Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens

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.