Dataset Information

When mycologists describe new species, not all relevant information is provided (clearly enough).

ABSTRACT: Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years' worth (2009-2018) of species descriptions of extant fungal taxa - 1,097 studies describing at most ten new species - in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal species descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions - be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures.

SUBMITTER: Durkin L

PROVIDER: S-EPMC7498475 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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When mycologists describe new species, not all relevant information is provided (clearly enough).

Durkin Louisa L Jansson Tobias T Sanchez Marisol M Khomich Maryia M Ryberg Martin M Kristiansson Erik E Nilsson R Henrik RH

MycoKeys 20200910

Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years' worth (2009-2018) of species descriptions of extant fungal taxa - 1,09 ...[more]

PMID: 32982558

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Project description:BACKGROUND: The basic process of RNA splicing is conserved among eukaryotic species. Three signals (5' and 3' splice sites and branch site) are commonly used to directly conduct splicing, while other features are also related to the recognition of an intron. Although there is experimental evidence pointing to the significant species specificities in the features of intron recognition, a quantitative evaluation of the divergence of these features among a wide variety of eukaryotes has yet to be conducted. RESULTS: To better understand the splicing process from the viewpoints of evolution and information theory, we collected introns from 61 diverse species of eukaryotes and analyzed the properties of the nucleotide sequences relevant to splicing. We found that trees individually constructed from the five features (the three signals, intron length, and nucleotide composition within an intron) roughly reflect the phylogenetic relationships among the species but sometimes extensively deviate from the species classification. The degree of topological deviation of each feature tree from the reference trees indicates the lowest discordance for the 5' splicing signal, followed by that for the 3' splicing signal, and a considerably greater discordance for the other three features. We also estimated the relative contributions of the five features to short intron recognition in each species. Again, moderate correlation was observed between the similarities in pattern of short intron recognition and the genealogical relationships among the species. When mammalian introns were categorized into three subtypes according to their terminal dinucleotide sequences, each subtype segregated into a nearly monophyletic group, regardless of the host species, with respect to the 5' and 3' splicing signals. It was also found that GC-AG introns are extraordinarily abundant in some species with high genomic G + C contents, and that the U12-type spliceosome might make a greater contribution than currently estimated in most species. CONCLUSIONS: Overall, the present study indicates that both splicing signals themselves and their relative contributions to short intron recognition are rather susceptible to evolutionary changes, while some poorly characterized properties seem to be preserved within the mammalian intron subtypes. Our findings may afford additional clues to understanding of evolution of splicing mechanisms.

Project description:Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or "footprint") of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or have narrow geographic distributions, and are thus prone to future shifts away from the climatic conditions in these parks in current climates. In other cases, some parks are broadly similar to large geographic regions surrounding the park or have climatic envelopes that may persist into near-term climate change. Larger parks predict larger climatic envelopes, in current conditions, but on average the predicted area of climate envelopes are smaller in our single future conditions scenario. Individual units in a protected area network may vary in the potential for climate adaptation, and adaptive management strategies for the network should account for the landscape contexts of the geodiversity or climate diversity within individual units. Conservation strategies, including maintaining connectivity, assessing the feasibility of assisted migration and other landscape restoration or enhancements can be optimized using analysis methods to assess the spatial properties of protected area networks in biogeographic and macroecological contexts.

Dataset Information

When mycologists describe new species, not all relevant information is provided (clearly enough).

Publications

When mycologists describe new species, not all relevant information is provided (clearly enough).

Similar Datasets

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