Study: DNA Barcodes to ID Fish Eggs


Sea Grant Trainee Alice Harada lowers a net off the Scripps pier in La Jolla to collect fish eggs.


Ron Burton


Marine Biology

Scripps Institution of Oceanography

UC San Diego


Alice Harada

Sea Grant Trainee
Marine Biology
Scripps Institution of Oceanography

UC San Diego


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Alice Harada, a first-year marine biology graduate student at Scripps Institution of Oceanography, UC San Diego. Photo: C. Johnson


November 2, 2012

Contact: Christina S. Johnson,, 858-740-4319

Sea Grant Trainee Alice Harada (above) lowers a net off the Scripps pier in La Jolla to collect fish eggs. DNA from the eggs will be extracted, amplified and sequenced to identify the species of fish that produced the eggs.

Her work is part of an ongoing Sea Grant project to optimize molecular approaches for quickly, inexpensively and reliably identifying fish eggs and larvae, in light of rapid advances in DNA sequencing technologies.

If successful, scientists will be one big step closer to having a much-needed tool for monitoring fish reproductive success, the timing and location of fish spawning, how these vary with environmental conditions and their link to natural variations in fish population sizes. It could also detect new, non-native fish species, as well as shifts in species' ranges.

“We want to find the fastest, best way to analyze samples of fish eggs,” explains UC San Diego’s Scripps Institution of Oceanography professor Ron Burton, the lead investigator on the project, titled High-Throughput Molecular Identification of Fish Eggs and Larvae.


Fish eggs in vials sorted by visual markers such as size, shape and color. Photo: C. Johnson

Fish eggs collected during ichthyoplankton surveys are typically sorted by their size, shape and other visually distinguishing characteristics. Each group of eggs is identified to species level, if possible, and counted. Such counts are used to estimate the number of spawning adults, an important parameter for evaluating stock health and setting harvesting guidelines. The problem is that sometimes eggs are incorrectly grouped together. “Fisheries biologists cannot visually tell apart some of the most common fish egg species, Burton says. Yet, they use these counts to establish fish spawning biomass.

Previously, Burton and former Sea Grant Trainee Lani Gleason applied DNA barcoding approaches to an archived record of fish eggs, collected during the CalCOFI cruises, that had been sorted, speciated and counted based on egg morphologies (see image above). That analysis showed that fish eggs were often misidentified. Particularly problematic was the whole flatfish family. Pacific halibut, sand dabs and diamond turbot were often confused.

With the fish egg collecting now going on at the pier, the goal is to establish what species are reproducing inshore locally; the probes for the CalCOFI project were
“tuned” for common pelagic fish species found farther off the coast. Once this is done, biologists will reevaluate the best approach for genetically indentifying the local inshore fish community.

One of the major objectives of the region's new marine reserve network is to protect larger, older female fishes that produce the most eggs and hence are most important to replenishing fish populations. The twice-weekly monitoring at the pier may shed light on whether this anticipated benefit is indeed occuring, or can be detected, and for which fish species.