Sexual origins of British Aspergillus nidulans isolates

Why outcross? The abandon-ship hypothesis in a facultative outcrossing/selfing fungal species

Most species able to reproduce both sexually and asexually (facultative sexual species) invest more in sexual reproduction in stressful environment conditions. According to the abandon-ship hypothesis, plasticity for investment in sexual reproduction may have been selected in these species, allowing unfit genotypes to generate progeny carrying new advantageous allelic combinations. We tested this hypothesis in Aspergillus nidulans, a fungus able to reproduce asexually, or sexually, by outcrossing and/or haploid selfing (i.e. fusion of genetically identical haploid nuclei, causing immediate genome-wide homozygosity). We crossed various strains of A. nidulans in a non-stressful environment and a stressful environment containing a non-lethal dose of fungicide. Without stress, crosses preferentially generated haploselfed fruiting bodies, whereas stressful conditions significantly increased the outcrossing rate. Our results strongly support the abandon-ship hypothesis and suggest that, for parents with low fitness, the costs of investing in sexual reproduction may be compensated by the production of fitter progeny carrying beneficial allele combinations. Similarly, the progeny generated by outcrossing was less fit than that produced by haploid selfing in non-stressful environments, but fitter in stressful conditions, suggesting that outcrossing may have short-term advantages in stressful environments in A. nidulans.

Aspergillus: sex and recombination

The genus Aspergillus is one of the most widespread groups of fungi on Earth, comprised of about 300-350 species with very diverse lifestyles. Most species produce asexual propagula (conidia) on conidial heads. Despite their ubiquity, a sexual cycle has not yet been identified for most of the aspergilli. Where sexual reproduction is present, species exhibit either homothallic (self fertile) or heterothallic (obligate outcrossing) breeding systems. A parasexual cycle has also been described in some Aspergillus species. As in other fungi, sexual reproduction is governed by mating-type (MAT) genes, which determine sexual identity and are involved in regulating later stages of sexual development. Previous population genetic studies have indicated that some supposedly asexual aspergilli exhibit evidence of a recombining population structure, suggesting the presence of a cryptic sexual cycle. In addition, genome analyses have revealed networks of genes necessary for sexual reproduction in several Aspergillus species, again consistent with latent sexuality in these fungi. Knowledge of MAT gene presence has then successfully been applied to induce sexual reproduction between MAT1-1 and MAT1-2 isolates of certain supposedly asexual aspergilli. Recent progress in understanding the extent and significance of sexual reproduction is described here, with special emphasis on findings that are relevant to clinically important aspergilli.

The mode of reproduction in natural populations of ascomycetous fungus, Emericella nidulans, from Israel

The mode of reproduction of the soil ascomycetous fungus Emericella nidulans of Israeli populations was studied using 15 microsatellite (simple sequence repeats or SSR) trinucleotide markers. The study was performed in three canyons: two located in the northern part of Israel (Mount Carmel and western Upper Galilee) and one in the southern Negev desert. In each canyon, E. nidulans strains were isolated from the opposite slopes and (in the desert canyon) the valley bottom. Testing the reproductive structure of the populations indicated the presence of sexuality in the northern population and predominant clonality in the desert population. The predominantly clonal character of the desert population of E. nidulans was explained by the assumption that for relevant multilocus systems of a fungus, only several haplotypes can survive in the rather constant, extremely stressful desert conditions. Additionally, the very low density of E. nidulans populations in the soil of the desert canyon, which reduces the probability of finding a sexual partner, might favour predominant clonality via selfing. Increasing sexuality in E. nidulans populations on the north-facing slopes of the northern canyons may be a result of biotic stress (pressure of competitive fungal species), due to the more mild ecological conditions in these canyons.

RNA silencing gene truncation in the filamentous fungus Aspergillus nidulans

The genus Aspergillus is ideally suited for the investigation of RNA silencing evolution because it includes species that have experienced a variety of RNA silencing gene changes. Our work on this subject begins here with the model species Aspergillus nidulans. Filamentous ascomycete fungi generally each encode two of the core RNA silencing proteins, Dicer and Argonaute, but A. nidulans appears to have lost one of each to gene truncation events. Although a role in growth, development, or RNA silencing was not detected for the truncated genes, they do produce spliced and poly(A)-tailed transcripts, suggesting that they may have an undetermined biological function. Population analysis demonstrates that the truncated genes are fixed at the species level and that their full-length orthologs in a closely related species are also unstable. With these gene truncation events, A. nidulans encodes only a single intact Dicer and Argonaute. Their deletion results in morphologically and reproductively normal strains that are incapable of experimental RNA silencing. Thus, our results suggest that the remaining A. nidulans RNA silencing genes have a "nonhousekeeping" function, such as defense against viruses and transposons.

Sexual and vegetative compatibility genes in the aspergilli

Gene flow within populations can occur by sexual and/or parasexual means. Analyses of experimental and in silico work are presented relevant to possible gene flow within the aspergilli. First, the discovery of mating-type (MAT) genes within certain species of Aspergillus is described. The implications for self-fertility, sexuality in supposedly asexual species and possible uses as phylogenetic markers are discussed. Second, the results of data mining for heterokaryon incompatibility (het) and programmed cell death (PCD) related genes in the genomes of two heterokaryon incompatible isolates of the asexual species Aspergillus niger are reported. Het-genes regulate the formation of anastomoses and heterokaryons, may protect resources and prevent the spread of infectious genetic elements. Depending on the het locus involved, hetero-allelism is not tolerated and fusion of genetically different individuals leads to growth inhibition or cell death. The high natural level of heterokaryon incompatibility in A. niger blocks parasexual analysis of the het-genes involved, but in silico experiments in the sequenced genomes allow us to identify putative het-genes. Homologous sequences to known het- and PCD-genes were compared between different sexual and asexual species including different Aspergillus species, Sordariales and the yeast Saccharomyces cerevisiae. Both het- and PCD-genes were well conserved in A. niger. However some point mutations and other small differences between the het-genes in the two A. niger isolates examined may hint to functions in heterokaryon incompatibility reactions.

Molecular karyotyping and chromosome length polymorphism in Cochliobolus sativus

Fungi are known to have variable genomes that can generate new virulence types capable of attacking important crop plants. To assess chromosome length polymorphisms in the barley spot blotch pathogen (Cochliobolus sativus), we analyzed the karyotypes of 16 isolates using contour-clamped homogeneous electric field (CHEF) electrophoresis. The collection of isolates studied were from diverse regions of the world (USA, Canada, Japan, Brazil, Uruguay, and Poland) and included representatives comprising the three known C. sativus pathotypes of 0, 1, and 2. Under two different running conditions, the number of CHEF bands observed ranged from 8 to 13 with a size range of 0.85 to 3.80 mega-bases (Mb). Each of the 16 isolates showed a unique banding pattern, except for two North Dakota isolates ND90Pr and ND91-Bowman, which were very similar. Single-copy DNA probes, previously assigned to each of the 15 chromosomes identified in reference isolate ND93-1, were hybridized to Southern blots of CHEF-separated chromosomes and revealed highly polymorphic chromosomes among isolates. Chromosomal rearrangements (translocations, deletions, duplications) were found in several isolates. DNA markers previously found linked to VHv1, a gene in pathotype 2 isolates conferring virulence on barley cultivar Bowman, also were used as probes in hybridizations with the CHEF blots. The results showed that the chromosome carrying the virulence gene in pathotype 2 isolates is larger than its counterpart without the gene in other isolates. This suggests that the genomic region carrying the virulence locus VHv1 is unique to pathotype 2 isolates. This study provides useful information on genome structure and divergence, which is essential for advancing our understanding of the genetics and biology of C. sativus.

Selection arena in Aspergillus nidulans

The selection arena hypothesis states that overproduction of zygotes--a widespread phenomenon in animals and plants--can be explained as a mechanism of progeny choice. As a similar mechanism, the ascomycetous fungus Aspergillus nidulans may overproduce dikaryotic fruit initials, hereafter called dikaryons. Then, progeny choice might involve selection on which of these dikaryons will thrive to produce thousands of zygotes. These zygotes each produce eight sexual spores which together fill up one fruiting body. In this study, we test the selection arena hypothesis in this homothallic fungus that produces both sexual and asexual spores. We analyzed two mitochondrial and 15 auxotrophic mutations for consequences on sexual and asexual reproduction. We found that many of these mutations confer sexual self-sterility as a pleiotropic effect under conditions of normal asexual spore production. This confirms an important prediction of the selection arena, namely that dikaryons carrying a (slightly) deleterious mutation are not able to proliferate and produce sexual spores. The selection arena ensures that reproductive energy is invested mainly in dikaryons and thus sexual spores of good genetic quality.

Alternative reproduction pathway in Aspergillus nidulans

Recombinant haploid segregants were recovered in filamentous fungus Aspergillus nidulans (Eidam) G. Winter directly from the heterokaryons instead of diploid segregants (process described earlier as parameiosis). In spite of the reproductive complexity of A. nidulans, parameiosis has only now been observed in this fungus. Since parameiosis was characterized by the occurrence of genetic recombination inside heterokaryotic hyphae, master strains (uvs+) and uvs mutants with high rate of both mitotic exchanges or chromosome nondisjunction were used to form heterokaryons. Two groups of mitotic segregants were recovered directly from heterokaryons--aneuploids and stable haploids. Heterokaryons formed with uvs mutants produced a higher number of parameiotic segregants compared to the heterokaryons formed with uvs+ strains. Segregants were analyzed by nutritional markers, acriflavine resistance and conidial color. Normal meiotic behavior of haploid recombinants was observed.

Intra-species chromosome-length polymorphism in Geotrichum candidum revealed by pulsed field gel electrophoresis

Geotrichum candidum is an ascomycetous anamorph yeast-like fungus found in various habitats. It is a component of the natural flora of milk and is used as a maturing agent for both soft and hard cheeses. This microorganism displays phenotypic variability and may act as an opportunist pathogen, causing geotrichosis. Cytological analysis of G. candidum strain ATCC 204307 showed this strain to have eight chromosomes. We prepared chromosomal DNA from 13 strains of G. candidum differing in habitat and morphotype. We used pulsed field gel electrophoresis (PFGE) in two sets of conditions to determine the size of the chromosomal DNA molecules. The strains investigated had five to eight chromosomes, 0.6 to 4.5 Mb in size. We estimated genome size in these 13 strains to be between 11 and 19 Mb. Pulsed-field gel electrophoresis profiles showed a high degree of polymorphism, indicating considerable variability between strains. Genome size and the presence of large chromosomes appeared to be correlated with morphotype. Strains with a mold-like or intermediate morphotype tended to have larger genomes than strains with a yeast-like morphotype did.

Sexual diploids of Aspergillus nidulans do not form by random fusion of nuclei in the heterokaryon

The sexual stage of Aspergillus (Emericella) nidulans consists of cleistothecia containing asci, each with eight ascospores. The fungus completes the sexual cycle in a homokaryotic or a heterokaryotic mycelium, respectively. The common assumption for the last 50 years was that different nuclear types are not distinguishable when sexual development is initiated. When cultured on a medium limited for glucose supplemented with 2% sorbitol, sexual development of A. nidulans is slowed and intact tetrads can be isolated. Through tetrad analysis we found that unlike haploid nuclei fuse preferentially to the prezygotic diploid nucleus. When heterokaryons are formed between nuclei of different genetic backgrounds, then recombinant asci derived from opposite nuclei are formed exclusively. Strains in the same heterokaryon compatibility group with moderate differences in their genetic backgrounds can discriminate between the nuclei of a heterokaryon and preferentially form a hybrid diploid nucleus, resulting in 85% recombinant tetrads. A. nidulans strains that differ at only a single genetic marker fuse the haploid nuclei at random for formation of diploid nuclei during meiosis. These results argue for a genetically determined "relative heterothallism" of nuclear recognition within a heterokaryon and a specific recruitment of different nuclei for karyogamy when available.

Electrophoretic characterization of Aspergillus nidulans strains with chromosomal duplications

Pulsed-field gel electrophoresis was used to characterize strains of Aspergillus nidulans with a chromosomal duplication Dp(I-II). Morphologically deteriorated and improved variants of these strains were also analyzed. The electrophoretic karyotype demonstrated that in two duplicated strains (A and B) the 4.2 Mb band, which corresponds to chromosome II, was absent and a new band was observed. Hybridization studies using the uapA (chromosome I) and wA (chromosome II) genes demonstrated that the new band corresponded to chromosome II plus the duplicated segment of chromosome I. The size of the chromosomal duplication was approximately 1.0 Mb. Analysis of the chromosomal bands of a morphologically improved strain showed that the duplicated segment of chromosome I was completely lost. The morphologically deteriorated variants V9 and V17 had the same karyotype as the duplicated strains. However, the deteriorated variant V5 lost part of chromosome I and had a rearrangement involving chromosome V. This rearrangement may have resulted from the mutagenic treatment used to obtain the genetic markers. Pulsed-field gel electrophoresis was found to be an excellent tool for locating chromosomal rearrangements.

Clonal Spread of Sclerotium cepivorum in Onion Production with Evidence of Past Recombination Events

Three field populations of Sclerotium cepivorum from Ontario and Que-bec in Canada, one field sample from the North Island of New Zealand, as well as isolates from other onion- and garlic-growing areas were classified in mycelial compatibility groups (MCGs) and further characterized by DNA fingerprints and DNA sequence polymorphisms at six genomic regions. MCGs in the population samples were genetically distinct clones. Members of a clone belonged to a unique MCG with an associated multi-locus genotype and DNA fingerprint. The structure in each field population was predominantly clonal based on the repeated sampling of genotypes over a wide geographic area. Only three clones were identified within each of the population samples. The hypothesis that these clones were introduced to the three agricultural production areas is supported by their recovery from additional locations. Some evidence for past recombination was detected when genotypes from the three population samples and from other locations were pooled.

Population structure and dynamics of Magnaporthe grisea in the Indian Himalayas

The population genetics of Magnaporthe grisea, the rice blast pathogen, were analyzed in a center of rice diversity (the Uttar Pradesh hills of the Indian Himalayas) using multilocus and single-, or low-copy, DNA markers. Based on DNA fingerprinting with the multilocus probe MGR586 and single-locus probes, 157 haplotypes clustered into 56 lineages (at >/=70% MGR586 band similarity, each with unique single-locus profiles) and high diversity indices were detected among 458 isolates collected from 29 sites during 1992-1995. Most valleys sampled had distinct populations (73% of the lineages were site specific) with some containing one or a few lineages, confirming the importance of clonal propagation, and others were very diverse. Widely distributed lineages suggested that migration occurs across the region and into the Indo-Gangetic plains. Repeated sampling at one site, Matli, (170 isolates, 1992-1995) yielded 19 lineages and diversity significantly greater than that reported from similar samples from Colombia and the Philippines. Analysis of allelic associations using pairwise comparisons and multilocus variance analysis failed to reject the hypothesis of gametic phase equilibrium. The Matli population shifted from highly diverse in 1992 to almost complete dominance by one lineage in 1995. Such population dynamics are consistent with recombination followed by differential survival of clonal descendants of recombinant progeny. At another site, Ranichauri, population (n = 84) composition changed from 2 to 11 lineages over 2 yr and yielded additional evidence for equilibrium. Sexually fertile and hermaphrodite isolates of both mating types were recovered from rice in both Matli and Ranichauri. We demonstrate that Himalayan M. grisea populations are diverse and dynamic and conclude that the structure of some populations may be affected to some extent by sexual recombination.

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

The evolutionary biology and population genetics underlying fungal strain typing

Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.

Random association among alleles in clonal populations of Sclerotinia sclerotiorum

Multiple loci identified in DNA fingerprints were used to test for random association in two agricultural populations of S. sclerotiorum. In linkage disequilibrium tests among pairs of loci with frequencies between 0.1 and 0.9, 44.5 and 80.5% of pairs of loci were consistent with random association in the clone-corrected samples of the Canadian canola and the North Carolina cabbage populations, respectively. In estimates of corrected (Bonferroni) P value, 70.66 and 98.89% of pairs of loci were in random association. All four possible genotypes for each pair of loci were observed in the Canadian canola sample, consistent with random association among loci. In multilocus association tests across all loci, however, significant association was observed in both populations. In the Canadian canola population, 40 possible heterokaryons were identified. Our data suggest that populations of S. sclerotiorum are predominantly clonal and that occasional genetic exchange and recombination, and not mutation alone, may be a source of new genotypes.

Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus

Aspergillus flavus, like approximately one-third of ascomycete fungi, is thought to be cosmopolitan and clonal because it has uniform asexual morphology. A. flavus produces aflatoxin on nuts, grains, and cotton, and assumptions about its life history are being used to develop strategies for its biological control. We tested the assumptions of clonality and conspecificity in a sample of 31 Australian isolates by assaying restriction site polymorphisms from 11 protein encoding genes and DNA sequences from five of those genes. A. flavus isolates fell into two reproductively isolated clades (groups I and II). The lack of concordance among gene genealogies among isolates in one of the clades (group I) was consistent with a history of recombination. Our analysis included five strains of the closely related industrial fungus A. oryzae, all of which proved to be clonally related to group I.

In vitro reconstruction of the Aspergillus (= Emericella) nidulans genome

A physical map of the 31-megabase Aspergillus nidulans genome is reported, in which 94% of 5,134 cosmids are assigned to 49 contiguous segments. The physical map is the result of a two-way ordering process, in which clones and probes were ordered simultaneously on a binary DNA/DNA hybridization matrix. Compression by elimination of redundant clones resulted in a minimal map, which is a chromosome walk. Repetitive DNA is nonrandomly dispersed in the A. nidulans genome, reminiscent of heterochromatic banding patterns of higher eukaryotes. We hypothesize gene clusters may arise by horizontal transfer and spread by transposition to explain the nonrandom pattern of repeats along chromosomes.

Molecular epidemiology of Cryptococcus neoformans in Brazil and the United States: evidence for both local genetic differences and a global clonal population structure

Little is known about the global molecular epidemiology of the human pathogenic fungus Cryptococcus neoformans. We studied 51 clinical and environmental (pigeon excreta) isolates from two cities in Brazil (Belo Horizonte and Rio de Janeiro) by analyzing their carbon assimilation patterns, electrophoretic karyotypes, restriction fragment length polymorphisms (RFLPs) with the C. neoformans repetitive element-1 (CNRE-1), and URA5 sequences. Results were compared to those previously obtained for isolates from New York City by the same DNA typing methods. Computer-assisted analysis of RFLPs and contour-clamped homogeneous electrophoresis (CHEF) patterns and URA5 sequences was performed to generate dendrograms. Some environmental and clinical isolates were found to be indistinguishable by CHEF, CNRE-1 RFLP, and URA5 sequence analyses. Similarly, some isolates from Rio de Janeiro and Belo Horizonte were indistinguishable by the three DNA typing techniques. Overall, Brazilian isolates appeared to be less heterogeneous by DNA analysis than isolates from other regions. Several Brazilian isolates were highly related to New York City isolates. Phylogenetic analysis of the sequences obtained for the Brazilian isolates and those obtained for New York City isolates was congruent with the dendrogram generated from the CNRE-1 RFLP data. In summary our results indicate (i) that the discriminatory power of the DNA typing method differs for Brazilian and New York City strains, with the order being CNRE-1 RFLP analysis > URA5 sequence analysis > CHEF analysis and CHEF analysis > URA5 sequence analysis > CNRE-1 RFLP analysis, respectively; (ii) that there are differences in local genetic diversity for Brazilian and New York City isolates; (iii) that there is additional evidence linking clinical isolates to those in pigeon excreta; and (iv) that some isolates from Brazil and New York City are closely related, consistent with the global dispersal of certain pathogenic strains.

Genetic diversity among clinical and environmental isolates of Aspergillus fumigatus

To determine if cases of invasive aspergillosis (IA) were caused by strains of Aspergillus fumigatus with unique characteristics, strains from immunosuppressed patients with IA were compared to strains obtained from sputa of patients with cystic fibrosis and to strains from the environment. An extremely high genomic diversity was observed among the 879 strains typed by Southern blotting with a retrotransposon-like element from A. fumigatus (C. Neuvéglise, J. Sarfati, J. P. Latgé, and S. Paris, Nucleic Acids Res. 24:1428-1434, 1996). Analysis of Southern blot hybridization patterns showed the absence of clustering between environmental isolates and clinical isolates from patients with IA or cystic fibrosis. In addition, strains could not be clustered depending on their geographical location. This study implies that practically any strain of A. fumigatus is potentially pathogenic and can provoke a case of IA when it encounters a favorable environment in an immunosuppressed host.

The evolutionary biology of Fusarium oxysporum

Fusarium oxysporum is an anamorphic species that includes both pathogenic and nonpathogenic strains. Plant pathogenic forms cause a wilt disease and are grouped into formae speciales based on their host range; some are further subdivided into pathogenic races. Many formae speciales are comprised of multiple clonal lineages and, in some cases, a pathogenic race is associated with more than one clonal lineage, suggesting independent origins. Although some evidence suggests one pathogenic race may give rise to another, recent derivation of a pathogen from a nonpathogen has not been documented. Most new occurrences of Fusarium wilt appear to be the result of a recent introduction rather than an independent local origin of the pathotype. Asexual propagation is the dominant influence on population structure in F. oxysporum and the absence of sexual reproduction is not likely to prevent this pathogen from continuing to inflict significant damage on susceptible crop hosts.

Female fertility and mating type effects on effective population size and evolution in filamentous fungi

The idealized individual in many fungal species is a haploid self-sterile hermaphrodite that may be propagated by asexually produced spores or that may reproduce sexually. In field populations, polymorphism occurs for female-sterile/hermaphrodite status, and female-sterile mutants, which function only as males during sexual reproduction, may comprise > 50% of the population. The effective population number may be based on the number of strains of different mating type or the relative frequency of hermaphrodites. The female-sterile mutants are at a selective disadvantage every time sexual reproduction occurs, and must have an advantage during vegetative propagation to persist at a significant frequency. When a high frequency of female-sterile strains is observed in field populations, it indicates that vegetative propagation is a significant component of the fungus' natural history. Depending on the mutation rate to female sterility and the selective advantage of the female-sterile strains during vegetative propagation, the ratio of sexual:asexual generations can range from 1:15 to 1:2300 for species in the Gibberella fujikuroi complex. The relative rarity of sexual reproduction may permit female-sterile strains to accumulate to a level such that local populations could completely lose sexuality and appear as asexual (imperfect) species.

Towards a unified evolutionary genetics of microorganisms

I propose here that evolutionary genetics, apart from improving our basic knowledge of the taxonomy and evolution of microbes (either eukaryotes or prokaryotes), can also greatly contribute to applied research in microbiology. Evolutionary genetics provides convenient guidelines for better interpreting genetic and molecular data dealing with microorganisms. The three main potential applications of evolutionary genetics in microbiology are (a) epidemiological follow-up (with the necessity of evaluating the stability of microbial genotypes over space and time); (b) taxonomy in the broad sense (better definition and sharper delimitation of presently described taxa, research of hidden genetic subdivisions); and (c) evaluation of the impact of the genetic diversity of microbes on their relevant properties (pathogenicity, resistance to drugs, etc). At present, two main kinds of population structure can be distinguished in natural microbial populations: (a) species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species with occasional bouts of short-term clonality fall into this category); (b) species that are strongly subdivided by either cryptic speciation or clonal evolution. Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations. Moreover, a codified selection of markers with appropriate molecular clocks (in other words: adapted levels of resolution) is sorely needed to answer distinct questions that address different scales of time and space: experimental, epidemic, and evolutionary. The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field. I propose a synthetic approach, relying on the statistical improvements and technical standardizations called for above, to settle a unified evolutionary genetics of microorganisms, valid whatever the species studied, whether eukaryotic (parasitic protozoa and fungi) or prokaryotic (bacteria). Apart from benefits for basic evolutionary research, the anticipated payoff from this synthetic approach is to render routine and common-place the use of microbial evolutionary genetics in the fields of epidemiology, medicine, and agronomy.

Mitochondrial inheritance in Aspergillus nidulans

Mitochondrial chloramphenicol and oligomycin resistance mutations were used to investigate mitochondrial inheritance in A. nidulans. Mitochondrial RFLPs could not be used to distinguish between paternal and maternal mitochondria because none were detected in the 54 isolates investigated. Several thousand ascospores from each of 111 hybrid cleistothecia from 21 different crosses between 7 heterokaryon incompatible isolates were tested for biparental inheritance. All mitochondrial inheritance was strictly uniparental. Not one instance of paternal inheritance of mitochondria was observed. The implications of our results for the theory that uniparental inheritance evolved to avoid cytoplasmic conflict are discussed. Possible explanations for the maintenance of strict uniparental inheritance of mitochondria in an inbreeding homothallic organism are suggested. The chloramphenicol resistance marker was inherited preferentially to the oligomycin resistance marker probably due to the inhibited energy production of mitochondria with the oligomycin resistance mutation. The maternal parent was determined for 93 hybrid cleistothecia from 17 crosses between 7 different strains. Contrary to previous reports A. nidulans strains functioned as both maternal and paternal parent in most crosses.

Molecular epidemiology of apparent outbreak of invasive aspergillosis in a hematology ward

During a 2-month period, five patients suffering from invasive infections caused by Aspergillus flavus or Aspergillus fumigatus were identified in the Hematology Department of the University Hospital Dijkzigt (Rotterdam, The Netherlands). To study the epidemiological aspects of invasive aspergillosis, strains from these patients and from the hospital environment, isolated during extensive microbiological screening, were subjected to genotyping. A novel DNA extraction technique, involving freezing, grinding, and direct lysis in guanidium isothiocyanate-containing buffers of mycelial material, was applied. DNA isolation was followed by typing by random amplification of polymorphic DNA (RAPD) analysis. This showed that strains isolated from all patients infected with the same fungal species were genotypically distinct, thus providing evidence against the possibility of an ongoing, single-source nosocomial outbreak. Strains could also be differentiated from strains of geographically diverse origins. However, an A. flavus strain from one of the patients was also frequently encountered in the hospital environment. As all environmental strains were collected after this patient had been diagnosed with invasive disease, the epidemiological value of this observation could not be ascertained. Intensive investigations showed no single source of A. flavus or other aspergilli. RAPD genotyping proved that the outbreak of invasive aspergillosis in the hematology ward consisted of a series of unrelated events and was not due to a common source within the hospital. RAPD fingerprinting of aspergilli may greatly facilitate future investigations of the epidemiology of invasive disease caused by these pathogens.

Wild chromosomal variants in Aspergillus nidulans

Pulsed-field gel electrophoresis and a chromosome-specific cosmid DNA library were used to determine the karyotypes of wild-type Aspergillus nidulans isolates from around the world. Overall, little structural variation was found, with a few major exceptions. One isolate possessed a non-essential B-chromosome of about 1.0 million base pairs (mb). Another isolate had undergone a non-reciprocal translocation of about 1.6 mb of chromosome VI onto chromosome VIII. Other than these chromosomal differences, these isolates appeared phenotypically normal. To analyze its effects on meiosis, the translocation isolate was outcrossed with another wild-type derivative that had a normal electrophoretic karyotype. This cross produced a range of phenotypes, including duplicated progeny that had a barren phenotype similar to that described for Neurospora partial disomics. The duplication was somewhat vegetatively unstable. This is the first association of sterility with chromosomal duplication in A. nidulans.

Parallel computing of physical maps--a comparative study in SIMD and MIMD parallelism

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are proposed and applied to the problem of chromosome reconstruction via clone ordering. Perturbation methods and problem-specific annealing heuristics are proposed and described. The SIMD algorithms are implemented on a 2048 processor MasPar MP-2 system which is an SIMD 2-D toroidal mesh architecture whereas the MIMD algorithms are implemented on an 8 processor Intel iPSC/860 which is an MIMD hypercube architecture. A comparative analysis of the various SIMD and MIMD algorithms is presented in which the convergence, speedup, and scalability characteristics of the various algorithms are analyzed and discussed. On a fine-grained, massively parallel SIMD architecture with a low synchronization overhead such as the MasPar MP-2, a parallel simulated annealing algorithm based on multiple periodically interacting searches performs the best. For a coarse-grained MIMD architecture with high synchronization overhead such as the Intel iPSC/860, a parallel simulated annealing algorithm based on multiple independent searches yields the best results. In either case, distribution of clonal data across multiple processors is shown to exacerbate the tendency of the parallel simulated annealing algorithm to get trapped in a local optimum.

Recombination and the multilocus structure of fungal populations

This review examines the relationship between recombination and the multilocus structure of populations. This discussion of population structure is based on the pattern of genetic variation within populations, especially the frequencies of multilocus genotypes, which can be used for making inferences about recombination. Three questions are addressed: Is population structure consistent with a random mating hypothesis? Is there evidence for recombination? How frequently does recombination occur?

Chromosome-length polymorphism in fungi

The examination of fungal chromosomes by pulsed-field gel electrophoresis has revealed that length polymorphism is widespread in both sexual and asexual species. This review summarizes characteristics of fungal chromosome-length polymorphism and possible mitotic and meiotic mechanisms of chromosome length change. Most fungal chromosome-length polymorphisms are currently uncharacterized with respect to content and origin. However, it is clear that long tandem repeats, such as tracts of rRNA genes, are frequently variable in length and that other chromosomal rearrangements are suppressed during normal mitotic growth. Dispensable chromosomes and dispensable chromosome regions, which have been well documented for some fungi, also contribute to the variability of the fungal karyotype. For sexual species, meiotic recombination increases the overall karyotypic variability in a population while suppressing genetic translocations. The range of karyotypes observed in fungi indicates that many karyotypic changes may be genetically neutral, at least under some conditions. In addition, new linkage combinations of genes may also be advantageous in allowing adaptation of fungi to new environments.