Controlled vocabulary
Terms and definitions
Free foreverCommon Measure maintains this vocabulary as part of its specification. Definitions are versioned. Where the field genuinely disagrees, we say so rather than picking a side quietly.
This vocabulary is maintained by Common Measure and will pass to the science committee on formation. Terms are open to challenge. Where a definition changes, the previous version remains published and the change is recorded.
Where a published standard defines a term, we adopt its definition rather than writing our own, and say so in the entry. CSA W214:21, Environmental DNA (eDNA) reporting requirements and terminology, is a published National Standard of Canada; we will align this vocabulary to it, and to other terminology standards as they are published, and record the change.
A
Adaptive sampling
A method in which the sequencing instrument decides in real time which DNA strands to keep reading and which to reject.
Used on nanopore platforms to enrich for target organisms during a run rather than before it. It performs a similar job to hybridization capture but in software instead of chemistry, which means the target list is a file that can be published and versioned rather than a physical reagent set.
Airborne eDNA
Genetic material suspended in air, collected by drawing air through a filter.
An emerging approach used for terrestrial biodiversity, plant and fungal survey, and biosecurity screening at ports and shipping containers. Collection volumes and residence times differ substantially from aquatic sampling, so thresholds developed for water do not transfer directly.
Amplicon
A segment of DNA produced by copying a specific region many times using PCR.
Metabarcoding works by amplifying the same marker region across many organisms at once, then sequencing the resulting amplicons. Amplicon length matters for comparability. Results based on a 313 base-pair fragment are not directly interchangeable with results based on a 400 base-pair fragment of the same gene.
ASV — Amplicon Sequence Variant
An exact sequence recovered from a sample, retained without being grouped with similar sequences.
ASVs are reproducible across studies in a way that OTUs are not, because they are not defined by a clustering threshold chosen by whoever ran the analysis. This is why ASVs are increasingly preferred where results need to be compared across laboratories or across years.
Assurance record
A permanent, immutable record of how a detection was produced.
It captures molecule type and marker, collection timestamp, filter and preservation method, replicate structure, which assays were run on which samples, control results, thresholds applied, and pipeline and reference database versions. A detection is not evidence until this record exists.
Autosampler
An instrument that collects and filters water samples automatically on a programmed schedule, without an operator present.
Autosamplers make high-frequency monitoring practical but collect samples sequentially, which means closely spaced samples are not true simultaneous replicates. Treating sequential samples taken 15 to 60 minutes apart as simultaneous can substantially bias estimates of sampling and temporal variance.
B
Benthic
Relating to the bottom of a waterbody, whether freshwater or marine.
Benthic sediment holds genetic material that has settled out of the water column, often integrating a longer period than a water sample. Sediment and water from the same location can return substantially different species lists, and neither is wrong.
Bioassessment
Evaluating the ecological condition of a waterbody by examining the organisms living in it.
In the United States this is done under the Clean Water Act, traditionally by collecting and visually identifying benthic macroinvertebrates. Metabarcoding can produce comparable indices from a water sample, which is one of the largest potential applications of environmental DNA in the country. Soil biological condition is assessed by analogous methods in agricultural and reclamation contexts.
Biosecurity
Screening for the arrival of unwanted organisms at a point of entry.
Ports, airports, shipping containers, plant nurseries and ballast water are all monitored this way. Detections carry immediate operational consequences, which makes defensibility more important here than almost anywhere else.
Bulk sample
A sample consisting of whole organisms rather than shed genetic material.
Common in terrestrial invertebrate work, where a trap catch is homogenized and sequenced together. It is not strictly environmental DNA, but it uses the same markers and pipelines and faces the same comparability problems.
C
Chain of custody
The documented sequence of everyone who handled a sample, and when.
Standard practice in regulated environmental testing and largely absent from environmental DNA workflows. Where a result may be challenged, an unbroken chain of custody is often the difference between evidence and an interesting observation.
Control
A sample run alongside real samples to detect contamination or failure.
Three kinds matter. A field blank is clean water processed with the same equipment in the same place, testing for contamination during collection. An extraction control uses only laboratory reagents, testing the laboratory. A no-template control runs the reaction with no DNA added, testing the reaction itself. A result reported without its controls is very difficult to defend.
Conformance
Meeting every requirement stated by a specification.
For the Common Measure assurance record, conformance means every required field is answered in the form the specification permits. A conformant record may still contain declared gaps; conformance describes whether the record follows the specification, while completeness describes how much is known.
Cq — quantification cycle
The number of PCR cycles required before a signal becomes detectable.
A lower Cq means more target DNA was present at the start. Because Cq depends on reaction conditions, the same Cq value from two laboratories does not necessarily mean the same concentration.
D
Digital PCR — dPCR
A method that divides a sample into thousands of tiny separate reactions and counts how many contain the target.
It gives absolute quantification without needing a standard curve, and tolerates inhibitors better than conventional qPCR. Like qPCR it is targeted. It can only find what it was designed to look for.
Discordance — phylogenetic-taxonomic
A mismatch between the named species and the genetic evidence.
Under-splitting is where one accepted name contains several genetically distinct lineages. Over-splitting is where taxonomy recognizes several species that cannot be genetically separated. Under-splitting is a serious problem for targeted assays: an assay built for one lineage can miss another lineage carrying the same name.
E
eDNA — environmental DNA
Genetic material shed by organisms into their environment, collected from water, soil, sediment or air rather than from the organism itself.
Every living thing sheds cells, mucus, scales, pollen and spores. Filtering a water sample, coring a soil profile, or drawing air through a membrane captures that material, and sequencing it reveals which species have recently been present. DNA persists for days to weeks and can travel, so a detection indicates recent presence, not a living local population.
Effective range
The time or distance beyond which two measurements are no longer meaningfully correlated.
In eDNA time series it is the lag beyond which concentrations at two moments are effectively independent. It is notoriously difficult to estimate. Published estimates from a single well-designed study ranged from roughly two to ten hours, with confidence intervals spanning half an hour to two weeks.
eRNA — environmental RNA
RNA shed into the environment, which degrades within minutes to hours and therefore indicates recent biological activity.
DNA is the blueprint and persists after death; RNA is the working copy and falls apart quickly once a cell stops functioning. Finding environmental RNA means something living was active at that place very recently, which is why it is used to confirm that a detection represents a living local population.
Extraction
The laboratory step that separates DNA or RNA from the filter and everything else caught on it.
Extraction chemistry affects how much genetic material is recovered, and different kits give different yields from the same filter. It is one of several points where two laboratories following the same nominal method can produce different numbers.
F
FASTQ
The standard file format holding raw sequencing output, the sequence reads themselves, before any interpretation.
A species list is a laboratory's interpretation of the FASTQ, made using the reference database and software available on the day. The FASTQ can be reanalyzed years later against improved references; the species list cannot. Anyone commissioning sequencing should request the FASTQ files, including controls.
Filter membrane
The porous disc that captures genetic material as water is drawn through it.
Two types are common. Mixed cellulose ester (MCE) is a depth filter, retaining particles both on and within the matrix. Polyethersulfone (PES) is a surface filter. MCE has been shown to recover more than ten percent more DNA than PES under the same conditions, a systematic difference caused by the consumable, not the method.
FreshnessGate
The principle that molecules degrading at different rates can be used together as a clock for how recently an organism was present.
Environmental DNA persists for days; environmental RNA disappears within hours. If the fast-degrading signal is present, the organism was there recently. If only DNA is found, the detection may reflect material that arrived days earlier from elsewhere.
H
Hybridization capture
A method that uses synthetic RNA baits to pull target DNA out of a sample before sequencing.
It enriches for organisms of interest without the amplification bias introduced by PCR, and recovers longer sequences than typical metabarcoding. The bait panel determines what can be found, which means a proprietary panel functions as a private standard.
I
Inhibition
Interference from substances in the sample that suppress the PCR reaction and cause false negatives.
Humic acids, tannins and sediment are common culprits in environmental samples. Well-run laboratories test for inhibition on every reaction using an internal positive control, and a result reported without an inhibition check may be a non-detection caused by chemistry rather than biology.
ISO 17805
The international standard specifying how environmental DNA is sampled, captured and preserved from water.
Published in 2026, and also adopted as a European standard. It covers filtration, contamination control, filter and preservative selection, and the metadata that should accompany a sample. It does not cover sediment, biofilms, sampling design, extraction, or anything downstream of preservation.
ISO/IEC 17025
The international standard for the competence of testing and calibration laboratories.
Accreditation under it is a statement about a laboratory's management systems and technical competence, awarded by an accreditation body. It is frequently confused with method approval, which it is not, and with conformance to a data standard, which it also is not.
ITIS — Integrated Taxonomic Information System
The United States federal reference for accepted scientific names.
Where a result will be used by a US agency, taxonomy aligned to ITIS is generally expected. Different reference databases follow different taxonomic authorities, which is one reason species lists from two laboratories can differ even when the underlying sequences agree.
L
Leaf swab
Collecting genetic material from a plant surface using a swab or wash.
Used for pathogen surveillance, pollinator work and arthropod detection in agriculture and forestry. Surface material is more recent and more local than soil, which makes interpretation different again.
Limit of detection
The lowest concentration a method can reliably distinguish from zero.
Related terms are the limit of blank, the highest signal expected from a blank sample, and the limit of quantitation, the lowest concentration that can be measured with acceptable precision. A non-detection means only that the target was below the limit of detection for that sample.
M
Marker
The specific region of the genome an assay targets.
Common markers include CO1 for animals and invertebrates, 12S for fish, 16S for bacteria, and ITS2 for plants and fungi. Two laboratories using different markers on the same water are answering different questions, and their species lists cannot be directly combined.
Metabarcoding
Sequencing a shared genetic marker across every organism in a sample at once, then matching the results against a reference database.
It answers the open question, what is here, rather than a single-species question. It is used for freshwater community surveys, marine baselines from water and sediment, and soil fauna and fungal inventories. It is limited by reference coverage: an organism can only be named if its sequence is already in the database, so poorly represented species come back as a genus, a family, or nothing at all.
Metagenomics
Sequencing all the genetic material in a sample without targeting any particular region.
It is comprehensive but inefficient for biodiversity monitoring, because the vast majority of reads come from microbial background rather than the organisms of interest.
Methylation
Chemical marks on DNA that vary with an organism's life stage and condition.
Methylation patterns differ between juveniles and adults, which makes it possible in principle to infer life stage from environmental samples. On some sequencing platforms these marks can be read directly from native DNA without additional chemistry.
N
Nanopore sequencing
A sequencing method that reads DNA by passing a strand through a tiny pore and measuring changes in electrical current.
It produces long reads, can run in the field, can detect methylation directly, and supports adaptive sampling. Read accuracy per base has historically been lower than short-read platforms, though the gap has narrowed considerably.
O
Occurrence record
A formal assertion that a given organism was present at a given place and time.
This is the unit that biodiversity databases store and regulators consult. Converting a molecular detection into an occurrence record requires deciding what confidence threshold, replicate structure and control performance are sufficient, decisions that are policy as much as science, and that no single laboratory can make on behalf of the others.
OTU — Operational Taxonomic Unit
A group of similar sequences clustered together and treated as one entity.
The clustering threshold is chosen by whoever runs the analysis, commonly 97 percent similarity, which means OTUs from different studies are not directly comparable. This is a principal reason results from two laboratories cannot simply be placed side by side.
P
PCR — polymerase chain reaction
A technique that makes many copies of a specific DNA region so it can be detected or sequenced.
It underlies both metabarcoding and targeted assays. PCR introduces bias — some sequences amplify more readily than others — which is one reason read counts do not translate directly into abundance.
Pelagic
Relating to the open water column, away from the bottom and the shore.
Pelagic sampling is the dominant mode in marine biodiversity survey and in fisheries applications. Depth becomes a primary variable in a way it rarely is in shallow freshwater work.
Persistent identifier
A permanent code assigned to a sequence so it can be tracked across runs, laboratories and years, independent of what it is currently named.
Species names are revised as taxonomy improves; a persistent identifier is not. Anchoring records to identifiers, with names attached as versioned annotations, means a taxonomic revision updates the record rather than breaking it.
Pollen metabarcoding
Identifying plant species from pollen using the ITS2 marker.
Applied to pollinator diets, honey authentication, airborne allergen monitoring and vegetation survey. It uses a different marker and a different reference library from animal work, and the two are frequently run on the same samples.
Polydisperse
Occurring across a wide range of particle sizes.
Environmental DNA is polydisperse. It exists as free molecules, as fragments bound to sediment, and inside intact cells. Different filter pore sizes capture different fractions, which contributes to the large variation between replicate samples taken from the same water.
Primer
A short synthetic DNA sequence that tells the PCR reaction where to start copying.
Primer choice determines which organisms are amplified and which are missed. Two laboratories using different primer sets for nominally the same marker will produce different species lists from identical water.
Provenance
The documented origin and handling history of a result.
In environmental DNA, provenance means knowing which sampler, filter, preservation method, pipeline version and reference database version produced a given detection. Without it, a result cannot be reproduced or compared with any confidence.
Pseudoreplication
Treating measurements that are not independent as though they were.
Samples collected close together in time or space are correlated. Analyzing them as independent underestimates uncertainty and inflates the rate of false positives, producing apparent relationships between eDNA concentration and environmental variables that disappear once the correlation is properly modeled.
Q
qPCR — quantitative PCR
A targeted method that tests for one specific species and estimates how much of its DNA is present.
It is more sensitive than metabarcoding for its target and produces genuinely quantitative results, but finds only what it was designed to find. Most United States invasive species monitoring is built on qPCR assays.
R
Reference database
The library of known sequences against which sample reads are matched to assign names.
Common databases include BOLD, GenBank, SILVA and UNITE. They differ in coverage, curation and taxonomic authority, and they change continually, which means the same raw data analyzed a year apart can yield a different species list. Recording the database version used is essential to reproducibility.
Relative efficiency
The proportion of target genetic material present in a sample that is ultimately recovered and available for analysis.
Absolute efficiency cannot be measured in the field because the true amount in the water is unknown, but relative efficiency between two methods can be compared. It reflects the whole workflow — collection, filtration, preservation and extraction — not any single step.
Replicate
A repeated measurement, of which there are three distinct kinds that are routinely confused.
A technical replicate is the same extract run multiple times, measuring laboratory variation. A field replicate is a separate sample collected at the same place and time, measuring sampling variation. A temporal replicate is a sample collected at the same place at a different time. Reporting a count of replicates without specifying which kind makes a result impossible to interpret.
Rhizosphere
The zone of soil immediately surrounding plant roots.
Biologically distinct from bulk soil a few centimeters away, with much higher microbial activity. Sampling design has to state which is being collected, because the two are not comparable.
S
Sampling variance
Variation between samples caused by the stochastic capture of genetic material during collection and processing, rather than by real change in the environment.
It is large. In one intensively sampled river site, sampling and short-term temporal variation together meant a measured concentration could plausibly fall anywhere between roughly a quarter and four times the expected value — from a single laboratory using a single method. Soil and sediment show comparable or greater variation, driven by patchiness at centimeter scales.
Sediment core
A vertical sample of accumulated sediment, sampled as a column.
Depth in a core corresponds loosely to time, which makes cores valuable for establishing historical baselines in lakes, estuaries and marine basins. DNA degrades with depth, so recovery falls off and dating assumptions become load-bearing.
Self-preserving filter
A filter housing that dries and stabilizes captured genetic material in the field, removing the need for a cold chain.
It also removes the step of transferring a filter by hand, which is a common point of contamination. For RNA, field stabilization is not optional. Without it the signal is gone before the sample reaches a laboratory.
Sequencing depth
The number of reads generated per sample.
Deeper sequencing recovers rarer organisms but costs more. Two samples sequenced to different depths will yield different species counts even if the underlying communities are identical, so depth must be recorded and accounted for before results are compared.
Soil core
A vertical sample of soil taken with a corer rather than scraped from the surface.
Standard practice in terrestrial and agricultural biodiversity work. Depth, diameter and whether the core was homogenized all affect the result and all have to be recorded.
Substrate
The material a sample is taken from: water, sediment, soil, air or a surface.
Substrate determines almost everything downstream: how much material is recovered, how long the signal persists, what controls are appropriate, and what a detection means. Results from different substrates at the same site are complementary, not interchangeable.
T
Taxonomic assignment
The step that converts a sequence into a species name by matching it against a reference database.
The outcome depends on which database was used, which version, what similarity threshold was applied, and how ambiguous matches were resolved. Two laboratories can agree completely on the underlying sequences and still report different species lists.
Temporal variance
Real change in the amount of genetic material at a site over time, as distinct from variation introduced by sampling.
Separating the two requires true replicates collected as close together in time as possible. Where they cannot be separated, it is impossible to tell whether a change in results reflects the ecosystem or the measurement.
Threshold
A cut-off value determining what counts as a detection.
Thresholds are applied at several points: minimum read count, minimum similarity to a reference sequence, minimum number of positive replicates. They are chosen, not discovered, and different choices produce different species lists from identical data. Recording the thresholds applied is part of the assurance record.
Trophic marker
A genetic marker chosen to reveal what an organism has eaten.
Used in diet studies from scat, gut contents and pollen loads, across terrestrial, freshwater and marine systems. It shares pipelines with environmental DNA but the sample is an organism rather than the environment.
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