Species of Interest

Longfin Smelt (Spirinchus thaleichthys):

Longfin smelt are a small species of semi-anadromous pelagic fish native to the San Francisco Estuary (SFE) and the lower portions of its many tributaries. Longfin smelt are currently believed to live for 2-3 years and grow to a total length of 124-150 mm, however their age and growth is still being actively studied. As indicated in their name, longfin smelt can be distinguished from other local smelt species by their elongated pectoral fins, which almost reach to the base of their pelvic fins. Their diet consists of small crustaceans, particularly mysids, and they are frequently preyed upon by a variety of birds, larger fishes, and marine mammals making them a crucial forage fish for the local ecosystems.

An adult, juvenile, and larval longfin smelt caught during our annual broodstock trawls. Adults typically inhabit deeper, more saline waters while juveniles and larva are confined to fresher, shallower habitats.

Mysid shrimp caught during an otter trawl. Mysids are the preferred food source for longfin smelt given their small size and high relative abundance.


Longfin smelt, like most bony fish, are broadcast spawners with females laying external eggs which are subsequently fertilized by mature males. Peak spawning occurs between February and April when mature individuals will move into shallower, less saline waters to lay their eggs on finer sediments. Although they are capable of tolerating a wide range of salinities, recruitment rates have been found to increase along with high freshwater inputs, which typically correlate to wetter years. Currently, the OGFL is exploring the reproductive potential of longfin smelt, also known as fecundity, to help estimate population growth rates. Longfin smelt are sexually dimorphic, with males possessing a prominent anal fin and turning a slightly darker color as they mature.


A side-by-side comparison of male and female longfin smelt. Note the enlarged anal fin on the male as well as the darker dorsal region and caudal fin. Longfin smelt can be distinguished from other local smelt species by their elongated pectoral fins, which almost reach to the base of their pelvic fins.


Artistic rendering of the longfin smelt life cycle. Adults enter the marine habitat and estuarine habitat, and return to lower saline waters during the spawning season.


Longfin smelt are currently recognized as a threatened species under the California Endangered Species Act (ESA), and efforts are currently being made to have them listed as a federally protected species. The largest current threats to their survival include entrainment, a decrease in freshwater inflows, pollutants, invasive species, and a decline in overall genetic diversity. Currently, longfin smelt are being cultured at the UC Davis Fish Conservation and Culture Laboratory (FCCL) in an attempt to help support and restore wild populations.

CDFW profile on longfin smelt:  https://wildlife.ca.gov/Conservation/Fishes/Longfin-Smelt



OGFL Publications:


Captive Rearing of Longfin Smelt Spirinchus Thaleichthys: First Attempt of Weaning Cultured Juveniles to Dry Feed

Growth, Osmoregulation, and Ionoregulation of Longfin Smelt (Spirinchus thaleichthys) Yolk-Sac Larvae at Different Salinities

Spatial Heterogeneity in Prey Availability, Feeding Success, and Dietary Selectivity for the Threatened Longfin Smelt


Genome-Wide Analysis Reveals Regional Patterns of Drift, Structure, and Gene Flow in Longfin Smelt (Spirinchus thaleichthys) in the Northeastern Pacific

Effects of Temperature on Hatching and Growth Performance of Embryos and Yolk-Sac Larvae of a Threatened Estuarine Fish: Longfin Smelt (Spirinchus thaleichthys)


Newly Discovered Spawning and Recruitment of Threatened Longfin Smelt in Restored and Under-Explored Tidal Wetlands

Silicon Valley’s Threatened Longfin Smelt: Evidence of Spawning and Recruitment in a Restored Tidal Wetland


Is Extinction Inevitable for Delta Smelt and Longfin Smelt? An Opinion and Recommendations for Recovery


The Use of Otolith Strontium Isotopes to Identify Critical Nursery Habitat for a Threatened Estuarine Fish


Assessing Nursery Habitat Quality for Native Smelts (Osmeridae) in the Low-Salinity Zone of the San Francisco Estuary



Delta Smelt (Hypomesus transpacificus):

Delta smelt are a small species of migratory forage fish endemic to the San Francisco Estuary. Both longfin and delta smelt belong to the family Osmeridae, and therefore share many of the same physical, ecological, and behavioral characteristics. Delta smelt are annual fish typically living for only a year, and ranging in size from 60 mm to 120 mm. They are zooplanktivorous and feed on a variety of smaller crustaceans that inhabit the turbid, cooler waters within the estuary. Like longfin smelt, they are an important forage fish in the estuary, acting as a food source for a variety of birds, marine mammals, and larger fish.

Image of  delta smelt caught by the OGFL, and an artistic rendering of a delta smelt .Note the pectoral fins, which are significantly smaller than that of the longfin smelt. Delta smelt are nearing extinction in the wild, with sightings becoming increasingly uncommon.

Delta smelt are euryhaline, and readily transition between salinities throughout their life cycle. After hatching in the spring, developing delta smelt will migrate from fresher waters into the lower salinity zones within the estuary. Here they will continue to mature through the fall until they migrate upstream in winter to prepare for the annual spawning event in the spring. Like longfin smelt, delta smelt have also been observed to experience elevated recruitment rates during years with higher amounts of precipitation.


A graphic depicting the life cycle of delta smelt. They prefer to spawn in fresher waters, including estuarine and riverine habitats where they will remain through the duration of their adult lives.


Delta smelt are currently listed on both the California and federal Endangered Species Act (ESA). They are recognized as an important indicator species, meaning that their health closely reflects that of their native waterways. They face many of the same threats as longfin smelt including entrainment, toxic substances, competition and predation from invasive species, a decrease in freshwater inputs, and a loss in genetic diversity as a result of their dwindling populations. Delta smelt are now nearing complete extinction, with wild populations currently representing less than 1% of their historic abundance. Delta smelt are also being cultured at the UC Davis FCCL to help bring wild populations back to a sustainable level.

CDFW profile on delta smelt:  https://wildlife.ca.gov/Conservation/Fishes/Delta-Smelt



OGFL Publications:


Visual, Spectral, and Microchemical Quantification of Crystalline Anomalies in Otoliths of Wild and Cultured Delta Smelt

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits With Native Delta Smelt 

Polygenic Discrimination of Migratory Phenotypes in an Estuarine Forage Fish 


Experimental Validation of Otolith-Based Age and Growth Reconstruction Across Multiple Life Stages of a Critically Endangered Estuarine Fish 

Patterns and Predictions of Condition Indices in a Critically Endangered Fish 

Otolith-Based Approaches Indicate Strong Effects of Environmental Variations on Growth of a Critically Endangered Estuarine Fish 


Complex Life Histories Discovered in a Critically Endangered Fish 

Calibrating Temperature Reconstructions from Fish otolith Oxygen Isotope Analysis for California’s Critically Endangered Delta Smelt 


Role of Freshwater Floodplain-Tidal Slough Complex in the Persistence of the Endangered Delta Smelt 

Delta Smelt and Water Politics in California 

Use of Single Nucleotide Polymorphisms Identifies Backcrossing and Species Misidentification Among Three San Francisco Estuary Osmerids 


Is Extinction Inevitable for Delta Smelt and Longfin Smelt? An Opinion and Recommendations for Recovery 


Delta smelt: Life History and Decline of a Once-Abundant Species in the San Francisco Estuary 


Contaminant and Food Limitation Stress in an Endangered Estuarine Fish 


Tagging the Next Generation: Validation of Trans-Generational Chemical Tagging for an Endangered Fish 

Pre-Screen Loss and Fish Facility Efficiency for Delta Smelt at the South Delta’s State Water Project, California 


Classification of Larval and Adult Delta Smelt to Nursery Areas by Use of Trace Elemental Fingerprinting 

Modification of the Biological Intercept Model to Account for Ontogenetic Effects in Laboratory Reared Delta Smelt (Hypomesus transpacificus


Assessing Nursery Habitat Quality for Native Smelts (Osmeridae) in the Low-Salinity Zone of the San Francisco Estuary 


Retrospective Determination of Natal Habitats for an Estuarine Fish with Otolith Strontium Isotope Ratios 




White Sturgeon (Acipenser transmontanus):

White sturgeon are a species of demersal fish native to the west coast, and are the largest freshwater fish in North America. Historic records indicate that some individuals have been observed to reach sizes of over 6 meters, and live to be well over one hundred years old. They typically inhabit rivers and estuaries along the west coast, but adults have been known to travel into shallow coastal waters. Juveniles consume a wide variety of benthic invertebrates, while adult diets primarily consist of larger fish.

An artistic rendering of a white sturgeon. Like sharks, sturgeon have what is known as a heterocercal tail, with their vertebrae extending up into the upper lobe of their caudal fin, making it larger than the lower lobe.

Unlike most of the fish studied in the OGFL, sturgeon possess a mostly cartilaginous skeleton. This makes it difficult to use otoliths to reconstruct life history profiles, as their otoliths are poorly ossified. Instead, we used their calcified fin rays which can provide important information on their age and migration patterns throughout the system.

A processed sturgeon fin ray. Fin rays are occasionally used in place of otoliths for fish with less ossified bones.


In the winter, mature adults migrate from deltas and estuaries upstream to fresher waters where spawning occurs from February to May. White sturgeon mature late in life, at around 10-16 years old, and spawning events occur once every 2 years for males and once every 2-4 years for females. During these spawning events female sturgeon lay upwards of 5,000 eggs per kilogram of body weight, with an average adult producing upwards of 200,000 eggs in a single season. 


A white sturgeon caught during the OGFL’s month trawl survey. The bone plates along its body are known as scutes, and are sharp ossified tissues used for defense.


While white sturgeon are currently not listed as endangered, they are categorized as a species of concern by the state of California. This is due to their low reproductive potential, as well as the numerous threats they face including habitat degradation, pollutants, entrainment of early life stages, vessel strikes, and poaching. Currently a carefully managed recreational fishery exists for white sturgeon, which allows for the capture and harvest of fish.

CDFW profile on white sturgeon:  https://wildlife.ca.gov/Conservation/Fishes/Sturgeon/White-Sturgeon



OGFL Publications:


Diversity in Habitat Use by White Sturgeon Revealed Using Fin Ray Geochemistry 


Ontogenetic Patterns in the Calcification and Element Incorporation in Fin Rays of Age-0 White Sturgeon 


Validating Fin Ray Microchemistry as a Tool to Reconstruct the Migratory History of White Sturgeon 




Chinook Salmon(Onchorynchus tshawytscha):

Chinook salmon are anadromous salmonids, and are economically critical to the regions they inhabit, with commercial and recreational salmon fisheries generating an estimated $900 million annually. They are the largest of the Pacific salmon, reaching sizes of almost 5 feet and over 100 pounds, and have earned the nickname “king salmon” as a result of their large size. Juveniles feed on a variety of aquatic and terrestrial invertebrates, while adults are primarily piscivorous. They are preyed upon by a variety of larger fish as well as birds and both terrestrial and aquatic mammals.


Chinook salmon are an economically important fish to the state of California, bringing in an estimated $900 million annually through recreational and commercial fisheries.


Chinook salmon reach maturity between 2-7 years old and lay their eggs in shallow gravel nests known as redds. Like all Pacific salmon, chinook are semelparous, meaning that they die shortly after spawning due to its high energetic cost. These regular die-off events are instrumental to the success of many ecosystems, as the input of available nutrients and energy benefits many other species. Chinook salmon exhibit a variety of life histories that make them resilient to the dynamic ecosystems they inhabit. They are categorized into distinct populations by the season in which they migrate upstream to spawn: spring, winter, fall, and late fall.


A deceased male chinook salmon. Males can be identified by their more pronounced hook-jaw, also known as a kype. Males also tend to develop a significant hump just before their dorsal fin.


Fall-run chinook migrate upstream between July and February, and typically spawn between October and December. They are currently the most abundant, and support the largest commercial and recreational fishery. Fall and late-fall-run chinook overlap in their run time as late-fall chinook run from mid-October to December, however they spawn from January until mid-April.

Spring-run chinook make their run in late March, and finish in September. Spawning occurs from mid-August through early October. They were once the most abundant run in the area, however in recent years they have undergone significant hybridization with fall-run chinook causing their populations to dwindle.

Winter-run chinook start to migrate in December and typically finish by August. They spawn from mid-April through August. Winter-run chinook are disproportionately affected by the construction of dams, as they historically spawned further upstream than the other populations. This habitat loss has caused their populations to decline dramatically in recent decades.


Artistic renderings of chinook salmon. Given their highly diverse life histories, individuals within this species can often look very different from one another. 


Fall and late-fall-runs are considered to be species of concern, while spring and winter-run chinooks are classified as endangered. They experience many of the same threats, though the degree to which the population is impacted is highly dependent on their individual life histories. These threats include water diversions, fish harvest, habitat loss, and dam construction which impedes their spawning runs.

CDFW profile on chinook salmon:  https://wildlife.ca.gov/Conservation/Fishes/Chinook-Salmon

NOAA profile on chinook salmon:  https://www.fisheries.noaa.gov/species/chinook-salmon



OGFL Publications:


Geochemical Tools Identify the Origins of Chinook Salmon Returning to a Restored Creek


Fishery Collapse, Recovery, and the Cryptic Decline of Wild Salmon on a Major California River

San Francisco Estuary:

The San Francisco Estuary (SFE) is the largest estuary in California, and is a crucial component of the local ecosystems and surrounding communities. It provides water to approximately 25 million people, and supports a wide array of aquatic species including numerous birds, mammals, and fishes. Due to the persistent drought experienced in the central valley, a large portion of water is diverted from the estuary and its connected tributaries to meet agricultural demands. This region experiences roughly half of the state’s total precipitation in the form of snow or rain, making it an important resource growing water intensive crops including almonds, avocados, rice, olives, and many others. While these diversions are important for the agricultural industry, they also reduce the volume of freshwater entering the estuary and can directly harm local species by trapping them in the water diversion systems.

Significant portions of the system are surrounded by mountains, resulting in copious amounts of run-off entering the estuary. This combined with the large amount of fertilizers present from surrounding farmlands results in a phenomenon known as eutrophication. Excess nutrients such as phosphorus and nitrogen cause phytoplankton populations to increase exponentially. When the nutrients have been exhausted, the phytoplankton die off and their remains are rapidly decomposed. The decomposition process requires an input of oxygen in order to function, causing dissolved oxygen levels to drop drastically. This results in hypoxic water conditions, which can seriously impact the health of the residential species.


The estuary is divided into 5 major sections: North Bay, Central Bay, South Bay, Suisun Bay, and the Delta. When conducting field work, the OGFL typically samples from Alviso marsh located in the southernmost portion of south bay. Here we perform otter trawls for both our monthly biodiversity surveys, and our longfin smelt broodstock collections. Notice how large portions of the bay are surrounded by mountains.


Many of the rivers in the estuary system have been altered dramatically by the construction of dams. These structures prevent many native diadromous species from making their runs up or downstream, negatively affecting the spawning process. This includes species such as salmon, trout, sturgeon, and many others. Dam removal efforts have started to gain traction in recent years, in order to help maintain the health of migratory species as well as the ecosystems they inhabit.

The San Francisco Estuary has an unusually high density of invasive species, and is known to be one of the most invaded bodies of water in the world. It hosts approximately 85 invasive species, with more than half being classified as harmful to the local ecosystems. Some prominent species include striped bass, Asian clams, Chinese mitten crabs, and various Japanese gobies. Some of these species, such as striped bass, are intentionally introduced to bolster a recreational fishery, while others may enter unintentionally through sources such as ship ballast water, or the aquarium trade.

San Francisco Estuary Partnership Profile:  https://www.sfestuary.org/our-estuary/about-the-estuary/