Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

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.

Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56-33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.

Watershed and fire severity are stronger determinants of soil chemistry and microbiomes than within-watershed woody encroachment in a tallgrass prairie system

Fire can impact terrestrial ecosystems by changing abiotic and biotic conditions. Short fire intervals maintain grasslands and communities adapted to frequent, low-severity fires. Shrub encroachment that follows longer fire intervals accumulates fuel and can increase fire severity. This patchily distributed biomass creates mosaics of burn severities in the landscape-pyrodiversity. Afforded by a scheduled burn of a watershed protected from fires for 27 years, we investigated effects of woody encroachment and burn severity on soil chemistry and soil-inhabiting bacteria and fungi. We compared soils before and after fire within the fire-protected, shrub-encroached watershed and soils in an adjacent, annually burned and non-encroached watershed. Organic matter and nutrients accumulated in the fire-protected watershed but responded less to woody encroachment within the encroached watershed. Bioavailable nitrogen and phosphorus and fungal and bacterial communities responded to high-severity burn regardless of encroachment. Low-severity fire effects on soil nutrients differed, increased bacterial but decreased fungal diversity and effects of woody encroachment within the encroached watershed were minimal. High-severity burns in the fire-protected watershed led to a novel soil system state distinct from non-encroached and encroached soil systems. We conclude that severe fires may open grassland restoration opportunities to manipulate soil chemistry and microbial communities in shrub-encroached habitats.

On the relativity of species, or the probabilistic solution to the species problem

For centuries, both scientists and philosophers have discussed the nature of species resulting in c. 35 species concepts proposed to date. However, in our opinion, none of them incorporated neither recent advances in evolutionary genomics nor dimensionality of species in befitting depth. Our attempt to do so resulted in the following conclusions. Due to the continuous nature of evolution (regardless of its rate and constancy), species are inevitably undefinable as natural discontinuous units (except those originating in saltatory speciation) whenever the time dimension is taken into consideration. Therefore, the very existence of species as a natural discontinuous entity is relative to its dimensionality. A direct consequence of the relativity of species is the duality of speciators (e.g., incipient species) meaning that, in a given time, they may be perceived as both being and not being a species. Finally, the most accurate way to reflect both the relativity of species and the duality of speciators in species delimitation is probabilistic. While the novelty of these ideas may be questionable, they still deserve more extensive attention from the biological community. Here, we hope to draw such attention by outlining one of the possible pathways towards a new kind of probabilistic species delimitation methods based on the probability of irreversible divergence of evolutionary lineages. We anticipate that our probabilistic view of speciation has the potential to facilitate some of the most serious and universal issues of current taxonomy and to ensure unity of the species-level taxonomy across the tree of life.

Seven new Serendipita species associated with Australian terrestrial orchids

Serendipita is one of the main fungal genera that form mutualistic associations with species of orchids (Orchidaceae). Here, seven new Serendipita species associated with various Australian orchid genera are described. These Serendipita species were originally characterized by multilocus DNA sequence species delimitation analyses (three mtDNA and four nuclear genes) and confirmed as distinct with addition of further isolates and reanalysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S). Culture morphology and microscopic features are presented for each species, three of which are binucleate and four multinucleate. For the ITS region, the seven species have within-species sequence divergence between 1.07% and 4.31%, and all but one of the species pairs is separated by interspecific divergence of at least 4.35%. The newly described Serendipita species, S. australiana, S. communis, S. occidentalis, S. rarihospitum, S. secunda, S. talbotii, and S. warcupii, are shown to be separate species from S. vermifera on the basis of comparison against a sequence from the type. Isolates originally identified by Warcup as Sebacina "vermifera" from Caladenia orchids are revised and shown to belong to three of the species newly described here. Some non-Caladenia isolates identified by Warcup as S. "vermifera" are also shown to be non-conspecific with the type of S. vermifera. On the basis of ITS sequences, 346 isolates from 26 other studies, previously identified under provisional designations, are accommodated under the novel species. The species of Serendipta described here associate with the Australian orchid genera Caladenia, Cyanicula, Elythranthera, Ericksonella, Eriochilus, Glossodia, and Pheladenia. Most of the novel Serendipita species occur widely across Australia, often with widely distributed hosts, but one species, Serendipita rarihospitum, associates with narrowly distributed orchid species.

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.

Cryphonectria carpinicola sp. nov. Associated with hornbeam decline in Europe

Since the early 2000s, reports on declining hornbeam trees (Carpinus betulus) are spreading in Europe. Two fungi are involved in the decline phenomenon: One is Anthostoma decipiens, but the other etiological agent has not been identified yet. We examined the morphology, phylogenetic position, and pathogenicity of yellow fungal isolates obtained from hornbeam trees from Austria, Georgia and Switzerland, and compared data with disease reports from northern Italy documented since the early 2000s. Results demonstrate distinctive morphology and monophyletic status of Cryphonectria carpinicola sp. nov. as etiological agent of the European hornbeam decline. Interestingly, the genus Cryphonectria splits into two major clades. One includes Cry. carpinicola together with Cry. radicalis, Cry. decipiens and Cry. naterciae from Europe, while the other comprises species known from Asia-suggesting that the genus Cryphonectria has developed at two evolutionary centres, one in Europe and Asia Minor, the other in East Asia. Pathogenicity studies confirm that Car. betulus is a major host species of Cry. carpinicola. This clearly distinguished Cry. carpinicola from other Cryphonectria species, which mainly occur on Castanea and Quercus.

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.

Habitat-Specific Clock Variation and Its Consequence on Reproductive Fitness

The circadian clock controls daily activities at the cellular and organismic level, allowing an organism to anticipate incoming stresses and to use resources accordingly. The circadian clock has therefore been considered a fitness trait in multiple organisms. However, the mechanism of how circadian clock variation influences organismal reproductive fitness is still not well understood. Here we describe habitat-specific clock variation (HSCV) of asexual reproduction in Neurospora discreta, a species that is adapted to 2 different habitats, under or above tree bark. African (AF) N. discreta strains, whose habitat is above the tree bark in light-dark (LD) conditions, display a higher rhythmicity index compared with North American (NA) strains, whose habitat is under the tree bark in constant dark (DD). Although AF-type strains demonstrated an overall fitness advantage under LD and DD conditions, NA-type strains exhibit a habitat-specific fitness advantage in DD over the LD condition. In addition, we show that allelic variation of the clock-controlled gene, Ubiquinol cytochrome c oxidoreductase (NEUDI_158280), plays a role in HSCV by modulating cellular reactive oxygen species levels. Our results demonstrate a mechanism by which local adaptation involving circadian clock regulation influences reproductive fitness.

Are species-pairs diverging lineages? A nine-locus analysis uncovers speciation among species-pairs of the Lobaria meridionalis-group (Ascomycota)

In spite of considerable effort to verify the theory of species-pairs, uncertainty still exists about the relationship between sexually or vegetatively reproducing populations of morphologically indistinguishable, sympatric lichen species. The current paper studies putative species-pairs within the Asian Lobaria meridionalis-group, using a nine-locus and time calibrated species-tree approach. Analyses demonstrate that pairs of sexually or vegetatively reproducing lineages split into highly supported monophyletic clades-confirming molecularly the species-pair concept for the L. meridionalis-group. In the broader context of evolution and speciation dynamics in lichenized fungi, this paper attempts to synthesize molecular findings from the last two decades to promote a more modern perception of the species-pair concept. Taxonomically, eight species were found to currently conform to the L. meridionalis-group, which differentiated during the Pliocene and Pleistocene. The coincidence of paleoclimatic events with estimated dates of divergence support a bioclimatic hypothesis for the evolution of species in the L. meridionalis-group, which also explains their current eco-geographic distribution patterns. Greater recognition for species with a long and independent evolutionary history, which merit high conservation priority, will be especially critical for preserving geographically restricted endemics from Southeast Asia, where habitat loss is driving rapid declines.

Natural Variation of the Circadian Clock in Neurospora

Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.

New species of Talaromyces isolated from maize, indoor air, and other substrates

Talaromyces strains isolated from maize seeds and the built environment were examined taxonomically because they could not be identified as previously described species. Using phenotypic analysis, DNA sequencing, and phylogenetic and concordance analyses, the authors discovered and described 10 new species in sect. Islandici and 1 new species in sect. Subinflati. Taxonomic novelties in sect. Islandici are Talaromyces delawarensis, T. herodensis, T. juglandicola, T. kilbournensis, T. novojersensis, T. ricevillensis, T. rogersiae, T. siglerae, T. subtropicalis, and T. tiftonensis, and the species from sect. Subinflata is T. tzapotlensis. The isolate of T. siglerae is unusual in Talaromyces because it produced a Sagenomella-like anamorph, but phylogenetic analysis placed it in Talaromyces. Talaromyces rotundus is known from a few isolates, but searches with internal transcribed spacer (ITS) sequences in GenBank revealed that it is commonly endolichenous with Lasallia hispanica. Talaromyces wortmannii also has a role as an endophyte of the aquatic plant Persicaria amphibia, based on ITS sequence records from GenBank.

Fungal Genomes and Insights into the Evolution of the Kingdom

The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

Multi-gene phylogeny of the genus Lobaria: Evidence of species-pair and allopatric cryptic speciation in East Asia

PREMISE OF THE STUDY

Accurate species delimitation has critical implications for ecological and conservation studies. The lichen genus Lobaria is widely distributed in old-growth forests. Particularly in East Asia, this genus includes many rare and poorly known taxa that are circumscribed as morpho- or chemospecies, as well as species-pairs.

METHODS

To critically examine the relationships between species identified via morphological and chemical criteria, phylogenetic species recognition (PSR) was applied to the genus Lobaria. Morphological and chemical patterns of 87 individuals were examined and three independent nuclear loci were sequenced. The East Asian L. meridionalis-group was additionally studied using split decomposition and haplotype network analysis.

KEY RESULTS

The genus Lobaria and most of its species were strongly supported statistically. Split decomposition and haplotype networks suggest complex evolutionary histories of species within the East Asian L. meridionalis-group.

CONCLUSIONS

Phylogenetic analyses confirmed the monophyly of the genus Lobaria, including L. anomala. Within Lobaria, three major clades were found. These clades associate with different photobionts and comprise 18 known species and 5 undescribed species. Several chemical compounds were found to be neither stable nor invariant characters. Some taxa of the L. meridionalis-group appear to be monophyletic but remain as allopatric cryptic species. In three clades, this study found evidence for diversification processes between isidiate and nonisidiate specimens (species-pair). These findings are discussed in the context of evolutionary hypotheses for speciation processes.

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.

Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle

There is strong community-wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single-locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.

A Comparison of Standard and High-Fidelity PCR: Evaluating Quantification and Detection of Pathogen DNA in the Presence of Orchid Host Tissue

The polymerase chain reaction (PCR) has been used with increasing frequency for detecting and identifying plant pathogens. Although PCR is sensitive, research has shown that amplification of target microbial DNA from within another organism, such as an arthropod or plant, can be inhibited by the presence of host DNA. In this study, the sensitivity of standard and high-fidelity PCR, which incorporates a second DNA polymerase with proofreading ability, to detect and amplify DNA from the fungal pathogen Pseudocercospora odontoglossi while in the presence of Cattleya orchid DNA, was compared. Different dilutions of plasmids containing internal transcribed spacer (ITS)1, 5.8S, and ITS2 rDNA from P. odontoglossi were spiked with Cattleya orchid plant DNA. The high-fidelity PCR could detect and amplify as few as 207 plasmids containing the fungal DNA, whereas the standard PCR required over 200 million copies. The high-fidelity PCR was more efficient than conventional PCR in detecting Sclerotium rolfsii and a Dickeya sp. from freshly inoculated orchid plants, demonstrating its increased sensitivity in early detection of fungal and bacterial pathogens that are difficult to discriminate early in disease development.

Penicillium menonorum, a new species related to P. pimiteouiense

Penicillium menonorum is described as a new monoverticillate, non-vesiculate species that resembles P. restrictum and P. pimiteouiense. On the basis of phylogenetic analysis of DNA sequences from four loci, P. menonorum occurs in a clade with P. pimiteouiense, P. vinaceum, P. guttulosum, P. rubidurum, and P. parvum. Genealogical concordance analysis was applied to P. pimiteouiense and P. parvum, substantiating the phenotypically defined species. The species P. rubidurum, P. guttulosum, and P. menonorum were on distinct branches statistically excluded from inclusion in other species and have distinct phenotypes.

Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta

Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.

The fungi: 1, 2, 3 ... 5.1 million species?

PREMISE OF THE STUDY

Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist.

METHODS

Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa.

KEY RESULTS

Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered.

CONCLUSIONS

Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

Elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. Even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. Here, we have circumvented these issues in the microbial eukaryote Neurospora crassa by using a "reverse-ecology" population genomic approach that is free of a priori assumptions about candidate adaptive alleles. We performed Illumina whole-transcriptome sequencing of 48 individuals to identify single nucleotide polymorphisms. From these data, we discovered two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. We conducted high-resolution scans for chromosomal regions of extreme divergence between these populations and found two such genomic "islands." Through growth-rate assays, we found that the subtropical Louisiana population has a higher fitness at low temperature (10 °C) and that several of the genes within these distinct regions have functions related to the response to cold temperature. These results suggest the divergence islands may be the result of local adaptation to the 9 °C difference in average yearly minimum temperature between these two populations. Remarkably, another of the genes identified using this unbiased, whole-genome approach is the well-known circadian oscillator frequency, suggesting that the 2.4°-10.6° difference in latitude between the populations may be another important environmental parameter.

Genus Hamigera, six new species and multilocus DNA sequence based phylogeny

Genus Hamigera was erected for Talaro-myces species that make asci singly instead of in chains. Initially it contained two species, H. avellanea and H. striata. We describe six new species in the genus, H. fusca, H. inflata, H. insecticola, H. pallida, H. paravellanea and H. terricola. Merimbla ingelheimensis is a distinct anamorphic species in the Hamigera clade. None of our DNA sequence data (BT2, calmodulin, ITS, 1su rDNA, RPB2, Tsr1 and Mcm7) supported the placement of H. striata in the same clade as H. avellanea, thus we accepted Talaromyces striatus. In addition to Hamigera species we examined the phylogenetic disposition of Warcupiella spinulosa, Penicillium megasporum, Penicillium arenicola and Merimbla humicoloides. Despite nominal similarity of some of these species to Merimbla, none of these species are part of the Hamigera clade and M. humicoloides is placed in Penicillium to have a monophyletic genus Hamigera.

Phylogenetic and biological species diversity within the Neurospora tetrasperma complex

The objective of this study was to explore the evolutionary history of the morphologically recognized filamentous ascomycete Neurospora tetrasperma, and to reveal the genetic and reproductive relationships among its individuals and populations. We applied both phylogenetic and biological species recognition to a collection of strains representing the geographic and genetic diversity of N. tetrasperma. First, we were able to confirm a monophyletic origin of N. tetrasperma. Furthermore, we found nine phylogenetic species within the morphospecies. When using the traditional broad biological species recognition all investigated strains of N. tetrasperma constituted a single biological species. In contrast, when using a quantitative measurement of the reproductive success, incorporating characters such as viability and fertility of offspring, we found a high congruence between the phylogenetic and biological species recognition. Taken together, phylogenetically and biologically defined groups of individuals exist in N. tetrasperma, and these should be taken into account in future studies of its life history traits.

Penicillium parvulum and Penicillium georgiense, sp. nov., isolated from the conidial heads of Aspergillus species

Two new Penicillium species were isolated from peanut-field soils in Georgia. The species were noted particularly because they sporulated on the conidial heads of Aspergillus species. Phenotypic descriptions were prepared with standard media. LSU-rDNA sequences were determined for the new species and compared to existing homologous sequences from Penicillium species with parsimony analysis. The monoverticillate species, P. parvulum, was related most closely to E. cinnamopurpureum, while the furcate species, P. georgiense, appeared in the tree near P. thiersii. Because P. parvulum was closely related to E. cinnamopurpureum additional loci were sequenced (beta-tubulin and calmodulin) for these and some other closely related species to establish the status of the species through genealogical concordance. Some proposed synonymies from prior studies were examined and resolved.

The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic neurospora

Comparative sequencing studies among a wide range of taxonomic groups, including fungi, provide the overall pattern that reproductive genes evolve more rapidly than other genes, and this divergence is believed to be important in the establishment of reproductive barriers between species. In this study, we investigated the molecular evolution of the pheromone receptor genes pre-1 and pre-2 of strains belonging to 12 and 13 heterothallic taxa, respectively, of the model genus Neurospora. Furthermore, we examined the regulatory pattern of both pheromone precursor and receptor genes during sexual crosses of Neurospora crassa and Neurospora intermedia, for which reinforcement of interspecific reproductive barriers in sympatry previously has been documented. We conclude that the part encoding the C-terminal intracellular domain of pre-1 and pre-2 genes evolves rapidly. Both stochastic and directional processes drive this divergence; both genes contain neutrally evolving codons, and in addition, pre-1 contains codons evolving under positive selection, whereas in pre-2 we found highly variable regions with numerous repeats encoding glycine, threonine, or aspartic acid. In addition, we found regulatory changes of the pheromone and receptor genes during crosses between N. crassa and N. intermedia with different reproductive success. Gene expression levels are higher in the interspecific sympatric crosses with low reproductive success than in their intraspecific and/or allopatric equivalents, both at the stage of initial communication and contact and later at postfertilization stages. Taken together, our data indicate that pheromones and receptors are important key players during reproductive isolation between Neurospora species, and this study provides a general framework for future studies on the role of reproductive proteins for reproductive isolation.