THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification

Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies

Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis, a disease confined to Latin America and of marked importance in the endemic areas due to its frequency and severity. This species is considered to be clonal according to mycological criteria and has been shown to vary in virulence. To characterize natural genetic variation and reproductive mode in this fungus, we analyzed P. brasiliensis phylogenetically in search of cryptic species and possible recombination using concordance and nondiscordance of gene genealogies with respect to phylogenies of eight regions in five nuclear loci. Our data indicate that this fungus consists of at least three distinct, previously unrecognized species: S1 (species 1 with 38 isolates), PS2 (phylogenetic species 2 with six isolates), and PS3 (phylogenetic species 3 with 21 isolates). Genealogies of four of the regions studied strongly supported the PS2 clade, composed of five Brazilian and one Venezuelan isolate. The second clade, PS3, composed solely of 21 Colombian isolates, was strongly supported by the alpha-tubulin genealogy. The remaining 38 individuals formed S1. Two of the three lineages of P. brasiliensis, S1 and PS2, are sympatric across their range, suggesting barriers to gene flow other than geographic isolation. Our study provides the first evidence for possible sexual reproduction in P. brasiliensis S1, but does not rule it out in the other two species.

Recombination within sympatric cryptic species of the insect pathogenic fungus Metarhizium anisopliae

Metarhizium anisopliae is an insect pathogenic fungus with a worldwide distribution. It is being developed and used as a biocontrol agent against a wide range of insect pests but relatively little is known of the life history of this fungus. We tested hypotheses concerning reproductive isolation and recombination in a sample of heat-active (ability to grow at 37 degrees C) and cold-active (ability to grow at 8 degrees C) sympatrically occurring isolates of M. anisopliae from Ontario, Canada by assaying nucleotide sequence variation at six polymorphic loci: the internally transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat, and portions of calmodulin (CAL), chitin synthase (CHS), subtilisin-like protease (PR1), neutral trehalase (NTL) and actin (ACT)-encoding genes. The most parsimonious trees constructed showed a topology consistent with the heat-active and cold-active isolates as two monophyletic groups. We then applied Genealogical Concordance Phylogenetic Species Recognition (GCPSR) to the genealogical trees and concluded that the transition from concordance among branches to incongruity among branches delimited two species of M. anisopliae within Ontario. The GCPSR of two species was supported by intraspecific incongruity within each species when tested using the Partition Homogeneity test, indicating recombination. The GCPSR of two species also corresponded to the heat-active and cold-active groups. As the groups are morphologically indistinguishable we applied the term 'cryptic species'. Therefore, the sympatrically occurring heat-active and cold-active isolates represent different cryptic species with a history of recombination among isolates within each species.

Advances in molecular diagnosis of toxigenic Fusarium species: a review

The development of advanced molecular diagnosis for the critical toxigenic Fusarium species is considered in this review. The specific topics discussed are (1) isolation of mating type genes of Gibberella complex, (2) molecular detection of Fusarium-producing fumonisins, (3) molecular detection of Fusarium-producing trichothecenes and enniatins. Particular attention is given to the development of PCR assays for genes involved in the toxin biosynthesis that would permit the early detection of Fusarium species-producing toxins and potentially even reveal which particular toxin may be present within a food or feed product. Most of these data have been obtained within the 'De-Tox Fungi' project supported by the European Commission (QLK1-CT-1998-01380).

Genetic evidence of local adaptation of wheat yellow rust (Puccinia striiformis f. sp. tritici) within France

Puccinia striiformis f. sp. tritici (PST), a clonal basidiomycete causing yellow rust disease on wheat, has a long record of 'overcoming' cultivar resistance introduced by breeders. Despite the long dispersal capacity of its spores, the French population of PST presents a strong geographical structure, with the presence of a specific pathotype (array of avirulence genes) at high frequencies in the south of France. The genetic diversity underlying this differentiation was analysed by microsatellite and AFLP markers. A total of 213 French isolates belonging to 10 pathotypes collected over a 15-year period were investigated. For each of the 12 microsatellites used, polymorphism resulted from a unique allelic variant associated to the south-specific pathotype. This pathotype was characterized by 40 specific markers over the total of 63 polymorphins detected using 15 AFLP primer combinations. Phylogeographical analysis indicated a strictly clonal structure of the population, and a strong genomic divergence between the northern population and a south-specific clone. Both virulence and molecular data show that the northern French population belongs to the northwestern European population, whereas the southern clone is most likely related to a Mediterranean population, the two subpopulations resulting from the ancient divergence of two clonal lineages. While the virulence complexity in the northern population may be explained by the successive introduction of corresponding resistance genes in cultivars, the maintenance of a simple virulence type in southern France, despite gene flow between the two populations, may be explained in terms of host cultivars repartition and local adaptation to specific host or climatic conditions.

Genetic structure of populations of Alternaria brassicicola suggests the occurrence of sexual recombination

Substantial polymorphism was detected between isolates from five populations of Alternaria brassicicola attacking Cakile maritima along the New South Wales coast of Australia, with a maximum of two genotypes being shared between population pairs. Of ten pair-wise population comparisons, six had no pathogen genotypes in common; only one genotype occurred five times, and most (93 %) were found only once. Although an UPGMA based on Nei's measure of genetic distance separated the five populations, a cluster analysis using individual isolates failed to group them according to population, indicating significant gene flow. An analysis of molecular variance indicated ca 14% of the variation occurred between populations, representing moderate population differentiation over the spatial scale of the study. Tests of the relative contribution of clonality and sexual recombination indicated low, albeit significant levels of linkage disequilibrium in all populations. The level of linkage disequilibrium, and the high genotype diversity, provides support for the contention that a hitherto unidentified sexual stage might be a significant factor in the life-cycle of A. brassicicola.

Endogenous lipogenic regulators of spore balance in Aspergillus nidulans

The ability of fungi to produce both meiospores and mitospores has provided adaptive advantages in survival and dispersal of these organisms. Here we provide evidence of an endogenous mechanism that balances meiospore and mitospore production in the model filamentous fungus Aspergillus nidulans. We have discovered a putative dioxygenase, PpoC, that functions in association with a previously characterized dioxygenase, PpoA, to integrate fatty acid derived oxylipin and spore production. In contrast to PpoA, deletion of ppoC significantly increased meiospore production and decreased mitospore development. Examination of the PpoA and PpoC mutants indicate that this ratio control is associated with two apparent feedback loops. The first loop shows ppoC and ppoA expression is dependent upon, and regulates the expression of, nsdD and brlA, genes encoding transcription factors required for meiospore or mitospore production, respectively. The second loop suggests Ppo oxylipin products antagonistically signal the generation of Ppo substrates. These data support a case for a fungal "oxylipin signature-profile" indicative of relative sexual and asexual spore differentiation.

Comparative analysis of environmental and clinical populations of Cryptococcus neoformans

Cryptococcus neoformans is a major, global cause of meningoencephalitis in immunocompromised patients. Despite advances in the molecular epidemiology of C. neoformans, its population structure and mode of reproduction are not well understood. In the environment, it is associated with avian guano or vegetation. We collected nearly 800 environmental isolates from three locations in the United States (viz., North Carolina, California, and Texas) and compared them with one another and with clinical isolates from North Carolina. As expected, they consisted of the most prevalent serotypes, serotypes A and D, as well as serotype AD hybrids. The majority of environmental isolates were obtained from pigeon excreta. All environmental and clinical isolates of serotype A or D had the MATalpha mating-type allele. However, the AD hybrids included MATa alleles typical of serotypes A and D. Using an amplified fragment length polymorphism fingerprinting technique with two primer pairs, we identified 12 genotypes among the isolates of serotype A. Six of these genotypes were present in both the clinical and the environmental populations. However, one of the most prevalent environmental genotypes was absent from the clinical samples, and two other genotypes were isolated only from patients. The combined molecular data suggest that this environmental population of C. neoformans is predominantly clonal, although there was evidence for recent or past recombination.

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.

The prevalence and evolution of sex in microorganisms

The origin of sex and how sex is maintained are among the biggest puzzles in biology. Most investigations into this problem have focused on complex eukaryotes like animals and plants. This mini-review summarizes recent progress in our understanding of the evolution of sex, highlighting results from studies of experimental and natural populations of microorganisms. Increasing evidence indicates that sexual reproduction in natural populations of viruses, bacteria, and eukaryotic microbes is much more prevalent than previously thought. In addition, investigations using experimental microbial populations are providing important parameters relevant to our understanding of the origin and maintenance of sex. It is argued that microbes are excellent model organisms to explore the mechanisms responsible for the evolution of sex.

Population Structure of Seedborne Phaeosphaeria nodorum on New York Wheat

ABSTRACT Population genetic and epidemiological studies have resulted in different hypotheses about the predominant source of primary inoculum in the Phaeosphaeria nodorum-wheat pathosystem (i.e., sexually derived, windborne ascospores versus asexual or seedborne inoculum). We examined the genetic structure of seedborne populations of P. nodorum as a further step toward evaluating the hypothesis that seedborne inoculum is an important contributor to foliar epidemics in New York's rotational wheat fields. In all, 330 seedborne isolates from seven field populations were genotyped at 155 amplified fragment length polymorphism loci. Seedborne populations possessed high levels of genotypic diversity, with virtually every isolate (326/330) having a unique haplotype. As in previous population genetic studies of P. nodorum, we found low levels of gametic disequilibrium, although we could reject the null hypothesis of random mating with the index of association test for two populations. Thus, genotypically diverse and seemingly panmictic populations of P. nodorum that have been observed in wheat foliage could be derived from seedborne primary inoculum. Although sexual reproduction and recombination may contribute to the diversity of foliar populations of P. nodorum, population genetic data do not rule out seed as a source of primary inoculum. Further experimentation will be needed to determine definitively the relative importance of windborne ascospores and seed-borne asexual inoculum in epidemics of Stagonospora nodorum blotch in New York.

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.

Reproduction inAspergillus fumigatus: sexuality in a supposedly asexual species?

Aspergillus fumigatus has long been considered to reproduce only by asexual means. However, accumulating evidence suggest that a sexual stage for A. fumigatus may yet be identified. We describe results from published and ongoing studies involving population genetic analyses, genome analysis, studies of mating-type gene presence and distribution, expression of sex-related genes, and taxonomic work which support the assertion that A. fumigatus has the potential to reproduce by sexual means. The consequences of sexual reproduction for the population biology and disease management of the species are discussed. The possible mechanisms of evolution of asexuality are then considered. It is proposed that asexual species may arise in one step by mutation or loss of a key gene(s), and/or there may be a 'slow decline' in sexual fertility within the species as a whole. Thus, it is argued that species should not be considered simply as sexual or asexual, but rather as individual isolates being present on a continuum of sexual fertility, with the implications for understanding sexuality/asexuality in A. fumigatus discussed.

Geographic isolation of Diplodia scrobiculata and its association with native Pinus radiata

Diplodia pinea (syn. Sphaeropsis sapinea) is a well-known latent pathogen of Pinus spp. with a worldwide distribution. As such, this fungus is native where pines are endemic in the northern hemisphere and it has been introduced into all countries of the Southern Hemisphere where pines are exotic. The newly described D. scrobiculata (formerly known as the B morphotype of D. pinea) is thought to have a much more limited distribution. D. scrobiculata was first reported as an endophyte and weak pathogen of P. banksiana, where it was found to coexist with D. pinea. Diplodia scrobiculata is now known to have a much broader distribution in Northern America and Europe. In this study, seven Simple Sequence Repeat (SSR) markers were used to evaluate genetic diversity and gene flow between populations of D. scrobiculata. Results indicate a strong geographic isolation between populations of D. scrobiculata from different regions in North America, with unique alleles fixed in the different populations. The data fits the isolation by distance model indicating limited dispersal. Geographic isolation in combination with isolation by distance suggests prolonged reproductive isolation. Intensive collections of endophytes from native P. radiata in California have yielded only D. scrobiculata and not the significantly more pathogenic D. pinea. SSR analysis of three populations of D. scrobiculata from native P. radiata identified many shared alleles among the populations and moderate to high gene flow between them. The three Californian populations are distant and distinct from populations of D. scrobiculata from elsewhere. Under stress conditions, P. radiata is known to be very susceptible to D. pinea in plantations in the Southern Hemisphere. Native P. radiata is currently experiencing severe stress due to pitch canker caused by Fusarium circinatum. Such stress would provide ideal conditions for an associated outbreak of D. pinea. Thus, it is critical to prevent the movement of D. pinea into the last remaining native stands of P. radiata.

Patterns of genetic variation in Phialocephala fortinii across a broad latitudinal transect in Canada

Dark septate root endophytes (DSE) are an artificial assemblage of fungi that have darkly pigmented, septate hyphae and that are frequent or distinctive intracellular associates of roots of apparently healthy plants. Based on isolates obtained from the roots of Salix spp., the distribution of a common DSE fungus, Phialocephala fortinii, was examined along a latitudinal transect in Canada running from the high arctic to the 49 degrees N parallel. Non-sporulating isolates were provisionally identified as P. fortinii through analysis of DNA sequence data of the ITS2 region of rDNA. P. fortinii was isolated frequently from boreal and arctic habitats, but rarely from grassland habitats. Patterns of genetic variation were examined through analysis of amplified fragment length polymorphisms (AFLP). All AFLP profiles were unique with the majority of genetic variation occurring among individuals within the collecting sites at each latitude. Neighbour-joining analysis of genetic distances yielded eight well-supported clusters, three of which included individuals from more than one latitude. Some linkage disequilibrium, possibly due to partial clonality, was detected.

Evidence for subdivision of the root-endophyte Phialocephala fortinii into cryptic species and recombination within species

The genetic structure of the root-endophyte Phialocephala fortinii was analyzed in three study sites using 11 single-copy RFLP probes. A total of 541 strains isolated from surface-sterilized, fine roots (diameter 0.5-3 mm) of Norway spruce (Picea abies) were examined. The average gene diversity (H) was high in all three study sites. Cluster analysis showed that up to four well-separated clusters of multi-locus haplotypes were present within the sites. Significant population subdivision was detected among these clusters, suggesting that groups of multi-locus haplotypes were reproductively isolated and that P. fortinii is a species complex composed of several cryptic species. This hypothesis was supported by ISSR-PCR which showed clusters consistent with those of the multi-locus haplotypes identified by RFLP analysis. In contrast, ITS sequence analysis did not allow to separate the species as clearly. The index of association (IA) did not deviate significantly from zero within any cryptic species, suggesting that recombination occurs within these species. Cryptic species occurred sympatrically. Thalli of two cryptic species were detected in the same 5-mm-long root segment in one instance. No significant differentiation was observed among populations of the same cryptic species in forest stands located approximately 5 km from each other. This finding is consistent with significant gene flow over this spatial scale. In addition, several isolates with both identical multi-locus haplotype and identical ISSR fingerprint were found at each study site indicating genotype flow or a recent common history between study sites.

Genetic Diversity Among Alternaria solani Isolates from Potatoes in South Africa

Genetic diversity among isolates of Alternaria solani, the causal agent of early blight of potato, from various potato-growing regions in South Africa (SA), was determined using virulence assays, vegetative compatibility (VC) tests, and random amplified microsatellite (RAMS) primers. The virulence assays showed low virulence levels for the largest part of the population, but failed to otherwise characterize the population diversity. The VC tests revealed 19 VC groups (VCGs), indicating a relatively high level of diversity among the isolates. There was little correlation between geographic origin of isolates and VCGs. Analysis of RAMS profiles revealed 27% genetic diversity among 46 isolates. This value is relatively high for an asexually reproducing fungus, but is similar to values obtained previously by authors studying A. solani. Distance analysis of the RAMS profiles also provided no evidence for geographical clustering of isolates. VCG and RAMS profiles indicated that isolates are randomly spread across SA. This fact, together with the high diversity of A. solani in SA, indicates that the fungus has a high potential to adapt to resistant cultivars or fungicides. This information can aid in the breeding and deployment of A. solani-resistant potato varieties, and in early blight disease management in SA.

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.

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.

Vegetative compatibility groups in indigenous and mass-released strains of the entomopathogenic fungus Beauveria bassiana: likelihood of recombination in the field

Using nitrate non-utilizing (nit) mutants, we determined vegetative compatibility groups (VCG) among strains of Beauveria bassiana representing strains indigenous to North America, isolated from diverse insect hosts, and strains that have been mass released for insect control. Genetic similarity among these strains was analyzed using random amplified polymorphic DNA (RAPD) markers. Our data revealed 23 VCGs among the 34 strains tested, with most of these groups comprised of only a single strain. We also observed a VCG comprised of eight genetically similar strains isolated from Colorado potato beetles (CPB). Co-inoculation studies of CPB larvae with complementary nit mutants from the same or from different VCGs revealed heterokaryosis in four out of five same-VCG pairs, with only 5-17% of the sporulating cadavers generating few parasexual recombinants. In contrast, none of the infected beetles treated with non-compatible pairs generated recombinants. The large number of VCGs observed and the low frequency of in vivo recombination limited to vegetatively compatible strains indicate that this self/non-self recognition system may be an effective barrier preventing genetic exchange between dissimilar strains in the field.

Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus

Tetrachaetum elegans Ingold is a saprobic aquatic hyphomycete for which no sexual stage has yet been described. It occurs most commonly during the initial decay of tree leaves in temperate freshwater habitats and typically sporulates under water. Dispersal of the aquatic fungus takes place primarily in the water column and has a large passive component. Differences in substrate composition (e.g. quality of leaf litter) may also play a role in the distribution of different species or genotypes. The population genetic structure of T. elegans was studied using amplified fragment length polymorphism (AFLP) multilocus fingerprints. The populations were isolated from the leaf litter of three different tree genera, sampled in nine streams distributed throughout a mixed deciduous forest. Molecular markers were developed for 97 monosporic isolates using four selective primer pairs. A total of 247 fragments were scored, of which only 32 were polymorphic. Significant stream differentiation was detected for the isolates considered in this study. Analysis of molecular variance revealed that 20% of the genetic variation observed was the result of differences between streams. No correlation between genetic and geographical distances was found but a few multilocus genotypes were observed in different locations. Altogether these results suggest that environmental barriers play a role in the population structure of this aquatic fungus. No clear-cut effect of leaf litter composition on genetic variation could be demonstrated. Finally, tests of linkage disequilibrium between the 32 polymorphic AFLP loci as well as simulations did not provide a final answer regarding clonality in T. elegans. Indeed, it was possible to reject linkage equilibrium at different sampling levels and show that full linkage was unlikely.

Stepwise Evolution of Races in Fusarium oxysporum f. sp. ciceris Inferred from Fingerprinting with Repetitive DNA Sequences

ABSTRACT Plant pathogens often exhibit variation in virulence, the ability to cause disease on host plants with specific resistance, evident from the diversity of races observed within pathogen species. The evolution of races in asexual fungal pathogens has been hypothesized to occur in a stepwise fashion, in which mutations to virulence accumulate sequentially in clonal lineages, resulting in races capable of overcoming multiple host plant resistance genes or multiple resistant cultivars. In this study, we demonstrate a simple stepwise pattern of race evolution in Fusarium oxysporum f. sp. ciceris, the fungus that causes Fusarium wilt of chickpeas. The inferred intraspecific phylogeny of races in this fungus, based on DNA fingerprinting with repetitive sequences, shows that each of the eight races forms a monophyletic lineage. By mapping virulence to each differential cultivar (used for defining races) onto the inferred phylogeny, we show that virulence has been acquired in a simple stepwise pattern, with few parallel gains or losses. Such a clear pattern of stepwise evolution of races, to our knowledge, has not been demonstrated previously for other pathogens based on analyses of field populations. We speculate that in other systems the stepwise pattern is obscured by parallel gains or losses of virulence caused by higher mutation rates and selection by widespread deployment of resistant cultivars. Although chickpea cultivars resistant to Fusarium wilt are available, their deployment has not been extensive and the stepwise acquisition of virulence is still clearly evident.

Historical and contemporary multilocus population structure of Ascochyta rabiei (teleomorph: Didymella rabiei) in the Pacific Northwest of the United States

The historical and contemporary population genetic structure of the chickpea Ascochyta blight pathogen, Ascochyta rabiei (teleomorph: Didymella rabiei), was determined in the US Pacific Northwest (PNW) using 17 putative AFLP loci, four genetically characterized, sequence-tagged microsatellite loci (STMS) and the mating type locus (MAT). A single multilocus genotype of A. rabiei (MAT1-1) was detected in 1983, which represented the first recorded appearance of Ascochyta blight of chickpea in the PNW. During the following year many additional alleles, including the other mating type allele (MAT1-2), were detected. By 1987, all alleles currently found in the PNW had been introduced. Highly significant genetic differentiation was detected among contemporary subpopulations from different hosts and geographical locations indicating restricted gene flow and/or genetic drift occurring within and among subpopulations and possible selection by host cultivar. Two distinct populations were inferred with high posterior probability which correlated to host of origin and date of sample using Bayesian model-based population structure analyses of multilocus genotypes. Allele frequencies, genotype distributions and population assignment probabilities were significantly different between the historical and contemporary samples of isolates and between isolates sampled from a resistance screening nursery and those sampled from commercial chickpea fields. A random mating model could not be rejected in any subpopulation, indicating the importance of the sexual stage of the fungus both as a source of primary inoculum for Ascochyta blight epidemics and potentially adaptive genotypic diversity.

Structures of the mating-type loci of Cordyceps takaomontana

Nucleotide sequences of the mating-type loci MAT1-1 and MAT1-2 of Cordyceps takaomontana were determined, which is the first such report for the clavicipitaceous fungi. MAT1-1 contains two mating-type genes, MAT1-1-1 and MAT1-1-2, but MAT1-1-3 could not be found. On the other hand, MAT1-2 has MAT1-2-1. A pseudogene of MAT1-1-1 is located next to MAT1-2.

Diversity of Epidemic Populations of Gibberella zeae from Small Quadrats in Kansas and North Dakota

ABSTRACT Gibberella zeae (anamorph Fusarium graminearum) causes Fusarium head blight (FHB) of wheat and barley and has been responsible for several billion dollars of losses in the United States since the early 1990s. We isolated G. zeae from the top, middle, and bottom positions of wheat spikes collected from 0.25-m(2) quadrats during severe FHB epidemics in a single Kansas (KS) field (1993) and in a single North Dakota (ND) field (1994). Three amplified fragment length polymorphism (AFLP) primer pairs were used to resolve 94 polymorphic loci from 253 isolates. Members of a subset of 26 isolates also were tested for vegetative compatibility groups (VCGs). Both methods indicated high levels of genotypic variability and identified the same sets of isolates as probable clones. The mean number of AFLP multilocus haplotypes per head was approximately 1.8 in each population, but this value probably underestimates the true mean due to the small number of samples taken from each head. Isolates with the same AFLP haplotype often were recovered from different positions in a single head, but only rarely were such apparently clonal isolates recovered from more than one head within a quadrat, a pattern that is consistent with a genetically diverse initial inoculum and limited secondary spread. The KS and ND samples had no common AFLP haplotypes. All G. zeae isolates had high AFLP fingerprint similarity (>70%, unweighted pair group method with arithmetic means similarity) to reference isolates of G. zeae lineage 7. The genetic identity between the KS and ND populations was >99% and the estimated effective migration rate was high (Nm approximately 70). Tests for linkage disequilibrium provide little evidence for nonrandom associations between loci. Our results suggest that these populations are parts of a single, panmictic population that experiences frequent recombination. Our results also suggest that a variety of population sampling designs may be satisfactory for assessing diversity in this fungus.

Molecular and physiological characterization of Italian isolates of Pyrenochaeta lycopersici

Corky root of tomato caused by Pyrenochaeta lycopersici is a disease of concern in Italy and for many tomato growing areas in the world. Isolates of the fungus were characterized at both the physiological and molecular level. The optimal in vitro growth temperature for all isolates was 23 degrees C. All Italian isolates of P. lycopersici showed similar RAPD and esterase banding patterns. No relevant polymorphisms were detected after enzymatic digestion of PCR-amplified ITS and IGS regions. The overall results indicate a low degree of genetic variability within a collection of 43 Italian isolates. These data are of interest in breeding programs for resistance against corky root of tomato and they provide useful information for the development of molecular diagnostic tools for the rapid identification and detection of P. lycopersici.

Population Genetic Structure of Tapesia acuformis in Washington State

ABSTRACT Eyespot of wheat is caused by Tapesia yallundae and T. acuformis. Historically, T. yallundae has been considered the more important causal agent of the disease in Washington state and consists of a large homogeneous population with a genetic structure consistent with both sexual and asexual reproduction. T. acuformis has increased significantly in Washington in the past 10 years and apothecia were found recently under natural field conditions, indicating that T. acuformis may have a more important role in eyespot of wheat than previously was thought. To determine the genetic structure of T. acuformis in Washington, 141 single conidial isolates were sampled from four subpopulations in the eastern wheat-growing region of the state. Isolates were scored for mating type and six amplified fragment length polymorphism markers. All markers segregated in a 1:1 ratio and were determined to be unlinked based on genetic analysis of 24 progeny from an in vitro cross. No significant differences in allele frequencies (0.127 < P < 0.809) were found among individual loci across the four subpopulations and over all loci based on contingency table analysis of the log-likelihood ratio statistic G(2). Likewise, no overall differences between subpopulations were detected using the population differentiation statistic theta (theta = -0.004, P = 0.537). Random mating could not be rejected within each subpopulation or for the combined data using clone-corrected data sets based on (i) 1:1 ratio of mating-type, (ii) multilocus gametic disequilibrium analyses (index of association), (iii) phylogenetic analyses (parsimony tree length permutation test), and (iv) genotypic diversity analyses. T. acuformis has a genetic structure similar to that of sympatric populations of T. yallundae in Washington, with both sexual and asexual reproduction contributing to the structuring of this species.

Gibberella from A (venaceae) to Z (eae)

Gibberella species are destructive plant pathogens, although many are more familiar under their Fusarium anamorph names. The recent synthesis of phylogenetic, biological, and morphological species approaches has revitalized taxonomy of a genus that was first described almost 200 years ago. Twelve sexual species of Gibberella of agricultural importance were selected for this review to represent phylogenetic, biological, and chemical diversity of the genus. Even closely related Gibberella species can differ in reproductive mode, geographic and host distribution, plant pathogenesis, and production of toxins and other biologically active metabolites. Gibberella species have proven amenable to meiotic and molecular genetic analysis; A complete genome sequence of G. zeae should soon be available. Combining gene disruption strategies with new genomics technologies for expression profiling should help plant pathologists to understand the pathological and evolutionary significance of biological and chemical diversity in Gibberella and to identify novel strategies for disease control.

Population genetic structure of Pyrenophora teres Drechs. the causal agent of net blotch in Sardinian landraces of barley (Hordeum vulgare L.)

Monoconidial cultures of Pyrenophora teres, the causal agent of barley net blotch, were isolated from leaves collected from six populations of the barley landrace "S'orgiu sardu" growing in five agro-ecological areas of Sardinia, Italy, and genotyped using AFLPs. The 150 isolates were from lesions of either the "net form" (P. teres f. sp. teres) or the "spot form" (P. teres f. sp. maculata) of the disease. Of 121 AFLP markers, 42%, were polymorphic. Cluster analysis resolved the isolates into two strongly divergent groups (F(ST) = 0.79), corresponding to the net (45% of the isolates) and the spot (55% of the isolates) forms (designated the NFR and SFR groups, respectively). The absence of intermediate genotypes and the low number of shared markers between the two groups indicated that hybridization between the two formae is rare or absent under the field condition of Sardinia. Five of the barley populations hosted both forms but in different proportions. The SFR populations were similar in overall polymorphism to the NFR populations. However, compared to the SFR form, the NFR occurred in all fields sampled and showed a higher population divergence (F(ST) = 0.43 versus F(ST) = 0.09 with all isolates; F(ST) = 0.37 versus F(ST) = 0.06 with clone corrected samples) probably due to a lower migration rate. AFLP fingerprints resolved 117 distinct genotypes among the 150 isolates sampled (78%), 87% in SFR and 68% in NFR isolates. Although the absolute numbers may be a function of the number of AFLP markers assayed, the relative difference suggests that clonality is more prevalent among the NFR isolates (with 11 of 46 haplotypes observed more than once), compared with SFR isolates (7 of 71 haplotypes). Both digenic and multilocus linkage disequilibrium analyses suggested that sexual reproduction occurs at significant levels within the NFR and SFR populations, and that the relative contribution of sexual and asexual reproduction varies among different environments.

Shared ITS DNA substitutions in isolates of opposite mating type reveal a recombining history for three presumed asexual species in the filamentous ascomycete genus Alternaria

About 15,000 species of ascomycete fungi lack a known sexual state. For fungi with asexual states in the anamorph genera Embellisia, Ulocladium, and Alternaria, six species have known sexual states but more than 50 species do not. In sexual filamentous ascomycetes, opposite mating type information at the MAT1 locus regulates mating and the opposite mating type genes each have a clonal, non-recombining phylogenetic history. We used PCR to amplify and sequence fragments of the opposite mating type genes from three supposedly asexual species, A. brassicae, A. brassicicola and A. tenuissima. Each haploid fungal isolate had just one mating type, but both mating types were present in all the three species. We sequenced the ribosomal ITS regions for isolates of opposite mating type, for the three asexual species and four known related sexual species. In a phylogenetic analysis including other ITS sequences from GenBank, the three asexual species were not closely related to any of the known sexual species. Isolates of opposite mating type but the same species had identical ITS sequences. During any period of asexual evolutionary history, lineages of each mating type would have had a separate evolutionary history and any ITS substitutions shared between isolates of opposite mating type would have had to accumulate by convergence. Allowing for varying substitution rates and assuming a Poisson distribution of substitutions, the probability that isolates of opposite mating type shared an ITS substitution through convergence was low. This suggests that isolates of opposite mating type of A. brassicae, A. brassicicola and A. tenuissima were exchanging substitutions through sexual or parasexual reproduction while the ITS was evolving. If sexuality was lost, it was lost after the period of evolutionary history represented by the shared substitutions.

Clonal reproduction and limited dispersal in an environmental population of Cryptococcus neoformans var gattii isolates from Australia

Cryptococcus neoformans var. gattii is a causative agent of cryptococcosis and is thought to have a specific ecological association with a number of Eucalyptus species in Australia. However, the role that the tree plays in the life cycle of the fungus and the nature of the infectious propagule are not well understood. This study set out to examine whether sexual recombination is occurring in a natural population of C. neoformans var. gattii and whether the fungus disseminates between colonized trees. Thirty C. neoformans var. gattii isolates, consisting of both the alpha and a mating types, were collected from 13 Eucalyptus camaldulensis trees growing along a riverbank in Renmark, South Australia. The genetic diversity within the population was studied by using amplified fragment length polymorphism fingerprinting, and each isolate was assigned a unique multilocus genotype. Population genetic analyses of the multilocus data found no evidence of genetic exchange between members of the population, indicating a clonal population structure. Canonical variate analysis was then used to study the relationship between isolates from different colonized trees. Isolates from individual trees were strongly correlated, and it appeared that dispersal between trees was not occurring to any appreciable extent. These results suggest that the eucalypt may not be the primary niche for C. neoformans var. gattii but that the decaying wood present in hollows on these trees may provide a favorable substrate for extensive clonal propagation of the yeast cells.

Ecological stress and sex evolution in soil microfungi

The elucidation of the origin and maintenance of sex is a major unsolved problem in evolutionary biology. A number of hypotheses have been elaborated, but the scarcity of empirical data limits further progress. During recent years, the general inclination has changed towards pluralistic models of sex evolution, due partly to an increased diversity of studied organisms. Fungi are among the most promising organisms for testing sexual causation, as demonstrated in recent laboratory experiments. However, reconciling theory and evidence necessitates critical field observations. Here, we report new estimates of the distribution of morphologically sexual and asexual soil microfungi in nature, which indicate a remarkable trend towards increased sexuality with increasing climatic stress.

Multilocus population structure of Tapesia yallundae in Washington State

Population genetic structure of the fungal wheat pathogen Tapesia yallundae in Washington State was determined using genetically characterized amplified fragment length polymorphic (AFLP) markers and mating-type (MAT1-1 or MAT1-2). Segregation and linkage relationships among 164 AFLP markers and MAT were analysed using 59 progeny derived from an in vitro cross. Alleles at 158 AFLP loci and the mating-type locus segregated in a 1:1 ratio. Ten unlinked markers were chosen to determine genetic and genotypic diversity and to test the hypothesis of random mating and population differentiation among five subpopulations of T. yallundae representative of the geographical distribution of wheat production in eastern Washington. Among 228 isolates collected, overall gene diversity was high (h = 0.425) and a total of 91 unique multilocus genotypes (MLG) were identified, with 32 MLG occurring at least twice. The overall population genetic structure was consistent with random mating based on the segregation of mating-type, index of association (IA), parsimony tree length permutation test (PTLPT) and genotypic diversity analyses. However, clonal genotypes were found within each subpopulation and were also distributed among the five subpopulations. No significant differences in allele frequencies were found among the five subpopulations for all 10 loci based on contingency table analysis (G2) and Wier & Cockerham's population differentiation statistic theta (theta = -0.008, P = 0.722). T. yallundae appears to consist of a large homogeneous population throughout eastern Washington with both sexual and asexual reproduction contributing to the observed population genetic structure despite no report of sexual fruiting bodies of T. yallundae occurring under natural field conditions.

Estimating the spontaneous mutation rate of loss of sex in the human pathogenic fungus Cryptococcus neoformans

Few events have evolutionary consequences as pervasive as changes in reproductive behavior. Among those changes, the loss of the ability to undergo sexual reproduction is probably the most profound. However, little is known about the rate of loss of sex. Here I describe an experimental system using the fungus Cryptococcus neoformans and provide the first empirical estimate of the spontaneous mutation rate of loss of sex in fungi. Two critical steps in sexual reproduction in C. neoformans were examined: mating and filamentation. Mating, the fusion of cells of opposite sexes, is a universal first step in eukaryotic sexual reproduction. In contrast, filamentation, a prerequisite process preceding meiosis and sexual spore development, is restricted to C. neoformans and a few other fungal species. After approximately 600 mitotic divisions under favorable asexual growth conditions, mean abilities for mating and filamentation decreased significantly by >67 and 24%, respectively. Similarly, though statistically not significant, the mean vegetative growth rates also decreased and among the mutation accumulation lines, the vegetative growth rates were negatively correlated to the mating ability. The estimated mutation rates to decreases in mating ability and filamentation were in excess of 0.0172 and 0.0036, respectively. The results show that C. neoformans can be a highly attractive model for analyses of reproductive system evolution in fungi.

Cenococcum geophilum populations show a high degree of genetic diversity in beech forests

• The asexual ectomycorrhizal fungus Cenococcum geophilum, known for its wide host and habitat range, has been suggested to provide isolate-dependant drought protection to fine roots. However, little is known about its genetic structure at the fine scale. • Genetic diversity and population structure of C. geophilum at the regional and stand scales was surveyed in five beech (Fagus silvatica) forests in northeastern France. The stands were selected for their contrasting climatic and edaphic features to assess the effect of environmental factors on population structure. • The genetic diversity of C. geophilum was estimated using RAPD, PCR/RFLP of the rDNA internal transcribed spacer (ITS) and PCR/RFLP and sequencing of an anonymous sequence characterized amplified region (SCAR) on ectomycorrhizas and sclerotia-derived mycelial cultures. • A high degree of genetic diversity was observed between and within beech stands in C. geophilum populations. These results suggest the occurrence of a high rate of mitotic or meiotic recombination and an effect of stand features on population structure.

Genetic analysis of pathogenic and nonpathogenic Fusarium oxysporum from tomato plants

Forty-three Fusarium oxysporum strains and one Fusarium solani strain were analyzed for genetic diversity. These strains represent a wide range of geographic locations and were collected primarily from tomato (Lycopersicon esculentum) roots. Among all 43 F. oxysporum strains, 21 were not pathogenic to tomato, 20 were pathogenic, including 13 strains of Fusarium oxysporum lycopersici and seven strains of Fusarium oxysporum radicis-lycopersici, and two were other formae speciales of the fungus. Genetic diversity of all 43 strains was assessed by vegetative compatibility group (VCG), sequence analysis of the rDNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene, and amplified fragment length polymorphism (AFLP). Most of the F. o. lycopersici strains were assigned to VCG 0030, while most nonpathogenic ones were incompatible with each other. ITS region analysis grouped the strains into four clusters. The nonpathogenic F. oxysporum strains were in two groups, while the pathogenic strains were placed in two different groups. Pathogenic and nonpathogenic strains were also separated into different clusters based on AFLP data, although some nonpathogenic strains grouped with pathogenic strains. The population of pathogenic strains was less diverse than that of the nonpathogenic strains, suggesting that the pathogenic strains were possibly of monophyletic origin. For both pathogenic and nonpathogenic F. oxysporum strains, no relationship was observed between the genetic profiles and geographic origin; this may indicate that pathogens did not originate independently at each locality.Key words: Fusarium oxysporum, VCG, rDNA (ITS) sequence, AFLP.

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.

A multiplex PCR test for determination of mating type applied to the plant pathogens Tapesia yallundae and Tapesia acuformis

A multiplex PCR test for determining mating type of the pathogens Tapesia yallundae and Tapesia acuformis is described. The test involves three primers: a "common" primer annealing to DNA sequence conserved in the flanking region of both mating-type idiomorphs and two specific primers annealing to sequence in either the MAT-1 or the MAT-2 idiomorphs. Locating the specific primers in different positions relative to the common primer yielded PCR products of 812 or 418 bp from MAT-1 and MAT-2 isolates, respectively. The test was used successfully to determine the mating type of 118 isolates of T. yallundae and T. acuformis from Europe, North America, and New Zealand. Isolates of both mating types were found on all continents for both species despite the rarely observed occurrence of sexual reproduction of T. acuformis. The multiplex test design should be applicable to other ascomycete species, of use in studies of MAT distribution and facilitating sexual crossing by identifying compatible isolates.

Species concepts in the Cylindrocladium floridanum and Cy. spathiphylli complexes (Hypocreaceae) based on multi-allelic sequence data, sexual compatibility and morphology

Much attention has recently been devoted to the delimitation of species units in Cylindrocladium (Cy.). In this regard the present study focuses on the taxa within the unresolved Cy. floridanum and Cy. spathiphylli species complexes. Maximum parsimony analyses of DNA sequences of ITS, beta-tubulin and histone regions of rRNA genes, and mating experiments revealed a geographically isolated species of Cylindrocladium in the Cy. spathiphylli (teleomorph: Calonectria spathiphylli) species complex. Cy. pseudospathiphylli sp. nov. (teleomorph: Ca. pseudospathiphylli sp. nov.) is described as a new phylogenetic, biological and morphological species. It is distinguished from Cy. spathiphylli by being homothallic, having smaller macroconidia, and distinct DNA sequences of beta-tubulin and histone genes. Similarly, parsimony analysis of a combined data set also indicated several phylogenetic species to exist within Cy. floridanum (teleomorph: Ca. kyotensis). Based on differences in vesicle morphology and conidium dimensions, the Canadian population of Cy. floridanum, formerly known as Cy. floridanum Group 2, is described as Cy. canadense sp. nov., while a further collection from Hawaii is described as Cy. pacificum sp. nov.