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San Diego researchers seek key to understanding volatile anchovy population shifts

A huge school of anchovy looked like a moving underwater shadow in images captured when the small fish gathered near San Diego’s Scripps Pier in 2014.

It was part of a boom cycle for the fish with a notoriously volatile population.

New research published in the current edition of the journal Nature Communications unlocks some of the mystery surrounding the reasons for the fluctuating population.


Anchovies are popular with humans, especially in Caesar salads, and they are an important part of the underwater food web.

The schools of fish feed marine mammals, seabirds and other larger fish. When anchovies are plentiful the marine environment thrives. During times of scarcity, hunger and starvation can hit, like the sea lion mortality event between 2013 and 2016.

Large schools indicate anchovy are common along the Southern California coast during boom cycles.

“It is especially notable because we see a lot of them. There’s a lot of anchovies out there,” said Rasmus Swalethorp, a researcher at the Scripps Institution of Oceanography

When there are a lot of anchovies that usually also means the marine environment is thriving.


“You have a lot of nutrients coming up from the deep ocean that are fueling phytoplankton production and skewing the whole food chain that the anchovies rely on to grow and survive,” Swalethorp said.

The new paper looks at the conditions present during the different cycles and it found the food chain plays a role.

When the anchovies are abundant, anchovy larvae are part of a shorter food chain, meaning there are fewer intermediate species between phytoplankton, single-cell plants and the anchovy’s mouth.

The food chain is longer, with more intermediate steps, during population busts.

Researchers at Scripps and the National Oceanic and Atmospheric Association’s Southwest Fisheries Science Center in La Jolla made their observations using a unique database known as the California Cooperative Oceanic Fisheries Investigations (CalCOFI) library.

CalCOFI has ocean sample collections full of vials. Those small tubes contain plankton and fish larvae.

“We’ve been keeping track of 800 species of fishes since the 1940’s,” said Andrew Thompson, a biologist at the Southwest Fisheries Science Center.

The study examined samples between 1960 and 2005, measuring the anchovy population as well as other parts of the sample.

When the sampling began in the late 1940s very few samples had anchovy larvae, a very different picture than samples from 2023.

“Today, we have maybe a thousand individuals in a single plankton tube, so orders of magnitudes difference in numbers,” Thompson said.

By examining the samples in different years, researchers can compare the anchovy populations and extrapolate what the food web was.

But understanding the food web is only one part of a complex web that combines to create boom or bust cycles for the small fish. Researchers still have a lot to learn.

“The short answer is we don’t exactly know,” said Swalethorp. “We know a lot of things that are important, but our ability to really measure that and measure the broad spatial and temporal scales that covers their populations is very limited.”

Researchers also hope knowing about the length of the food chain will help them predict what the anchovy population will be.