Geology topics

Matthew B B. Laramie

Publications and source records attributed to Matthew B B. Laramie.

3 recordsLinked to original sources

USGS2026

Detecting bumble bees in the wild using environmental DNA: Development and validation of a qPCR assay for the endangered Franklin’s bumble bee (Bombus franklini)

Environmental DNA (eDNA) sampling is a noninvasive alternative to conventional methods of surveying insects that may be particularly useful for detecting pollinators. We developed a quantitative polymerase chain reaction (qPCR) assay to detect the DNA of Franklin’s bumble bee ( Bombus franklini ) from flower samples and conducted an initial test of the assay using samples collected within and around the historical range of the species. We further analyzed all samples using metabarcoding. Our qPCR assay successfully amplified B. franklini DNA and exhibited no cross-reactivity with nontarget bumble bee DNA during in silico and in vitro testing. We did not detect B. franklini DNA from field-collected flower samples using either qPCR or metabarcoding. However, metabarcoding analysis revealed DNA of at least 16 other bumble bee species. This finding underscores the potential utility of eDNA sampling for surveying bumble bees. Nondetection of B. franklini from field-collected flower samples may be due to the extreme rarity of the species; B. franklini is endangered and has not been observed in the wild since 2006. Our B. franklini assay is among the first bee-specific qPCR assays ever developed and provides proof of concept for additional assays that may improve detection rates of rare and endangered bees.

California, Oregon↗

USGS2025

Field test of the self-preserving eDNA filter and the importance of calibration when changing methods during long-term monitoring

Filtering water is currently the primary field method used for collecting aquatic environmental DNA (eDNA). One of the drawbacks of filtering is the need to transfer the filter from the filter housing to a preservative-filled container in the field. New products are being developed to avoid this handling step, but comparative studies are needed to ensure that the results produced by new protocols are transferable within and across eDNA monitoring programs. To meet this need, we evaluated two filter preservation methods (self-preserving filter housing vs. ethanol) of the 5.0-μm polyethersulfone (PES) filter membrane in a field trial typical of stream fisheries eDNA sampling. We compared DNA detection and yield for free-swimming rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), from streams in Washington, United States, and British Columbia, Canada, while accounting for the effects of two environmental covariates: stream discharge and water temperature. As these streams were part of an ongoing fisheries eDNA monitoring program, we also compared these methods to the original protocol, which used a 0.45-μm cellulose nitrate (CN) filter membrane and ethanol preservative. We found that the self-preserving filter housings collected and preserved eDNA well and provided similar results to identical filters preserved in ethanol. The 5.0-μm PES filters preserved in ethanol significantly outperformed the original protocol in terms of both DNA detection and yield, highlighting the importance of calibration of eDNA results when changing sampling methods during an ongoing monitoring program.

british Columbia, Washington↗

USGS2025

Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease

Throughout the canyons of the Colorado and Uncompahgre Plateaus, water is a limited resource for wildlife, with patchy distribution and seasonal availability. Tributary creeks within these canyons drain into mainstem rivers, providing habitat and breeding sites for native amphibians. Yet, little is known about the diversity and distribution of amphibians that live in these harsh, dynamic environments. In addition, the rivers that border these canyon tributaries may serve as corridors for nonnative species and disease. The American Bullfrog ( Lithobates catesbeianus ) is a nonnative species in western Colorado known to prey on native amphibians and act as a reservoir for pathogens such as Batrachochytrium dendrobatidis ( Bd ). From 2019 to 2022, we surveyed for amphibians using visual encounter surveys (VES) and environmental DNA (eDNA) surveys throughout the McInnis Canyons National Conservation Area (MCNCA), the Dominguez–Escalante National Conservation Area (DENCA), and the Dolores River Canyon Wilderness Study Area (DRCWSA). Our primary goals were to document the diversity and distribution of native amphibians in the canyonlands and evaluate potential threats to these species from bullfrogs and Bd . We confirmed that sensitive species, such as the Great Basin Spadefoot ( Spea intermontana ) and the Northern Leopard Frog ( Lithobates pipiens ), inhabit these protected areas. In most cases, bullfrogs were not detected within ephemeral tributaries, but bullfrog DNA was detected in some tributaries at the confluence with the mainstem rivers. In Mee Canyon (MCNCA), however, bullfrogs were found within the tributary, up to 3 km from the Colorado River. A bullfrog individual removed from this canyon tested positive for Bd , and diet contents suggested that native amphibians are potential prey in this system. Nonnative predators and disease pose a threat to native amphibians, alongside environmental changes such as drought and hydrological shifts driven by ongoing climate change.

Colorado↗