Range wide structure and diversity in longfin smelt

For more information contact Mandi Finger: ajfinger@ucdavis.edu

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.

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Map of longfin range taken from Federal Register

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.

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Abundance indices of longfin smelt taken from Federal Register

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. This project is in collaboration with Miller Lab member Ismail Saglam, and Jim Hobbs, both UC Davis.



Preliminary results

We have found that substantial population structure exists throughout the range of longfin smelt, as indicated by the NGSAdmix plot below:


Population codes: YBAK (Yakutat Bay, AK), PTLC/HRLC (Harrison and Pitt Lakes, Canada), LWSH (Lake Washington, WA), COLR (Columbia River, WA). Bay area locations: ALVS (Alviso Slough), PETA (Petaluma), CHPI (Chipps Island), SFBY (San Francisco Bay), SUIB (Suisun Bay).

Note that all of the “pink” fish were caught in the Bay Area. The green individual may be a mis-labelling error (most likely) or perhaps a fish swam down from up north (less likely). We found very little structure within the Bay Area.

Unfortunately, we need additional samples from the populations north of the Bay Area to really see how much the fish could be moving. Specifically, we need additional samples from the Humboldt and Columbia River Estuaries. With this data though, we can definitively say that the SFE population of longfin smelt is genetically distinct from longfin populations in Washington, Canada, and Alaska.

Stay tuned.



Department of Water Resources


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