Delta smelt

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Delta smelt
Hypomesus transpacificus.jpg
Scientific classification Red Pencil Icon.png
Kingdom: Animalia
Phylum: Chordata
Class: Actinopterygii
Order: Osmeriformes
Family: Osmeridae
Genus: Hypomesus
H. transpacificus
Binomial name
Hypomesus transpacificus
McAllister, 1963

The delta smelt (Hypomesus transpacificus) is an endangered [1] [2] slender-bodied smelt, about 5 to 7 cm (2.0 to 2.8 in) long, in the family Osmeridae. Endemic to the upper Sacramento-San Joaquin Estuary of California, it mainly inhabits the freshwater-saltwater mixing zone of the estuary, except during its spawning season, when it migrates upstream to fresh water following winter "first flush" flow events (around March to May). [3] It functions as an indicator species for the overall health of the Delta's ecosystem. [4]


Because of its one-year lifecycle and relatively low fecundity, it is very susceptible to changes in the environmental conditions of its native habitat. [5] Efforts to protect the endangered fish from further decline have focused on limiting or modifying the large-scale pumping activities of state and federal water projects at the southern end of the estuary, thereby limiting water available to farming. However, these efforts have not prevented the species from becoming functionally extinct in the wild. [6]

Taxonomy and evolution

H. olidus

H. nipponensis

H. japonicus

H. pretiosus

H. transpacificus

Phylogeny of the genus Hypomesus. [7]

The delta smelt is one of five currently recognized species within the genus Hypomesus , which is part of the larger smelt family, Osmeridae. The genus has been subject to many revisions since it was first classified by Gill in 1863. [8] The first major revision occurred in 1963, when the family Osmeridae was re-examined by Canadian ichthyologist Donald Evan McAllister. Expanding on Japanese researcher Hamada's earlier determination that H. olidus was not a monolithic widespread species, but rather one of three distinct species of Hypomesus, McAllister assigned them new names, and further delineated what he believed were four subspecies. This was the first description of H. transpacificus, named for its supposed occurrence on both sides of the Pacific, and also "to the friendship of Japanese and Canadian ichthyologists." He separated these geographically isolated populations into separate subspecies: H. t. transpacificus and H. t. nipponensis. [8]

Modern analysis of the genus would elevate all of McAllister's subspecies to full species status, based on fin ray counts and the number of chromatophores between their mandibles, a change which genetic analysis has supported. [7] [9] In fact, genetic analysis would conclude that despite their morphological similarities, H. nipponensis and H. transpacificus are actually members of different phylogenetic clades. [10]

The abbreviated distribution of Hypomesus species along both the east and west sides of the Pacific Ocean suggests that their common ancestor had a range that would have crossed the Pacific. Researchers have hypothesized that climatic changes may have reduced the range of the ancestral species during cooling periods, which would have created a reproductive barrier, allowing speciation to occur. [7] Although the low number of species in the genus and high levels of homoplasy have frustrated attempts to determine whether the northern Pacific H. olidus or H. nipponensis are the basal species of Hypomesus, [7] the most recent speciation event in Hypomesus is known to have been between the two native east Pacific species, H. pretiosus and H. transpacificus. This is plausibly due to a geographic isolation of a widespread eastern Pacific ancestor, of which some members were isolated in a freshwater basin in western California, possibly in the lakes that would have been located in the southern San Joaquin Valley during the Pleistocene epoch. [7]


The delta smelt is endemic to the Sacramento–San Joaquin River Delta in California, where it is distributed from the Suisun Bay upstream through the delta in Contra Costa, Sacramento, San Joaquin, and Solano Counties. The delta smelt is a pelagic (lives in the open water column away from the bottom) and euryhaline species (tolerant of a wide salinity range). It has been collected from estuarine waters with salinities up to 14 parts per thousand.

Historically, delta smelt were distributed from San Pablo Bay upstream to Sacramento on the Sacramento River and Mossdale on the San Joaquin River, which varied seasonally and with freshwater outflow. [11] Today, large areas of historic delta smelt habitat and designated critical habitat have become unsuitable for some life history stages of the species, though key environmental characteristics (e.g. temperature, salinity, water depth) of these areas have not changed. [12] [13] Delta smelt disappeared from the southern portion of their historic habitat in the late 1970s, which coincides with substantial increases in the amounts of water exported from the delta. Water export operations likely have a great effect on the distribution, abundance, and genetic diversity of delta smelt. [14]


The delta smelt is semelparous, living one year and dying after its first spawning. Their spawning occurs in spring in river channels and tidally influenced backwater sloughs upstream of the mixing zone where salt water meets fresh water. The Sacramento and San Joaquin Rivers then transport the delta smelt larvae downstream to the mixing zone, normally located in the Suisun Bay. Young delta smelt then feed and grow in the mixing zone before starting their upstream spawning migration in late fall or early winter.

The delta smelt is preyed upon by larger fish, especially striped bass and largemouth bass, which are introduced species in the Sacramento-San Joaquin Delta. [15]

Endangered status

Historically, delta smelt were relatively abundant in the upper Sacramento-San Joaquin Estuary, with populations declining dramatically in the 1980s. [16] They were listed as threatened by both federal and state governments in 1993, and sustained record-low abundance indices, prompted their listing as endangered under the California Endangered Species Act in 2010. [17] [18] Critical habitat was listed for delta smelt on December 19, 1994. [19]

Delta smelt are threatened with extinction due to anthropogenic alterations to their ecosystem, including urbanization, non-native species, water diversions, contaminants, and the conversion of complex tidal habitats to leveed channels. [20] A survey in April 2015 found only one individual delta smelt. Although the fish is almost extinct in the wild, extant populations remain in a captive-breeding program at UC Davis and in a fish hatchery operated by the U.S. Fish and Wildlife Service near Shasta Dam. [6]

Court protection

In 2005, the U.S. Fish and Wildlife Service (FWS) issued a biological opinion that the Central Valley Project and the California State Water Project were not having an adverse effect on the recovery of the delta smelt. [21] The Natural Resources Defense Council sued, and in 2007, Fresno U.S. District Court Judge Oliver Wanger found the biological opinion was arbitrary and capricious and ordered protections for the delta smelt while the document was redone. [22]

In 2008, at the close of the court's deadline, the FWS issued a new biological opinion. [23] This time, the FWS came to the opposite of its earlier conclusion, finding the water projects were jeopardizing the continued existence of the delta smelt. [24] When six new plaintiffs sued, Judge Wanger preliminarily ordered the FWS to give him weekly justifications of delta flow restrictions and appointed four scientists as his own expert witnesses. [25] After haranguing FWS expert witnesses as “zealots”, [26] in December 2010 Judge Wanger, again, found the FWS BioOp was arbitrary and capricious and, again, ordered the FWS to complete a new one. [27]

In 2014, a divided panel of the Ninth Circuit Court of Appeals reversed Judge Wanger. [28] While the new biological opinion was “a ponderous, chaotic document, overwhelming in size”, it was found not arbitrary and capricious. [29] The Ninth Circuit affirmed that the water projects were jeopardizing the existence of the delta smelt, and given TVA v. Hill's command that endangered species must be saved "whatever the cost", Circuit Judge Jay Bybee opined that California could only use the smelts' water after receiving an exemption from the God Squad. [30] In January 2015 the U.S. Supreme Court declined review without comment. [31]

The smelt is unpopular among farmers, with a common complaint being that 200,000 acres of farmland have been left fallow due to "four buckets of minnows". [32] Although allegations have been made that this protection has hurt California's agricultural sector, with the devastation of hundreds of thousands of acres of farmland and the loss of tens of thousands of jobs in the Central Valley, [33] a 2009 UC Davis study estimated that job losses due to smelt protection were closer to 5,000. [34] An additional 16,000 job losses in the Central Valley were attributed to the drought California had been experiencing in recent years.[ citation needed ]

See also

Related Research Articles

Smelt (fish) Family of fishes

Smelts are a family of small fish, the Osmeridae, found in the North Atlantic and North Pacific Oceans, as well as rivers, streams and lakes in Europe, North America and Northeast Asia. They are also known as freshwater smelts or typical smelts to distinguish them from the related Argentinidae, Bathylagidae, and Retropinnidae.

San Joaquin River Longest river of Central California, United States

The San Joaquin River is the longest river of Central California in the United States. The 366-mile (589 km) long river starts in the high Sierra Nevada, and flows through the rich agricultural region of the northern San Joaquin Valley before reaching Suisun Bay, San Francisco Bay, and the Pacific Ocean. An important source of irrigation water as well as a wildlife corridor, the San Joaquin is among the most heavily dammed and diverted of California's rivers.

Sacramento–San Joaquin River Delta Inland river delta and estuary in Northern California

The Sacramento–San Joaquin River Delta, or California Delta, is an expansive inland river delta and estuary in Northern California. The Delta is formed at the western edge of the Central Valley by the confluence of the Sacramento and San Joaquin rivers and lies just east of where the rivers enter Suisun Bay. The Delta is recognized for protection by the California Bays and Estuaries Policy. Sacramento–San Joaquin Delta was designated a National Heritage Area on March 12, 2019. The city of Stockton is located on the San Joaquin River on the eastern edge of the delta. The total area of the Delta, including both land and water, is about 1,100 square miles (2,800 km2). Its population is around 500,000 residents.

California Central Valley grasslands

The California Central Valley grasslands is a temperate grasslands, savannas, and shrublands ecoregion in California's Central Valley. It a diverse ecoregion containing areas of desert grassland, prairie, savanna, riparian forest, marsh, several types of seasonal vernal pools, and large lakes such as now-dry Tulare Lake, Buena Vista Lake, and Kern Lake.

Yolo Bypass

The Yolo Bypass is one of the two flood bypasses in California's Sacramento Valley located in Yolo and Solano Counties. Through a system of weirs, the bypass diverts floodwaters from the Sacramento River away from the state's capital city of Sacramento and other nearby riverside communities.

Delta–Mendota Canal

The Delta–Mendota Canal is a 117-mile-long (188 km) aqueduct in central California, United States. The canal was designed and completed in 1951 by the U.S. Bureau of Reclamation as part of the Central Valley Project to supply freshwater to users downstream of the San Joaquin River. Freshwater is diverted into the Madera Canal and Friant-Kern Canal at Friant Dam.

Suisun Marsh Largest brackish water marsh on west coast of US

Located in northern California the Suisun Marsh has been referred to as the largest brackish water marsh on west coast of the United States of America. The marsh land is part of the San Francisco Bay tidal estuary, and subject to tidal ebb and flood. The marsh is home to many species of birds and other wildlife, and is formed by the confluence of the Sacramento and San Joaquin rivers between Martinez and Suisun City, California and several other smaller, local watersheds. Adjacent to Suisun Bay, the marsh is immediately west of the legally defined Sacramento-San Joaquin Delta as well as part of the San Francisco Bay estuary.

<i>Hypomesus</i> Genus of fishes

Hypomesus is a genus of smelts (Osmeridae), consisting of five species found in the northern hemisphere.

Longfin smelt Species of fish

The longfin smelt is a smelt that is found in several estuaries and lakes along the northern Pacific coast of North America.

Big River (California) River in Mendocino County, California (USA), south of Mendocino Village

The Big River is a 41.7-mile-long (67.1 km) river in Mendocino County, California, that flows from the northern California Coast Range to the Pacific Ocean at Mendocino, Mendocino County, California. From the mouth, brackish waters extend 8 miles (13 km) upstream, forming the longest undeveloped estuary in the state.

Sonoma Creek Stream in California

Sonoma Creek is a 33.4-mile-long (53.8 km) stream in northern California. It is one of two principal drainages of southern Sonoma County, California, with headwaters rising in the rugged hills of Sugarloaf Ridge State Park and discharging to San Pablo Bay, the northern arm of San Francisco Bay. The watershed drained by Sonoma Creek is roughly equivalent to the wine region of Sonoma Valley, an area of about 170 square miles (440 km2). The State of California has designated the Sonoma Creek watershed as a “Critical Coastal Water Resource”. To the east of this generally rectangular watershed is the Napa River watershed, and to the west are the Petaluma River and Tolay Creek watersheds.

Green sturgeon Species of fish

The green sturgeon is a species of sturgeon native to the northern Pacific Ocean, from China and Russia to Canada and the United States.

The Peripheral Canal was a series of proposals starting in the 1940s to divert water from California's Sacramento River, around the periphery of the San Joaquin-Sacramento River Delta, to uses farther south. The canal would have attempted to resolve a problem with the quality of water pumped south. Pumps create such a powerful suction that the boundary between freshwater to saltwater has shifted inland, negatively affecting the environment. The pumps have increased by 5 to 7 million acre feet the amount of water exported each year to the Central Valley and Southern California. However, the peripheral canal as proposed would have reduced the overall freshwater flow into the Delta and move the freshwater-saltwater interface further inland, causing damage to Delta agriculture and ecosystems.

Ecology of the San Francisco Estuary

The San Francisco Estuary together with the Sacramento–San Joaquin River Delta represents a highly altered ecosystem. The region has been heavily re-engineered to accommodate the needs of water delivery, shipping, agriculture, and most recently, suburban development. These needs have wrought direct changes in the movement of water and the nature of the landscape, and indirect changes from the introduction of non-native species. New species have altered the architecture of the food web as surely as levees have altered the landscape of islands and channels that form the complex system known as the Delta.

Oliver Winston Wanger is a former United States District Judge of the United States District Court for the Eastern District of California.

Stone Lakes National Wildlife Refuge Wildlife refuge near Sacramento, California

The Stone Lakes National Wildlife Refuge, located south of Sacramento, California, lies within the Sacramento-San Joaquin delta, the destination of thousands of migrating waterfowl, shorebirds, and other water birds. The refuge was established in 1994.

<i>Hypomesus nipponensis</i> Species of fish

Hypomesus nipponensis is an important food fish native to the lakes and estuaries of Hokkaido, Japan. It has been introduced in other locations, including the San Francisco Delta of the United States. It is raised in fisheries, and is very similar in appearance to the delta smelt.

Marsh Creek (California)

Marsh Creek is a stream in east Contra Costa County, California in Northern California which rises on the eastern side of Mount Diablo and flows 30 miles (48 km) to the Sacramento–San Joaquin River Delta at Oakley, California, near Big Break Regional Shoreline. The creek flows through Marsh Creek State Park (California), where water is impounded to form Marsh Creek Reservoir, then through the city of Brentwood, California.

Sites Reservoir Proposed reservoir in Sacramento Valley, California

Sites Reservoir is a proposed $5.2-billion offstream reservoir project west of Colusa in the Sacramento Valley of northern California, to be built by the California Department of Water Resources. The project would pump 470,000 to 640,000 acre feet per year of the winter flood flow from the Sacramento River upstream of the Sacramento–San Joaquin River Delta, through existing canals to an artificial lake 14 miles (23 km) away. Annual yield will depend on precipitation and environmental restrictions.

California Water Fix and Eco Restore, formerly known as the Bay Delta Conservation Plan, is a $15 billion plan proposed by Governor Jerry Brown and the California Department of Water Resources to build two large, four-story tall tunnels to carry fresh water from the Sacramento River under the Sacramento-San Joaquin Delta toward the intake stations for the State Water Project and the Central Valley Project.


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  8. 1 2 McAllister DE (1963). "A revision of the smelt family, Osmeridae". National Museum of Canada Bulletin. Department of National Affairs and National Resources. 191: 29–31.
  9. Sweetnam DA (1995). "Field identification of delta smelt and wakasagi". Interagency Ecological Program for the Sacramento-San Joaquin Estuary Newsletter (Spring): 1–3.
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  11. Radtke, LD (1966) Distribution of smelt, juvenile sturgeon and starry flounder in the Sacramento-San Joaquin Delta. In: Fish bulletin. California Department of Fish and Game, Sacramento, pp 115–129
  12. CDFG (2003) Comment letter on the five-year status review of the delta smelt. California Department of Fish and Game, California, p 6
  13. Miller J, Swanson C, Poole KS (2006) Emergency petition to list the delta smelt (Hypomesus transpacificus) as an endangered species under the Endangered Species Act. Center for Biological Diversity, Bay Institute, & Natural Resources Defense Council.
  14. Bennett, WA (2005) Critical assessment of the delta smelt population in the San Francisco Estuary, California. San Francisco Estuary Watershed Sci 3:1–71.
  15. Raymond Bark; Brent Bridges; Dr. Mark D. Bowen (2008). "2008 Tracy Research Study: Plan Predator Impacts on Salvage Rates of Juvenile Chinook salmon and Delta Smelt". Archived from the original on June 29, 2010. Retrieved 2009-06-26.
  16. Newman KB (2008) Sample design-based methodology for estimating delta smelt abundance. San Francisco Estuary Watershed Sci 6:1–18.
  17. CDFG (2010) State & federally listed endangered & threatened animals of California. California Department of Fish & Game,State of California, The Natural Resources Agency, California.
  18. Federal Register 58:12863; March 5, 1993
  19. Federal Register 59:65256
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  21. "Federal Judge Throws Out Biological Opinion for Threatened Delta Smelt". 2007-05-25.
  22. Natural Resources Defense Council v. Kempthorne, 506 F. Supp. 2d 322 (E.D. Cal. 2007).
  24. Jenkins, Matt (10 December 2010). "California's Tangled Water Politics". High Country News . 42 (22). Retrieved 22 May 2015.
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  27. San Luis & Delta-Mendota Water Auth. v. Salazar, 760 F. Supp. 2d 855, 863 (E.D. Cal. 2010).
  28. citing San Luis & Delta-Mendota Water Authority v. Jewell, 747 F.3d 581 (9th Cir. 2014).
  29. Id., see oral argument video at .
  30. San Luis & Delta-Mendota Water Authority v. Jewell, 747 F.3d 581 (9th Cir. 2014) citing Eric M. Yuknis, Note, Would a “God Squad” Exemption under the Endangered Species Act Solve the California Water Crisis?, 38 B.C. Envtl. Aff. L. Rev. 567 (2011).
  31. "State Water Contractors v. Jewell".
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  34. Howitt, R., Josue Medellin-Azuara, Duncan MacEwan. "Measuring the Employment Impact of Water Reductions" Department of Agriculture and Resource Economics and Center for Watershed Sciences, UC Davis, September 2009