Voyager: How many fish species are in the Scripps DNA database so far?

The list of fish species found in California’s marine environment numbers more than 800 and is growing steadily. So far, only about 500 of those observed species have had DNA extracted to add to the tissue collection at Scripps Institution of Oceanography at UC San Diego.

The variety of observed species is quite extraordinary. The species range from the harmless but largest living fish in the world, the whale shark, Rhincodon typus, and the notorious white shark, Carcharodon carcharias, to many tiny species such as the saddled prickleback, Lumpenopsis clitella, which is just over two inches long and not discovered until 2003.

Nearly half of these species have been observed only on rare occasions, sometimes only once. Reasons for the scarcity vary. In some cases, a fish typically lives outside of California waters and only occasionally ventures to local waters. Others inhabit poorly sampled areas, such as the deep sea.

One reason that more of the observed fish species haven’t been added to the tissue collection is due to preservation procedures. When fish specimens were originally collected, they were preserved in formalin, a saturated solution of formaldehyde, water, and another agent, typically methanol. However, formalin can break up DNA, making it unsuitable for analysis. To address this problem, Scripps researchers began using ethanol in 1993 for DNA sampling because ethanol helps to keep the DNA intact for cataloging.

The tissue collection at Scripps Oceanography continues to grow steadily and ultimately will become part of a larger project that intends to barcode all living organisms, the “International Barcode of Life.”

-- Ron Burton, director, Marine Biology Research Division

To learn more about using barcodes to identify fish species, read our story “Life Behind Bars” at explorations.ucsd.edu/Features/2009/Life_Behind_Bars/.