A DNA metabarcoding approach to monitoring fish spawning and population connectivity in Coastal Southern and Central California

Project Number
Project Date Range
Funding Agency
California Ocean Protection Council (OPC)
Focus Area(s)
Sustainable Fisheries and Aquaculture

Changes in global climate are affecting many parameters of the ocean environment including temperature, pH, nutrient levels and oxygen concentrations. These changes, along with direct anthropogenic impacts, may be altering the distribution and abundance of marine fish in California's coastal ecosystems with potentially significant consequences on commercial and recreational fisheries. Although changes in distributions of adult fish are often immediately observed, new patterns of reproduction can be harder to identify, and in some cases, may only affect adult populations years later. 

Using samples collected weekly for two years at five shore stations — spanning from La Jolla in the south to Santa Cruz in the north — this project examined the species diversity in fish eggs in California, with a focus on how egg diversity varied in space and time.

The research team found an increased diversity of species at the four southern sites, confirming earlier results. (For example, there were only eight species represented in over 2,000 eggs sampled in San Luis Obispo, while 22 species were identified in fewer eggs further south in Santa Monica and Newport.) Despite this overall low diversity, eggs of the Pacific sand sole were only found at the northern sites.

Originally, this project proposed the use of a technique known as “metabarcoding” to analyze eggs. Metabarcoding sequences the combined genetic materials drawn from all of the eggs in a sample and estimates the proportional abundance of each species. The technique is less precise than “barcoding,” which analyzes the genetic material from each egg separately, but it can be cheaper and faster. In this project, however, the low number of eggs collected in many samples made barcoding economically competitive.

It was not possible to analyze population connectivity using egg samples across geographic sites as had been planned, since the species diversity in northern study sites was lower than expected. Only speckled sanddabs provided sufficient material for such analysis, which is ongoing.