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Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
<p>The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNA-based candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report three species new to North America – <em>Calogaya ferrugineoides</em> (H. Magn.) Arup, Froden & Sochting, <em>Endocarpon deserticola</em> T. Zhang, X. L. Wei & J. C. Wei and <em>Xanthocarpia ferrari</em> (Bagl.) Frödén, Arup & Søchting – verified using ITS sequencing data. In addition, <em>Circinaria squamulosa</em> sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data – including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon – provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semi-arid climates.</p>
Fig. 3 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 3. Timing of chytridiomycosis-associated amphibian declines. (A) Declines by year. Bars indicate the number of declines in a given year, stacked by decline severity. For species for which the exact year of decline is uncertain, the figure shows the middle year of the interval of uncertainty, as stated by experts or inferred from available data. (B) Cumulative declines. Curves indicate the cumulative number of declines in each decline-severity category over time. In (A) and (B), the arrows mark the discovery of chytridiomycosis in 1998.
Fig. 2 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 2. Taxonomic distribution of chytridiomycosis-associated amphibian declines. Each bar represents one species, and color denotes the severity of its decline. Concentric circles indicate, from inner to outer, order (Caudata or Anura), family, and genus. Full names are given only for families and genera that include>5 and>2 species, respectively; details for all taxa are in table S4. Within each taxonomic level, sublevels are ordered alphabetically. Protruding bars indicate species for which there is evidence of recovery. [Photo credits (left to right): Telmatobius bolivianus, I.D.l.R.; Atelopus zeteki, B.G.; and Craugastor crassidigitus, B.G.]
Fig. 4 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 4. Severity of chytridiomycosis-associated amphibian declines in relation to the geographic and elevational ranges of species. (A) Declines in relation to geographic range. Each dot indicates a species, located randomly along the perimeter of a circle with radius equal to the log10 of the species's geographic range in kilometers squared. (B) Declines in relation to elevational range. Horizontal bars, boxes, and vertical bars indicate, respectively, mean, first and second quartiles, and 95% quantiles of elevation ranges within each category of decline severity.
Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 1. Global distribution of chytridiomycosis-associated amphibian species declines. Bar plots indicate the number (N) of declined species, grouped by continental area and classified by decline severity. Brazilian species are plotted separately from all other South American species (South America W); Mesoamerica includes Central America, Mexico, and the Caribbean Islands; and Oceania includes Australia and New Zealand. No declines have been reported in Asia. n, total number of declines by region. [Photo credits (clockwise from top left): Anaxyrus boreas, C. Brown, U.S. Geological Survey; Atelopus varius, B.G.; Salamandra salamandra, D. Descouens, Wikimedia Commons; Telmatobius sanborni, I.D.l.R; Cycloramphus boraceiensis, L.F.T.; Cardioglossa melanogaster, M.H.; and Pseudophryne corroboree, C. Doughty]
Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 1. Global distribution of chytridiomycosis-associated amphibian species declines. Bar plots indicate the number (N) of declined species, grouped by continental area and classified by decline severity. Brazilian species are plotted separately from all other South American species (South America W); Mesoamerica includes Central America, Mexico, and the Caribbean Islands; and Oceania includes Australia and New Zealand.
Fig. 1 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 1. Global distribution of chytridiomycosis-associated amphibian species declines. Bar plots indicate the number (N) of declined species, grouped by continental area and classified by decline severity. Brazilian species are plotted separately from all other South American species (South America W); Mesoamerica includes Central America, Mexico, and the Caribbean Islands; and Oceania includes Australia and New Zealand. No declines have been reported in Asia. n, total number of declines by region. [Photo credits (clockwise from top left): Anaxyrus boreas, C. Brown, U.S. Geological Survey; Atelopus varius, B.G.; Salamandra salamandra, D. Descouens, Wikimedia Commons; Telmatobius sanborni, I.D.l.R; Cycloramphus boraceiensis, L.F.T.; Cardioglossa melanogaster, M.H.; and Pseudophryne corroboree, C. Doughty]
Fig. 2 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 2. Taxonomic distribution of chytridiomycosis-associated amphibian declines. Each bar represents one species, and color denotes the severity of its decline. Concentric circles indicate, from inner to outer, order (Caudata or Anura), family, and genus. Full names are given only for families and genera that include>5 and>2 species, respectively; details for all taxa are in table S4. Within each taxonomic level, sublevels are ordered alphabetically. Protruding bars indicate species for which there is evidence of recovery. [Photo credits (left to right): Telmatobius bolivianus, I.D.l.R.; Atelopus zeteki, B.G.; and Craugastor crassidigitus, B.G.]
Fig. 4 in Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity
Fig. 4. Severity of chytridiomycosis-associated amphibian declines in relation to the geographic and elevational ranges of species. (A) Declines in relation to geographic range. Each dot indicates a species, located randomly along the perimeter of a circle with radius equal to the log10 of the species's geographic range in kilometers squared. (B) Declines in relation to elevational range. Horizontal bars, boxes, and vertical bars indicate, respectively, mean, first and second quartiles, and 95% quantiles of elevation ranges within each category of decline severity.
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
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Data from: Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities
Arbuscular mycorrhizal fungi (AMF) are key regulators of ecosystem processes, yet how their biodiversity works in ecosystems remains poorly understood. We documented the extent to which taxonomic resolution influenced the effect of biodiversity of AMF taxa on plant performance (growth, nutrient uptake and stress tolerance) in a meta-analysis of 902 articles. We found that the effect of biodiversity of AMF taxa depended on taxonomic resolution. Plant performance was positively promoted by AMF family richness, while no effect was found for fungal species richness. In addition, negative effect was found between AMF phylogenetic diversity and plant growth. This pattern can be explained by functional conservatism within AMF families and functional differentiation among AMF families. Synthesis. Conservation of AMF communities to maintain a full complement of ecosystem functions requires the presence of diverse families and not simply diverse species within a family. This finding may be of key importance for the function of ecosystems under various environmental perturbations to which AMF families may respond differently.
FIG. 16 in Fungal Biodiversity Profiles 101-110
FIG. 16. — Maximum Likelihood (ML) phylogram inferred from raxmlGUI 2.0 (Edler et al. 2019) based on nrITS sequences of Russula. One thousand bootstrap replicates were analyzed to obtain nodal support values. Bootstrap support values (>70%) obtained from ML analysis are shown above or below the branches at nodes. Two collections of the novel Indian species are indicated in red and the holotype in bold.
FIG. 13 in Fungal Biodiversity Profiles 101-110
FIG. 13. — Phylogram based on analysis of both published and still unpublished ITS sequence data (by B. Dima & V. Papp) showing the position of Rhodophana within Entolomataceae and the various operational taxonomic units that need to be named in Europe. Phylogenetic tree inferred from nrDNA ITS sequences using PhyML 3.1 (Guindon & Gascuel 2003) with the following settings: GTR+I+G model of evolution, gamma distribution of 10 rate categories, and tree topology search as SPR. Branch support was tested using the non-parametric, Shimodaira-Hasegawa version of the approximate likelihood-ratio test (SH-aLRT). PhyML SH-aLRT support values (>50) are indicated at the branches. Clades represented by at least one unpublished sequence are compressed. All published sequences from repositories are shown in brackets. Newly generated sequences for our new species are highlighted in boldface. Bar indicates 0.05 expected change per site per branch.
Linked collectors and determiners for: Fungal Biodiversity Centre (CBS) - Fungi strains.
Natural history specimen data linked to collectors and determiners held within, "Fungal Biodiversity Centre (CBS) - Fungi strains". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/82dc5194-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/82dc5194-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/82dc5194-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/82dc5194-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
FIG. 11. — Lactarius aurantiobrunneus X.H in Fungal Biodiversity Profiles 81-90
FIG. 11. — Lactarius aurantiobrunneus X.H. Wang, sp. nov. (HKAS 101912, holotype): A, basidiospores; B, pleuromacrocystidia; C, lamella edge; D, pileipellis. Scale bars: A, 5 μm; B, 20 μm; C, D, 25 μm.
FIG. 23 in Fungal Biodiversity Profiles 81-90
FIG. 23. — Maximum parsimony Strict consensus tree illustrating the phylogeny of Serpula dendrocalami C.L. Zhao, sp. nov., and related species in Serpula based on nLSU sequences. Branches are labeled with parsimony bootstrap values (before slash) higher than 50% and Bayesian posterior probabilities (after slash) equal to and more than 0.95. The nLSU dataset included sequences from 16 fungal specimens representing 8 species. The dataset had an aligned length of 1411 characters, of which 1158 characters are constant, 69 are variable and parsimony-uninformative, and 184 are parsimony-informative. Maximum parsimony analysis yielded 4 equally parsimonious trees (TL = 321, CI = 0.854, HI = 0.146, RI = 0.947, RC = 0.808). Best model for the nLSU dataset estimated and applied in the Bayesian analysis: GTR+I+G, lset nst = 6, rates = invgamma; prset statefreqpr = dirichlet (1,1,1,1). Bayesian analysis and ML analysis resulted in a similar topology as MP analysis, with an average standard deviation of split frequencies = 0.003841 (BI). This phylogenetic analysis demonstrated that our species was closely related to S. similis (Berk. & Broome) Ginns. Nuclear LSU region was amplified with primer pairs LR0R and LR7 (http://www.biology.duke.edu/fungi/mycolab/primers.htm). The PCR procedure for nLSU was as follows: initial denaturation at 94 °C for 1 min, followed by 35 cycles at 94 °C for 30 s, 48 °C 1 min and 72 °C for 1.5 min, and a final extension of 72 °C for 10 min. The PCR products were purified and directly sequenced at Kunming Tsingke Biological Technology Limited Company. All newly generated sequences were deposited at GenBank (Table 1). Branches are labeled with parsimony bootstrap values (before slash) higher than 50% and Bayesian posterior probabilities (after slash) equal to and more than 0.95.
Data from: Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities
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