eDNA Archives - Genidaqs | Fisheries Science, eDNA & Population Genetics

{artemis}: Cutting-Edge qPCR Analysis Toolkit for eDNA/eRNA Research

Gregg — Tue, 22 Jul 2025 20:03:44 +0000

Introducing {artemis}: A Breakthrough R Package for qPCR-Based eDNA Analysis from the Genidaqs Group

We’re thrilled to share a major advancement from the Genidaqs Group—our latest contribution to the environmental science and biotechnology community: the release of a powerful new open-source R package called {artemis}. Specifically developed for environmental DNA (eDNA) analysis, {artemis} is set to transform how researchers approach biodiversity monitoring, ecosystem assessment, and conservation decision-making.

🔍 What is {artemis}?

{artemis} is a cutting-edge statistical software package for R, purpose-built to analyze quantitative Polymerase Chain Reaction (qPCR) data—an essential technique in modern eDNA research. Unlike conventional models, {artemis} is engineered to account for the complex dynamics and variability inherent in qPCR datasets, leading to:

More accurate eDNA quantification
Reduced statistical bias
Improved predictive modeling
Enhanced interpretation of biodiversity signals

This makes {artemis} a crucial tool for aquatic ecology, species detection, and molecular environmental monitoring.

🌱 Why {artemis} Matters in Environmental Science and Conservation

One of the most impactful features of {artemis} is its ability to optimize eDNA survey design. By simulating field sampling strategies with real or synthetic qPCR data, researchers can:

Strategically plan surveys for maximum detection efficiency
Reduce wasted effort and resources
Increase the probability of detecting rare or elusive species
Justify sampling protocols with data-driven predictions

This capability directly supports more efficient conservation planning, adaptive ecosystem management, and evidence-based decision-making.

🌍 Scientific and Environmental Impact

The launch of {artemis} represents a significant leap forward in the field of eDNA analytics. It empowers scientists, ecologists, and conservation professionals to:

Rapidly assess environmental samples for species presence
Detect subtle changes in ecosystem health
Compare multiple survey designs based on expected detection success
Interpret eDNA and even eRNA data with greater clarity and confidence

By streamlining complex qPCR data analysis, {artemis} helps accelerate responses to urgent conservation challenges such as invasive species monitoring, endangered species protection, and ecosystem restoration.

💼 What This Means for Genidaqs

For Genidaqs, {artemis} reinforces our position as a leader in environmental data science and quantitative ecology. It reflects our deep commitment to:

Delivering innovative, data-driven environmental solutions
Advancing scientific research in ecological monitoring
Supporting actionable strategies for biodiversity conservation

We are proud to offer tools that not only push the boundaries of environmental research but also deliver real-world impact for ecosystems and communities alike.

📖 Learn More

Dive into the full technical details and case studies in our recent peer-reviewed publication:

DOI: 10.1002/edn3.277

Have questions or want to collaborate on environmental DNA projects? We’d love to hear from you. Stay connected as we continue to integrate {artemis} into our field operations and research programs.

Let’s Start Your Project. Contact Us

The post {artemis}: Cutting-Edge qPCR Analysis Toolkit for eDNA/eRNA Research appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Advancing eDNA Monitoring in San Francisco Bay Estuary

Scott Blankenship — Thu, 10 Apr 2025 20:50:19 +0000

Genidaqs recently partnered with the U.S. Geological Survey and fellow collaborators on an innovative study exploring how different eDNA sampling techniques perform in detecting fish communities—especially the elusive longfin smelt—in restored tidal wetlands of the San Francisco Bay Estuary.

Traditional fish sampling methods were compared with two eDNA-based approaches: standard filtration using Sterivex™ filters and a high-volume tow net method. USGS sampled Hamilton Wetlands, Sonoma Baylands, Tolay Creek, and a South Bay control sites. Longfin Smelt inhabit these wetlands. These sites represent different restoration strategies, allowing us to assess fish communities in wetlands formed naturally through tidal sediment accretion and those restored using beneficially reused dredged material.

EDNA samples were collected using both water sampling methods. Analysis used two molecular techniques, qPCR and metabarcoding, to evaluate species presence and fish community composition. This dual approach provided a more comprehensive assessment of the aquatic biodiversity at each site.

Longfin Smelt

The study revealed several important findings. We detected Longfin smelt eDNA at all four locations, with qPCR demonstrating higher sensitivity than metabarcoding in species detection. The “high-volume” tow net method potentially filtered more water than the filter-based method, which appeared to improve detection rates—especially for rare species like longfin smelt. Additionally, tow net sampling identified a greater number of species, indicating higher species richness across the sites. In contrast, samples collected via Sterivex™ filters displayed more variability in community composition, suggesting that each method may offer unique ecological insights.

This collaborative effort highlights the growing value of high-volume eDNA techniques for estuarine monitoring. By combining qPCR’s targeted sensitivity with the broader species detection of metabarcoding, researchers can gain a more complete picture of fish communities in dynamic hydrologic environments. These findings offer promising implications for future conservation and wetland restoration efforts.

Read the full publication here:
https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.560

Let’s Start Your Project. Contact Us

The post Advancing eDNA Monitoring in San Francisco Bay Estuary appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Dam Removal on Klamath River Provides Unique Scientific Opportunities

Gregg — Mon, 12 Feb 2024 10:52:00 +0000

The removal of four dams along the Klamath River represents a unique opportunity to study the impacts of large-scale dam removal on river ecology. To establish an invaluable genetic baseline, the study team (Genidaqs, RES) collected and preserved over 400 eDNA and eRNA samples from locations across the Klamath River before dam removal. Post-removal eDNA collections are ongoing.

For a wider perspective on overall Klamath River Restoration, see arcgis storymaps here.

This “molecular library” provides a genetic snapshot of which fish and other aquatic species were present prior to Dam removal and where higher abundances may occur. As dam removal alters the river ecosystem, we plan to compare this pre-removal genetic catalogue with future eDNA surveys to quantify resulting changes in biodiversity and species distribution.

Environmental DNA analysis allows non-invasive, cost-effective monitoring compared to traditional survey methods. Our team took care to capture sufficient genetic material for future genomic analyses like species detection, community metabarcoding, and population demography inference.

This genetic time capsule will enable unprecedented study of how dam removal impacts aquatic biology at the population scale as well as demonstrate a process for how these kinds of large-scale collaborative assessments could occur.

If you’re interested in collaborating, we’d love to discuss analysis plans to unlock insights from this rare ecological dataset. Let’s connect to explore partnerships to better understand and support river restoration!

Let’s Start Your Project. Contact Us

The post Dam Removal on Klamath River Provides Unique Scientific Opportunities appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Monitoring Delta Smelt Environmental DNA (eDNA)

Carlton — Mon, 01 Jan 2018 17:52:00 +0000

The Delta Smelt (Hypomesus transpacificus, McAllister) is a small pelagic fish (120 mm maximum length) endemic to the San Francisco Estuary that has experienced a significant decline in population abundance over the past few decades. Dramatic alterations of the estuary have been ongoing since the Gold Rush (mid 19th century), with the current ecosystem inhospitable to native species. The inadequacy of existing habitat to sustain Delta Smelt is exemplified by decreasing population abundance observed in long term monitoring programs, with declines becoming particularly acute in the early 2000’s. The low encounter rates (high frequency of zero catches) results in survey estimate imprecision, although measurement precision is not reported for abundance indices. Additionally, low population abundance restricts “take” under the State and Federal Endangered Species Act, which limits activities permitted to target Delta Smelt. Current monitoring is insufficient to associate species occurrence with relevant habitat attributes; however, monitoring enhancements needed to evaluate population recovery cannot be implemented due to perceived impacts. Therefore, alternative approaches are needed to obtain biological information on rare, cryptic species that do not require “take” authorization. One of the most compelling approaches likely applies molecular diagnostic methods that detect species-specific DNA in the environment (Environmental DNA; eDNA).

Environmental DNA methods provide a means to address limitations of visual surveys, because they are 1) cost effective and feasible to deploy over a large survey area 2) unambiguously identify target organisms and 3) are sensitive, capable of detecting trace amounts of DNA in sampled material. The eDNA approach differs from traditional sampling in that a given survey does not capture the target organisms themselves, but the biological material those organisms leave in their environment. To use Delta Smelt eDNA information effectively in a regulatory context, a mathematical model is required that describes the relationship between DNA detection (positives, negatives) and the three main variables (volume, distance and biomass) influencing detection of DNA particles within an aquatic unidirectional or tidally-influences system. The relationship is needed to reliably determine that when a positive detection for Delta Smelt occurs one can estimate how far away the DNA could have traveled (given a biomass). Focused experiments have been designed to fill in the most pressing gaps in our current knowledge needed to inform our existing models and test performance under realistic field conditions.

Let’s Start Your Project. Contact Us

The post Monitoring Delta Smelt Environmental DNA (eDNA) appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Joint Base Lewis-McChord Oregon Spotted Frog eDNA

Carlton — Sat, 30 Dec 2017 23:08:00 +0000

Most of the land bases where US Army installations reside are ecologically significant – providing refuge for a large number of the nation’s threatened and endangered plants and animals. Restrictions caused by threatened and endangered species and their critical habitat can have a detrimental impact on the military’s ability to “train as we fight.” The Army indicates that compliance with the Endangered Species Act (ESA) is the number one environmental encroachment on training and readiness (AERTA 2012). In response, the Army is committed to ensuring the long-term viability and continuity of training ranges while meeting land stewardship requirements. As more herpetofaunal species become a conservation concern, it becomes increasingly important for Army land managers to document the species that currently exist on their lands and, through proactive management, potentially avoid conflicts between conservation measures and military training. Joint Base Lewis-McCord (JBLM), Washington houses one such at-risk amphibian species, the Oregon spotted frog (Rana pretiosa). The Oregon spotted frog is an aquatic species found only in the Pacific Northwest and, as of 2014, was federally listed as Threatened by the United States Fish and Wildlife Service (UFWS). JBLM has engaged in a robust relocation program to supplement populations of spotted frog on the installation but success of these efforts has been difficult to document or quantify. Oregon Spotted Frogs are very difficult to survey for due to their infrequent terrestrial movements and their propensity to call underwater. Survey efforts based on visual and/or call surveys has documented few individuals but this likely underrepresents actual abundances.

Sampling for environmental DNA (eDNA) for Oregon Spotted Frogs could be a more effective approach for surveying and monitoring. eDNA sampling involves obtaining genetic material directly from environmental samples (e.g. breeding ponds) without actually physically identifying frog individuals. The objective of this project was to sample for Oregon Spotted Frogs via eDNA to determine timing and distribution of the species in breeding ponds on Joint Base Lewis-McCord, Washington.

Let’s Start Your Project. Contact Us

The post Joint Base Lewis-McChord Oregon Spotted Frog eDNA appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Detection of Adult Green Sturgeon Using Environmental DNA Analysis

Carlton — Mon, 11 Dec 2017 23:49:00 +0000

The objective of this study was to assess the effectiveness of the eDNA sampling technique as a survey of Environmental DNA (eDNA) is an emerging sampling method that has been used successfully for detection of rare aquatic species. The identification of sampling tools that are less stressful for target organisms has become increasingly important for rare and endangered species. A decline in abundance of the Southern Distinct Population Segment (DPS) of North American Green Sturgeon located in California’s Central Valley has led to its listing as Threatened under the Federal Endangered Species Act in 2006. While visual surveys of spawning Green Sturgeon in the Central Valley are effective at monitoring fish densities in concentrated pool habitats, results do not scale well to the watershed level, providing limited spatial and temporal context. Unlike most traditional survey methods, environmental DNA analysis provides a relatively quick, inexpensive tool that could efficiently monitor the presence and distribution of aquatic species. We positively identified Green Sturgeon DNA at two locations of known presence in the Sacramento River, proving that eDNA can be effective for monitoring the presence of adult sturgeon in large river systems. While further study is needed to understand uncertainties of the sampling method, our study represented the first documented detection of Green Sturgeon eDNA, indicating that eDNA analysis could provide a new tool for monitoring Green Sturgeon distribution in the Central Valley, complimenting traditional on-going survey methods.

Study description, eDNA methods and analysis protocols of this study have been published in Bergman PS, Schumer G, Blankenship S, Campbell E (2016) Detection of Adult Green Sturgeon Using Environmental DNA Analysis. PLoS ONE 11(4): e0153500.

For information consistency and data compatibility, Genidaqs uses the protocols described in this publication for all its aquatic eDNA work throughout the Western U.S.

Let’s Start Your Project. Contact Us

The post Detection of Adult Green Sturgeon Using Environmental DNA Analysis appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.

Burns Paiute Tribe Natural Resources Department: Development of eDNA Methods to Detect Presence of the Invasive Brook Trout after Eradication

Carlton — Mon, 11 Dec 2017 23:16:00 +0000

Nonnative brook trout exist in high numbers in the Upper Malheur River basin. In response to the identification of brook trout as a limiting factor to the recovery of ESA-listed bull trout in the basin (USFWS, 2002), the Burns Paiute Tribe Natural Resources Department (BPT) began brook trout suppression efforts in 2010. Since 2001, the Tribe has acquired two properties totaling 8,145 acres and managed for wildlife mitigation according to agreements with the Bonneville Power Administration (BPA). The Malheur River and its two main headwater tributaries, Big Creek and Lake Creek, flow through these properties. The preservation and enhancement of bull trout is important to BPT and helps guide management decisions on its property. Additionally, bull trout protection contributes to decisions concerning grazing and agricultural practices for other agencies, grazing allottees, and private landowners throughout the basin.

In conjunction with brook trout removal activities, BPT has partnered with Cramer Fish Sciences (CFS) since 2011 to develop an environmental DNA-based technique as a metric to monitor abundance trends. Environmental DNA (eDNA) is genetic material naturally shed by organisms that can be found in bulk environmental samples without isolating individual organisms. Samples were taken in both lacustrine and riverine environments twice annually (pre-spawn and post-spawn) for three field seasons and were compared to capture data. In 2014, eDNA sampling protocol shifted from taking whole water samples to using a peristaltic pump to capture DNA on a small contained filter. This technique has increased detection rates and is well suited for remote sampling locations. This project has demonstrated that the eDNA technology can generally detect brook trout presence in a body of water. Genetic sequencing of brook trout has also occurred through this partnership; however, variables due to the hydrology and physical conditions of sampling locations have not been tested. While many methodological uncertainties have been overcome and the use of eDNA technology has expanded tremendously in the last 5 years as a monitoring tool, these uncertainties must be remedied in order to expand the utility of this technology to other scenarios in species detection. For example, the maximum downstream distance for reliable detection of species is needed to structure sampling appropriately in order to both minimize costs and maximize detection probability. Another difficulty pertains to biomass, which positively correlates with DNA in the environment, but the relationship between the amount of DNA detected from within a water sample and the number of individuals (biomass) present is unclear.

With the framework now in place for monitoring species abundance using eDNA and the advancement of sampling methodology, the Burns Paiute Tribe seeks to maximize the potential of this technology. The goal of the Tribe is brook trout eradication in the Upper Malheur River basin. An integral part of this goal is the development of cost effective means to monitor eradication success. Therefore, the Tribe proposes to develop protocol specific to stream flows for sampling to detect species presence post-removal and as a means for early detection of new invasions. While eDNA has been used previously for the detection of rare and/or cryptic species (Teletchea, 2009; Jerde et al., 2011), condition-specific sampling intervals are lacking. The proposed project would consist of using known locations and quantities of fish and sampling downstream to determine the distance over which eDNA can be consistently detected. Sampling would occur twice per year for three years in diverse stream settings and environmental conditions that may contribute to eDNA carry distance. From information gained in these controlled trials, we will devise a protocol for appropriate sampling intervals based on stream flows that will yield high probabilities of detection, given presence.

Let’s Start Your Project. Contact Us

The post Burns Paiute Tribe Natural Resources Department: Development of eDNA Methods to Detect Presence of the Invasive Brook Trout after Eradication appeared first on Genidaqs | Fisheries Science, eDNA & Population Genetics.