The Planetary Genome: How We Are Finally Digitizing Earth’s Biosphere

Abstract

The early twenty-first century has witnessed a fundamental paradigm shift in the biological sciences, transitioning from the macroscopic observation of organisms to the molecular detection of their genetic traces. This report provides an exhaustive analysis of the current state of DNA barcoding and environmental DNA (eDNA) biomonitoring programs globally as of 2024-2025. Synthesizing data from over 120 distinct research outputs, policy documents, and technical reports, we examine the operationalization of these technologies across planetary ecosystems. We explore the massive infrastructural undertakings of the International Barcode of Life (iBOL) and BIOSCAN; the regulatory standardization efforts within the European Union via DNAqua-Net and CEN; the industrial-scale invasive species surveillance programs in North America; and the cutting-edge application of autonomous robotic samplers in the deep ocean. Furthermore, we dissect the methodological nuances—from the physics of DNA transport in aquatic systems to the bioinformatic algorithms used for taxonomic assignment—that underpin these efforts. The report concludes that while eDNA has matured into a robust tool for specific applications like invasive species detection, its global potential is currently constrained by reference library gaps, "dark taxa," and the need for harmonized international standards.

1. Introduction: The Measurement of Life in the Anthropocene

1.1 The Biodiversity Information Crisis

The biosphere is undergoing rapid transformation, driven by anthropogenic pressures such as climate change, habitat destruction, and the spread of invasive species. In this context, the ability to rapidly and accurately inventory biodiversity is not merely an academic exercise but a critical requirement for planetary stewardship. However, traditional biodiversity monitoring has long faced a "scalability crisis." Conventional methods—morphological identification of specimens caught in nets, traps, or observed via binoculars—are labor-intensive, invasive, and reliant on a shrinking pool of taxonomic experts.¹

The scope of this challenge is quantified by the "Linnaean shortfall"—the gap between the number of species described by science (approximately 1.8 million) and the estimated total number of species on Earth (ranging from 8.7 to over 18 million).² At current rates of description, it would take centuries to catalog life, during which time countless species will likely go extinct. This urgency has necessitated a technological leap: the digitization of identification through genetics.

1.2 From Barcoding to Biomonitoring: Availability of the Detectable Genome

The solution has emerged through two related but distinct molecular revolutions: DNA Barcoding and Environmental DNA (eDNA).

DNA Barcoding is the practice of sequencing a short, standardized region of the genome to identify a specimen. First proposed in 2003, it utilizes the cytochrome c oxidase I (COI) gene for animals and loci like rbcL and matK for plants.³ This effectively creates a "barcode" for every species, allowing non-experts to identify organisms if they have access to a sequencing machine and a reference library.

Environmental DNA (eDNA) takes this a step further. It is based on the premise that all living organisms shed genetic material—skin cells, mucus, gametes, feces, and decaying tissue—into their environment. By sampling the medium (water, soil, air, or snow) rather than the organism itself, researchers can detect the "genetic shadow" of species presence.⁴

1.3 The Current Landscape (2024-2025)

As of 2025, we are witnessing the consolidation of these technologies into large-scale, national, and international monitoring infrastructures. The field has moved beyond "proof-of-concept" studies to "industrial application."

• Scale: Projects are no longer limited to single ponds or streams but encompass entire river basins (e.g., the Mississippi, the Danube) and ocean basins.⁶

• Technology: The workflow has evolved from simple PCR (detecting one species) to metabarcoding (detecting whole communities) and is now integrating with autonomous robotics to remove the human element from sampling.⁸

• Standardization: The "Wild West" era of disparate protocols is ending, replaced by ISO standards and rigorous Quality Assurance Project Plans (QAPPs) designed to make eDNA data legally defensible in court and policy.¹⁰

This report details these developments, structured to provide both a high-level strategic overview and a deep-dive into the scientific mechanisms driving this global transformation.

2. The Biological and Physical Basis of eDNA

To understand the engineering and design of global monitoring programs, one must first appreciate the biological and physical properties of the analyte itself: the DNA molecule in the environment.

2.1 Sources and State of eDNA

eDNA is a complex mixture of genetic material. It exists in two primary states:

1. Intracellular DNA: DNA encapsulated within whole cells (e.g., shed skin cells, bacteria, single-celled algae) or organelles (mitochondria). This form is more protected from degradation.

2. Extracellular DNA: Free-floating DNA released from cell lysis or excretion. This form is highly vulnerable to enzymatic shearing and hydrolysis.⁴

In aquatic environments, the "particle size" of eDNA varies. While some DNA is dissolved, the majority of detectable eukaryotic eDNA is associated with particles between 1 and 10 micrometers (μm). This dictates the filtration strategies used in global programs, which typically employ filters with pore sizes ranging from 0.22 μm to 0.45 μm to capture this cellular debris while allowing water to flow through.⁴

2.2 Fate and Transport: The Hydrology of Genes

Once released, eDNA does not stay static. It is transported by currents and subjected to degradation. Understanding "eDNA ecology"—how long it lasts and how far it travels—is crucial for interpreting detection results.

• Degradation: DNA degrades exponentially in the environment. Factors accelerating degradation include high temperatures, ultraviolet (UV) radiation, and microbial activity (which consumes DNA as a nutrient). In temperate waters, eDNA signals can persist for days to weeks; in tropical, high-microbial environments, they may last only hours.¹ This creates a "temporal window" for detection. A positive result indicates the organism was present relatively recently.

• Transport: In lotic (flowing) systems like rivers, eDNA flows downstream. A detection at Point A does not mean the fish is at Point A; it means the fish is upstream. Research has shown that eDNA can travel kilometers, but the signal dilutes with distance and discharge volume.¹³ This "transport distance" is a critical variable in the probabilistic models used by agencies like the US Fish and Wildlife Service (USFWS) to pinpoint invasive carp populations.⁷

2.3 Environmental Matrices

While water is the most common medium, 2024-2025 has seen an explosion in the use of other matrices:

• Soil: Used for terrestrial biodiversity assessments. Soil eDNA binds to clay particles and humic substances, which can protect it from degradation but also makes extraction difficult due to inhibition.¹⁴

• Snow: A breakthrough application in the Arctic involves melting snow from animal tracks to retrieve nuclear DNA (nDNA). Because snow is cold and low in microbial activity, it acts as a freezer, preserving DNA shed from footpads.¹⁶

• Air: The use of air samplers (e.g., MD8) to capture airborne DNA (eAir) is revolutionizing the monitoring of vascular plants and canopy-dwelling animals that are otherwise hard to sample.⁴

3. The Methodological Pipeline: From Field to Sequence

Global biomonitoring programs rely on a standardized workflow. Variation at any step can render data incomparable, which is why standardization bodies (discussed in Section 6) are so focused on this pipeline.

3.1 Step 1: Sample Collection and Filtration

The gold standard for aquatic sampling involves filtering water to concentrate the DNA.

• Manual vs. Automated: Traditionally, water was collected in bottles and filtered in a lab. However, this introduces a lag time where DNA can degrade. Modern programs are moving toward in situ filtration using backpack samplers (e.g., Smith-Root) or autonomous vehicles that filter water at the point of collection and add a preservative (like ethanol or Longmire’s buffer) immediately.⁹

• Filter Types: Cellulose nitrate and glass fiber filters are common. The choice depends on the turbidity of the water; highly turbid water (like the Mississippi River) clogs fine filters quickly, requiring larger pore sizes or pre-filtration steps.¹⁸

3.2 Step 2: DNA Extraction and Inhibition

Back in the laboratory, the DNA must be released from the filter and purified. A major challenge here is inhibition. Environmental samples often contain humic acids, tannins, and other compounds that inhibit the polymerase chain reaction (PCR)—the enzymatic process used to amplify DNA.

• Cleaning the Sample: Extraction kits (e.g., Qiagen DNeasy) are used to "wash" the DNA. If inhibitors remain, the PCR will fail, leading to a "false negative" (failing to detect a species that is actually present).

• Quality Control: rigorous programs, such as the Asian Carp monitoring in the US, employ "inhibition controls"—synthetic DNA spiked into a sample to check if the reaction works. If the spike is not detected, the sample is flagged as inhibited.¹¹

3.3 Step 3: Amplification (qPCR vs. Metabarcoding)

This is the divergent point in the workflow, depending on the monitoring goal.

3.3.1 Targeted Detection (qPCR/ddPCR)

When the goal is to manage a specific species (e.g., an invasive carp or an endangered newt), scientists use Quantitative PCR (qPCR) or Droplet Digital PCR (ddPCR).

• Mechanism: These methods use "primers" and "probes"—short strands of synthetic DNA designed to bind only to the target species' DNA. If the target is present, the reaction produces a fluorescent signal.

• Quantification: qPCR allows researchers to estimate the quantity of DNA (copy number) in the sample. This is often used as a proxy for biomass or abundance, although the relationship is complex and influenced by environmental variables.¹²

• Use Case: This is the workhorse of federal biosecurity programs (e.g., USFWS, Australian border control) because it is highly sensitive and species-specific.⁷

3.3.2 Community Detection (Metabarcoding)

When the goal is a general biodiversity survey, Metabarcoding is used.

• Mechanism: Instead of species-specific primers, "universal primers" are used. These bind to highly conserved regions of the genome shared by a whole group of organisms (e.g., the "MiFish" primers for all bony fish).

• Sequencing: The PCR product—a mixture of DNA from all the species in the sample—is sequenced on a High-Throughput Sequencing (HTS) platform (e.g., Illumina NovaSeq). This generates millions of "reads."

• Use Case: This is used for ecosystem health assessments, food web reconstruction, and BIOSCAN-style planetary inventories.²¹

3.4 Step 4: Bioinformatics and Taxonomic Assignment

The final output of the sequencer is a massive text file of DNA sequences. Converting this into a list of species names is the domain of bioinformatics.

• The Algorithm: The computer must match each sequence to a known species in a reference database.

• K-mer Analysis: Algorithms break sequences into short, fixed-length chunks (k-mers) and look for unique patterns. This is faster than aligning entire sequences.²³

• Lowest Common Ancestor (LCA): Often, a short DNA sequence is identical across several closely related species (e.g., different species of rockfish). In these cases, the algorithm cannot assign the sequence to a species level. Instead, it assigns it to the "Lowest Common Ancestor"—the genus or family level that encompasses all the matches. This conservative approach prevents false identifications.²⁵

• The Reference Database Gap: The accuracy of this process is entirely dependent on the quality of the reference library (e.g., BOLD, GenBank). If a species has never been sequenced, it cannot be identified. It becomes a "Dark Taxon"—a distinct genetic cluster that lacks a Latin name.¹⁴

4. Global Infrastructure: The Mega-Science of Barcoding

While the methodology is complex, the implementation is being streamlined through massive international collaborations. The central nervous system of this global effort is the International Barcode of Life (iBOL) consortium.

4.1 iBOL and the BIOSCAN Mission

Established in 2008 and headquartered in Canada, iBOL is a treaty-like coalition of over 25 nations committed to building a digital identification system for all multicellular life.

• Phase 1: BARCODE 500K (2010-2015): This initial phase successfully barcoded 500,000 species, proving the viability of the COI barcode as a universal standard.²⁷

• Phase 2: BIOSCAN (2019-2026): The current phase aims to scale this up to 2.5 million species. BIOSCAN is not just about collecting barcodes; it is about applying them to understand species interactions (symbiosis, predation) and dynamics (population shifts due to climate change).²

• Future Phase: Planetary Biodiversity Mission (PBM): Planned to launch after BIOSCAN, this mission aims to complete the inventory of multi-cellular life by 2045.²⁷

4.2 Museomics: Unlocking the Past

A critical strategy for BIOSCAN to fill the "reference database gap" is Museomics. Natural history museums hold millions of specimens collected over centuries, many of which are now rare or extinct.

• The Process: By extracting DNA from these dried, pinned, or alcohol-preserved specimens, researchers can populate the reference libraries without needing to mount expensive expeditions to recapture rare species.

• Impact: This provides the "ground truth" for eDNA studies. If an eDNA survey in a remote river detects a sequence that matches a museum specimen collected in 1900, it confirms the persistence of that species.¹⁴

5. Regional Case Study: North America and the War on Invasive Species

In North America, the primary driver for eDNA adoption has not been academic discovery, but economic defense. The Great Lakes fishery is valued at over $7 billion annually, and it is threatened by the invasion of Asian Carp.

5.1 The Asian Carp Threat

"Asian Carp" refers collectively to four species: Bighead, Silver, Grass, and Black Carp. Introduced in the 1970s for aquaculture and sewage treatment, they escaped into the Mississippi River basin and have been moving northward. The Silver and Bighead carp are planktivores that can outcompete native fish larvae, threatening the entire food web.⁷

The defense line is the Chicago Area Waterway System (CAWS), a series of canals connecting the Mississippi drainage to the Great Lakes. Traditional monitoring (electroshocking, netting) is inefficient at detecting low-density populations at the "leading edge" of an invasion.

5.2 The Federal Response: USFWS and USACE

The US Fish and Wildlife Service (USFWS) and US Army Corps of Engineers (USACE) have operationalized eDNA surveillance on an industrial scale.

• Program Scale: Since 2013, the USFWS Whitney Genetics Laboratory (WGL) has processed tens of thousands of water samples annually. This is a year-round operation involving trained field crews and high-throughput robotic liquid handlers in the lab.⁷

• Technological Evolution: The program started with conventional PCR (cPCR) but transitioned to quantitative PCR (qPCR) in 2015. This shift allowed for higher sensitivity and the ability to estimate relative DNA concentration.²⁹

• Quality Assurance (QAPP): The program operates under a strict Quality Assurance Project Plan. This document governs every aspect of the workflow, from how many times a bottle is rinsed to the temperature of the sample during transport. This legalistic rigor is necessary because a positive detection can trigger costly management actions, such as closing shipping locks.⁷

5.3 The "Trigger" Problem: Probabilistic Modeling

A major challenge in the early years was interpreting positive results. Does a positive eDNA sample mean a live fish is present? Or did the DNA arrive via a bird, a boat hull, or sewage (secondary vectors)?

To address this, the agencies developed a probabilistic model.

• Refined Interpretation: A single positive sample is not treated as definitive proof of a population. Instead, it contributes to a probability score.

• Decision Matrix: If the number of positive samples exceeds a certain threshold, it triggers a "Response Action"—intensive physical sampling (electrofishing/netting) to capture the fish. This coupling of molecular surveillance with physical verification is now the global model for invasive species management.⁷

• Recent Detections (2023-2024): The system continues to prove its worth. Recent surveys detected invasive carp eDNA in Taylorsville Lake, Kentucky, and upstream of barriers in South Dakota, prompting immediate investigation.¹⁹

6. Regional Case Study: Europe and the Quest for Regulatory Standards

While North America focuses on pest control, Europe is focused on regulatory integration. The European Union's Water Framework Directive (WFD) is one of the most ambitious pieces of environmental legislation in the world, requiring member states to achieve "Good Ecological Status" in all surface waters.

6.1 DNAqua-Net: Harmonizing a Continent

The challenge for Europe is its political geography. Rivers like the Danube or the Rhine flow through multiple countries. If France uses one method to measure biodiversity and Germany uses another, the data cannot be combined to assess the river's health.

• The Initiative: DNAqua-Net (COST Action CA15219) was launched to solve this. It brought together over 500 scientists from 49 countries to harmonize eDNA protocols.

• The Goal: To replace or strictly augment the traditional biological quality elements (fish, invertebrates, algae) of the WFD with DNA-based metrics. Traditional methods are expensive and vary by season; DNA methods offer a standardized, potentially automatable alternative.³²

6.2 The Rise of ISO Standards

Europe has led the development of formal ISO (International Organization for Standardization) standards for biomonitoring.

• CEN/TC 230: The European Committee for Standardization's Technical Committee 230 (Water Analysis) formed Working Group 28 specifically for DNA and eDNA methods.

• ISO 16578 (2022): This standard, "Molecular biomarker analysis — Requirements for microarray detection," specifies how to validate the specificity of DNA probes. It requires rigorous in silico testing against databases to ensure a probe intended for Species A doesn't accidentally bind to Species B.¹⁰

• Metabarcoding Standards: New standards are currently in development (e.g., prEN ISO 17805) specifically for sampling water for metabarcoding, addressing the need for uniform filtration and preservation protocols across the EU.³⁵

7. Regional Case Study: Australasia and the Great Barrier Reef

Australia faces a unique threat: the biological destruction of the Great Barrier Reef (GBR) by the Crown-of-Thorns Starfish (COTS).

7.1 The COTS Crisis

The Crown-of-Thorns Starfish (Acanthaster cf. solaris) is a corallivore that undergoes massive population explosions, consuming living coral tissue. These outbreaks are a major cause of coral cover loss.

• The Detection Problem: COTS outbreaks often start in deep water or cryptic habitats. Traditional "manta tow" surveys (towing a diver behind a boat) only detect adult starfish when they are already numerous and destroying the reef.

• The Need for Early Warning: Managing COTS requires detecting them at the "pre-outbreak" or larval stage, allowing control teams to intervene before the population explodes.³⁷

7.2 AIMS and the "Dipstick" Revolution

The Australian Institute of Marine Science (AIMS) has developed a world-leading eDNA program for COTS.

• Larval Detection: Using eDNA, AIMS researchers can detect the presence of COTS larvae in the plankton, identifying "initiation zones"—reefs where outbreaks originate.³⁸

• Lateral Flow Assays (LFA): In a move to democratize the technology, AIMS developed a "dipstick" test. Utilizing isothermal amplification technology (detecting DNA at a constant temperature without the heating/cooling cycles of PCR), this test works like a pregnancy test.

• Field Application: A tourism operator or park ranger can take a water sample, dip the strip, and see a colored line if COTS DNA is present. This removes the need for a laboratory, allowing for real-time decision-making on the reef.⁵

8. The Technological Frontier: Autonomous Systems

The future of eDNA lies in removing the human sampler entirely. The costs of ship time and field crews are the limiting factors in global monitoring. Robotics offers a solution.

8.1 The MBARI Environmental Sample Processor (ESP)

The Monterey Bay Aquarium Research Institute (MBARI) has pioneered the Environmental Sample Processor (ESP), often dubbed a "lab in a can."

• Capabilities: The ESP is a robotic device that automates the entire workflow: it draws in water, filters it, applies preservatives, and can even perform DNA extraction and processing in situ.

• 3G-ESP and LRAUVs: The third-generation ESP is compact enough to fit inside a Long-Range Autonomous Underwater Vehicle (LRAUV). These torpedo-like robots can patrol the ocean for weeks, diving to 300 meters, collecting samples based on pre-programmed triggers (e.g., "sample if chlorophyll levels spike").⁸

• Real-time Data: While most samples are archived for later analysis, advanced ESP modules can transmit data via satellite, providing near real-time alerts for harmful algal blooms or specific pathogens.⁴¹

8.2 Commercial Autosamplers

Commercial companies are also entering this space. Smith-Root, known for electrofishing, produces the "Spyglass" and other autosamplers.

• Utility: These units can be deployed on riverbanks or pylons to take samples at set intervals (e.g., every 6 hours). This high-temporal resolution is impossible with manual sampling and allows researchers to track daily cycles of eDNA release or capture pulses of DNA during storm events.⁹

• Integration: These systems are being integrated into networks like USGS READI-Net, aiming to create a national grid of autonomous biological weather stations.⁴³

9. Global Gaps, Emerging Frontiers, and Ethics

9.1 The "Parachute Science" Problem

A review of global eDNA literature reveals a stark geographic bias. The majority of studies and infrastructure are located in the Global North (Europe, North America, Japan).

• Brazil and the Amazon: In megadiverse regions like Brazil, there is a growing push to build local capacity. A 2024 review noted that while eDNA studies in Brazil are increasing, there is a risk of "parachute science"—where foreign researchers collect samples and export them for analysis, leaving no infrastructure or expertise behind. Developing local sequencing hubs is a priority for the Global South.⁴⁴

• MENA Region: The Middle East and North Africa face technical challenges. The high salinity and temperature of the Red Sea and Persian Gulf accelerate DNA degradation. Additionally, reference libraries for these unique ecosystems are underdeveloped, leading to poor taxonomic assignment for local species.⁴⁵

9.2 The "Dark Taxa" and Database Bias

The ultimate limit of eDNA is the reference database. In many invertebrate surveys, 80-90% of the sequences detected do not match any named species in the database.

• Dark Taxa: These are species that exist genetically but have no Linnaean name. They represent a massive, invisible component of biodiversity.

• The Fix: Initiatives like BIOSCAN are racing to sequence more specimens, while bioinformaticians are developing methods to analyze "taxonomy-free" data, using the genetic clusters (OTUs or ASVs) themselves as the unit of measurement for biodiversity health.²⁷

9.3 Tracking the Rare and Elusive: Polar Bears and Snow

One of the most poetic and technically impressive applications of 2024-2025 is the extraction of eDNA from snow tracks.

• The Breakthrough: Researchers in the Arctic have successfully amplified nuclear DNA (nDNA) from polar bear footprints. Unlike mitochondrial DNA (mtDNA), which is abundant but only identifies the species, nDNA allows for the identification of individuals and their sex.¹⁶

• Implication: This allows for "genetic mark-recapture" studies without ever seeing or disturbing the animal. It represents a humane, non-invasive future for wildlife biology in fragile ecosystems.⁴⁷

10. Conclusion

As we move through the mid-2020s, DNA barcoding and eDNA biomonitoring have graduated from experimental novelties to essential pillars of planetary management. The trajectory is clear: the field is moving toward automation, standardization, and globalization.

We are transitioning from a world where we catch fish to count them, to a world where we sense their presence through the chemical traces they leave behind. The convergence of robotics (LRAUVs), genomics (HTS), and big data (BIOSCAN) is creating a "planetary nervous system"—a network of sensors capable of monitoring the pulse of the biosphere in near real-time.

However, significant challenges remain. The "digital divide" between the Global North and South must be bridged to prevent a skewed understanding of global biodiversity. Reference libraries must be completed to illuminate the "dark matter" of the biological world. And regulatory frameworks must continue to evolve to accept molecular data as legal evidence.

Ultimately, eDNA represents our best hope for overcoming the Linnaean shortfall. In the race against extinction, it provides the speed and scale necessary to understand what we are losing, and perhaps, how to save it.

Table 1: Summary of Key Regional eDNA Initiatives

Region	Program / Initiative	Primary Focus	Key Technology	Operational Status (2025)
Global	iBOL / BIOSCAN	Species Discovery & Library Building	Barcoding (COI), Metabarcoding	Scaling to 2.5 million species; laying groundwork for Planetary Biodiversity Mission.27
North America (USA)	USFWS / USACE	Invasive Species (Asian Carp)	Targeted qPCR, Probabilistic Modeling	Operational year-round surveillance in Mississippi/Great Lakes basins.7
Europe	DNAqua-Net / CEN	Regulatory Standardization (WFD)	Metabarcoding, ISO Standards	Developing harmonized standards for EU-wide river monitoring.32
Australia	AIMS / GBRMPA	Coral Reef Protection (COTS)	Lateral Flow Assays ("Dipsticks"), eDNA	Operational early warning system; citizen science integration.39
Japan	ANEMONE	Biodiversity Network	Metabarcoding	Nationwide biodiversity monitoring network utilizing citizen science.48
Arctic	WWF / MIX Research	Rare Mammal Tracking	Snow track nuclear DNA	Proof-of-concept for individual identification of Polar Bears.16

Table 2: Comparative Analysis of eDNA Detection Methods

Feature	Targeted Detection (qPCR / ddPCR)	Community Detection (Metabarcoding)
Target	Single species (e.g., Silver Carp).	Multiple species / Whole communities (e.g., all fish).
Specificity	High (Species-specific primers).	Variable (Depends on "universal" primers and database).
Sensitivity	Extremely High (can detect few copies).	High, but rare species can be swamped by abundant ones.
Quantification	Possible (Copy number estimation).	Difficult (Read count is a poor proxy for abundance).
Cost	Low per sample (once assay is developed).	Higher per sample (sequencing costs).
Primary Use	Biosecurity, Invasive Species, Rare/Endangered Species.	Biodiversity Audits, Ecosystem Health, Food Web Analysis.
Key Limitation	Must know what you are looking for in advance.	Dependent on reference library; "Dark Taxa" issue.

Works cited

1. Technology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation? - Metabarcoding and Metagenomics, accessed January 12, 2026, https://mbmg.pensoft.net/article/130834/

2. BIOSCAN - International Barcode of Life, accessed January 12, 2026, https://ibol.org/bioscan/

3. BIOSCAN: DNA barcoding to accelerate taxonomy and biogeography for conservation and sustainability - Canadian Science Publishing, accessed January 12, 2026, https://cdnsciencepub.com/doi/10.1139/gen-2020-0009

4. Environmental DNA (eDNA) Technology in Biodiversity and Ecosystem Health Research: Advances and Prospects - NIH, accessed January 12, 2026, https://pmc.ncbi.nlm.nih.gov/articles/PMC12789655/

5. Stick 'em up: new test can detect crown-of-thorns starfish as quickly as a home pregnancy kit, accessed January 12, 2026, https://www.aims.gov.au/information-centre/news-and-stories/stick-em-new-test-can-detect-crown-thorns-starfish-quickly-home-pregnancy-kit

6. A strategy for successful integration of DNA-based methods in aquatic monitoring - JRC Publications Repository, accessed January 12, 2026, https://publications.jrc.ec.europa.eu/repository/handle/JRC129289

7. USFWS Great Lakes Region 2021 eDNA Report, accessed January 12, 2026, https://www.fws.gov/sites/default/files/documents/eDNA-2021-Report-Final-May%202022.pdf

8. Autonomous eDNA collection using an uncrewed surface vessel over a 4200, accessed January 12, 2026, https://www.vliz.be/imisdocs/publications/395906.pdf

9. eDNA Autosampler - Smith-Root, accessed January 12, 2026, https://www.smith-root.com/edna/edna-autosampler

10. ISO 16578:2022 - e-standart, accessed January 12, 2026, https://e-standart.gov.az/Standard/Details/09d4e2d1-047c-4511-a49e-7b27326e6ba7

11. Quality Assurance Project Plan- eDNA Monitoring of Bighead and Silver Carps - U.S. Fish and Wildlife Service, accessed January 12, 2026, https://www.fws.gov/sites/default/files/documents/2024-03/qapp_2015_508compliant.pdf

12. Advancing the environmental DNA and RNA toolkit for aquatic ecosystem monitoring and management - PMC - NIH, accessed January 12, 2026, https://pmc.ncbi.nlm.nih.gov/articles/PMC11927557/

13. Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program, accessed January 12, 2026, https://cdnsciencepub.com/doi/10.1139/cjfas-2012-0478

14. Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring | BioScience | Oxford Academic, accessed January 12, 2026, https://academic.oup.com/bioscience/article/75/12/1083/8251452

15. Comparison of soil eDNA to camera traps for assessing mammal and bird community composition and site use - NIH, accessed January 12, 2026, https://pmc.ncbi.nlm.nih.gov/articles/PMC11246831/

16. Tracking Polar Bears with DNA from Snowy Footprints | World Wildlife Fund, accessed January 12, 2026, https://www.worldwildlife.org/news/stories/secrets-in-the-snow/

17. Evaluation of environmental DNA (eDNA) collected from tracks in the snow as a means to monitor individual polar bears (Ursus maritimus) in the Chukchi and Beaufort Seas, accessed January 12, 2026, https://www.north-slope.org/wp-content/uploads/2022/04/NSB-DWM_PRR-2019-01_Preliminary_Research_Report_Polar_Bear_eDNA_2019.10.17.pdf

18. Environmental DNA (eDNA) - U.S. Fish and Wildlife Service, accessed January 12, 2026, https://www.fws.gov/sites/default/files/documents/BMP%20Complete%20Final%20Draft%204.1.22%20-%20REM%20LJW.pdf

19. Using eDNA to elucidate Silver and Bighead Carp range expansion in two Missouri River tributaries in eastern South Dakota | bioRxiv, accessed January 12, 2026, https://www.biorxiv.org/content/10.1101/2023.11.15.567277v2.full-text

20. National eDNA Reference Centre - EcoDNA, accessed January 12, 2026, https://www.ecodna.org.au/nrc

21. DNA Metabarcoding: Current Applications and Challenges - ACS Publications, accessed January 12, 2026, https://pubs.acs.org/doi/10.1021/acs.jafc.5c06002

22. Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring - PMC - PubMed Central, accessed January 12, 2026, https://pmc.ncbi.nlm.nih.gov/articles/PMC8920846/

23. Taxonomic Assignment - GitHub Pages, accessed January 12, 2026, https://cloud-span.github.io/nerc-metagenomics06-taxonomic-anno/01-taxonomic/index.html

24. A survey of k-mer methods and applications in bioinformatics - PMC - NIH, accessed January 12, 2026, https://pmc.ncbi.nlm.nih.gov/articles/PMC11152613/

25. A post about k-mers - this time for taxonomy! - Living in an Ivory Basement, accessed January 12, 2026, http://ivory.idyll.org/blog/2017-something-about-kmers.html

26. Flexi answers - What is the lowest common ancestor? | CK-12 Foundation, accessed January 12, 2026, https://www.ck12.org/flexi/biology/mammal-ancestors/what-is-the-lowest-common-ancestor/

27. International Barcode of Life project (iBOL) Barcode Index Numbers (BINs) - GBIF, accessed January 12, 2026, https://www.gbif.org/dataset/4cec8fef-f129-4966-89b7-4f8439aba058

28. International Barcode of Life – Illuminate Biodiversity, accessed January 12, 2026, https://ibol.org/

29. FWS Midwest Region 3 FAC Bighead and Silver Carp eDNA Monitoring Dashboard, accessed January 12, 2026, https://www.arcgis.com/apps/dashboards/52b22abe9c4d4575adfe851a946f444d

30. FY 2021 Asian Carp Action Plan and Items, accessed January 12, 2026, https://icrcc.fws.gov/sites/carp/files/2024-03/2021-asian-carp-action-plan-amended.pdf

31. Invasive carp eDNA detected in Taylorsville Lake - Kentucky Department of Fish & Wildlife, accessed January 12, 2026, https://fw.ky.gov/News/Pages/Invasive-carp-eDNA-detected-in-Taylorsville-Lake.aspx

32. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe - RIO Journal, accessed January 12, 2026, https://riojournal.com/article/11321/

33. Monitoring Biodiversity with eDNA and DNAqua-Net - COST, accessed January 12, 2026, https://www.cost.eu/monitoring-biodiversity-dnaqua-net/

34. INTERNATIONAL STANDARD ISO 16578 iTeh STANDARD PREVIEW (standards.iteh.ai), accessed January 12, 2026, https://cdn.standards.iteh.ai/samples/80968/751ba76928864c1ba79fbf62b94b9f72/ISO-16578-2022.pdf

35. What is eDNA method standardisation and why do we need it? - ResearchGate, accessed January 12, 2026, https://www.researchgate.net/publication/388972178_What_is_eDNA_method_standardisation_and_why_do_we_need_it

36. What is eDNA method standardisation and why do we need it? - SCCWRP FTP, accessed January 12, 2026, https://ftp.sccwrp.org/pub/download/DOCUMENTS/JournalArticles/1436_eDNAMethodStandardisation.pdf

37. Monitoring crown-of-thorns starfish | AIMS - The Australian Institute of Marine Science, accessed January 12, 2026, https://www.aims.gov.au/research-topics/environmental-issues/crown-thorns-starfish/monitoring-crown-thorns-starfish

38. Operationalising and implementing crown-of- thorns starfish (COTS) environmental DNA (eDNA) monitoring on the Great Barrier Reef, accessed January 12, 2026, https://barrierreef.org/uploads/CCIP-D-03-Final-Report-eDNA-Monitoring.pdf

39. Early detection of crown-of-thorns starfish possible with enhanced technique | AIMS, accessed January 12, 2026, https://www.aims.gov.au/information-centre/news-and-stories/early-detection-crown-thorns-starfish-possible-enhanced-technique

40. An autonomous vehicle coupled with a robotic laboratory proves its worth - MBARI, accessed January 12, 2026, https://www.mbari.org/news/an-autonomous-vehicle-coupled-with-a-robotic-laboratory-proves-its-worth/

41. Environmental Sample Processor (ESP) - MBARI, accessed January 12, 2026, https://www.mbari.org/technology/environmental-sample-processor-esp/

42. Automated eDNA Sampling - Siren, accessed January 12, 2026, https://siren.fort.usgs.gov/static-page/automated-edna-sampling

43. Smith-Root eDNA Autosampler tested in new USGS READI-Net study, accessed January 12, 2026, https://www.smith-root.com/news/smith-root-edna-autosampler-tested-in-new-usgs-readi-net-study

44. DNA metabarcoding and environmental DNA across Brazilian biomes: trends, challenges, and conservation applications | bioRxiv, accessed January 12, 2026, https://www.biorxiv.org/content/10.64898/2025.12.11.693676v1.full-text

45. Environmental DNA Metabarcoding in Marine Ecosystems: Global Advances, Methodological Challenges, and Applications in the MENA Region - MDPI, accessed January 12, 2026, https://www.mdpi.com/2079-7737/14/11/1467

46. Capturing environmental DNA in snow tracks of polar bear, Eurasian lynx and snow leopard towards individual identification - Frontiers, accessed January 12, 2026, https://www.frontiersin.org/journals/conservation-science/articles/10.3389/fcosc.2023.1250996/full

47. Sampling polar bear footprints in the snow for conservation insights - WWF.CA, accessed January 12, 2026, https://wwf.ca/stories/sampling-polar-bear-footprints-edna/

contents, accessed January 12, 2026, https://ednasociety.org/wp-content/uploads/2025/07/eDNA_NL06_EN.pdf