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6 results for “Fungal barcode”
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>
DNA barcode analyses improve accuracy in fungal species distribution models
<p class="western"><span>Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase of occurrence data sets has generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of many groups is not completely settled. This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions. We analyze distribution models for three morphospecies from the corticioid genus <i>Xylodon</i> (Hymenochaetales, Basidiomycota), comparing models based on species names on vouchers specimens with models derived from species identified by DNA barcode. Differences in the contribution of predictors driving the distribution of each modeled taxon and the extent of their ranges were studied. Records under <i>X</i><i>ylodon</i><i> paradoxus</i>, <i>X</i>.<i> flaviporus</i> and <i>X</i>. <i>raduloides</i> were obtained from fungarium collections and GenBank repository. Two grouping criteria were used: (1) specimens were grouped by their collection or sequence voucher names and (2) specimens were grouped following molecular identification using ITS sequences through barcoding gap species recognition (BGSR). Climatic, geographic and biotic variables were used to predict the potential distribution of each taxon through MaxEnt algorithm. From the three morphospecies selected according to voucher names, up to 19 species candidates were detected using BGSR. Climatic variables were the most important predictors in distribution models made from names on voucher specimens, but their importance decreased when BGSR was applied. In general, the extent of species distributions was more restricted for taxa under BGSR. Our results show that taxonomic uncertainty has a strong effect in <i>Xylodon</i> species distribution models. Misleading results can be obtained when cryptic species or identification errors mask the actual diversity of the presence records. Preserved specimens in natural history collections offer the possibility to assess if the species name on labels matches the current species recognition criteria.</span></p>
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
Open the record for dataset details and reuse information.
DNA barcode analyses improve accuracy in fungal species distribution models
Open the record for dataset details and reuse information.
Figure 2 from: Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Divakar P, Lumbsch T, St. Clair L (2013) DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 7: 1-22. https://doi.org/10.3897/mycokeys.7.4508
Figure 2 - A Cartoon representation of the maximum likelihood ITS topology obtained from 240 Rhizoplaca melanophthalma sensu lato specimens in Leavitt et al. (in review). Values at each node indicate non-parametric-bootstrap support; only support values > 50% are indicated B Box plots of ITS genetic distances within each new species, all intraspecific distances, and all interspecific distances. In each box plot, the box shows the interquartile range (IQR) of the data. The IQR is defined as the difference between the 75th percentile and the 25th percentile. The solid and dotted line through the box represent the median and the average length, respectively; and C The coalescent-based species-tree for the Rhizoplaca melanophthalma species-complex estimated from five genetic markers (ITS, IGS, group I intron, β-tubulin, and MCM7 loci) in Leavitt et al. 2011a.
Figure 1 from: Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Divakar P, Lumbsch T, St. Clair L (2013) DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 7: 1-22. https://doi.org/10.3897/mycokeys.7.4508
Figure 1 - Variation in morphology and habit within Rhizoplaca melanophthalma sensu lato. Scale bar = 5 mm.
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