Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection

Distribution of Cronartium x flexili, an interspecific hybrid of two fungal tree rust pathogens, in subalpine forest ecosystems of western USA

Interspecific hybridization plays a key role in the evolution of novel fungal pathogens, and when it occurs between native and invasive species, can lead to potentially serious consequences. In this study, we examined the temporal and spatial distribution of a recently detected hybrid (Cronartium x flexili) of two tree pathogens, invasive to North America Cronartium ribicola and native Cronartium comandrae. In total, 726 and 1452 aecia from 178 Pinus contorta ssp. latifolia and 357 Pinus flexilis trees were collected from 26 sites in four national forests in 2019-2021. Using morphological and molecular analyses, 71 aecia collected from 25 P. flexilis trees had intermediate morphology and contained heterozygous SNPs in two genomic regions. Population analyses revealed the presence of multiple hybrid genotypes randomly distributed among sites and years. No aecia from P. contorta ssp. latifolia were identified as hybrids suggesting unidirectional gene flow from native C. comandrae to invasive C. ribicola. Aeciospores from 2 hybrid aecia produced urediniospores on Ribes nigrum. Overall, these results suggest that, even though low in frequency, C. x flexili is persistent in the region and has pathogenic potential. Hybrid expansion into the large range of susceptible pines could have cascading impacts on forest health.

Rapid evolution of pre-zygotic reproductive barriers in allopatric populations

IMPORTANCE

A population diversifies into two or more species-such a process is known as speciation. In sexually reproducing microorganisms, which barriers arise first-pre-mating or post-mating? In this work, we quantify the relative strengths of these barriers and demonstrate that pre-mating barriers arise first in allopatrically evolving populations of yeast, Saccharomyces cerevisiae. These defects arise because of the altered kinetics of mating of the participating groups. Thus, our work provides an understanding of how adaptive changes can lead to diversification among microbial populations.

Meiotic drive is associated with sexual incompatibility in Neurospora

Evolution of Bateson-Dobzhansky-Muller (BDM) incompatibilities is thought to represent a key step in the formation of separate species. They are incompatible alleles that have evolved in separate populations and are exposed in hybrid offspring as hybrid sterility or lethality. In this study, we reveal a previously unconsidered mechanism promoting the formation of BDM incompatibilities, meiotic drive. Theoretical studies have evaluated the role that meiotic drive, the phenomenon whereby selfish elements bias their transmission to progeny at ratios above 50:50, plays in speciation, and have mostly concluded that drive could not result in speciation on its own. Using the model fungus Neurospora, we demonstrate that the large meiotic drive haplotypes, Sk-2 and Sk-3, contain putative sexual incompatibilities. Our experiments revealed that although crosses between Neurospora intermedia and Neurospora metzenbergii produce viable progeny at appreciable rates, when strains of N. intermedia carry Sk-2 or Sk-3 the proportion of viable progeny drops substantially. Additionally, it appears that Sk-2 and Sk-3 have accumulated different incompatibility phenotypes, consistent with their independent evolutionary history. This research illustrates how meiotic drive can contribute to reproductive isolation between populations, and thereby speciation.

Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales)

Among many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

Neurospora from Natural Populations: Population Genomics Insights into the Life History of a Model Microbial Eukaryote

The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research.

Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity

BACKGROUND

Hybridization is a central mechanism in evolution, producing new species or introducing important genetic variation into existing species. In plant-pathogenic fungi, adaptation and specialization to exploit a host species are key determinants of evolutionary success. Here, we performed experimental crosses between the two pathogenic Microbotryum species, M. lychnidis-dioicae and M. silenes-acaulis that are specialized to different hosts. The resulting offspring were analyzed on phenotypic and genomic levels to describe genomic characteristics of hybrid offspring and genetic factors likely involved in host-specialization.

RESULTS

Genomic analyses of interspecific fungal hybrids revealed that individuals were most viable if the majority of loci were inherited from one species. Interestingly, species-specific loci were strictly controlled by the species' origin of the mating type locus. Moreover we detected signs of crossing over and chromosome duplications in the genomes of the analyzed hybrids. In Microbotryum, mitochondrial DNA was found to be uniparentally inherited from the a2 mating type. Genome comparison revealed that most gene families are shared and the majority of genes are conserved between the two species, indicating very similar biological features, including infection and pathogenicity processes. Moreover, we detected 211 candidate genes that were retained under host-driven selection of backcrossed lines. These genes and might therefore either play a crucial role in host specialization or be linked to genes that are essential for specialization.

CONCLUSION

The combination of genome analyses with experimental selection and hybridization is a promising way to investigate host-pathogen interactions. This study manifests genetic factors of host specialization that are required for successful biotrophic infection of the post-zygotic stage, but also demonstrates the strong influence of intra-genomic conflicts or instabilities on the viability of hybrids in the haploid host-independent stage.

Heterospecific mating interactions as an interface between ecology and evolution

Reproductive interference (costly interspecific sexual interactions) is well-understood to promote divergence in mating-relevant traits (i.e. reproductive character displacement: RCD), but it can also reduce population growth, eventually leading to local extinction of one of the species. The ecological and evolutionary processes driven by reproductive interference can interact with each other. These interactions are likely to influence whether the outcome is coexistence or extinction, but remain little studied. In this paper, we first develop an eco-evolutionary perspective on reproductive interference by integrating ecological and evolutionary processes in a common framework. We also present a simple model to demonstrate the eco-evolutionary dynamics of reproductive interference. We then identify a number of factors that are likely to influence the relative likelihoods of extinction or RCD. We discuss particularly relevant factors by classifying them into four categories: the nature of the traits responding to selection, the mechanisms determining the expression of these traits, mechanisms of reproductive interference and the ecological background. We highlight previously underappreciated ways in which these factors may influence the relative likelihoods of RCD and local extinction. By doing so, we also identify questions and future directions that will increase our holistic understanding of the outcomes of reproductive interference.

Diversity and Postzygotic Evolution of the Mitochondrial Genome in Hybrids of Saccharomyces Species Isolated by Double Sterility Barrier

Eukaryotic species are reproductively isolated by sterility barriers that prevent interspecies fertilization (prezygotic sterility barrier) or the fertilization results in infertile offspring (postzygotic sterility barrier). The Saccharomyces species are isolated by postzygotic sterility barriers. Their allodiploid hybrids form no viable gametes (ascospores) and the viable ascospores of the allotetraploids cannot fertilize (conjugate). Our previous work revealed that this mechanism of reproductive isolation differs from those operating in plants and animals and we designated it double sterility barrier (the failure of homeologous chromosomes to pair and the repression of mating by mating-type heterozygosity). Other studies implicated nucleo-mitochondrial incompatibilities in the sterility of the Saccharomyces hybrids, a mechanism assumed to play a central role in the reproductive isolation of animal species. In this project the mitochondrial genomes of 50 cevarum (S. cerevisiae × S. uvarum) hybrids were analyzed. 62% had S. cerevisiae mitotypes, 4% had S. uvarum mitotypes, and 34% had recombinant mitotypes. All but one hybrid formed viable spores indicating that they had genomes larger than allodiploid. Most of these spores were sterile (no sporulation in the clone of vegetative descendants; a feature characteristic of allodiploids). But regardless of their mitotypes, most hybrids could also form fertile alloaneuploid spore clones at low frequencies upon the loss of the MAT-carrying chromosome of the S. uvarum subgenome during meiosis. Hence, the cevarum alloploid nuclear genome is compatible with both parental mitochondrial genomes as well as with their recombinants, and the sterility of the hybrids is maintained by the double sterility barrier (determined in the nuclear genome) rather than by nucleo-mitochondrial incompatibilities. During allotetraploid sporulation both the nuclear and the mitochondrial genomes of the hybrids could segregate but no correlation was observed between the sterility or the fertility of the spore clones and their mitotypes. Nucleo-mitochondrial incompatibility was manifested as respiration deficiency in certain meiotic segregants. As respiration is required for meiosis-sporulation but not for fertilization (conjugation), these segregants were deficient only in sporulation. Thus, the nucleo-mitochondrial incompatibility affects the sexual processes only indirectly through the inactivation of respiration and causes only partial sterility in certain segregant spore clones.

Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens

Hybridization is increasingly recognized as an important force impacting adaptation and evolution in many lineages of fungi. During hybridization, divergent genomes and alleles are brought together into the same cell, potentiating adaptation by increasing genomic plasticity. Here, we review hybridization in fungi by focusing on two fungal pathogens of animals. Hybridization is common between the basidiomycete yeast species Cryptococcus neoformans × Cryptococcus deneoformans, and hybrid genotypes are frequently found in both environmental and clinical settings. The two species show 10-15% nucleotide divergence at the genome level, and their hybrids are highly heterozygous. Though largely sterile and unable to mate, these hybrids can propagate asexually and generate diverse genotypes by nondisjunction, aberrant meiosis, mitotic recombination, and gene conversion. Under stress conditions, the rate of such genetic changes can increase, leading to rapid adaptation. Conversely, in hybrids formed between lineages of the chytridiomycete frog pathogen Batrachochytrium dendrobatidis (Bd), the parental genotypes are considerably less diverged (0.2% divergent). Bd hybrids are formed from crosses between lineages that rarely undergo sex. A common theme in both species is that hybrids show genome plasticity via aneuploidy or loss of heterozygosity and leverage these mechanisms as a rapid way to generate genotypic/phenotypic diversity. Some hybrids show greater fitness and survival in both virulence and virulence-associated phenotypes than parental lineages under certain conditions. These studies showcase how experimentation in model species such as Cryptococcus can be a powerful tool in elucidating the genotypic and phenotypic consequences of hybridization.

Assortative mating in sympatric ascomycete fungi revealed by experimental fertilizations

Mate recognition mechanisms resulting in assortative mating constitute an effective reproductive barrier that may promote sexual isolation and speciation. While such mechanisms are widely documented for animals and plants, they remain poorly studied in fungi. We used two interfertile species of Epichloë (Clavicipitaceae, Ascomycota), E. typhina and E. clarkii, which are host-specific endophytes of two sympatrically occurring grasses. The life cycle of these obligatory outcrossing fungi entails dispersal of gametes by a fly vector among external fungal structures (stromata). To test for assortative mating, we mimicked the natural fertilization process by applying mixtures of spermatia from both species and examined their reproductive success. Our trials revealed that fertilization is non-random and preferentially takes place between conspecific mating partners, which is indicative of assortative mating. Additionally, the viability of hybrid and non-hybrid ascospore offspring was assessed. Germination rates were lower in E. clarkii than in E. typhina and were reduced in ascospore progeny from treatments with high proportions of heterospecific spermatia. The preferential mating between conspecific genotypes and reduced hybrid viability represent important reproductive barriers that have not been documented before in Epichloë. Insights from fungal systems will deepen our understanding of the evolutionary mechanisms leading to reproductive isolation and speciation.

Global distribution of mating types shows limited opportunities for mating across populations of fungi causing boxwood blight disease

Boxwood blight is a disease threat to natural and managed landscapes worldwide. To determine mating potential of the fungi responsible for the disease, Calonectria pseudonaviculata and C. henricotiae, we characterized their mating-type (MAT) loci. Genomes of C. henricotiae, C. pseudonaviculata and two other Calonectria species (C. leucothoes, C. naviculata) were sequenced and used to design PCR tests for mating-type from 268 isolates collected from four continents. All four Calonectria species have a MAT locus that is structurally consistent with the organization found in heterothallic ascomycetes, with just one idiomorph per individual isolate. Mating type was subdivided by species: all C. henricotiae isolates possessed the MAT1-1 idiomorph, whereas all C. pseudonaviculata isolates possessed the MAT1-2 idiomorph. To determine the potential for divergence at the MAT1 locus to present a barrier to interspecific hybridization, evolutionary analysis was conducted. Phylogenomic estimates showed that C. henricotiae and C. pseudonaviculata diverged approximately 2.1 Mya. However, syntenic comparisons, phylogenetic analyses, and estimates of nucleotide divergence across the MAT1 locus and proximal genes identified minimal divergence in this region of the genome. These results show that in North America and parts of Europe, where only C. pseudonaviculata resides, mating is constrained by the absence of MAT1-1. In regions of Europe where C. henricotiae and C. pseudonaviculata currently share the same host and geographic range, it remains to be determined whether or not these two recently diverged species are able to overcome species barriers to mate.

Gene exchange between two divergent species of the fungal human pathogen, Coccidioides

The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.

Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi

Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.

The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila

Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization. We also measured the magnitude of a premating barrier (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of all nine known extant species within the melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. Next, we partition postzygotic isolation into different components and find that, as expected, hybrid sterility evolves faster than hybrid inviability. These results lend support for the hypothesis that, in Drosophila, reproductive isolation mechanisms (RIMs) that act early in reproduction (or in development) tend to evolve faster than those that act later in the reproductive cycle. Finally, we tested whether there was evidence for reinforcing selection at any RIM. We found no evidence for generalized evolution of reproductive isolation via reinforcement which indicates that there is no pervasive evidence of this evolutionary process. Our results indicate that PMPZ RIMs might have important evolutionary consequences in initiating speciation and in the persistence of new species.

Mitonuclear interactions may contribute to fitness of fungal hybrids

Hybridization between species is being recognized as a major force in the rapid adaptive evolution of fungal plant pathogens. The first stages of interspecific hybridization necessarily involve nuclear-mitochondrial chimeras. In their 2001 publication, Olson and Stenlid reported that mitochondria control the virulence of first generation hybrids between the North American fungal pathogen Heterobasidion irregulare and its congeneric H. occidentale. By assessing saprobic ability and gene expression of H. irregulare × H. annosum sensu stricto hybrids and of their parental genotypes, we demonstrate that mitochondria also influence saprobic growth of hybrids. Moreover, gene expression data suggest that fungal fitness is modulated by an intimate interplay between nuclear genes and mitochondrial type, and is dependent on the specific mitonuclear combination.

Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens

An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.

Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity

The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.

Detection of genetic incompatibilities in non-model systems using simple genetic markers: hybrid breakdown in the haplodiploid spider mite Tetranychus evansi

When two related species interbreed, their hybrid offspring frequently suffer from reduced fitness. The genetics of hybrid incompatibility are described by the Bateson–Dobzhansky–Muller (BDM) model, where fitness is reduced by epistatic interactions between alleles of heterospecific origin. Unfortunately, most empirical evidence for the BDM model comes from a few well-studied model organisms, restricting our genetic understanding of hybrid incompatibilities to limited taxa. These systems are predominantly diploid and incompatibility is often complete, which complicates the detection of recessive allelic interactions and excludes the possibility to study viable or intermediate stages. Here, we advocate research into non-model organisms with haploid or haplodiploid reproductive systems and incomplete hybrid incompatibility because (1) dominance is absent in haploids and (2) incomplete incompatibility allows comparing affected with unaffected individuals. We describe a novel two-locus statistic specifying the frequency of individuals for which two alleles co-occur. This approach to studying BDM incompatibilities requires genotypic characterization of hybrid individuals, but not genetic mapping or genome sequencing. To illustrate our approach, we investigated genetic causes for hybrid incompatibility between differentiated lineages of the haplodiploid spider mite Tetranychus evansi, and show that strong, but incomplete, hybrid breakdown occurs. In addition, by comparing the genotypes of viable hybrid males and inviable hybrid male eggs for eight microsatellite loci, we show that nuclear and cytonuclear BDM interactions constitute the basis of hybrid incompatibility in this species. Our approach opens up possibilities to study BDM interactions in non-model taxa, and may give further insight into the genetic mechanisms behind hybrid incompatibility.

The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens

Hybridization in fungi has recently been recognized as a major force in the generation of new fungal plant pathogens. These include the grass pathogen Zymoseptoria pseudotritici and the powdery mildew pathogen Blumeria graminis triticale of triticale. Hybridization also plays an important role in the transfer of genetic material between species. This process is termed introgressive hybridization and involves extensive backcrossing between hybrid and the parental species. Introgressive hybridization has contributed substantially to the successful spread of plant pathogens such as Ophiostoma ulmi and O. novo-ulmi, the causal agents of Dutch elm disease, and other tree pathogens such as the rust pathogen Melampsora. Hybridization occurs more readily between species that have previously not coexisted, so-called allopatric species. Reproductive barriers between allopatric species are likely to be more permissive allowing interspecific mating to occur. The bringing together of allopatric species of plant pathogens by global agricultural trade consequently increases the potential for hybridization between pathogen species. In light of global environmental changes, agricultural development, and the facilitated long-distance spread of fungal plant pathogens, hybridization should be considered an important mechanism whereby new pathogens may emerge. Recent studies have gained insight into the genetics and biology of fungal hybrids. Here I summarize current knowledge about hybrid speciation and introgressive hybridization. I propose that future studies will benefit greatly from the availability of large genome data sets and that genome data provide a powerful resource in combination with experimental approaches for analyses of hybrid species.

Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.

Rapid and widespread de novo evolution of kin discrimination

Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation.

A Potential Case of Reinforcement in a Facultatively Sexual Unicellular Eukaryote

The origin of a new species requires a mechanism to prevent divergent populations from interbreeding. In the classic allopatric model, divided populations evolve independently and accumulate genetic differences. If contact is restored, hybrids suffer reduced fitness and selection may favor traits that prevent mistakes in mating, a process known as reinforcement. This decisive but transient phase is challenging to document and has been reported mostly in macroorganisms. Very little is known about the processes through which new microbial species originate. In particular, it is unclear whether microbial eukaryotes, many of which can reproduce sexually during complex life cycles, speciate in much the same way as do well-studied plants and animals. Using individual cellular mate choice trials, we investigated the mating behavior of sympatric and allopatric woodland populations of the yeast Saccharomyces paradoxus. We find evidence consistent with reinforcement, potentially representing an example of microbial speciation in progress.

Name changes in medically important fungi and their implications for clinical practice

Recent changes in the Fungal Code of Nomenclature and developments in molecular phylogeny are about to lead to dramatic changes in the naming of medically important molds and yeasts. In this article, we present a widely supported and simple proposal to prevent unnecessary nomenclatural instability.

Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens

895 I. 895 II. 896 III. 898 IV. 900 V. 902 VI. 904 VII. 905 905 References 905 SUMMARY: Speciation of fungal plant pathogens has been associated with host jumps, host domestication, clonal divergence, and hybridization. Although we have substantial insight into the speciation histories of several important plant pathogens, we still know very little about the underlying genetics of reproductive isolation. Studies in Saccharomyces cerevisiae, Neurospora crassa, and nonfungal model systems illustrate that reproductive barriers can evolve by different mechanisms, including genetic incompatibilities between neutral and adaptive substitutions, reinforcement selection, and chromosomal rearrangements. Advances in genome sequencing and sequence analyses provide a new framework to identify those traits that have driven the divergence of populations or caused reproductive isolation between species of fungal plant pathogens. These traits can be recognized based on signatures of strong divergent selection between species or through the association of allelic combination conferring hybrid inferiority. Comparative genome analyses also provide information about the contribution of genome rearrangements to speciation. This is particularly relevant for species of fungal pathogens with extreme levels of genomic rearrangements and within-species genome plasticity.

Evolutionary dynamics of sex-biased genes in a hermaphrodite fungus

Differential gene expression is believed to largely explain sexually dichotomous phenotypes. This phenomenon is especially significant in hermaphrodites, in which male and female sexual tissues have identical genotypes. Sex differences in transcription have been linked to molecular evolution: genes with higher expression in male compared with female sexual tissues (i.e., male-biased genes) have been associated with rapid gene divergence in various animals and plants, implying that selective differences exist among the sexual structures. In the present investigation, we examined expressed sequence tags, microarrays, and gene sequence data from the hermaphroditic fungus Neurospora crassa and confirmed selective differences of genes with disparate expression among male versus female sexual structures in this organism. The results held across various genotypes and stages of sexual development. Furthermore, our data showed that N. crassa comprises a rare example of an organism where female-biased genes evolve rapidly; they exhibited faster evolution at the protein level and reduced optimal codon usage compared with male-biased genes, sexually unbiased genes, and vegetative genes. Female-biased genes also had a greater portion of sites that experienced positive selection and showed stronger signals of selective sweeps than male-biased genes, suggesting that the rapid evolution is at least partly driven by adaptive evolution. Distinctive aspects of the reproductive biology of N. crassa which might explain the rapid evolution of female-biased genes are discussed, particularly the propensity for female-female competition during mating, as well as the multifunctional nature of male structures. The present findings open new opportunities to test hypotheses about sex-biased gene expression and molecular evolution.

Genome wide association identifies novel loci involved in fungal communication

Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species.

Many phenotypes of interest are controlled by multiple loci, and in biological systems identifying determinants of such complex traits is challenging. Here, we genotyped 112 wild isolates of Neurospora crassa and used this resource to identify genes that mediate a fundamental but poorly-understood attribute of this filamentous fungus: the ability of germinating spores to sense each other at a distance, extend projections toward one another, and fuse. Inheritance at a secretion gene, cse-1, was associated strongly with germling communication across wild strains; this association was validated in experiments showing reduced communication in a cse-1 deletion strain. By testing interacting partners of CSE1, and by assessing additional secretion and signaling factors whose inheritance associated more modestly with germling communication in wild strains, we identified eight other novel determinants of this phenotype. Our population of genotyped wild isolates provides a flexible and powerful community resource for the rapid identification of any varying, complex phenotype in N. crassa. The success of our approach, which used a phenotyping scheme far more tractable than would be required in a screen of the entire N. crassa gene deletion collection, serves as a proof of concept for association studies of wild populations for any organism.

Discovery of a sexual cycle in Aspergillus lentulus, a close relative of A. fumigatus

Aspergillus lentulus was described in 2005 as a new species within the A. fumigatus sensu lato complex. It is an opportunistic human pathogen causing invasive aspergillosis with high mortality rates, and it has been isolated from clinical and environmental sources. The species is morphologically nearly identical to A. fumigatus sensu stricto, and this similarity has resulted in their frequent misidentification. Comparative studies show that A. lentulus has some distinguishing growth features and decreased in vitro susceptibility to several antifungal agents, including amphotericin B and caspofungin. Similar to the once-presumed-asexual A. fumigatus, it has only been known to reproduce mitotically. However, we now show that A. lentulus has a heterothallic sexual breeding system. A PCR-based mating-type diagnostic detected isolates of either the MAT1-1 or MAT1-2 genotype, and examination of 26 worldwide clinical and environmental isolates revealed similar ratios of the two mating types (38% versus 62%, respectively). MAT1-1 and MAT1-2 idiomorph regions were analyzed, revealing the presence of characteristic alpha and high-mobility-group (HMG) domain genes, together with other more unusual features such as a MAT1-2-4 gene. We then demonstrated that A. lentulus possesses a functional sexual cycle with mature cleistothecia, containing heat-resistant ascospores, being produced after 3 weeks of incubation. Recombination was confirmed using molecular markers. However, isolates of A. lentulus failed to cross with highly fertile strains of A. fumigatus, demonstrating reproductive isolation between these sibling species. The discovery of the A. lentulus sexual stage has significant implications for the management of drug resistance and control of invasive aspergillosis associated with this emerging fungal pathogen.

Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi

Background

The broadly accepted pattern of rapid evolution of reproductive genes is primarily based on studies of animal systems, although several examples of rapidly evolving genes involved in reproduction are found in diverse additional taxa. In fungi, genes involved in mate recognition have been found to evolve rapidly. However, the examples are too few to draw conclusions on a genome scale.

Results

In this study, we performed microarray hybridizations between RNA from sexual and vegetative tissues of two strains of the heterothallic (self-sterile) filamentous ascomycete Neurospora intermedia, to identify a set of sex-associated genes in this species. We aligned Expressed Sequence Tags (ESTs) from sexual and vegetative tissue of N. intermedia to orthologs from three closely related species: N. crassa, N. discreta and N. tetrasperma. The resulting four-species alignments provided a dataset for molecular evolutionary analyses. Our results confirm a general pattern of rapid evolution of fungal sex-associated genes, compared to control genes with constitutive expression or a high relative expression during vegetative growth. Among the rapidly evolving sex-associated genes, we identified candidates that could be of importance for mating or fruiting-body development. Analyses of five of these candidate genes from additional species of heterothallic Neurospora revealed that three of them evolve under positive selection.

Conclusions

Taken together, our study represents a novel finding of a genome-wide pattern of rapid evolution of sex-associated genes in the fungal kingdom, and provides a list of candidate genes important for reproductive isolation in Neurospora.

The Colletotrichum acutatum species complex

Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum.

TAXONOMIC NOVELTIES

New combinations - Colletotrichum limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. lupini (Bondar) Damm, P.F. Cannon & Crous, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. New species - C. acerbum Damm, P.F. Cannon & Crous, C. australe Damm, P.F. Cannon & Crous, C. brisbanense Damm, P.F. Cannon & Crous, C. cosmi Damm, P.F. Cannon & Crous, C. costaricense Damm, P.F. Cannon & Crous, C. cuscutae Damm, P.F. Cannon & Crous, C. guajavae Damm, P.F. Cannon & Crous, C. indonesiense Damm, P.F. Cannon & Crous, C. johnstonii Damm, P.F. Cannon & Crous, C. kinghornii Damm, P.F. Cannon & Crous, C. laticiphilum Damm, P.F. Cannon & Crous, C. melonis Damm, P.F. Cannon & Crous, C. orchidophilum Damm, P.F. Cannon & Crous, C. paxtonii Damm, P.F. Cannon & Crous, C. pseudoacutatum Damm, P.F. Cannon & Crous C. pyricola Damm, P.F. Cannon & Crous, C. rhombiforme Damm, P.F. Cannon & Crous, C. scovillei Damm, P.F. Cannon & Crous, C. sloanei Damm, P.F. Cannon & Crous, C. tamarilloi Damm, P.F. Cannon & Crous, C. walleri Damm, P.F. Cannon & Crous. Typifications: Epitypifications - C. acutatum J.H. Simmonds, C. limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. nymphaeae (Pass.) Aa, C. phormii (Henn.) D.F. Farr & Rossman, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. Lectotypifications - C. nymphaeae (Pass.) Aa, C. orchidearum Allesch.

Colletotrichum - current status and future directions

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.

Large-scale introgression shapes the evolution of the mating-type chromosomes of the filamentous ascomycete Neurospora tetrasperma

The significance of introgression as an evolutionary force shaping natural populations is well established, especially in animal and plant systems. However, the abundance and size of introgression tracts, and to what degree interspecific gene flow is the result of adaptive processes, are largely unknown. In this study, we present medium coverage genomic data from species of the filamentous ascomycete Neurospora, and we use comparative genomics to investigate the introgression landscape at the genomic level in this model genus. We revealed one large introgression tract in each of the three investigated phylogenetic lineages of Neurospora tetrasperma (sizes of 5.6 Mbp, 5.2 Mbp, and 4.1 Mbp, respectively). The tract is located on the chromosome containing the locus conferring sexual identity, the mating-type (mat) chromosome. The region of introgression is confined to the region of suppressed recombination and is found on one of the two mat chromosomes (mat a). We used Bayesian concordance analyses to exclude incomplete lineage sorting as the cause for the observed pattern, and multilocus genealogies from additional species of Neurospora show that the introgression likely originates from two closely related, freely recombining, heterothallic species (N. hispaniola and N. crassa/N. perkinsii). Finally, we investigated patterns of molecular evolution of the mat chromosome in Neurospora, and we show that introgression is correlated with reduced level of molecular degeneration, consistent with a shorter time of recombination suppression. The chromosome specific (mat) and allele specific (mat a) introgression reported herein comprise the largest introgression tracts reported to date from natural populations. Furthermore, our data contradicts theoretical predictions that introgression should be less likely on sex-determining chromosomes. Taken together, the data presented herein advance our general understanding of introgression as a force shaping eukaryotic genomes.

Introgression is a process by which genetic material from one species becomes infiltrated into another, genetically distinct species. Introgression usually occurs via sexual reproduction: individuals of two species mate and produce a hybrid offspring, then the offspring repeatedly backcross with one of the parental species. Introgression has long been recognized as a key process in evolution, as it may contribute to speciation, diversification, and adaptation to new environments. The importance and prevalence of introgression has been well established in plant and animal systems, and in this study we use a fungal model system, Neurospora, to study the introgression at the genomic level. We gathered genomic data from six genomes, and by comparative genomics we revealed genetic transfer of DNA regions of unprecedentedly large sizes, covering over 50% of the mating-type chromosomes, and used phylogenetic analyses to reveal the origin and direction of the transfer. Introgression was found solely on the mating-type chromosomes, which contradicts theoretical predictions for sex-determining chromosomes. We argue that this unexpected pattern is due to the fact that fungi do not have differentiated sexes (female/male) and thereby are free from sex-biased evolutionary forces. Instead, we suggest that introgression between fungal species may result in reinvigoration of genomic regions exposed to suppressed recombination.

The tempo and modes of evolution of reproductive isolation in fungi

Reproductive isolation is an essential ingredient of speciation, and much has been learned in recent years about the evolution of reproductive isolation and the genetics of reproductive barriers in animals and plants. Fungi have been neglected on these aspects, despite being tractable model eukaryotes. Here, we used a model fitting approach to look at the importance of different barriers to gene flow to explain the decrease of reproductive compatibility with genetic distance in fungi. We found support for the occurrence of reinforcement in the presyngamy compatibility among basidiomycetes. In contrast, no evidence for reinforcement was detected in ascomycetes, concurring with the idea that host/habitat adaptation in this group can pleiotropically cause reproductive isolation. We found no evidence of a snowballing accumulation of postsyngamic reproductive incompatibilities in either ascomycetes or the complex of anther smut fungi. Together with previous studies, our results suggest that ecologically based barriers to gene flow and karyotypic differences may have an important role in hybrid inviability and sterility in fungi. Interestingly, hybrid sterility appeared to evolve faster than hybrid inviability in fungi.

Emerging fungal threats to animal, plant and ecosystem health

The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.