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Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Authors:
Juan Carlos Zamora at Conservatoire et Jardin botaniques de la Ville de Genève
Juan Carlos Zamora
Måns Svensson at Uppsala University
Måns Svensson
Roland Kirschner at National Taiwan University
Roland Kirschner
Ibai Olariaga at Rey Juan Carlos University
Ibai Olariaga
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Abstract and Figures

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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Supplementary resources (2)

Supporting Figure 1
Data
October 2021
Slavomir Adamcik · Teuvo Tapio Ahti · S A A Martyn Ainsworth · László Albert · Stefan Ekman
Supporting Figure 1
Data
June 2018
Juan Carlos Zamora · Måns Svensson · Roland Kirschner · Ibai Olariaga · Stefan Ekman
... This article is based on Proposal 338 of Thiele et al. (2023b), but altered so that it is the Nomenclature Committee for Fungi rather than the General Committee that has responsibility for maintaining the list of repositories and the list of journals. , and the realisation that the huge amount of potentially new species would take decades or centuries to describe, there were calls to facilitate the description of new species based on environmental sequencing (De Beer et al. 2016;, which were refuted by others Zamora et al. 2018). ...
... While an overwhelming majority of mycologists were against a formal naming of species based on single gene sequences, as evidenced by the lack of support of previous proposals to enable the typification of names by sequence data, it seems useful that environmental sequences would be given citable identifiers, similar to GenBank numbers, protein codes, or deep space objects. But, such a naming system for OTUs based on short sequences needs to be quite different from giving a definite species name, due to the uncertainty associated with such names, as discussed previously Zamora et al. 2018). ...
Proposals for consideration at IMC12 to modify provisions related solely to fungi in Chapter F of the International Code of Nomenclature for algae, fungi, and plants
Article
Full-text available
  • Aug 2024
Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.
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... Hawksworth et al., 2016;Meierotto et al., 2019), but these proposals have been heavily criticised (e.g. Zamani et al., 2021;Zamora et al., 2018). We strongly advocate for an integrative taxonomy framework, where multiple lines of evidence are considered (Dayrat, 2005;Will et al., 2005). ...
Temporal trends in global reptile species descriptions over three decades
Article
Full-text available
  • Nov 2024
  • SYST BIODIVERS
Despite the urgency imposed by the current biodiversity crisis, many species remain undescribed, facing extinction before their formal recognition by science. Accelerating species descriptions is thus imperative. However, descriptions should be robust and based on good taxonomic practice, which may enhance long-term nomenclatural stability that is crucial for scientific research and conservation planning. Yet, few studies have assessed the robustness of species description. Here, we evaluated temporal trends in species descriptions of nearly 4,000 squamate reptiles spanning more than three decades (from 1990 to 2023). We observed an average increase of about 115% in the number of lines of evidence used in descriptions, such as pholidosis, morphometrics, and genes sequenced for molecular analysis. Type-series size decreased by nearly half for lizards but remained roughly constant for snakes, while page length dedicated to descriptions showed an upward trajectory for both taxa, increasing 42.7% on average over time. Furthermore, our study highlights the positive correlation between robust species descriptions (i.e. measured by the number of lines of evidence provided, type-series size, and number of pages) and taxonomic reviews, as well as the impact of collaborative efforts, with more authors on descriptions associated with greater lines of evidence and pages. Overall, descriptions of reptiles have become more thorough and robust over recent decades. The proportion of species descriptions that included molecular analysis has grown over time, with more than half of all species described annually in recent years having molecular data. Despite hundreds of new reptile species being described annually, the potential invalidation of many species in the future may jeopardise current conservation efforts. Therefore, thorough, accurate descriptions are important in addressing the biodiversity crisis and providing reliable data for biodiversity analyses and conservation planning.
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... Secretaries' comments Much has been written on the pros and cons of introducing types that are DNA sequences (e.g. Thines et al. 2018;Zamora et al. 2018;Lücking et al. 2021;Nilsson et al. 2023). ...
Synopsis of proposals on fungal nomenclature: a review of the proposals concerning Chapter F of the International Code of Nomenclature for algae, fungi, and plants submitted to the XII International Mycological Congress, 2024
Article
Full-text available
  • Aug 2024
A commentary is provided on the seven formally published proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) that will be dealt with by the Fungal Nomenclature Session (FNS) of the 12th International Mycological Congress (IMC12) in August 2024. The proposals deal with: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. Information is also provided on the composition and role of the Fungal Nomenclature Bureau, the operation of the FNS and the pre-Congress Guiding vote.
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... These rearrangements inevitably forced researchers to redefine generic and specific concepts, and to revise the criteria for new species (Aime et al. 2021). The use of molecular (e.g., barcoding genes) and morphological (e.g., culture characteristics and sexual and asexual morphs) data to delimit species, genera and families, as addressed in several studies, ultimately should clarify and stabilize nomenclature (Zamora et al. 2018;Kandemir et al. 2020;Lücking et al. 2020;Jiang et al. 2020;Crous et al. 2021). ...
200 years of taxonomic confusion: Sporendonema and allies
Article
Full-text available
  • Mar 2024
  • ANTON LEEUW INT J G
The genus Sporendonema (Gymnoascaceae, Onygenales) was introduced in 1827 with the type species S. casei for a red mould on cheese. Cheese is a consistent niche for this species. Sphaerosporium equinum is another species classified in Gymnoascaceae and has also been reported from cheese. Recently, other habitats have been reported for both Sporendonema casei and Sphaerosporium equinum. The present study aimed to investigate the taxonomy of Sporendonema and Sphaerosporium, as well as a close neighbour, Arachniotus. Two strains of Hormiscium aurantiacum, another related cheese-associated species were also included in the analyses. Strains were evaluated in terms of macro- and micromorphology, physiology including salt tolerance, growth rate at different temperatures, casein degradation, cellulase activity, lipolytic activity, and multi-locus phylogeny with sequences of the nuclear ribosomal internal transcribed spacer region, the D1-D2 region of the large subunit and partial β-tubulin locus sequences. The results showed that the analysed species were congeneric, and the generic names Arachniotus and Sphaerosporium should be reduced to the synonymy of Sporendonema. Therefore, four new combinations as well as one lectotype and one epitype were designated in Sporendonema. Two strains attributed to Sphaerosporium equinum from substrates other than cheese were found to be phylogenetically and morphologically deviant and were introduced as a new species named Sporendonema isthmoides.
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... Whilst the initial proposals were voted down in both instances, the latter by substantial margins in the preliminary "guiding vote" (>85% of voters rejected both proposals; May and Miller 2018), the proposals were instead passed on to a special-purpose committee (Turland et al. 2017;May and Redhead 2018) and the general proposal remains prominent in the literature with the use of DNA sequences as types still considered favourably by some mycologists (Wu et al. 2019;Lücking et al. 2021;Nilsson et al. 2023). This proposal has been criticised on a number of technical and disciplinary grounds (Thines et al. 2018;Zamora et al. 2018). One issue, however, that appears to have been undiscussed is how the names will be given to DNA-only types. ...
Call me by your name: Considerations of DNA sequences as types within wider discussions on fungal nomenclature
Article
  • Dec 2023
This paper discusses the interaction between two substantial debates in taxonomy and nomenclature: The potential introduction of DNA-only types into fungal taxonomy and whether certain species names are offensive and should be changed. It argues that the acceptance of DNA sequences as types will likely lead to a proliferation of eponyms (species named after a person or persons) and that this will render them more likely to censure thus creating a point of instability in the fungal nomenclature. More fundamentally, it seeks to highlight the cultural and aesthetic attraction of names and to promote wider conversation on why we consider the Latin binomial central in our description of species.
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... Therefore, our phylogenetic results agree with Lücking et al. [79] that comparison of sequences with GenBank blastn alone [42][43][44] is insufficient for accurate taxonomic characterisation because the reference databases used for molecular identifications are still incomplete and often contain erroneously named sequences. Furthermore, in our opinion only the integrative approach is acceptable if we seek for stabilised and operable taxonomy [80]. ...
The Lignicolous Genus Entonaema: Its Phylogenetic-Taxonomic Position within Hypoxylaceae (Xylariales, Fungi) and an Overview of Its Species, Biogeography, and Ecology
Article
Full-text available
  • Aug 2023
The lignicolous saprotrophic genus Entonaema contains six formally accepted species: E. liquescens (type species), E. cinnabarinum, E. globosum, E. dengii, E. moluccanum, and E. siamensis. Its stromatic ascomata develop on the surface of dead wood remnants; they are rather large, globose to irregularly shaped, and vividly coloured. The fresh stroma interior is filled with a liquid matter. In early studies, the genus was considered to have a preference for tropical habitats, while in more recent field research, numerous collections have been added from warm, temperate areas of Europe, North America, and Asia. Our taxonomic and phylogenetic studies were based on freshly collected E. cinnabarinum from Croatia and E. liquescens from the USA. A phylogenetic study of the sequence alignment of four concatenated gene regions (ITS, LSU, rpb2, and β-tub) revealed the true taxonomic position of Entonaema within Hypoxylaceae (Xylariales), a sister to Hypoxylon carneum. Detailed macroscopic and microscopic descriptions of E. cinnabarinum are accompanied by drawings and colour photographs, while the study of E. liquescens is focused on stromatal microchemical reaction. With new information, the worldwide identification key to the putative species of Entonaema is proposed. Ecological data and biogeographical patterns were studied using all available and reliable sources of recorded data. Climatic preferences of the two most widespread Entonaema species, E. liquescens and E. cinnabarinum, are discussed in detail.
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Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes)
Article
Full-text available
  • Aug 2024
Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophospora kesseensis, Hoforsa rebekkae, Kahvena rebeccae, Kelottijaervia shannonae, Kungsaengena shadiae, Langduoa dianae, Lehetua indrekii, Lokruma stenii, Moostea stephanieae, Nikkaluokta mahdiehiae, Parnigua craigii, Riederberga sylviae, Ruua coralieae, Tammsaarea vivikae and Unemaeea nathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversispora bareae, Diversispora nevadensis, Fuscutata cerradensis, Fuscutata reticulata, Viscospora deserticola and Parvocarpum badium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the “dark matter fungi”.
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The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes
Article
Full-text available
  • Jan 2024
  • INT J SYST EVOL MICR
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the ‘Code of Nomenclature of Prokaryotes Described from DNA Sequence Data’ (‘SeqCode’), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
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200 years of taxonomic confusion: Sporendonema and allies
Preprint
Full-text available
  • Nov 2023
The genus Sporendonema was introduced in 1827 with the type species S . casei . for a red mold on cheese. Cheese is a consistent niche for this species. Sphaerosporium equinum is another species classified in Gymnoascaceae ( Onygenales ) and has also been reported from cheese. Recently, other habitats have been reported for both Sporendonema casei and Sphaerosporium equinum . The present study aimed to investigate the taxonomy of Sporendonema and Sphaerosporium , as well as a close neighbor, Arachniotus . Hormiscium aurantiacum , another related cheese-associated species was also included in the analyses. Strains were evaluated in terms of colony morphology, micromorphology, salt tolerance, growth rate at different temperatures, casein degradation, cellulase activity and multilocus phylogeny with sequences of the nuclear ribosomal internal transcribed spacer region, the D1-D2 region of the large subunit and partial β-tubulin locus sequences. The results showed that the analysed species were congeneric, and the generic names Arachniotus and Sphaerosporium should be reduced to the synonymy of Sporendonema . Therefore, four new combinations as well as one lectotype and one epitype were designated in Sporendonema . Two strains attributed to Sphaerosporium equinum from substrates other than cheese were found to be phylogenetically and morphologically deviant and were introduced as a new species named Sporendonema isthmoides .
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Report of the Special‐purpose Committee on DNA Sequences as Types, established at the XIX International Botanical Congress in Shenzhen, China
Article
Full-text available
  • Oct 2023
A Special‐purpose Committee on DNA Sequences as Types was established at the XIX International Botanical Congress (IBC) in Shenzhen, China in 2017, with a mandate to report to the XX IBC with recommendations on a preferred course of action with respect to DNA sequences as potential types under the International Code of Nomenclature for algae, fungi, and plants . This report provides a synthesis of the deliberations from the Special‐purpose Committee on this issue. We discuss two potential options for dealing with the problem that many species, especially of microfungi and microalgae, can be discovered and delimited using eDNA sequencing but cannot currently be formally named due to the requirement in the Code that either a specimen or illustration be nominated as holotype. One option is to expand the definition of “type” to include DNA sequences, while a second option would allow some taxa to be named without types, the application of their names instead being determined using a DNA sequence. This report should be read in concert with two formal proposals for potential amendments to effect these options, published in this issue of Taxon .
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When Should We Describe Species?
Article
Full-text available
  • Dec 2017
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Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections
Article
Full-text available
  • Apr 2018
Global herbarium collections house a vast number of plant specimens stretching back over centuries. They include rare and extinct species, important historical collections, and valuable type specimens that could help to resolve long-standing taxonomic issues. Historical plant collections also provide unique windows into past evolutionary processes and population histories that do not exist with modern data alone. However, because the DNA in such specimens is often degraded and scarce, manipulation and analysis of their genetic material can be challenging. Recent developments in non-destructive genetic sampling and working with very small quantities of genomic DNA, especially in next-generation sequencing and bioinformatic analysis of ancient DNA, now make the majority of herbarium specimens potentially accessible to phylogenetic, population genetic, and barcoding studies. For example, studies of DNA from long time series of Ipomoea batatas and Anacamptis palustris collections revealed linkages between anthropogenic activity and changes in haplotype distribution. These time series also enable the identification of genes under recent selection in the genomes of both the plants and their pathogens, as was shown for Phytophthora infestans, a microbial pathogen of Solanum tuberosum. Here, we summarize the major challenges in using historical plant DNA in evolutionary studies and review genetic studies integrating herbarium specimens. We expect future genetic studies of historical herbarium specimens to use genomic, metagenomic, and population genetic approaches to: investigate how plant populations respond to environmental change; infer temporal changes in genetic diversity; identify genes under recent selection; and investigate past plant pathogen epidemics.
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Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex
Article
Full-text available
  • Jun 2018
The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.
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New light on names and naming of dark taxa
Article
Full-text available
  • Feb 2018
A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as “dark taxa” or “dark matter fungi”. As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.
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Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
Article
Full-text available
  • Oct 2017
  • MOL BIOL EVOL
Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a dataset of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from datasets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
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Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
Article
Full-text available
  • Sep 2017
Background: The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. Results: Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. Conclusions: CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.
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Estimation of levels of gene flow from DNA sequence data.
Article
  • Oct 1992
  • GENETICS
We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).
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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications
Article
  • Dec 2017
Recent scientific and technological advances have improved and streamlined our ability to recognise and describe fungal species. Detailed comparative genomics studies have also expanded our understanding of species boundaries. Against this background, we explore the nature of fungal species and consider how this impacts our understanding of their genetics and evolution. The current body of evidence suggests that fungal species are unique evolutionary units that are separated from one another by boundaries that are "porous" under certain conditions ("semipermeable" in analogy to the differential permeability of membranes). Overall, the penetrability of these boundaries depends on the relatedness between donor and recipient species, the spatial proximity of related species to one another during their evolution, and the evolutionary potential associated with the breach of a boundary. Furthermore, the semipermeable nature of species boundaries fundamentally affects the population genetics of a species, with potentially profound effects on its overall evolution and biology. This also influences the methodologies used in taxonomy, because some species appear capable of maintaining their genetic isolation despite extensive penetrability of their boundaries. Most analytical procedures are also not able to distinguish the signals of species boundary permeability from those associated with incomplete lineage sorting or intraspecific diversity. Collectively, these issues greatly complicate how we study and name fungi. An awareness of the nature of species, their boundaries and the biological and genomic signatures of boundary breaches, will enhance our ability to identify them and, perhaps more importantly, to develop realistic strategies to manage and manipulate their growth and distribution.
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Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus
Article
  • Sep 2017
  • EUR J PROTISTOL
Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.
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