Vertebrate DNA in water

I remember the famous limnologist G. Evelyn Hutchinson was once mocked as supposedly believing that he could determine all there was to know about a lake simply by sticking one, perhaps two, fingers in a lake.

I am not sure how many fingers it would take, but with environmental DNA one can convince themselves that we are getting pretty close with just a few fingers worth of water.

Almost everything that touches a stream or lake should leave some DNA behind. We tested that a bit with some filtered stream samples from Nebraska taken by NE DEQ. Across a wide range of streams in eastern Nebraska, we amplified vertebrate DNA (here fishes and mammals) to see what animals were leave  DNA signatures behind.

Turns out a lot.

On the mammal side, a lot of human DNA, which might be from handling the samples, but also cattle, skunk, muskrat, beaver, deer and mice.

On the fish side, we found about 20 species of fish, including long nose gar, common carp, silver carp (!), fathead minnow, quillback, longnose sucker, and spotfin shiner.

Keys  to using eDNA for vertebrates is a combination of choosing the right primer and getting enough sequencing depth to capture as much of the assemblage as possible. These data were pulled from ~300,000 reads across ~25 sites. Doing it right will likely take at least an order of magnitude more sequencing depth.

Still, it’s encouraging to see so many species in our data.

We’re continuing to work on the issue, so stay tuned…