and the recently named L. biglobosa. Parsimony and distance analyses further separated groups within both species, usually corresponding to specific host plants or geographic origin, e.g. L. maculans 'brassicae' from cultivated Brassica, L. maculans 'lepidii'. from Lepidium sp., L. biglobosa 'brassicae', from various Brassica species, L. biglobosa 'thlaspii' from Thlaspi arvense, L. biglobosa 'erysimii' from Erysimum sp., and L. biglobosa 'canadensis' mostly found in central Canada. The oldest L. maculans specimens maintained in international collections clustered with either L. maculans 'brassicae', L. biglobosa 'brassicae', or a still different group closely related to L. biglobosa 'thlaspii'. The evolutionary relationships between the seven infraspecific groups are discussed in terms of phytopathological relevance and species isolation linked with specific life cycle, geographic isolation or host specificity.

Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote

We critically examined methods for recognizing species in the model filamentous fungal genus Neurospora by comparing traditional biological species recognition (BSR) with more comprehensive applications of both BSR and phylogenetic species recognition (PSR). Comprehensive BSR was applied to a set of 73 individuals by performing extensive crossing experiments and delineating biological species based on patterns of reproductive success. Within what were originally considered two species, N. crassa and N. intermedia, we recognized four reproductively isolated biological species. In a concurrent study (Dettman et al. 2003), we used genealogical concordance of four independent nuclear loci to recognize phylogenetic species in Neurospora. Overall, the groups of individuals identified as species were similar whether recognized by reproductive success or by phylogenetic criteria, and increased genetic distance between parents was associated with decreased reproductive success of crosses, suggesting that PSR using genealogical concordance can be used to reliably recognize species in organisms that are not candidates for BSR. In one case, two phylogenetic species were recognized as a single biological species, indicating that significant phylogenetic divergence preceded the development of reproductive isolation. However, multiple biological species were never recognized as a single phylogenetic species. Each of the putative N. crassa x N. intermedia hybrids included in this study was confidently assigned to a single species, using both PSR and BSR. As such, no evidence for a history of hybridization in nature among Neurospora species was observed. By performing reciprocal mating tests, we found that mating type, parental role, and species identity of parental individuals could all influence the reproductive success of matings. We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms.

Phylogeography of the fungal pathogen Histoplasma capsulatum

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.

Ascospore-derived isolate ofArthrodermabenhamiaewith morphology suggestive ofTrichophytonverrucosum

Sixty-one ascospores were isolated from an ascocarp produced by the mating of two Arthroderma benhamiae strains, RV 26678 and KMU4169, that differed in their mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) patterns and in the sequences of their nuclear ribosomal internal transcribed spacer (ITS) regions. RV 26678 is a genetically typical A. benhamiae isolate, while KMU4169, though morphologically indistinguishable from A. benhamiae, is an isolate with a deviating ITS sequence and with a mtDNA RFLP profile identical to that of T. verrucosum. One of the 61 progeny ascospores formed a colony, KMU5-46, that was quite different from both parental isolates. KMU5-46 is a faviform colony morphologically similar to Trichophyton verrucosum, although its mtDNA RFLP patterns and ITS sequences were identical to those of A. benhamiae parental strain RV 26678. The morphological alteration manifested in KMU5-46, as well as this isolate's complete loss of sexual response, indicates the possibility that the asexual T. verrucosum and the sexual A. benhamiae are conspecific.

Host-parasite relationships among bolete infecting Hypomyces species

Host specificity of the mycoparasite Hypomyces microspermus to the Xerocomus chrysenteron group has been observed, but primarily from European collections. Our objectives were to test host specificity among Hypomyces spp. associated with boletes in California oak-woodlands, investigate population biology of these parasites, and to initiate studies on host-parasite coevolution. Bolete samples were collected from four locations separated by up to 600 km. Hypomyces isolates were cultured and host tissue samples taken for molecular identification. Based on AFLP analysis, four distinct Hypomyces clades were found with little genotypic diversity within each group. ITS-rDNA regions of selected isolates from each group were sequenced and analyzed along with sequences from a previously published phylogeny. Isolates from two AFLP groups clustered with H. microspermus whereas isolates from the other two AFLP groups clustered with H. chrysospermus. ITS-RFLP followed by sequence analysis identified three bolete hosts: (1) X. dryophilus; (2) a Xerocomus species closely related to X. dryophilus with affinities to X. chrysenteron; and (3) a Xerocomus species related to the X. subtomentosus group, which is not closely related to X. dryophilus and X. chrysenteron. H. microspermus infected X. dryophilus and the species with affinities to X. chrysenteron, whereas H. chrysospermus infected the species with affinities to X. chrysenteron and the species related to the X. subtomentosus group. These results support previous observations that H. microspermus is host-specific to the X. chriysenteron group, and that H. chrysospermus is more of a generalist pathogen. We also conclude that host-parasite coevolution studies within this system will not be possible until a phylogeny of North American boletes is in place.

Molecular markers reveal genetic isolation and phylogeography of the S and F intersterility groups of the wood-decay fungus Heterobasidion annosum

The root-rot fungus Heterobasidion annosum (Fr.) Bref. species complex consists of three intersterility groups (S, F, and P), separated by their host affinity. The phylogenetic relationship of the species complex was studied, with the focus on the S and F groups, by comparing DNA sequences of four nuclear gene fragments: calmodulin, glyceraldehyde 3-phosphate dehydrogenase, heat stress protein 80-1, and elongation factor 1-alpha, and one anonymous locus, from 29 fungal isolates originating from Europe, Asia, and North America. The phylogeny of each separate gene locus as well as the combined dataset consisted of three main clades: European F group isolates, Euroasian S group isolates, and North American S group isolates, suggesting them to be separated into phylogenetic species. The results also support the hypothesis of an early separation between the S and F groups, indicating that their distribution have followed their host tree species for a considerable time period.

Analysis of nrDNA sequences and microsatellite allele frequencies reveals a cryptic chanterelle species Cantharellus cascadensis sp. nov. from the American Pacific Northwest

In the Pacific Northwest, yellow chanterelles have long been referred to as Cantharellus cibarius, synonymous with the European yellow chanterelle. Broad scale genetic surveys of North American chanterelles with C. cibarius-like morphology have demonstrated that the nrDNA internal transcribed spacer exhibits length variability, suggesting that this common morphology masks a species complex. Recently researchers have used morphological and genetic data to identify the yellow chanterelle most frequently harvested from American Pacific Northwest forests as C. formosus, a species once thought to be rare in the region. We present three genetic data sets and one morphological data set that characterize a previously undescribed, species of yellow chanterelle from the central Cascade Mountains of Oregon. Phylogenetic analyses of the nrDNA large subunit and ITS regions show that C. cascadensis sp. nov., along with two other yellow chanterelle taxa (C. cibarius var. roseocanus and European C. cibarius), are more closely related to white chanterelles (C. subalbidus) than they are to C. formosus. Data from five microsatellite loci provide evidence that C. formosus, C. subalbidus, and C. cascadensis sp. nov. do not interbreed when they co-occur spatially and temporally in Douglas fir-western hemlock forests. This demonstrates that these three sympatric chanterelles are biological species with boundaries congruent with those delineated by nrDNA phylogenetic clades. Morphological data indicate that the colour of the pileus and shape of the stipe can be used to separate fresh collections of the two yellow species now known to co-occur in Douglas fir-western hemlock forests in Oregon.

Interspecific hybridization in plant‐associated fungi and oomycetes: a review

Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.

Fungal multilocus sequence typing--it's not just for bacteria

Multilocus sequence typing uses nucleotide sequence from several genes to identify individual microbial pathogens. The data obtained for multilocus sequence typing can be used to recognize fungal species and to determine if the fungi are purely clonal, or if they also recombine. Genetic regions with more polymorphisms and microsatellites might be used to recognize populations within species and are well suited to Bayesian methods of assigning unknown individuals to populations of origin. Knowledge of species, populations and reproductive mode can help answer questions common to all emerging diseases: is the disease due to the recent spread of a pathogen, to the emergence of a virulent strain of an existing pathogen, or to a change in the environment that promotes disease?

Development of markers for simple sequence repeat-rich regions that discriminate between Pisolithus albus and P. microcarpus

Inter-simple sequence repeat PCR (ISSR-PCR) was used to develop markers for simple sequence repeat-rich (SSR) regions for investigation of genetic relatedness of Pisolithus isolates collected from eastern mainland Australia. Primers were designed to amplify ten SSR-rich regions and these were used to screen 14 Pisolithus isolates. Two amplified loci showed size polymorphisms among the isolates (regarded as polymorphic), two were monomorphic for all isolates, while the remainder amplified alleles for only some isolates. UPGMA analysis of the alleles for each isolate at each locus together with ITS-RFLP analysis, separated the isolates into groups. These two groups appear to correspond to isolates that ITS sequence data have previously separated as P. albus and P. microcarpus.

Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes of Sphaeropsis sapinea and distinguish a new species of Diplodia

Sphaeropsis sapinea is an opportunistic pathogen causing serious damage to conifers, pre-disposed by adverse environmental conditions or mechanical damage. Three different morphological forms of the fungus have been described and are commonly referred to as the A, B and C morphotypes. Isolates of the different morphotypes have also been separated based on differences in pathogenicity and molecular characteristics. These differences, however, overlap and have not been considered sufficiently robust to justify the description of separate taxa. The aim of this study was to consider relationships between isolates representing different S. sapinea morphotypes, using multiple gene genealogies inferred from partial sequences of six protein-coding genes and six microsatellite loci. Genealogies generated for the protein-coding genes and microsatellite loci were not congruent but both consistently grouped isolates representing the A and C morphotypes in separate but closely related clades. In contrast, isolates of the B morphotype grouped together in a clade that was equally different to the A and C morphotypes as it was to the clade encompassing isolates of Botryosphaeria obtusa. These results provide strong evidence to show that the B morphotype isolates are distantly related to S. sapinea and represent a discrete taxon, which we describe here as Diplodia scrobiculata sp. nov.

Phylogeny of bipolar Cladonia arbuscula and Cladonia mitis (Lecanorales, Euascomycetes)

Phylogenetic relationships and levels of geographic differentiation of two closely related bipolar taxa, Cladonia arbuscula and Cladonia mitis, were cladistically examined with ITS regions, SSU rDNA introns, partial beta-tubulin, and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) genes. In the combined analysis of the four genes, C. arbuscula was paraphyletic, while C. mitis, nested within C. arbuscula, formed a strongly supported monophyletic group. C. arbuscula samples were divided into three separate clades: "arbuscula I," appearing as basal to the other ingroup taxa, "arbuscula II," and "arbuscula III" (the latter represented by only one specimen), which were not correlated with any morphological trait. Only C. mitis specimens formed a morphologically and chemically distinct group. None of the main clades was correlated with geographic origin. The separate analyses were poorly resolved, and in most cases samples from "arbuscula I," "arbuscula II," and "arbuscula III" clades were intermixed. An incongruence test revealed conflict among the four gene regions in almost all cases. Only ITS regions and introns were not significantly incongruent, suggesting lack of recombination within the ribosomal DNA locus. Incomplete lineage sorting and recombination were considered to be the main reasons accounting for the incongruencies. The high proportion of shared polymorphisms between the "arbuscula I" and "arbuscula II" clades, especially found from the beta-tubulin gene and from the ITS regions, and the lack of corroborating morphological characters both indicate a short history of reproductive isolation among the groups. The lack of genetic differentiation among the northern and southern samples within the main clades indicates a relatively recent gene flow, which may have resulted from migrations during the Pleistocene glaciations or from more recent long-distance dispersal.

Relationships of Scopulariopsis based on LSU rDNA sequences

Relationships between Scopulariopsis species and allied fungi were studied by sequencing a 350 bp gene region of the large subunit ribosomal RNA gene (LSU rDNA). In addition, a limited morphological dataset of nine characters was included in the cladistic analysis. Nineteen mitosporic strains (nine Scopulariopsis, five Wardomyces, three Doratomyces, one Trichurus and one Scedosporium species) and 21 meiosporic strains (14 Microascus, 4 Kernia and 3 Pithoascus species) were studied. The data were analysed using parsimony methods. Based on the analyses, the studied microascaceous fungi are divided to 12 molecular lineages. Most of the opportunistic human pathogenic Scopulariopsis species are placed in one clade ('Microascus manginii Clade'). Most synnematous anamorphs with Scopulariopsis-like conidia (Doratomyces and Trichurus) are placed in another clade ('Microascus albonigrescens Clade'), together with Wardomyces. Microascus sensu lato can be divided into seven clades which also incorporate all studied Pithoascus, Scopulariopsis, Wardomyces and Trichurus species and most of the Doratomyces species. Most of the Kernia teleomorphs and one Doratomyces species are placed in a different main clade, together with Pseudallescheria and Petriella. Future alternatives in the taxonomy of Microascus include splitting the genus or redefining it to include deviating taxa. More molecular data need to be obtained and considered in either case.

Evolution of drug resistance in Candida albicans

The widespread deployment of antimicrobial agents in medicine and agriculture is nearly always followed by the evolution of resistance to these agents in the pathogen. With the limited availability of antifungal drugs and the increasing incidence of opportunistic fungal infections, the emergence of drug resistance in fungal pathogens poses a serious public health concern. Antifungal drug resistance has been studied most extensively with the yeast Candida albicans owing to its importance as an opportunistic pathogen and its experimental tractability relative to other medically important fungal pathogens. The emergence of antifungal drug resistance is an evolutionary process that proceeds on temporal, spatial, and genomic scales. This process can be observed through epidemiological studies of patients and through population-genetic studies of pathogen populations. Population-genetic studies rely on sampling of the pathogen in patient populations, serial isolations of the pathogen from individual patients, or experimental evolution of the pathogen in nutrient media or in animal models. Predicting the evolution of drug resistance is fundamental to prolonging the efficacy of existing drugs and to strategically developing and deploying novel drugs.