Geology topics

Yer Lor

Publications and source records attributed to Yer Lor.

6 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↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2023

Dead-end hollow fiber ultrafiltration capture of environmental DNA for freshwater mussel (Unionidae) species detection with metabarcoding

Insufficient water sample volumes can be a limiting factor for detecting species with environmental DNA (eDNA) from aquatic habitats. We compared detections of freshwater mussel (Unionidae) communities using large water sample volumes and dead-end hollow fiber ultrafiltration (D-HFUF or DEUF) with traditional eDNA filtration methods that use relatively small water sample volumes. Unionid species were detected in approximately 50-L D-HFUF eDNA samples with two mitochondrial DNA metabarcoding markers (COI and ND1) and compared to species detection results from eDNA captured from commonly used 1-L samples filtered with polyethersulfone (PES) filters at three lotic sites in Georgia and Missouri. Of the 431,560 COI and 1,035,472 ND1 reads from all environmental samples of both filter types that passed quality control, 95% (410,755 reads) of COI reads and 85% (883,472 reads) of ND1 reads were assigned to a unionid species. Nineteen different freshwater mussel species were detected across all D-HFUF samples, and 11 species were detected across all PES samples. Reads assigned to the genus Elliptio could not be resolved beyond the genus level with either marker. From D-HFUF samples, 15 and 16 mussel species were detected with the COI and ND1 markers, respectively. From PES samples, nine and seven species were detected with the COI and ND1 markers, respectively. More mussel species were detected at each site in D-HFUF samples than in PES samples regardless of whether results from both markers were combined or evaluated separately. Our results demonstrate the merit of further exploration and optimization of D-HFUF for capturing eDNA from high-volume water samples to facilitate detection of unionids and likely other aquatic organisms.

Environmental DNA↗

USGS2023

The relative importance of cisco (Coregonus artedi) in the diets of common loons (Gavia immer) among a set of cisco refuge lakes in Minnesota

Common loon ( Gavia immer (Brünnich, 1764)) foraging patterns and the relative importance of cisco ( Coregonus artedi Lesueur, 1818) in the diets of loons were evaluated for the Whitefish Chain of Lakes, a set of coldwater cisco refuge lakes in Minnesota, USA. Environmental DNA metabarcoding of loon fecal samples detected 15 fish species. Yellow perch ( Perca flavescens (Mitchill, 1814)), mimic shiner ( Notropis volucellus (Cope, 1865)), and cisco were the most prominent prey detected across the study lakes. We observed a shift in fish species consumed, with increases in detections of mimic shiner and cisco DNA among loon fecal samples collected in August and September. In some locations, suitable oxythermal habitat became restricted throughout the summer, forcing cisco into surface waters, which potentially increased their vulnerability to loon predation. Conversely, large foraging aggregations of loons were observed during late summer through fall at locations with ample oxythermal habitat and abundant cisco populations. We hypothesize that cisco were sought by loons as a high-calorie prey resource prior to migration. Conservation efforts directed at preserving water quality in important cisco refuge lakes are likely to benefit common loons through enhancement of both the forage base, for resident and migrating birds, and breeding habitat suitability.

Minnesota↗

USGS2021

Environmental DNA metabarcoding as a tool for biodiversity assessment and monitoring: Reconstructing established fish communities of north-temperate lakes and rivers

Aim To evaluate the ability of precipitation-based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well-studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on conventional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predict eDNA detection. Location Upper Great Lakes Region, North America. Methods Fish community composition was estimated for seven lakes and two Mississippi River navigation pools using sequence data from the mitochondrial 12S gene amplified from 10 to 50 water samples per waterbody collected in 50-mL centrifuge tubes at a single time point. Environmental DNA (eDNA) was concentrated without filtration by centrifuging samples to reduce per-sample handling time. Taxonomic detections from eDNA were compared to established community monitoring databases containing up to 40 years of sampling and a detailed habitat/substrate preference matrix to identify patterns of bias. Results Mitochondrial 12S gene metabarcoding detected 15%–47% of the known species at each waterbody and 30%–76% of known genera. Non-metric multidimensional scaling (NMDS) assessment of the community structure indicated that eDNA-detected communities grouped in a similar pattern as known communities. Discriminant analysis of principal components indicated that there was a high degree of overlap in habitat/substrate preference of eDNA-detected and eDNA-undetected species suggesting limited habitat bias for eDNA sampling. Main conclusions Large numbers of small volume samples sequenced at the mitochondrial 12S gene can describe the coarse community structure of freshwater systems. However, additional conventional sampling and environmental DNA sampling may be necessary for a complete diversity census.

Illinois, Iowa, Wisconsin↗

USGS2020

Using environmental DNA (eDNA) to detect the endangered Spectaclecase Mussel ( Margaritifera monodonta )

Margaritifera monodonta , or the Spectaclecase Mussel, is a federally endangered freshwater mussel species that has experienced a 55% reduction in range and is currently concentrated in 3 rivers in the Midwest region of the United States (Gasconade and Meramec rivers, Missouri, and St Croix River, Wisconsin). The detection of new populations by traditional survey methods has been limited because these mussels tend to occur under large rocks and boulders. Environmental DNA (eDNA) technology has been used to detect invasive and rare species, but its use for detection of rare, benthic-dwelling species in large flowing systems has been limited. Here, we propose using eDNA to assess known populations of M. monodonta . We designed a M. monodonta -specific quantitative polymerase chain reaction (qPCR) assay and tested it using water samples from multiple M. monodonta housing tanks, water samples from 2 known mussel beds on the St Croix River, and water samples from 3 known mussel beds on the Mississippi River. We observed higher overall eDNA detection rates on the St Croix River (30.2%) compared to the upper Mississippi River (0.60%). We also observed higher eDNA detection rates (73.3–93.1%) in 2018 for samples collected during the larval release period in May compared to samples collected in August after the reproductive period had ended (55.6–70.8%) on the St Croix River. We tested samples collected at 3 distances downstream from the 2 mussel beds found in the St Croix River, but we did not observe a substantial effect of distance on our detection rates. However, we did observe greater detection rates for samples collected near the bottom compared to at the surface. Our results indicate that this novel qPCR assay can successfully detect M. monodonta eDNA and could be used to rapidly screen locations to guide intensive physical searches for populations in riverine systems.

Wisconsin, Missouri↗