DOI: 10.5061/dryad.p5hqbzkr3
title: Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens

description: 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 – Calogaya
 ferrugineoides (H. Magn.) Arup, Froden &
 Sochting, Endocarpon deserticola T. Zhang, X. L. Wei
 & J. C. Wei and Xanthocarpia ferrari (Bagl.)
 Frödén, Arup & Søchting – verified using ITS sequencing data. In
 addition, Circinaria squamulosa 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.
description: Family-level multiple sequence alignments of the of the standard
 DNA barcoding marker – the internal transcribed spacer region
 (ITS).
description: <strong>Supplementary file S1.</strong> List
 of Herbarium records of lichens collected from the Glen Canyon National
 Recreation Area – search of the Consortium of North American Lichen
 Herbaria on 26 February 2021.
 <strong>Supplementary file S2.</strong> Family-level
 multiple sequence alignments of the of the standard DNA barcoding marker –
 the internal transcribed spacer region (ITS).
 <strong>Supplementary file S3.</strong> Photographic
 documentation of sampled lichens.
 <strong>Supplementary file S4.</strong> Family-level
 topologies inferred from multiple sequence alignments of the standard DNA
 barcoding marker – the internal transcribed spacer region (ITS).
 <strong>Supplementary file S5.</strong> Caliciaceae:
 A. Buellia elegans (Leavitt sl19085). Candelariaceae: B. Candelariella
 antennaria (Leavitt sl19083); C. Candelariella aurella (Leavitt sl19098);
 D. Candelariella citrina (Leavitt sl19124); E. Candelariella rosulans agg.
 1 (Leavitt sl19038); F. Candelariella rosulans agg. 2 (Leavitt sl19044);
 G. Candelariella rosulans agg. 3 (Leavitt sl19128). H. Unknown cf.
 Candelariales (Leavitt sl19049). Catillariaceae: I. Thalloidima sedifolium
 (Leavitt sl19051). Collemataceae: J.Enchylium aff. polycarpon (Leavitt
 sl19118); K. Scytinium plicatile (Leavitt sl19045); L. Enchylium aff.
 polycarpon (Leavitt sl19127). Parmeliaceae: M. Montanelia saximontana
 (Leavitt sl19093); N. Xanthoparmelia aff. plittii (Leavitt sl19079); (O)
 Xanthoparmelia maricopensis (Leavitt sl19102. Lichenotheliaceae: P. Heppia
 lutosa (Leavitt sl19120). Physciaceae: Q.Phaeophyscia aff. hirsuta 1
 (Leavitt sl19082); R. Phaeophyscia cf. hirsuta (Leavitt sl19090); S.
 Phaeophyscia aff. hirtella 1 (Leavitt sl19081); T. Phaeophyscia aff.
 hirtella 2 (Leavitt sl19132); U. Rinodina aff. luridata 3 (Leavitt
 sl19042); V. Rinodina cf. athallina 2 (Leavitt sl19067); W. Rinodina aff.
 luridata 1 (Leavitt sl19047); X. Rinodina aff. luridata 2 (Leavitt
 sl19060). Psoraceae: Y. Protoblastina aff. rupestris (Leavitt sl19099).
 Stereocaulaceae: Z. Lepararia aff. membranacea (Leavitt sl19101). i.
 Lepararia aff. vouauxii (Leavitt sl19116). Thelotremataceae: ii.
 Diploschistes scruposus (Leavitt sl19107). All specimens housed at
 BRY-C.