RSPB Scotland partnered with NatureMetrics on a pilot eDNA study across five Scottish lochs. The aim was to better understand the lochs’ ecology and how suitable they are as habitat for the common scoter, a rare breeding duck.

The data revealed ecological differences between the lochs that affect their suitability for the scoter, and turned up new records of hard-to-survey and protected species along the way.

A few pairs of common scoter breed in Scottish lochs each year. In some lochs they compete with brown trout for invertebrate prey. But where small fish such as minnows and sticklebacks are present, trout feed on those instead, easing the pressure on the scoters.

Knowing which fish live in each loch is therefore key to predicting competition, but that information is hard to come by. The standard method, gill-netting, is invasive for the fish and needs significant time and resources. As a result, it’s rarely carried out, and fish communities are poorly known, especially smaller species that anglers don’t catch or record.

RSPB wanted to test whether eDNA could fill this gap by characterising fish communities, with a focus on trout and small fish species. The scoter itself wasn’t expected to be detected, as sampling took place outside its breeding season.

eDNA was collected from four lochs in the Flow Country and from Loch Loyne in the West Highlands. At each loch, subsamples were taken at multiple points around the perimeter, combined in a sample bag and filtered through a single NatureMetrics aquatic eDNA kit.

The samples were then analysed in our laboratory using our vertebrate eDNA service.

eDNA analysis revealed a wide range of Scottish vertebrate fauna, including 9 fish species, 9 birds, 4 mammals (including water vole) and 1 amphibian (common toad).

Fish communities largely matched known distributions, with some plausible new detections. These included the Critically Endangered European eel in Lochan nam Breac, and new records of nine-spined stickleback and European bullhead, both commonly under-recorded in conventional surveys.

An unexpected detection of carp in Loch Talaheel may have been linked to angling activity (either an illegal introduction or transfer of DNA via fishing tackle).

Minnows and three-spined sticklebacks were detected at high levels in three lochs but were absent from the other two (Loch Talaheel and Clar Loch), while brown trout were present in all five. This suggests common scoters will face greater competition for invertebrate prey in Loch Talaheel and Clar Loch, where trout have no smaller fish to feed on.

With just one sample per loch, the pilot gave RSPB improved data on fish communities and pinpointed the two lochs where scoters are likely to face the most competition for food. It also produced new records of protected and hard-to-survey species, including European eel and water vole, and showed eDNA to be a rapid, non-invasive tool for guiding conservation decisions in remote freshwater habitats.