Hidden in plain sight: Discovering the macro lichens of the American Southwest and Northern Mexico

Methods

Summary

Our field methods combine habitat mapping, structured floristic surveys, traditional taxonomic methods, photography, and DNA barcoding to document macrolichen diversity across the American Southwest and northern Mexico. Before fieldwork, we will use established U.S. Forest Service and Bureau of Land Management vegetation, elevation, climate, hydrology, and geological maps to identify representative ecological regions and specialized habitats for survey.

Within each selected area, two or more surveyors will conduct a structured “meander” survey across a mapped sampling unit. Rather than restricting searches to a fixed circular plot, surveyors will systematically move through the area while examining the full range of available microhabitats, including trees and shrubs, rock outcrops, soil, bryophyte mats, riparian margins, cliffs, seeps, and other moisture-rich or unusual habitats. Search effort and survey routes will be recorded, and species accumulation will be monitored to determine when additional searching is producing few or no new taxa.

Our initial field trials will take place in the Jemez Mountains of New Mexico, including the exceptionally mesic East Fork Jemez River canyon. These surveys will allow us to refine the protocol before expanding into additional Southwestern and northern Mexican mountain systems.

All recorded macrolichens will be photographed in situ, and representative specimens will be collected for microscopic, chemical, and molecular identification. The nuclear ribosomal ITS region (nrITS) will serve as our primary DNA barcode, with additional loci used when greater taxonomic resolution is needed. Voucher specimens will be deposited in publicly accessible herbaria, photographs and occurrence records will be shared through iNaturalist, and sequence data will be deposited in GenBank.

This integrated approach allows us to combine reproducible ecological sampling with the flexibility necessary to document rare species and specialized habitats that may be missed by conventional fixed-plot surveys.

Challenges

Fieldwork in the Southwest comes with several practical challenges, including snow at high elevations, extreme summer heat, monsoon storms, wildfire closures, difficult road access, and permitting restrictions. To reduce these risks, we will work within flexible seasonal windows and identify alternate survey areas in advance so fieldwork can continue even if individual sites become temporarily inaccessible.

Another challenge is that rare or cryptic lichens can be easy to miss or difficult to identify in the field. We will address this by combining structured habitat surveys with in situ photography, voucher collections, microscopy, chemical methods, and DNA barcoding. We will also track species accumulation during surveys so we can identify sites where additional sampling is needed before considering a habitat adequately documented.

Pre Analysis Plan

Our initial analysis will focus on building a complete and verifiable record of macrolichen diversity within each surveyed region. For every field site, we will compile a current species list based on field observations, voucher specimens, photographs, microscopy, chemical tests when necessary, and DNA barcode data for selected specimens.

All observed taxa will be documented through a shared iNaturalist project, where photographs, locality information, and occurrence records will be publicly accessible. Verified DNA sequences will be deposited in GenBank, and voucher specimens will be deposited in recognized herbarium collections so that records can be independently reexamined in the future.

We will compare our field records with existing herbarium specimens, published floras, iNaturalist observations, GenBank records, and other available biodiversity databases to identify new regional records, poorly documented taxa, possible range extensions, and species requiring additional taxonomic study.

Survey completeness will be evaluated using species accumulation through time and repeated field observations to identify habitats where additional collecting is needed. Rare, unusual, or potentially undescribed taxa will receive additional morphological and molecular study.

The primary project outcomes will be updated regional species lists, publicly available occurrence and photographic data, DNA barcode records, curated voucher specimens, and ultimately revised macrolichen floras for the surveyed regions of the American Southwest and northern Mexico. More detailed statistical analyses of diversity, climate, elevation, and community turnover may be developed as the geographic dataset grows.