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Range Wide Structure and Diversity in Longfin Smelt

Range Wide Structure and Diversity in Longfin Smelt

Background and Significance of Study

Relative to the infamous Delta Smelt, the state-threatened longfin smelt (Spirinchus thaleicthys) has been largely ignored in conservation discussions and water politics until recently. This is in part because longfin smelt are not endemic to the San Francisco Estuary (SFE) and San Joaquin-Sacramento Delta, unlike the Delta Smelt. Instead Longfin smelt range roughly from the SFE to Alaska. However the SFE population is not only the southernmost, but is also the largest.

Longfin smelt were once the most abundant fish in the upper estuary – even more abundant than Delta Smelt. Yet their numbers have plummeted in recent years, and they have been petitioned for listing under the ESA. The USFWS determined the SFE distinct population segment (DPS) of longfin smelt to be warranted but precluded.

The collapse of longfin smelt has generated research (much like the collapse of Delta Smelt), and the GVL has been contracted to use RAD-sequencing to examine the range-wide population structure and diversity of longfin smelt. We have sequenced roughly 150 longfin smelt from throughout the SFE. Individual longfin smelt from the Columbia River, Lake Washington, Harrison and Pitt Lakes in Canada, and Yakutat Bay, Alaska were added to the library for sequencing.

Project Status

As of August 2019, the sequencing and preliminary analyses are completed and a demographic analysis is nearly completed that shows the San Francisco Bay population of longfin smelt is the greatest source of genetic diversity to the adjacent populations (Humboldt Bay and the Columbia River estuary). This is surprising because it was not known that longfin could or would migrate northward along the coast. It's always interesting when genetic data can provide new information on a species!


Department of Water Resources

Jim Hobbs California Department of Fish and Wildlife

Ismail Saglam, Koc University, Istanbul, Turkey


USFWS longfin smelt fact sheet

Bay-Delta Fish you’ve never heard of: longfin smelt

New Bay Bridge headache: demolition could harm threatened smelt

Metropolitan Bay-Delta Committee hears a science update on the longfin smelt

Delta smelt’s unsung relative on the verge of extinction, too

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