Ophiostoma quercus: An unusually diverse and globally widespread tree-infecting fungus

Ophiostoma quercus (Ascomycota, Ophiostomatales) is a globally widespread, insect-vectored fungus that colonizes a wide diversity of hardwood and conifer hosts. Although the fungus is considered to be non-pathogenic, it is closely related to the fungi that cause Dutch elm disease. We examined the global diversity of O. quercus based on a ribosomal RNA marker and three unlinked gene regions. The fungus exhibited substantial morphological diversity. In addition, O. quercus had high genetic diversity in every continent from which it was collected, although the fungus was most diverse in Eurasia. There was no evidence of geographical clustering of haplotypes based on phylogenetic and network analyses. In addition, the phylogenetic trees generated based on the different markers were non-congruent. These results suggest that O. quercus has been repeatedly moved around the globe, because of trade in wood products, and that the fungal species most likely outcrosses regularly. The high genetic diversity of the fungus, as well as its ability to utilize a wide variety of arthropod vectors and colonize a tremendous diversity of tree host species makes O. quercus truly unique among ophiostomatoid fungi.     

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi

The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.     

Molecular systematics and taxonomic overview of the bird's nest fungi (Nidulariaceae)

Fungi in the Nidulariaceae, otherwise known as ‘bird's nest fungi’, are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.     

Old age, multiple formations or genetic plasticity? Clonal diversity in the uniparental Caucasian rock lizard, Lacerta dahli

Allozyme variation at 35 gene loci is investigated in 161 specimens of the uniparental Caucasian lizard Lacerta dahli from several locations in Armenia and Georgia. All individuals are heterozygotic at 12 loci, and homozygotic at 21 loci. Variation at two loci results in five uniparental clones. One clone is widespread whereas four are geographically restricted and are represented by only one or two individuals. Because successful formation of uniparental clones is rare, and because the biparental species forming them are now allopatric, the most probable explanation for the origin of the observed clonal diversity is either mutation or recombination within the common clone. The rare clones have lower levels of enzyme activity at four loci, suggesting that these organisms may be genetically deficient. Although the evidence points to change in a pre-existing clone, the possibility of multiple origins cannot be ruled out. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cosmopolitan metapopulations of free-living microbial eukaryotes

Metapopulations of macroscopic organisms tend to be geographically restricted, but free-living protists and other microbial eukaryotes present a different picture. Here we show that most organisms smaller than 1 mm occur worldwide wherever their required habitats are realised. This is a consequence of ubiquitous dispersal driven by huge population sizes, and the consequently low probability of local extinction. Organisms larger than 10 mm are much less abundant, and rarely cosmopolitan. The supporting data, together with the discovery that the 1-10 mm size range accommodates a transition from cosmopolitan to regionally-restricted distribution, were derived from extensive inventories of eukaryotic species in a freshwater pond (1278 species), and a shallow marine bay (785 species). All accessible records were examined to establish the extent of global coverage by these species. Some groups of microbial eukaryotes are severely undersampled (e.g. naked amoebae; marine meiofauna in the southern hemisphere) but this fails to weaken evidence that metapopulations of microbial eukaryotes are cosmopolitan.     

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

Background  

Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeographic relationships within this lineage at a global scale have been largely unknown. In this study, we obtained DNA sequences from a nearly complete taxon sampling of known species from Europe, Central America and North America. We inferred intra- and interspecific phylogenetic relationships as well as major morphological evolutionary trends within section Calochroi based on 576 ITS sequences, 230 ITS + 5.8S + D1/D2 sequences, and a combined dataset of ITS + 5.8S + D1/D2 and RPB1 sequences of a representative subsampling of 58 species.     

Lizards from the end of the world: phylogenetic relationships of the Liolaemus lineomaculatus section (Squamata: Iguania: Liolaemini)

The Liolaemus lineomaculatus section is a geographically widely distributed group of lizards from the Patagonian region of southern South America, and includes 18 described species representing the most southerly distributed Liolaemus taxa (the genus includes 228 species and extends from Tierra del Fuego north to south-central Peru). Despite high species diversity, the phylogenetic relationships of this section are unknown. In the present work we sampled all described species in the L. lineomaculatus section as well as currently undescribed candidate species to reconstruct the first complete phylogenetic hypothesis for the clade. Our data set included four anonymous nuclear loci, three nuclear protein-coding loci, and two mitochondrial genes. We compared results obtained with three different phylogenetic methods for the concatenated data set (Maximum Parsimony, Maximum Likelihood and Bayesian Inference) with a coalescent-based species tree approach (BEST), and recovered congruent, strongly-supported topological arrangements across all methods. We identified four main clades within the L. lineomaculatus section: the lineomaculatus, magellanicus, somuncurae, and kingii+archeforus groups, for which we estimated divergence times. We discuss the taxonomic implications of these results and how the future integration of phylogeographic, niche modeling and morphological approaches will allow testing biogeographical hypotheses in this clade.     

An ergot alkaloid biosynthesis gene and clustered hypothetical genes from Aspergillus fumigatus

The ergot alkaloids are a family of indole-derived mycotoxins with a variety of significant biological activities. Aspergillus fumigatus, a common airborne fungus and opportunistic human pathogen, and several fungi in the relatively distant taxon Clavicipitaceae (clavicipitaceous fungi) produce different sets of ergot alkaloids. The ergot alkaloids of these divergent fungi share a four-member ergoline ring but differ in the number, type, and position of the side chains. Several genes required for ergot alkaloid production are known in the clavicipitaceous fungi, and these genes are clustered in the genome of the ergot fungus Claviceps purpurea. We investigated whether the ergot alkaloids of A. fumigatus have a common biosynthetic and genetic origin with those of the clavicipitaceous fungi. A homolog of dmaW, the gene controlling the determinant step in the ergot alkaloid pathway of clavicipitaceous fungi, was identified in the A. fumigatus genome. Knockout of dmaW eliminated all known ergot alkaloids from A. fumigatus, and complementation of the mutation restored ergot alkaloid production. Clustered with dmaW in the A. fumigatus genome are sequences corresponding to five genes previously proposed to encode steps in the ergot alkaloid pathway of C. purpurea, as well as additional sequences whose deduced protein products are consistent with their involvement in the ergot alkaloid pathway. The corresponding genes have similarities in their nucleotide sequences, but the orientations and positions within the cluster of several of these genes differ. The data indicate that the ergot alkaloid biosynthetic capabilities in A. fumigatus and the clavicipitaceous fungi had a common origin.     

Epipactis helleborine shows strong mycorrhizal preference towards ectomycorrhizal fungi with contrasting geographic distributions in Japan

Epipactis helleborine (L.) Crantz, one of the most widespread orchid species, occurs in a broad range of habitats. This orchid is fully myco-heterotrophic in the germination stage and partially myco-heterotrophic in the adult stage, suggesting that a mycorrhizal partner is one of the key factors that determines whether E. helleborine successfully colonizes a specific environment. We focused on the coastal habitat of Japanese E. helleborine and surveyed the mycorrhizal fungi from geographically different coastal populations that grow in Japanese black pine (Pinus thunbergii Parl.) forests of coastal sand dunes. Mycorrhizal fungi and plant haplotypes were then compared with those from inland populations. Molecular phylogenetic analysis of large subunit rRNA sequences of fungi from its roots revealed that E. helleborine is mainly associated with several ectomycorrhizal taxa of the Pezizales, such as Wilcoxina, Tuber, and Hydnotrya. All individuals from coastal dunes were exclusively associated with a pezizalean fungus, Wilcoxina, which is ectomycorrhizal with pine trees growing on coastal dunes. Wilcoxina was not detected in inland forests. Coastal populations were indistinguishable from inland populations based on plant trnL intron haplotypes. Our results indicate that mycorrhizal association with geographically restricted pezizalean ectomycorrhizal fungi is a key control upon this orchid species' distribution across widely different forest habitats.     

Cryptic species in Stachybotrys chartarum

Stachybotrys chartarum has received much attention as a possible cause of sick-building syndrome. Because morphological species recognition in fungi can hide diversity, we applied a phylogenetic approach to search for cryptic species. We examined 23 isolates from the San Francisco Bay Area, and another seven from around the US. Using markers we developed for three polymorphic protein coding loci (chitin synthase 1, beta-tubulin 2, and trichodiene synthase 5), we infer that two distinct phylogenetic species exist within the single described morphological species. We have found no correlation between genetic isolation and geographic distance.     

Pseudo-nitzschia pungens (Bacillariophyceae): A cosmopolitan diatom species?

Genetic, reproductive and morphological variation were studied in 193 global strains of the marine diatom species Pseudo-nitzschia pungens (Grunow ex Cleve) Hasle to assess potential intraspecific variation and biogeographic distribution patterns. Genetic differentiation between allo- and sympatric strains was investigated using the ITS1–5.8S–ITS2 rDNA region. Three ITS clades were found. Clones of opposite mating type were sexually compatible within clades I or II, and viable F1 hybrid offspring were produced in crosses between them. The molecular differences between these clades were correlated with slight but consistent morphological differences. At present, nothing can be said about morphology and mating behavior for clade III clones because only ITS data were available. The three ITS clades showed different geographic distributions. Clade II was restricted to the NE Pacific, whereas clones belonging to clade III originated from geographically widely separated areas (Vietnam, China and Mexico). ITS clade I was recovered in all locations studied: the North Sea (Belgium, The Netherlands, France), the eastern and western N Atlantic (Spain, Canada), the NW and S Pacific (Japan, New Zealand) and the NE Pacific (Washington State). Clade I thus appears to be globally distributed in temperate coastal areas and provides the first strong evidence to date for the global distribution of a biologically, genetically and morphologically defined diatom species.     

Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: evidence for cryptic allopatric diversity

Underground environments are increasingly recognized as reservoirs of faunal diversity. Extreme environmental conditions and limited dispersal ability of underground organisms have been acknowledged as important factors promoting divergence between species and conspecific populations. However, in many instances, there is no correlation between genetic divergence and morphological differentiation. Lucifuga Poey is a stygobiotic fish genus that lives in Cuban and Bahamian caves. In Cuba, it offers a unique opportunity to study the influence of habitat fragmentation on the genetic divergence of stygobiotic species and populations. The genus includes four species and one morphological variant that have contrasting geographical distributions. In this study, we first performed a molecular phylogenetic analysis of the Lucifuga Cuban species using mitochondrial and nuclear markers. The mitochondrial phylogeny revealed three deeply divergent clades that were supported by nuclear and morphological characters. Within two of these main clades, we identified five lineages that are candidate cryptic species and a taxonomical synonymy between Lucifuga subterranea and Lucifuga teresinarum. Secondly, phylogeographic analysis using a fragment of the cytochrome b gene was performed for Lucifuga dentata, the most widely distributed species. We found strong geographical organization of the haplotype clades at different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. At a larger temporal scale, these processes could also explain the diversification and the distribution of the different species.     

Isolation and characterization of microsatellite loci from the entomopathogenic fungus Beauveria bassiana (Ascomycota: Hypocreales)

Beauveria bassiana, an entomogenous fungus used for the biological control of pest insects, comprises a globally‐distributed species complex of regionally endemic lineages. In order to study the population genetics of B. bassiana, detail species boundaries, conduct ecological studies of natural populations and track fates of experimentally‐released strains, sensitive genetic markers are required. We describe the isolation and characterization of eight microsatellite loci that amplify successfully from strains representative of the phylogenetic diversity in the B. bassiana complex.     

Chemotypic and genotypic diversity in the ergot alkaloid pathway of Aspergillus fumigatus

Aspergillus fumigatus is an opportunistic human pathogen that synthesizes a group of mycotoxins via a branch of the ergot alkaloid pathway. This fungus is globally distributed, and genetic data indicate that isolates recombine freely over that range; however, previous work on ergot alkaloids has focused on a limited number of isolates. We hypothesized that A. fumigatus harbors variation in the chemotype of ergot alkaloids and genotype of the ergot alkaloid gene cluster. Analysis of 13 isolates by high performance liquid chromatography revealed four distinct ergot alkaloid profiles or chemotypes. Five isolates completed the A. fumigatus branch of the ergot alkaloid pathway to fumigaclavine C. Six independent isolates accumulated fumigaclavine A, the pathway intermediate immediately before fumigaclavine C. One isolate accumulated only the early pathway intermediates chanoclavine-i and chanocla-vine-i aldehyde, and one isolate lacked ergot alkaloids altogether. A genetic basis for each of the observed chemotypes was obtained either by PCR analysis of the ergot alkaloid gene cluster or through sequencing of easL, the gene encoding the prenyl transferase that reverse prenylates fumigaclavine A to fumigaclavine C. Isolates also exhibited differences in pigmentation and sporulation. The ergot alkaloid chemotypes were widely distributed geographically and among substrate of origin.     

Phylogenetic trait conservation in the partner choice of a group of ectomycorrhizal trees

Ecological interactions are frequently conserved across evolutionary time. In the case of mutualisms, these conserved interactions may play a large role in structuring mutualist communities. We hypothesized that phylogenetic trait conservation could play a key role in determining patterns of association in the ectomycorrhizal symbiosis, a globally important trophic mutualism. We used the association between members of the pantropical plant tribe Pisonieae and its fungal mutualist partners as a model system to test the prediction that Pisonieae‐associating ectomycorrhizal fungi will be more closely related than expected by chance, reflecting a conserved trait. We tested this prediction using previously published and newly generated sequences in a Bayesian framework incorporating phylogenetic uncertainty. We report that phylogenetic trait conservation does exist in this association. We generated a five‐marker phylogeny of members of the Pisonieae and used this phylogeny in a Bayesian relaxed molecular clock analysis. We established that the most recent common ancestors of Pisonieae species and Pisonieae‐associating fungi sharing phylogenetic conservation of their patterns of ectomycorrhizal association occurred no more recently than 14.2 Ma. We therefore suggest that phylogenetic trait conservation in the Pisonieae ectomycorrhizal mutualism association represents an inherited syndrome which has existed for at least 14 Myr.     

湛江沿海潮间带产胞外纤溶活性酶类海洋真菌的生物多样性分析

【目的】研究湛江沿海硇洲岛和徐闻珊瑚礁自然保护区潮间带产胞外纤溶酶样酶和纤溶酶原激活物海洋真菌的生物多样性,为发掘新型溶栓药物奠定基础。【方法】采用马铃薯葡萄糖琼脂(PDA)和酵母膏蛋白胨葡萄糖(YPD)培养基分离培养海洋真菌,采用真菌r DNA转录间隔区1-5.8S r DNA-转录间隔区2(ITS1-5.8S-ITS2)片段的序列分析及其系统进化树构建的方法鉴定分离培养的海洋真菌,采用脱脂牛奶马铃薯葡萄糖琼脂(SM-PDA)培养基培养法筛选产胞外蛋白酶的海洋真菌,采用海水纤维蛋白马铃薯葡萄糖琼脂(FN-PDA)培养基培养法筛选产胞外纤溶酶样酶和/或纤溶酶原激活物的海洋真菌。【结果】从湛江沿海的硇洲岛和徐闻珊瑚礁自然保护区潮间带分离、培养和鉴定了海洋真菌446株,含真菌的98个种,分布于真菌域子囊菌门(Ascomycota)和担子菌门(Basidiomycota)的6个纲、18个目、46个科、65个属;其中产胞外蛋白酶的海洋真菌有265株,61个种,分布于41个属;产胞外纤溶酶样酶的海洋真菌有67株,22个种,分布于14个属;产胞外纤溶酶原激活物的海洋真菌有84株,23种,分布于13个属;优势属为曲霉属(Aspergillus),其次为青霉属(Penicillium)。【结论】湛江沿海潮间带可分离培养的产胞外纤溶酶样酶和纤溶酶原激活物的海洋真菌物种丰富多样,是发掘新型溶栓药的丰富资源。     

SPECIATIONAL HISTORY IN A DIVERSE CLADE OF HABITAT-SPECIALIZED SPIDERS (ARANEAE: NESTICIDAE: NESTICUS): INFERENCES FROM GEOGRAPHIC-BASED SAMPLING

This paper summarizes the results of an initial effort to reconstruct the speciational history of cave spiders (Nesticus) from the southern Appalachian Mountains of eastern North America. The Appalachian Nesticus fauna includes a large series of about 30 species distributed across islandlike cave and montane habitats. Many of the species are geographically restricted; all of the species are found in allopatry. Observed patterns of morphological variation and biogeographic evidence suggest that species diversification in this lineage may have occurred recently, perhaps in response to Pleistocene climatic fluctuations. To address questions about the spatial and temporal dynamics of Nesticus speciation, while accounting for potential phylogenetic difficulties, I have gathered nuclear and mitochondrial DNA sequences for a sample of individuals from 81 populations representing 28 Nesticus species. Analyses of these data indicate that considerable genetic divergence exists within and among currently recognized morphological species. Consistent with relatively deep species divergences, most of which likely predate the Pleistocene, is a prevailing pattern of phylogenetic concordance between taxonomic species and monophyletic gene tree lineages. The few deviations from monophyly detected can be tentatively attributed to a peripatric mode of speciation. Although species limits as inferred by the molecular data are generally concordant with patterns of morphological continuity and discontinuity in genitalia, there is evidence to suggest that cryptic phylogenetic lineages exist within some morphologically continuous units. This observation, in combination with the general depth of species lineages, makes any argument about rapid evolution in Nesticus genitalic characteristics unnecessary.     

Molecular phylogeny of pearl oysters and their relatives (Mollusca,Bivalvia, Pterioidea)

Background  

The superfamily Pterioidea is a morphologically and ecologically diverse lineage of epifaunal marine bivalves distributed throughout the tropical and subtropical continental shelf regions. This group includes commercially important pearl culture species and model organisms used for medical studies of biomineralization. Recent morphological treatment of selected pterioideans and molecular phylogenetic analyses of higher-level relationships in Bivalvia have challenged the traditional view that pterioidean families are monophyletic. This issue is examined here in light of molecular data sets composed of DNA sequences for nuclear and mitochondrial loci, and a published character data set of anatomical and shell morphological characters.     

Consideration of the taxonomy and biodiversity of Australian ectomycorrhizal fungi

Mycorrhiza management in forestry must be predicated on an understanding of fungal biology and ecology. A fundamental building block of the biology and ecology of any organism is accurate identification and an understanding of its relationship to other organisms. The taxonomy of the larger fungi has been largely based on morphological classification of sexual structures but now Taxonomy routinely incorporates mating studies, and biochemical and molecular data. Taxonomy may not revolutionize theories on mycorrhiza but can clarify some of the inconsistencies due to misrepresentation or over-generalizations and inappropriate conclusions drawn from studies with inaccurately identified fungi. To illustrate this, we discuss and example where incorrect fungal names were repeatedly erroneously applied in morphological and physiological research reports on this fungus, e.g. Laccaria laccata. In this case subsequent taxonomic study revealed the reason for the conflicting research results reported for this fungus. We discuss the status of identifying the ectomycorrhizal fungi in various forest communities in Australia and the relationships of this process to assessing their use in forestry. Recent intensive efforts to collect, isolate and identify Australian ectomycorrhizal fungi have revealed an enormous and unique species diversity, e.g., for truffle-like fungi, over 2000 collections from the last five years alone have yielded 2 new families, 24 new genera, and about 184 new species. Nearly 95% of the described and undescribed fungi from Australia are novel, with some 22 genera and 3 families endemic. In most cases the current systematic knowledge of mycorrhizal fungi is inadequate to support clear framework for Australian taxa. This reflects the traditional Northern Hemisphere view of the world, the uniqueness of the Australian fungal flora, and how poorly it is known. For example, the genus Hymenogaster had been widely acknowledged as the most reduced member of the Cortinariaceae. However recent work on Hymenogaster species from the Southern Hemisphere has offered a number of alternative affinities to various species. We also discuss the role proper identification of the organisms involved plays in understanding the ecosystem. Emphasis should be placed on how species diversity equates with physiological and genetic diversity and how a sound taxonomic understanding of species and their systematic position is essential to properly manage them. Accurate taxonomic information will continue to be required as the basis for assessing the role of ectomycorrhizal fungi in sustained ecological development. Of particular significance is the role of ectomycorrhizal fungi in maintenance of plant diversity in natural ecosystems and those disturbed by management. In conclusion, we present some key research areas involving the use of taxonomy that need priority attention.     

Geographic range size, seedling ecophysiology and phenotypic plasticity in Australian Acacia species

Aim The degree to which eco‐physiological traits critical to seedling establishment are related to differences in geographic range size among species is not well understood. Here, we first tested the idea that seedling eco‐physiological attributes associated with establishment differ between narrowly distributed and geographically widespread plant species. Secondly, we tested the notion that species occupying wide geographic ranges have greater phenotypic plasticity in response to the environment than contrasted species with more restricted distributions. Location Eastern Australia. Methods We compared five pairs of geographically restricted and widespread Acacia species grown under glasshouse conditions for differences in seedling relative growth rate and associated allocational, morphological and physiological traits. We then examined whether widespread species displayed greater phenotypic plasticity in these traits than narrowly distributed species in response to changes in soil water availability. Results Neither relative growth rate nor any measure of biomass accumulation or allocation differed significantly between seedlings of narrowly distributed and widespread species. In addition, the plasticity of biomass allocation was not greater in widespread species. However, the leaflets of widespread species had higher photosynthetic capacity and greater plasticity of water use efficiency than the leaflets of narrowly distributed species. Main conclusions We demonstrated fundamental differences in the physiology and plasticity of leaflets of widespread and narrowly distributed species. The greater plasticity of these seedling leaflet traits may allow widespread Acacia species to utilize a wider range of environmental conditions in relation to soil moisture than restricted Acacia species. However, we did not find corresponding differences in mean or plasticity of seedling growth and allocational traits. In general, we suggest that relationships between rarity and species traits are both context and taxon specific.