Do they stay or do they go? Tracking fish with DNA

A guest blog by Diana Baetscher

“Catch anything?”

Our boat pulled at the mat of giant kelp I had used to tie the bow line, drifting closer to the man’s kayak. The fisherman motioned to a few rockfish and told us that he was angling for a bigger prize: a cabezon, or better yet, lingcod.

I hold a baby rockfish before taking a very small tissue sample for genetic analysis. Dozens of fish wait their turn in the bucket below (Photo: Diana Baetscher).

I hold a baby rockfish before taking a very small tissue sample for genetic analysis. Dozens of fish wait their turn in the bucket below (Photo: Diana Baetscher).

We were having good luck catching rockfish too. But rather than taking the fish home for tacos, we snipped a tiny piece of fin, tucked it into an envelope, and released the fish back into the cold water of Carmel Bay. These fin clips contain DNA that I use to match adult rockfish with their babies by a rockfish-paternity test that I developed as part of my graduate research.

It might seem like a strange goal – finding matches between adult rockfish and their offspring – but our aim is to understand where baby fish end up when they are born in a marine protected area (MPA). Our method works because the adult rockfish we study are nearly stationary: they move approximately 100 square feet during their entire adult life. Baby rockfish, however, are pushed around by currents, wind, and waves. No one knows how much control these tiny fish have over where they travel, and ultimately, where they end up.

Baby rockfish drift and swim under the cover of the kelp canopy in Carmel Bay, California (Photo: Laughlin Barker).

Baby rockfish drift and swim under the cover of the kelp canopy in Carmel Bay, California (Photo: Laughlin Barker).

Ten years ago, scientists and policy-makers designed MPAs along the coast of central California to provide protected habitat and increase populations of fishes favored by fishermen. Research at that time suggested that many of the baby fish within the MPAs would leave and increase fishing opportunities. Other baby fish would stay inside the reserves and grow the population. Carmel Bay includes two such protected areas and we sample adult and baby fish both inside and outside these MPAs.

But we needed a way to test where the baby fish are going.

With DNA from thousands of rockfish, I look at dozens of genes, and in those genes, hundreds of individual base-pair differences: the single molecules that make each person – or fish – unique. This is how researchers compare bits of DNA that we have in common with our parents and siblings, but not with folks that are unrelated to us. And this is how I track down parent-rockfish and their babies that stay in Carmel Bay.

Single-molecule differences in the genes of fish (and people) allow researchers to match parents-and-offspring (Graphic: Diana Baetscher).

Single-molecule differences in the genes of fish (and people) allow researchers to match parents-and-offspring (Graphic: Diana Baetscher).

My research tests whether baby fish stay in the marine reserves where they are born and increase local populations, or settle outside of MPAs and boost fishing opportunities. My results studying rockfish in Carmel Bay suggest that fish might do both – some stay near their parents and others travel miles away. A combination of movement patterns keeps fish populations healthy and supports fisheries.

We catch another rockfish and wrangle it onboard, avoiding the sharp spines. I snip a tiny piece of fin tissue, and release the fish along the side of the boat, where it quickly swims beneath the kelp. I tuck my tissue sample into an envelope. Back at the lab, the DNA from this fish will provide some of the clues needed to track fish movement and ultimately allow us to manage our coastal fisheries sustainably.

Diana Baetscher is a PhD candidate in Ecology and Evolutionary Biology at UCSC and the Fisheries Ecology Division of NOAA’s Southwest Fisheries Science Center