Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt ( Hypomesus transpacificus ), a critically endangered estuarine fish associated with water. sampling the field was first paired trawl survey. Species-specific Taqman qPCR assay showed concordance between methods, weak signal. Informed by results sampling, an experiment designed to assess how turbidity and...

ABSTRACT We introduce a new software program, MaxTemp , that increases precision of the temporal method for estimating effective population size ( N e ) in genetic monitoring programs, which are increasingly used to systematically track changes global biodiversity. Scientists and managers typically most interested individual generations, either match with single‐generation estimates census or evaluate consequences specific management actions environmental events. Systematically sampling...

ABSTRACT Objective Current methods for larval fish preservation impede molecular analyses and hinder our ability to modernize monitoring programs using the latest technologies. We tested seven candidate preservatives (10% buffered formalin, 10% hydantoin, 50% ethanol, 70% DESS [a solution containing dimethyl sulfoxide, disodium EDTA, saturated NaCl], Excell Plus, DNA Shield) their preserve Delta Smelt Hypomesus transpacificus morphology while also allowing subsequent analyses. Methods...

Genetic adaptation to captivity is a concern for threatened and endangered species held in conservation hatcheries. Here, we present evidence of genetic hatchery the delta smelt (Fish Conservation Culture Laboratory, University California Davis; FCCL). The FCCL population genetically managed with parentage analysis addition wild fish each year. Molecular monitoring indicates little loss variation low differentiation between populations. Yet, found an increase offspring survival reproductive...

Abstract The Delta Smelt Hypomesus transpacificus , listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines wild. relies on accurate, efficacious, and reproducible molecular techniques help maintain captive population's overall genetic diversity minimize inbreeding. We created panel of single‐nucleotide polymorphisms (SNPs) support broodstock pedigree reconstruction improve upon current...

An extreme decline in Delta Smelt (Hypomesus transpacificus) abundance has led to a number of management actions support this endangered species, including the development and refinement culture techniques creation refuge population. The wild population diminished point that many scientific community believe supplementation using cultured fish needs be experimentally evaluated as possible tool. Concerns about include effectiveness action, its potential divert attention funding from other...

Abstract The once abundant delta smelt Hypomesus transpacificus is now on the verge of extinction. At UC Davis Fish Conservation and Culture Laboratory, a refuge population has been maintained since 2008 as safeguard against extinction to breed provide fish for research. Due artificial aquaculture operations, it assumed that are impacted by life in captivity leading questions about differences between cultured captive wild fish. This study looked at fork length ( FL ), body weight BW...

Conservation of endangered fishes commonly includes captive breeding, applied research, and management. Since 1996, a breeding program has existed for the federally threatened California Delta Smelt Hypomesus transpacificus , an osmerid fish endemic to upper San Francisco Estuary. Although this serves as refuge population, with experimental releases being initiated supplement wild it was uncertain how individuals would survive, feed, maintain condition outside hatchery conditions. We...

Seasonal floodplain wetland is one of the most variable and diverse habitats found in coastal ecosystems, yet it also highly altered by humans. The Yolo Bypass, primary Sacramento River California's Central Valley, USA, has been shown to provide various benefits native fishes when inundated. However, Bypass exists as a tidal dead-end slough during dry periods its value less studied this state. During recent drought (2012-2016), we higher abundance endangered Delta Smelt (Hypomesus...

The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns genetic structure, diversity and gene flow which are vital for management poorly understood this species. Here, we use genome-wide data to evaluate population structure across a broad latitudinal scale estuaries ranging from SFE Yakutat Bay Lake Washington, fine within Fraser River SFE. Results indicate high between major estuaries, fine-scale...

Abstract Adaptation to captivity in spawning programs can lead unintentional consequences, such as domestication that results reduced fitness the wild. The timing of sexual maturation has been shown be a trait under selection fish hatcheries, which affects fish's access mating opportunities and aligning their offspring's development with favorable environmental conditions. Earlier maturing may favored hatchery settings where managers provide artificially optimal growing conditions, but early...

Ten primer pairs were screened to develop single nucleotide polymorphism (SNP) TaqMan assays that will distinguish California golden trout and some rainbow trouts (Oncorhynchus mykiss sspp., O. m. aguabonita) from the Paiute Lahontan cutthroat clarkii seleniris, c. henshawi). From these 10 pairs, one mitochondrial five nuclear fixed SNP differences discovered developed into assays. These six be useful for characterizing monitoring hybridization between groups. Additional Oncorhynchus sspp....

Abstract The Owens Pupfish Cyprinodon radiosus represents many of the challenges managing threatened or endangered species in fragmented refuge populations. All six extant populations were examined to assess how management practices, including serial translocations and founder events, have influenced genetic diversity make recommendations for future management. Four sampled twice with 3–4 years intervening; two additional once. Populations genotyped at nine microsatellite loci; estimated...

Abstract Understanding reproductive behavior of sensitive species is crucial for their conservation. The Delta Smelt Hypomesus transpacificus a federally threatened, state-endangered fish whose poorly understood. We used genetic techniques to investigate the spawning cultured in conservation hatchery. conducted natural tank-spawning experiment total four separate tanks during two seasons. were allowed spawn order patterns using parentage analysis larvae produced. In total, 2,474 assigned...

Abstract Urbanization, habitat degradation, fragmentation, and invasive species have led to the severe decline or extirpation of many endemic southern California freshwater fish species, including Arroyo Chub Gila orcuttii , which has declined precipitously in recent years. Classified by Department Fish Wildlife as a high concern, is native Los Angeles, San Gabriel, Luis Rey, Santa Ana, Margarita rivers Malibu Juan creeks. To examine population structure genetic diversity within species'...

Abstract Objective Protecting biodiversity is important for preserving ecosystem functions and services, understanding the diversity present in a system necessary effective conservation. Lampreys display extensive morphology life history strategy. The extent of this underlying genetic patterns have not yet been fully characterized. Uncertainty about species boundaries operational taxonomic units hinders lamprey management Limited data collected on California lampreys ( Lampetra spp....

Delta Smelt Hypomesus transpacificus, is an endangered fish endemic to the California San Francisco Bay-Delta, USA. Extreme declines of wild population have prompted use cultured supplement since 2021 prevent extinction species. However, evidence adaptation captivity in conservation hatchery has raised concerns about captive-bred for supplementation and how these may differ from Smelt. We conducted a study over two consecutive years investigate effects varying levels captive ancestry on...

Abstract We introduce a new software program, MAXTEMP , that maximizes precision of the temporal method for estimating effective population size ( N e ) in genetic monitoring programs, which are increasingly used to systematically track changes global biodiversity. Scientists and managers typically most interested individual generations, either match with single-generation estimates census or evaluate consequences specific management actions environmental events. Systematically sampling...

Abstract A refugial population of the endangered delta smelt ( Hypomesus transpacificus ) has been maintained at Fish Conservation and Culture Laboratory (FCCL) UC Davis since 2008. Despite intense genetic management, fitness differences between wild cultured fish have observed FCCL. To investigate molecular underpinnings hatchery domestication, we used whole‐genome bisulfite sequencing to quantify epigenetic hatchery‐origin smelt. Differentially methylated regions (DMRs) were identified...

The threatened Paiute cutthroat trout ( Oncorhynchus clarkii seleniris , PCT) is endemic to Silver King Creek, California, USA, which was stocked with non-native beginning in 1930. Single nucleotide polymorphism (SNP) and microsatellite data reveal that the population Creek weakly structured composed of introgressed California golden mykiss aguabonita CAGT), hatchery rainbow RT), some native PCT. Two SNP groups were analyzed: (i) one mitochondrial five autosomal SNPs, diagnostic between...

Abstract Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed within the critically endangered Delta Smelt. Broadly categorizable as freshwater residents, we examined Restriction site Associated DNA sequencing data test for relationship between genetic...

Abstract The Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater O. ssp. complex and federally listed threatened under Endangered Species Act. However, genetic studies to date have revealed very little differentiation between PCT its closest relative, Lahontan (LCT) henshawi . These results casted doubt on whether genetically distinct or merely phenotypic variant of LCT. Here, we present genomic analysis populations resolve...

Abstract Global efforts to conserve declining amphibian populations have necessitated the development of rapid, reliable, and targeted survey methods. Environmental DNA surveys offer alternative or complementary methods traditional techniques. The California tiger salamander Ambystoma californiense (CTS) is endemic California, where it breeds in vernal pools. In past 25 y, CTS has faced a 21% loss known occurrences, largely through habitat loss, threatened by hybridization with an introduced...

Abstract Objective The ichthyofaunal diversity of the Great Basin is incompletely characterized, with Wall Canyon Sucker Catostomus sp. being one potential species. limited in distribution to drainage Surprise Valley, Washoe County, Nevada, USA. It was first documented and collected by C. L. Hubbs R. Miller 1934, no species description has been published date. Nonetheless, treated as a appeared various contexts within outside scientific literature such. Methods We conducted phylogenetic...