Species

The OGFL studies a variety of imperiled fish species in the San Francisco Estuary (SFE) & across the Globe.

SFE: Longfin Smelt, Delta Smelt, White Sturgeon, Chinook Salmon

Global: Tarek, Tapertail Anchovy, Lake Whitefish, Gulf Sturgeon

Longfin Smelt:

Longfin Smelt (Spirinchus thaleichthys) is a semi-anadromous forage fish native to the San Francisco Estuary (SFE) and estuaries across the northeastern Pacific Ocean. The species lives for up to 3 years and reaches a maximul length of approximately 150 mm. As indicated in the name, Longfin can be distinguished from other local smelt species by their elongated pectoral fins which nearly reach the base of the pelvic fins. The Longfin diet consists of small crustaceans, particularly copepods and mysid shrimp, and they are frequently preyed upon by a variety of birds, larger fishes, and marine mammals, making them a key component of estuarine and coastal food webs.

*Larval Longfin showing otoliths (lapillus and sagitta).*

The San Francisco Estuary (SFE) Longfin Smelt population is the southernmost genetically distinct source population for coastal habitats across California. Although once one of the most abundant species in the SFE, the population is now at < 1% of it’s historic (1980s) abundance levels. The species is currently listed as threatened under the California Endangered Species Act (CESA) and endangered under the federal ESA (as of 2024). Major threats to SFE Longin Smelt include entrainment at water export facilities, reduced freshwater outflow, pollution, and non-native species. Although conservatoin efforts are increasing, key questions remain about Longin’s basic biology including ontogentic patterns in maturation, fecundity, growth rates, adult and juvenile distributions, and magiratory behaviors. The OGFL has partnered with the CDFW to apply otolith-based age, growth, and geochemistry tools to quantify these patterns and help inform management and conservation of the SFE Longfin Smelt population.

*Transverse cross sections of juvenile and adult Longfin showing daily and annual rings, respectively.*

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 is most successful in years of high precipitatoin and freshwater outflow. Currently, the OGFL is exploring the reproductive potential of longfin smelt, also known as fecundity, to help estimate population growth rates.

The OGFL has collaborated with other researchers at UC Davis to develop the UCD Longfin Smelt Conservation Culture Program (LFSCCP), where the OGFL collects and supplies wild mature broodstock to the Fish Conservation and Culture Laboratory (FCCL), Bodega Marine Laboratory, or Putah Creek Facility, where they are spawned and offspring reared as part of a state-funded conservation program. CDFW profile on longfin smelt.

*Adult Longfin Smelt exhibit sexual dimorphism, with an enlarged anal fin and darker pigmentation in reproductively mature males.*

*Post-larval Longfin Smelt showing the distinctive triangular air bladder.*

Conceptual model of the Longfin life cycle. Postlarve and juveniles leave fresh and low-salinity estuarine habitats to enter coastal marein habitats where they rear until returning to tidal freshwater habitats to spawn at age2.

OGFL Longfin Smelt Publications:

Delta Smelt:

Delta Smelt (Hypomesus transpacificus) is a pelagic migratory forage fish endemic to the San Francisco Estuary, CA. Like Longfin Smelt, Delta Smelt belong to the family Osmeridae, thus the two species share several physical, ecological, and behavioral characteristics. Unlike Longfin, Delta Smelt exhibit andannual life cycle, reach maximum sizes of aproximately 100 mm, and remain in low-salinity habitats of the Upper San Francisco Estuary. They forage primarily on small crustaceans (e.g., copepods) and larval fishes. 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 a Delta Smelt caught by CDFW. Note the pectoral fins, which are significantly smaller than that of the longfin smelt.*

Delta Smelt is listed as critically endangered by the IUCN Red List, endangered by the California Endangered Species Act (CESA), and threatened by the federal Endangered Species Act (ESA). It serves as as an important indicator species, meaning that populatoin dynamics likely reflect the ecological integrity of the Upper San Francisco Estuary. The species faces numerous threats including entrainment and habitat modification due to water exports, pollution, trophic disruption due to water managment and invasive clams, and competition and predation from non-native fishes. Delta Smelt are at the brink of extinction, with most fish in the wild having been cultured at the UC Davis FCCL; whereas wild-spawned individauls are now rarely observed. CDFW profile on delta smelt.

*Whole otoliths of Delta Smelt from 30 days (larva) to 271 days (subadult) post hatch.*

Delta Smelt exhibit a complex migratory life history, moving ontogenetically between tidal freshwater and brackishwater habitat. After hatching in the spring, many developing larvae will disperse 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. However, this migratory (MIG) life history is not exhibited by all individuals, with some remaining upstream as freshwater residents (FWR), and others being born in or near brackish water habitats and remaining there for most of their lives (BWR).

*Conceptual diagram of the complex life cycle of Delta Smelt, based on Hobbs et al. 2019. Artwork by Adi Khen*.

OGFL Delta Smelt Publications:

White Sturgeon:

White Sturgeon (Acipenser transmontanus) is a species of demersal fish native to the west coast and is 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. Individuals typically inhabit rivers and estuaries in the northeastern Pacific Ocean, with some making large migrations across the ocean into between estauries of major rivers. Juveniles consume a wide variety of small benthic invertebrates, while adults consume larger benthic inverebrates and fish. In the winter, mature adults migrate upstream from estuarine and coastal habitats into major rivers where spawning occurs from February to May. White sturgeon mature late in life, at around 10-16 years old, with spawning occuring only once every 2-4 years, and with females laying upwards of 200,000 eggs in a single season.

*A juvenile White Sturgeon captured in Lower South San Francisco Bay.*

White Sturgeon are currently not listed as endangered; however, it is considered a species of concern by the state of California and has recently been petitioned for protected status under CESA and ESA. 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, poaching, and harmful algal blooms. A carefully managed catch and eaerecreational fishery exists for white sturgeon, which allows for the capture and harvest of fish. CDFW profile on White Sturgeon.

Unlike most of the fish studied in the OGFL, sturgeon possess vateritic (abnormal) otoliths. Instead of otoliths, we used their leading calcified fin rays (“spine”) which can provide important information regarding each individual’s age and life-long migration behaviors.

OGFL White Sturgeon Publications:

Chinook Salmon:

OGFL Staff with a King Salmon off of Bodega Bay, CA.

Chinook (“King”) Salmon (Onchorynchus tshawytscha) is an anadromous species of salmon that is both economically and ecolgoical critical to the regions it inhabits. Commercial and recreational salmon fisheries generate an estimated $900 million annually. Juveniles feed on a variety of aquatic and terrestrial invertebrates, while adults forage largely on small fishes and krill. They are preyed upon by a variety of larger fish as well as birds and both terrestrial and aquatic mammals. They are the largest of the Pacific salmon, reaching sizes of almost 5 feet and over 100 pounds, reaching maturity between 2-7 years old, followed by dramatic migrations up major rivers where they lay their eggs in shallow gravel nests known as redds. Like all Pacific salmon, Chinook Salmon are 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 migratory 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. 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 and NOAA profile on Chinook Salmon.

*A juvenile Chinook. Artwork by Adi Khen.*

Fall-run and late-fall-run Chinook migrate upstream between July and February, with most spawning between October and December. Fall-run currently constitute the majority of Chinook Salmon in California, supporting the commercial and recreational fisheries. Fall and late-fall-run chinook overlap in their run time as late-fall chinook run from mid-October to December, however late-fall typically 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, dams now block them from most of their spawning habitats and hybridization with fall-run Chinook has further reduced their numbers.

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.

OGFL Chinook Salmon Publications:

Tarek:

Tarek (Alburnus tarichi) is an migratory cyprinid (minnow) that is native to Lake Van, Turkey. Lake Van is a teriminal alkaline lake, similar to Lake Mono and Pyramid Lake in Nevada. The chemistry of these terminal lakes makes them inhospitable to most fish species, but a few such as the Lahontan Cutthrout Trout, Cui-ui, and Tarek have adapted a unique physiology to survive in these inhospital waters. Although adult Tarek are physiologically adapted to the alkaline conditions in Lake Van, they must migrate up into freshwater streams in order to reproduce, with massive migrations of fish creating spectacles as they leap over waterfalls trying to get to freshwater spawning grounds.

*Lake Van lies within the Republic of Türkiye.*

This migrating popultion of Tarek supports important fisheries and cultural events around Lake Van. However, overfishing and degradation of spawning streams have impacted Tarek numbers, leading to converns about sustainability of the population. A key question remaining is which spawnging streams contribute most to the adult Tarek populaiton. The OGFL collaborated with Dr. Semra Saygin and Dr. Mahmut Elp at the Ondokuz Mayis University, Turkey, to apply otolith Sr isotope geochemistry to identify the relative importance of different spawning streams to the adult Tarek population in Lake Van.

*Only adult Tarek can survive the high alkalinity of terminal Lake Van. Thus they must make long spawning runs into freshwater streams to spawn.*

*Tarek make massive migration runs into freshwater streams to spawn, leaping over waterfalls and creating a spectacle with great cultural significance to fishing communities around Lake Van.*

As for most cyprinids (minnows), the lappili (vs sagittae in other spp) are the largest and most conducive to otolith-based aging and geochemical analyses. Several examples of Tarek lapilli that were sectioned and polished in the frontal plane are shown.

Results of geochemical analyses highlight that several streams appear to contribute more than others to the adult Tarek population in most years, but that all streams are likely contributing at various times. Thus protection of all spawning sites is likely improtant for long-term survival of the species.

Saygin, S, N Polat, M Willmes, LS Lewis, JA Hobbs, AA Atıcı, and M Elp. 2022. Strontium isotopes in otoliths reveal a diversity of natal origins for Tarek (Alburnus tarichi) in Lake Van, Turkey. Fisheries Research. https://doi.org/10.1016/j.fishres.2022.106441

Tapertail Anchovy:

Tapertail anchovy (Coilia nasus) is a large-bodied anadromous species of anchovy with a pointed tail. It is native to the western Pacific Ocean, where it makes seasonal migrations between coastal habitats and freshwater rivers to spawn. The population in China’s Yangtze River supports a highly valuable fishery, but is also threatened by overfishing and habitat degradation. The OGFL is working with Chinese collaborators Drs. Jian Yang and Tao Jiang at the Chinese Academy of Fishery Sciences to apply Sr isotope geochemistry to better understand migration behaviors of Tapertails and which habitats in the Yangtze appear most important for spawning and rearing.

*The OGFL is collaborating with researchers in China to study migrations of Tapertail Anchovies.*

*The Yangtze River in China, where Tapertail Anchovies live and spawn.*

Lake Whitefish:

Lake Whitefish (Coregonus clupeaformis) is a coldwater species of freshwater whitefish that is common to the Great Lakes and surrounding water ways of North America. It is the most valuable commerically harvested species in the Great Lakes due to its abundance and pleasant flavor. However, overfishing and habitat degradation are impacting Lake Whitefish populations. LWF are known to spawn in tributaries of the Great Lakes (e.g. in Greenbay, WI) or along offshore reefs where gravels and water quality remain suitable. The relative contributions of stream spawning however remains unknown, and has likely decreased due to degradation of stream habitats. Researchers at the University of Wisconsin, Green Bay, including Dr. Patrick Forsythe and his student Peter Rawinsky, are collaborating with the OGFL to use otolith elemental fingerprinting to better understand the relative contributions of stream spawning to Lake Whitefish in Green Bay.

Gulf Sturgeon:

Gulf Sturgeon (Acipenser oxyrhynchus desotoi) is a subspecies of Atlantic Sturgeon that is native the the northern coast of the Gulf of Mexico. Like White Sturgeon in California, it is an ancient, long-lived, anadromous species that lives in coastal marine environments as an adult, running up major rivers in Mississippi (e.g., the Pearl and Pascagula Rivers) to spawn. Historically, it supported a valuable fishery, but overfishing and habitat degradatoin have severely impact its populations. Researchers at Mississipi State University, including Dr. Peter Allen and his student Matt Olson, are working with the OGFL to apply geochemical tools to calcified Gulf Sturgeon Fin rays to better understand the migratory behaviors of this species into and out of its major spawning habitats in Mississippi.

Otolith Geochemistry & Fish Ecology Laboratory

Species

Tarek:

Tapertail Anchovy:

Lake Whitefish:

Gulf Sturgeon:

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