Fungi are more important to our lives than is assumed by the general public. They can comprise both devastating pathogens and plant-associated mutualists in nature, and several species have also ...become important workhorses of biotechnology. Fungal diversity research has in a short time transcended from a low-tech research area to a method-intensive high-tech discipline. With the advent of the new genomic and post-genomic methodologies, large quantities of new fungal data are currently becoming available each year. Whilst these new data and methodologies may help modern fungal diversity researchers to explore and discover the yet hidden diversity within a context of biological processes and organismal diversity, they need to be reconciled with the traditional approaches. Such a synthesis is actually difficult to accomplish given the current discouraging situation of fungal biology education, especially in the areas of biodiversity and taxonomic research. The number of fungal diversity researchers and taxonomists in academic institutions is decreasing, as are opportunities for mycological education in international curricula. How can we educate and stimulate students to pursue a career in fungal diversity research and taxonomy and avoid the situation whereby only those few institutions with strong financial support are able to conduct excellent research? Our short answer is that we need a combination of increased specialization and increased collaboration, i.e. that scientists with specialized expertise (e.g., in data generation, compilation, interpretation, and communication) consistently work together to generate and deliver new fungal knowledge in a more integrative manner – closing the gap between both traditional and modern approaches and academic and non-academic environments. Here we discuss how this perspective could be implemented in the training of the ‘next generation fungal diversity researcher’.
Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of ...species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.
The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic revision by the first ...author detected a wide range of morphological variation. To confront the phenotypically based circumscription of these taxa and to resolve their relationships morphological and ITS rDNA data were obtained for 56 individuals representing eight Caloplaca species belonging to the C. saxicola group. We tested the monophyly of these eight morphospecies by performing maximum parsimony, maximum likelihood and two different types of Bayesian analyses (with and without a priori alignments). Restricting phylogenetic analyses to unambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species within the C. saxicola group. However, phylogenetic resolution of all or most of the eight species currently included as two distinct subgroups within the C. saxicola group was possible only by combining morphological characters and signal from ambiguously aligned regions with the unambiguously aligned ITS sites or when the entire ITS1 and 2 regions were not aligned a priori and included as an integral component of a Bayesian analysis (BAli-Phy). The C. arnoldii subgroup includes C. arnoldii, comprising four subspecies, and the C. saxicola subgroup encompasses seven species. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup and their relationships could not be resolved with combined ITS and morphological data. Unequivocal morphological synapomorphies for all species except C. arnoldii and C. pusilla are recognized and presented.
The vision of the
Earth BioGenome Project
1
is to complete reference genomes for all of the planet’s ~2M described eukaryotic species in the coming decade. To contribute to this global endeavour, ...the
Darwin Tree of Life Project
(DToL
2
) was launched in 2019 with the aim of generating complete genomes for the ~70k described eukaryotic species that can be found in Britain and Ireland. One of the early tasks of the DToL project was to determine, define, and standardise the important metadata that must accompany every sample contributing to this ambitious project. This ensures high-quality contextual information is available for the associated data, enabling a richer set of information upon which to search and filter datasets as well as enabling interoperability between datasets used for downstream analysis. Here we describe some of the key factors we considered in the process of determining, defining, and documenting the metadata required for DToL project samples. The manifest and Standard Operating Procedure that are referred to throughout this paper are likely to be useful for other projects, and we encourage re-use while maintaining the standards and rules set out here.
The monotypic, lichen-forming genus Ingvariella originally was segregated from Diploschistes and placed within the Thelotremataceae (Ostropales) based on aspects of exciple morphology. However, the ...I+ hymenium and amyloid ascus wall suggest affinities to families other than the Thelotremataceae. To assess the identity of Ingvariella and to investigate its placement within the Ostropales, we inferred phylogenetic relationships of I. bispora by comparison of mtSSU rDNA and nuLSU rDNA sequences for 59 species encompassing a broad array of ostropalean fungi by means of Bayesian, maximum likelihood and weighted maximum parsimony methods. Here we report that Ingvariella is a member of the Stictidaceae, sister to the mainly saprotrophic genus Cryptodiscus. The inclusion of the first saxicolous lichen-forming fungus within this family expands the broad ecological diversity of the Stictidaceae, where saprotrophic fungi, corticicolous lichen-forming fungi and lichenized and non-lichenized conspecific taxa have been described previously. We also present new insights into the relationships among other families within the Ostropales.
The
Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for ...this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of
Teloschistaceae. Our study confirmed the polyphyly of
Caloplaca,
Fulgensia and
Xanthoria, and revealed that
Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in
Caloplaca subgenus
Gasparrinia do not form a monophyletic entity.
Caloplaca aurantia,
C. carphinea and
C. saxicola s. str. groups were recovered as monophyletic. The subgenera
Caloplaca and
Pyrenodesmia were also polyphyletic. In the subgenus
Caloplaca, the traditionally recognized
C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.
Les Teloschistaceae (Lecanoromycetes, Ascomycota, líquens) són una família àmpliament distribuïda, amb una considerable heterogeneïtat morfològica i ecològica entre gèneres i grups d'espècies. En ...aquesta família, el gènere Caloplaca, es troba entre els més mal coneguts taxonòmicament parlant, i pot ser considerat com un dels més complexos i diversificats d'entre els líquens crustacis. La seva delimitació ha estat especialment problemàtica per la gran semblança existent entre les espècies lobulades de Caloplaca, i les d'altres gèneres de la família, com Xanthoria o Fulgensia. D'entre les espècies lobulades de Caloplaca, el grup de C. Saxicola ha resultat ser un dels més controvertits a nivell taxonòmic. L'objectiu principal d'aquest estudi ha estat realitzar la revisió taxonòmica i morfològica d'aquest grup, així com l'anàlisi filogenètica en seqüències de l'espaiador intern transcrit (ITS) del DNA ribosòmic del nucli.Com a resultat d'aquesta revisió, podem afirmar que els següents tàxons pertanyen al grup de C. saxicola: C. Arnoldii (Wedd.) Zahlbr.; C. Biatorina (A. Massal.) J. Steiner; C. Clauzadeana Gaya, Nav.-Ros. & Cl. Roux; C. Decipiens (Arnold) Blomb. & Forssell, C. Nana Gaya & Nav.-Ros.; C. Pseudofulgensia Gaya & Nav.-Ros.; C. Pusilla (A. Massal.) Zahlbr.; C. Rouxii Gaya, Nav.-Ros. & Llimona; C. Saxicola (Hoffm.) Nordin; C. schistidii (Anzi) Zahlbr. i C. tegularis sensu auct. Per altra banda, C. cirrochroa (Ach.) Th. Fr.; C. saxicola ssp. laceratula (Arnold ex Poelt) Clauzade & Cl. Roux; C. obliterans (Nyl.) Blomb. & Forssell i C. proteus Poelt han estat excloses d'aquest grup. En aquest estudi, s'han descrit també tres espècies noves: C. clauzadeana Gaya, Nav.-Ros. & Cl. Roux, C. nana Gaya & Nav.-Ros. and C. pseudofulgensia Gaya & Nav.-Ros.; i s'ha proposat un nom nou: C. rouxii Gaya, Nav.-Ros. & Llimona = C. saxicola ssp. miniata (Hoffm.) Clauzade & Cl. Roux.Tant a partir de la filogènia basada en dades d'ITS, com de la combinada amb caràcters morfològics i anatòmics, s'ha confirmat que, segons el concepte adoptat per nosaltres, el grup de C. saxicola és monofilètic. Així mateix, diverses de les espècies fins ara acceptades en aquest grup de Caloplaca han estat associades a valors de recolzament alts. Finalment, s'ha volgut confirmar la hipòtesi que considerava que les espècies lobulades de Caloplaca formen un grup monofilètic dins d'un mostreig taxonòmic més ampli de Teloschistaceae, en el que s'han inclòs tàxons que representen tots els grups d'espècies de Caloplaca. Amb aquest objectiu s'han realitzat anàlisis filogenètiques en seqüències d'ITS de 121 individus. Les relacions filogenètiques s'han examinat utilitzant les anàlisis de màxima parsimònia (MP) i inferència bayesiana (B) com a criteris d'optimització. Les diverses anàlisis realitzades no han permès provar amb bona confiança el monofiletisme de la família Teloschistaceae. No obstant això, el nostre estudi ha confirmat el polifiletisme de Caloplaca, Fulgensia, Teloschistes i Xanthoria. També s'ha pogut confirmar que les espècies tradicionalment incloses a Caloplaca subgènere Gasparrinia no formen una entitat monofilètica. C. aurantia, C. carphinea i C. saxicola s.str. són els únics grups que s'han recuperat monofilètics. Les nostres anàlisis també han posat en evidència que el gènere Letrouitia (Letrouitiaceae) pertany a les Teloschistaceae. En aquest estudi, la inclusió de senyal filogènetic a partir de les regions aliniades ambiguament a màxima parsimònia (caràcters INAASE i ARC recodificats) ha donat lloc a la millor reconstrucció filogenètica. Aquests caràcters han demostrat ser útils en filogènies a gran escala com la de les Teloschistaceae. Malgrat tot, amb un mostreig exhaustiu com el nostre, la incorporació d'aquests caràcters no ha resultat suficient per obtenir una resolució completa de les relacions filogenètiques. Per aquest motiu, en futurs estudis serà necessària la combinació de dades ITS amb les d'altres locus, i també l'addició de caràcters morfòlogics.
Teloschistaceae (Lecanoromycetes, lichen-forming Ascomycota) is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In this family, the lichen genus Caloplaca is among the least known taxonomically. The poor understanding of its species has often led to being overlooked, although it can be considered as one of the most diversified genus among the crustose lichens.Moreover, the delimitation of this genus has been always problematic due mostly to the strong similarity between lobed species of Caloplaca and species of other genera within Teloschistaceae, such as Xanthoria or Fulgensia. Among all lobed Caloplaca species, the Saxicola group has been the most controversial taxonomically.To provide a comprehensive and more natural classification of this group of lobed Caloplaca, we report here results from a taxonomical and morphological revision, and phylogenetic analyses that were carried out on sequences of the nuclear rDNA internal transcribed spacer region (ITS).Based on this ITS phylogeny, together with the morphological and anatomical characters, some of the so far accepted species of this group of Caloplaca were associated with high support values. The same was true for potentially new cryptic species with elusive diagnostic morphological and anatomical characters. Finally, we tested the hypothesis that the lobed Caloplaca species form a monophyletic group within a broader taxon sampling of the Teloschistaceae, including taxa representing all species groups of Caloplaca. Phylogenetic analyses were carried out on sequences from ITS region obtained from 121 individuals. The various analyses carried out did not allow us to prove with high confidence the monophyly of the family Teloschistaceae. However, our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that genus Teloschistes is also nonmonophyletic. We also confirmed here that lobed Caloplaca species do not form a monophyletic entity. C. aurantia, C. carphinea and C. saxicola s.str. groups were the only ones recovered as monophyletic.
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