Welcome to IMC 2018 International Mycological Congress
Conference Calendar

 

Displaying One Session

Symposia
Location
201 2nd Floor
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Symposia

Fungal species limits:  A global tree health perspective

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-1
Authors
  • M. Wingfield
  • B. Slippers
  • B. Wingfield
  • E. Steenkamp

Abstract

Abstract

Natural forests and plantations globally are increasingly threatened by disesases caused by fungal tree pathogens. The driving forces behind these diseases are complex. They emerge not only from accidental introductions of pathogens into new areas but also via host shifts and hybrisation events. Our ability to identify species, not only in a practical manner but also one that ensures effective and responsible quarantine is challenged. In the case of tree health, there are growing numbers of examples of pathogens where species names are used that poorly or at least ineffectively reflect the genetic nature of the pathogen. The “age of genomics” makes it possible to identify species to include a comprehensive knowledge of their genetic nature. This will improve our understanding of the global pathways of movement of tree pathogens and the quality of quarantine measures. But it is also realistic to understand that the depth of knowledge regarding species limits will be variable in different countries of the world and it will depend deeply on available resources to study tree pathogens.

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Symposia

A re-evaluation of species limits and distribution of the cupulate, blackish Helvella spp. in the Nordic countries

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-2
Authors
  • S. Løken
  • I. Skrede
  • T. Schumacher

Abstract

Abstract

This study represents an in-depth systematic study of a species complex of small and medium-sized cupulate-stipitate, blackish Helvella species. These species were formerly recognized as a single (but variable) morphospecies, i.e. Helvella corium. Recently this complex has been shown to represent a group of phylogenetic species, nested in (at least) two divergent evolutionary lineages of a broadly defined Helvella genus. Consequently, historically, the herbarium specimens of this species complex have for decades been stored and annotated as H. corium in the University herbaria. In the present project we identified and re-assessed the occurrence and distribution of the true phylogenetic species of this morphospecies complex in the Nordic countries. We examined and barcoded all material stored under the name Helvella corium in the Nordic University herbaria (O, TRH, BG, TROM, C, S, UPS, UME, GB). This was supplemented with fresh specimens from primarily under-studied, alpine regions of Norway collected in 2015-2017. DNA was extracted from ca. 500 specimens of which 436 specimens were successfully barcoded (HSP and/or RPB2). The oldest, successfully barcoded specimen was dating back to 1888. Species limits and evolutionary relationships of the complex were re-assessed, using an extended set of genetic markers (LSU, HSP, RPB2, EF-1α and 5.8S for 41 specimens). We performed Maximum likelihood and Bayesian inference analyses, including molecular species delimitation with STACEY (Beast2). Morphological characters of the individual species were subsequently re-evaluated across the identified lineages, followed by a character state analysis. Altogether, seven phylogenetic species were recognized: H. alpestris, H. macrosperma, H. nannfeldtii, H. alpicola, H. alpina, H. pseudoalpina sp. nov, and H. corium. The phylogeny received high bootstrap support for a monophyletic group consisting of H. nannfeldtii, H. alpestris and H. macrosperma, with H. alpicola as its sister species. H. alpina, H. pseudoalpina and H. corium represented a second evolutionary lineage separate from the other lineage by long branch length and high bootstrap support. The barcoded specimens have been used to map the distribution of the 7 phylospecies in the Nordic countries. Of the 436 barcoded specimens, 233 represented H. corium, 76 H. nannfeldtii, 39 H. alpestris, 23 H. alpina, 14 H. alpicola, 8 H. macrosperma, and 4 H. pseudoalpina. An additional 39 misidentified Helvella corium samples belonged to Helvella species outside the two lineages in question. H. corium is the only species that occur at all levels along a gradient from the temperate to the boreal to the arctic-alpine biome. The other six species seem restricted to the arctic-alpine biome, where they occupy different but overlapping habitats. The most common alpine species in the Nordic country seems to be H. nannfeldtii, which is assumed to have a circumpolar distribution.

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Symposia

Testing an operational approach to species delimitation in Hydnum (Cantharellales, Basidiomycota)

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-3
Authors
  • R. Swenie
  • P. Matheny

Abstract

Abstract

Hydnum is a genus of edible, commercially harvested ectomycorrhizal fungi with a global distribution. We constructed a phylogeny with ITS nucleotide sequences from North America, Europe, Asia and Australasia that reveals 64 putative species worldwide. A three-gene phylogeny constructed with ITS, TEF1 and RPB2 nucleotide sequences strongly supports relationships between major clades in the genus. Recently described species of Hydnum have been circumscribed on the basis of ITS sequence dissimilarity and morphological variation, this often microscopic in detail. However, several undescribed clades of Hydnum are morphologically cryptic with varying amounts of ITS sequence variation. Here, we test an operational threshold-based species delimitation approach in Hydnum in an evolutionary framework using a Bayesian general mixed-Yule coalescent model. In addition, we explore integrating ecological niche modeling into species delimitation methods.

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Symposia

What clinical mycologists need for species recognition?

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-4
Authors
  • W. Meyer

Abstract

Abstract

Fungal nomenclature is characterised by name changes, which are due to the fact that fungi where able to have multiple names, describing different asexual and sexual morphological stages, Article 59 of the Code of Botanical Nomenclature, as those different stages propagate independently and thus their shared identify is not always obvious. However, based on the molecular identity of the asexual and sexual stage of a fungus, the dual nomenclature was recently abolished. In addition, the increase in knowledge at the morphological, biochemical and genetic level, the increasing accumulation of strains as a result of systematic field studies, and the application of new, more discriminatory technologies, e.g. single/multiple gene/whole genome sequencing and MALDI-TOF, recognises ever more species-specific characteristics leading to the discovery of molecular sibling species. This has potentially a profound effect on clinical mycology, as it directly impacts on established fungal and disease names. Ideally, in a clinical setting, a fungal name should reflect, 1) a specific disease association; 2) inform about antifungal resistance to guide treatment decisions, 3) confirms with clear cut species-specific characteristics (morphological, molecular, biochemical) for a fast an accurate identification of a disease agent, and 4) reflect the true phylogenetic relationships between species. Molecular techniques are now capable to detect minute differences, in the absence of clear species delimitation data, cut off values and an overall lack of intra- and interspecies variation data. As such, science has to find a compromise between scientific progress and clinical confusion. In many cases the increased information is very helpful, e.g. in the case of antifungal resistant species, e.g. C. krusei = Pichia kudriavzeii. On the other hand, the detection of genetic diversity does progress faster than the finding of clinical relevant characteristics, e.g. Fusarium solani or C. neoformans/ C. gattii, which are now large species complexes, consisting of multiple, closely related and morphologically poorly distinguishable, "cryptic" species with similar antifungal susceptibility and currently unfinished studies to characterise the discovered genetic differences. Here it is necessary to provide nomenclature stability and simultaneously recognise ongoing speciation processes, by using the term “species complexes”.
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Symposia

Global phylogenomics and fungal species

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-5
Authors
  • D. Engelthaler
  • J. Monroy-Nieto
  • J. Bowers

Abstract

Abstract

Comparative phylogenomics can now provide empirical understanding of the relationships between lineages in fungal taxa. Prior to the advent of high-throughput whole genome sequencing, speciation had been typically accomplished through a variety of morphotyping, phenotyping and genotyping techniques. Given that such analysis is done on isolates gathered from clinical, veterinary or environmental convenience sampling, previous methods have been limited in their abilities to understand population structure or establish true genetic relatedness. Global, phenotypic and ecologic diversity are required to build a full species context. Phylogenomic examinations using next generation sequencing and bioinformatic tools are allowing for empirical high-resolution analysis of current and historical relationships among populations of fungi of interest. Here we analyze the genomes of representatives of the Coccidioides and Cryptococcus species complexes and model their evolutionary relationships. These analyses clearly identify the previously established subtypes and species and shed light on questions regarding a number of lineages within these species that may also warrant species designations. What is not clear is the genomic differentiation limits that actually distinguish subtypes and species. And while comprehensive taxonomic schemes with clear variation thresholds can now be established, diagnostic and treatment confusion may be inevitable in the move to rename identifiable taxonomic groups.

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Symposia

Species recognition: Can one type fit all applications

Session Number
S40
Location
201 2nd Floor, Puerto Rico Convention Center, San Juan, Puerto Rico
Date
07/21/2018
Time
08:30 AM - 10:30 AM
Presentation Number
S40-6
Authors
  • J. Taylor

Abstract

Abstract

Under the Evolutionary Species Concept, fungal species have been recognized by phenotype, mating tests and phylogenetics. Using conidial Neurospora as an example, phylogeny recognizes an order of magnitude more species than morphology and twice as many as mating tests. Now, genomic resequencing is revealing multiple population of interbreeding individuals within phylogenetic species. These populations lack structure and constitute the smallest taxonomic unit above the individual. Within species, there are no intrinsic barriers to mating among these populations, whose divergence is estimated in 100,000s of years (doi.org/10.1073/pnas.1014971108) rather than the millions of years required for the evolution of intrinsic mating barriers (doi.org/10.1371/journal.pgen.1002204). Therefore, between the biological reality of populations and the biological reality of evolved, intrinsic mating barriers, lie 3 million years where species recognition relies on phylogeny. Phylogenetic species recognition is an approach open to interpretation and adding quantification might make is application more uniform. The aforementioned population genomics offers a means of adding quantification to population-species recognition by simply adding a measure of genomic divergence to the taxon name. An example of such a measure is Nei and Li’s π (http://www.pnas.org/content/76/10/5269 ). Examples of this widely used and easily calculated measure of genetic variation will be presented (doi.org/10.1111/mec.13417, doi.org/10.1111/mec.13132). It may come as a shock that the now dominant method of species recognition shares little with the above-mentioned approaches, that is, species recognition by operational taxonomic units (OTUs) recovered from mycobiomes (doi:10.1038/nrmicro2963). Fungal OTU recognition currently relies on PCR amplification from environmental DNA of the rDNA repeat, which is necessarily inferior to the methods mentioned above. For example, even the most discriminating rDNA region, the internal transcribed spacer (ITS), lumps all Neurospora species, conidial and aconidial, into one OTU. Hope for a solution to the OTU problem comes from the recent publication of a fungal genome assembled from metagenomic data (doi:10.1101/gr.228429.117). This approach could provide the fungal genomes needed to recognize populations and species as described above. This approach is already being attempted with bacteria (doi:10.1038/ismej.2017.113), and may be easier to apply to fungi, where sexual reproduction produces discrete populations. If the history of fungal phylogenetic species recognition is a guide, technical obstacles will be easier to overcome than political obstacles, where increased transparency and access will be required to promote acceptance.

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