eDNA detection thresholds: what species can and cannot be found

Not every species is equally visible to eDNA. Some, like carp in a pond, are almost impossible to miss. Others, like a passing bobcat that drank once at a stream, are borderline invisible. Understanding what drives detection helps you interpret both the hits and the absences on your report.

Shedding rate

Fish shed constantly through gill exchange and mucus. Amphibians release enormous amounts of DNA as larvae. Mammals shed via urine, feces, hair, and skin. Reptiles shed skin in intact sheets a few times a year.

This ordering shows up in detection. Fish and amphibians are the easiest aquatic targets. Mammals are moderately easy from urine and scat but harder from casual passage. Reptiles are notoriously harder because their shedding is episodic.

Body size and biomass

Larger individuals and larger populations produce more DNA. A single trout in a headwater stream is a much smaller signal than a school of fifty. A resident colony of bats is easier to detect than a lone migrant.

This is why absence in a single sample is weak evidence — small populations of small-bodied species live at the edge of detection.

Habitat and residence time

An animal that lives in the sampled area sheds continuously into it. One that passes through leaves a brief pulse that may or may not still be detectable when the sample is taken.

This is also why lake sediment cores can reveal species that no longer live there — the residency was long enough historically to leave a durable record.

Primer coverage and database completeness

A species that binds the chosen primers well and is in the reference database will show up if it was there. A species that has a mismatch at the primer site, or that has never been sequenced, cannot be identified even if its DNA is in the sample.

This is why edge cases — a rare tropical insect, an undescribed fungus — can genuinely be present and still not appear by name in a report.

Frequently asked questions

Why did a species I know is here not show up?

Most likely reasons: it sheds little, it was outside the sample area at the moment, its DNA had degraded, or the primer set does not amplify it well.