Delta smelt’s unsung cousin seems verging on extinction, too

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The longfin smelt, so-named for its long pectoral fins, lives in the open water of San Francisco Estuary. Source: U.S. Bureau of Reclamation

By James Hobbs and Peter Moyle
Another native fish of the Sacramento-San Joaquin Delta appears to be rivaling the cliffhanger status of the delta smelt.

Relative to its historical abundance, the lesser-known longfin smelt has experienced an even bigger decline than delta smelt — and may be in bigger trouble — according to trawl surveys of Delta fishes.

In the past two years, catches of adult longfins have been close to zero, and a recent larval survey found alarmingly few of the smelt. The dramatic downturn is likely a result of the drought, as with the tinier delta smelt.

Lacks federal protection

Unlike its headline-grabbing relative, the longfin is not listed under the federal Endangered Species Act.

In 2012 the U.S. Fish and Wildlife Service determined that the Delta population of longfin smelt deserved protection, but designated the fish only as a candidate for listing. The less powerful California Endangered Species Act lists the species as threatened with extinction. Presumably, the federal protections for the delta smelt have benefited the longfin and other native fishes because it is the species most sensitive to changes in the Delta’s waterways.

The longfin and delta smelt were once common, thriving inhabitants of the Delta and elsewhere in the open waters of San Francisco Estuary. The longfin live two to three years longer than the delta smelt and grow twice as big – up to 5 inches long – big enough to have been an important part of the San Francisco Bay commercial smelt fishery in the 19th century.

Caption

Longfin smelt grow up to 5 inches, about twice the length of nature delta smelt. Photo by Randall Baxter/California Department of Fish and Wildlife

The longfin population was the most abundant fish in the upper estuary. The population has gone through several boom and bust periods (Figure 1).

The initial slump, in the 1980s, was at least partially the result of the invasion of the overbite clam, which has robbed pelagic fish of food. Starting in 2002, the population nosedived, following the trajectory of delta smelt and other species — a trend known as the Pelagic Organism Decline

Sampling programs all show population collapsing

Before 1980, the state’s Fall Midwater Trawl survey alone would catch thousands of individuals in a four-month season (September-December). Since 2002, only 10 – 100 fish have been captured per season.

A similar pattern is shown in the San Francisco Bay Study, a monthly fish survey that uses midwater and bottom otter trawls to sample from South San Francisco Bay to the North Delta. Together, the state surveys show a dramatic decline of longfin smelt throughout the estuary (Figure 2).

Likewise, our monthly sampling in Suisun Marsh, which UC Davis began in 1979, has shown a long-term decline of the smelt (Figure 3).

siderTom Cannon, an estuarine fisheries ecologist and biostatistician, was perhaps the first to sound the alarm over the estuary population of longfin smelt, in a recent California Fisheries Blog headlined, “They’re Gone.” 

Are they on the verge of extinction? The answer is not as clear as it seems to be for delta smelt, in part because so much less is known about longfin.

Recent UC Davis surveys have found longfin smelt in areas not previously monitored — Alviso Marsh in the lower South Bay, Napa-Sonoma Marsh, Petaluma River and the Cache-Lindsey Complex of the North Delta — raising the question of whether the smelt’s distribution has changed.

While the species clearly is in severe decline, it is possible that sampling programs are missing significant segments of the population. In summer and fall, substantial numbers inhabit coastal waters — outside areas surveyed.

However, all sampling programs within the estuary show longfin of all ages collapsing in the past few years,  suggesting an estuary-wide decline.

Drought impacts

The aggressive invasion of the overbite clam in San Francisco Estuary is blamed as one of the causes of the decline of delta and longfin smelt in recent years. Photo by Cynthia Brown/U.S. Geological Survey

The aggressive invasion of the overbite clam in San Francisco Estuary is blamed as one of the causes of the decline of delta and longfin smelt in recent years. Photo by Cynthia Brown/U.S. Geological Survey

The abundance of longfin smelt, particularly young-of-year, increases with the amount of freshwater flowing through the estuary (Figure 4). The fish also seems to have a low tolerance for warmer waters, with adults rarely found in water warmer than 64 degrees (18 degrees C) and young-of-year above 73 degrees (22 degress C) [Figure 5].

Warmer temperatures and less freshwater flow in the Delta are associated with drought, so if the drought continues, longfin smelt are likely to be extirpated from the estuary. Even if the drought ends, smelt numbers may be so low that recovery will be difficult and slow.

Recolonization from more northern populations is possible but highly uncertain, reflecting a need for more research on the basic biology of the species. We just hope the smelt will still be around to study.

James Hobbs is a research scientist and Peter Moyle if a professor of fish biology, both with the UC Davis Department of Wildlife, Fish and Conservation Biology. This article was originally posted on Aug. 31, 2015 and revised Sept. 1 with additional information and sources.

Further reading

Hobbs, J. A., C. Parker, J. Cook and M. Bisson. 2015. Technical Report: The distribution and abundance of larval and adult longfin smelt in the San Francisco Bay tributaries Year 1: Pilot Study. DOI: 10.13140/RG.2.1.3185.5843

Hobbs, J.A., L. L. Lewis, N. Ikemiyagi, T. Sommer and R. Baxter. 2010. “The use of otolith strontium isotopes (87Sr/86Sr) to identify nursery habitat for a threatened estuarine fish.” Environmental Biology of Fishes. 89:557-569. DOI 10.1007/s10641-010-9762-3

Merz, J.E., P.S. Bergman, J. F. Melgo and S. Hamilton. 2013. Longfin smelt: spatial dynamics and ontogeny in the San Francisco Estuary, California. California Fish and Game 99(3):122-148

Rosenfield, J. A. and R. Baxter. 2007. Population dynamics and distribution patterns of longfin smelt in the San Francisco Estuary. Transactions of the American Fisheries Society 136:1577-1592

PopTrends_chart.png

Figure 1.  Fall Midwater Trawl Survey abundance indices for most common Delta fishes, 1967 – 2014. (Axes scaled to abundance of longfin smelt, with breaks in y-axis for less abundant species) Source: California Department of Fish and Wildlife

 

The longfin and delta smelt were once abundant in the Delta and elsewhere in the open waters of San Francisco Estuary. The longfin live two to three years longer than the delta smelt and grow twice as big – up to 5 inches long – big enough to have been an important part of the San Francisco Bay commercial fishery in the 19th century.

Figure 2.  Abundance indices (standardized) for longfin smelt, 1980 – 2014. Source: California Department of Fish and Wildlife 

fig3_lfsmelt.png

Figure 3. Catch-per-minute otter trawling Suisun Marsh, 1980 – 2014. Source: UC Davis

 

 

Longfin smelt abundance in the Fall Midwater Trawl (log transformed) plotted against freshwater outflow (log transformed). Regressions lines for the 1967-1987 pre-Corbula years, 1988-2000 Corbula invasion period, and from 2002-2014 “modern-climate regime”. Corbula is an invasive clam that has reduced the food supply for longfin smelt and other pelagic species.

Figure 4.  Longfin smelt abundance in Fall Midwater Trawl plotted against Delta freshwater outflow (log transformed). Regression lines for 1967 – 1987 (pre-overbite clam invasion); 1988 – 2000 (during invasion); and 2002 – 2014 (post-invasion). The invasive overbite clam has robbed food from longfin smelt and other pelagic species. Source: California Department of Fish and Wildlife

Smoothed presence-absence data from the San Francisco Bay Study (Otter trawl + midwater trawl) for Age-0, Age-1 and Age-2 longfin smelt occurrence with water temperature. (data 1980-2013)

Figure 5.  Smoothed presence-absence data of longfin smelt — Age 0, Age 1 and Age 2 –with water temperature, 1980 – 2013. Source: San Francisco Bay Study (otter and midwater trawls) 

 

 

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6 Responses to Delta smelt’s unsung cousin seems verging on extinction, too

  1. Hi James, Peter,

    To say that the drought is causing the likely extinction of Delta and longfin smelt is like a coroner attributing death to heart failure but neglecting to mention the 45 caliber hole through it.

    Both Delta and longfin smelt, once perhaps the most abundant species in the estuary, survived the great mega-droughts over the last millennia. They may not survive the State Water Board’s serial weakening of minimal flow standards enacted to protect them. You cannot draw critical habitat during critical life stages of smelt into the Central Delta and expose them to lethal summer temperatures, while exporting half the net primary production, and expect them to survive.

    You mention Cannon’s recent post on CSPA’s fisheries blog. You might take a look at Tom’s Summer of 2013 and Summer of 2014, submitted as part of CSPA’s comments to the State Board regarding the weakening of standards over the last three years. We chronicled the collapse of Delta smelt and, unfortunately, our predictions are now occurring.

    This may be the first instance in the history of the state and federal endangered species acts of species going extinct because the agencies charged with their protection stood mute as minimal requirements for their protection were waived.

    Excessive diversion of water to irrigate the desert has sentenced the estuary to a perpetual drought. As the smelt go, so go many of the other pelagic species. And frankly, a number of anadromous species may not be far behind. Cheers!

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  2. Tom Cannon says:

    Stock, or spawner abundance, would explain much of the color shifts in your Figure 4 analysis.

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  3. Pingback: Science news and reports: Striped bass: The Central Valley’s most popular predator; Delta smelt’s unsung cousin seems verging on extinction; The diversity of periodically flowing streams; Today in El Nino advice: Don’t worry about the Blob;

  4. Pingback: Science news and reports: Striped bass: The Central Valley’s most popular predator; Delta smelt’s cousin verging on extinction; The diversity of periodically flowing streams; Today in El Nino advice: Don’t worry about the Blob; and more R

  5. jarosenfield says:

    You asked for longfin smelt stock-recruit relationships, we delivered! See this newly published research article: Nobriga, M.L. & J.A. Rosenfield. 2016. Population Dynamics of an Estuarine Forage Fish: Disaggregating Forces Driving Long-Term Decline of Longfin Smelt in California’s San Francisco Estuary, Transactions of the American Fisheries Society, 145:44-58.

    Highlights:
    (1) The number of Age 0 longfin produced per spawner (Age 2 fish) is modified by freshwater flow into San Francisco Bay’s estuary and that relationship has not changed (even due to the clam invasion) for at least ~50 years.
    (2) The number of spawning-aged fish produced per juvenile longfin smelt (i.e., survival) has declined over the past several decades, but the decline appears to be slow and somewhat consistent (e.g., no clear signal of any step-decline). Modeling population dynamics that include the effect of a step-decline in the food web produce results that are not distinguishable statistically from models that do not include a step-decline in the food web .
    (3) The life stages experiencing the survival decline are those that occur when the fish are distributed in brackish or marine waters; the unchanged, statistically significant, log-log relationship between juvenile longfin smelt abundance and freshwater flow through the Delta appears to affect the life stages that occur in the freshwater or low salinity zones of the estuary.
    (4) temperature was not a significant covariate of either spawner-recruit or recruit-spawner relationships.

    Finally, I agree with Jennings. Saying that longfin smelt were negatively affected by “drought” ignores the fact that on top of the natural water shortage, >>50% of the water available during this recent dry period did not reach the smelt’s home. And even the meager protections for the San Francisco Estuary (including Clean Water Act flow standards and endangered species act protections) were weakened or waived in two consecutive years. If you eliminate environmental safeguards, it should be no surprise that the environment suffers — but you can’t blame that on mother nature or the smelt.

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  6. jameedade says:

    Valuable ideas – I was fascinated by the info – Does anyone know if I can access a template DA 67-9-1 form to complete ?

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