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Stream restorations are increasingly critical for managing and recovering freshwater biodiversity in human-dominated landscapes. However, few studies have quantified how rehabilitative actions promulgate through aquatic communities over decades. Here, a long-term dataset is analyzed for fish assemblage change, incorporating data pre- and post-restoration periods, and testing the extent to which native assemblage stability has increased over time. In the late 1950s, a large capacity dam was installed on Putah Creek (Solano County, CA, USA), which altered the natural flow regime, channel structure, geomorphic processes, and overall ecological function. Notably, downstream flows were reduced (especially during summer months) resulting in an aquatic assemblage dominated by warm-water nonnative species, while endemic native species subsisted at low levels as subordinates. A court-mediated Accord was ratified in 2000, providing a more natural flow regime, specifically for native and anadromous fishes in the stream. The richness of nonnative species decreased at every site following the Accord, while the richness of native species increased or stayed constant. At the three most upstream sites, native species richness increased over time and ultimately exceeded nonnative richness. Native assemblage recovery was strongest upriver, closer to flow releases and habitat restoration activities, and decreased longitudinally downstream. Rank–abundance curves through time revealed that, while species evenness was low throughout the study, dominance shifted from nonnative to native species in the upstream sites coincident with rehabilitation efforts. Mean rank shifts decreased following flow rehabilitation; thus the assemblage became increasingly stable over time following flow rehabilitation. Putah Creek’s rehabilitation may represent a model for others interested in improving endemic freshwater communities in degraded ecosystems.

Effective conservation of endangered species requires knowledge of the full range of life-history strategies used to maximize population resilience within a stochastic and ever-changing environment. California’s endemic Delta Smelt ( Hypomesus transpacificus ) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as a semi-anadromous species, recent studies have challenged this lifecycle model for Delta Smelt, suggesting the species is an estuarine resident with several localized “hot-spots” of abundance. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life-history phenotypes including freshwater resident (FWR), brackish-water resident (BWR), and semi-anadromous (SA) fish. We further refined life-history phenotypes using an unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the semi-anadromous fish could be clustered into at least four additional life-history phenotypes that varied by natal origin, dispersal age and adult salinity history. These diverse life-history strategies should be incorporated into future conservation and management efforts aimed at preventing the extinction of Delta Smelt in the wild.

The Gulf sturgeon ( Acipenser oxyrinchus desotoi ) is a large, long-lived, anadromous fish inhabiting the northern Gulf of Mexico. This charismatic fish was hunted to near extinction in the early 1900s. In 1991 the subspecies was listed as threatened under the Endangered Species Act. Recovery continues to be challenged by threats such as habitat destruction, fisheries bycatch, and climate change. There are seven known natal rivers. Historically, each river was thought to contain a single, spring-spawning group. Recent studies have discovered several rivers (Suwannee, Choctawhatchee) contain a second, fall-spawning group. This study utilizes genetic techniques to investigate the proposed existence of a fall-spawning group in the Apalachicola River, Florida. Juvenile Gulf sturgeon were sampled between May and July, from 2013 to 2022. Four adults were also captured on the spawning grounds during October of 2022. Samples were genotyped for thirteen microsatellite loci to assess genetic population structure within the Apalachicola River. Analyses detected two distinct genetic groups (F ST  = 0.085). Dates of capture, length frequency distributions of juveniles, and genetic assignment of spawning adults allowed us to characterize these as separate spring- and fall-spawning groups. While approximately 90% of juveniles collected were assigned to the spring, only slight differences in genetic diversity were detected between groups. The temperature window for spawning was found to be three weeks shorter on average in the fall than the spring, highlighting the need for additional research into differing environmental or anthropogenic influences on these populations. The discovery of a fall-spawning group of Gulf sturgeon in the Apalachicola River improves our understanding of the representation, redundancy, and resiliency of the species and provides critical information for improved management of this river system.

The Atlantic sturgeon Acipenser oxyrinchus oxyrinchus is an anadromous species with a wide range along the Atlantic coast of North America. Because of overharvest and a variety of other anthropogenic stressors, the numbers of estuaries that currently host successful natural reproduction and the abundances of extant populations are depressed compared to historic numbers, resulting in its listing under the US Endangered Species Act as five Distinct Population Segments (DPS). Atlantic sturgeon are vulnerable to stressors not only within their natal estuaries but also at distant locales because of the highly migratory behavior of their subadult and adult life stages. In this study, we used our previously derived microsatellite DNA catalogue of 13 reference spawning populations and Individual-Based Assignment testing to determine the origin of 202 adult Atlantic sturgeon that were collected from the lower Altamaha River during spring, several months prior to their fall upriver spawning. We found that approximately one third (37%) of these adults assigned to populations other than the Altamaha, almost all (96%) to other populations within the South Atlantic DPS, a finding consistent with our earlier acoustic telemetry results. These results have management implications, including the likelihood of recolonization of depleted populations in the South Atlantic DPS and the compilation of reference population genetic profiles used in population delineation and mixed-stock analyses.

American shad (Alosa sapidissima) are an anadromous fish species native to North America that have an extensive range, but their populations are declining. Acoustic telemetry can play a vital role in better understanding the behavior and survival of this sensitive species, but successfully handling and tagging juvenile American shad can be challenging. We conducted several experiments to determine the best methods for collecting, transporting, holding, and tagging juvenile shad. Minimizing out-of-water handling and the use of a saltwater treatment during collection increased 24 h survival from 78 to 99% after transport. Saltwater was also fundamental in keeping tagged shad alive overnight. Shad as small as 50 mm, were implanted with a dummy acoustic transmitter using a pectoral incision method with no suture. In a 60 d holding evaluation, the tagged fish survived at a rate comparable to their non-tagged counterparts (81.5% for tagged, 70% for untagged). Tagged and untagged shad also had similar survival when exposed to a tank of predators. The results are important for improving conservation efforts for small, sensitive species of fish, like American shad.

Background Pacific salmon ( Oncorhynchus spp. ) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue. Results Candidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon ( O. nerka ) and Chinook salmon ( O. tshawytscha ) (cool, 13–14 °C and warm temperatures 18–19 °C) over 5–7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies. Conclusions The results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon.

Climate-change driven increases in water temperature pose challenges for aquatic organisms. Predictions of impacts typically do not account for fine-grained spatiotemporal thermal patterns in rivers. Patches of cooler water could serve as refuges for anadromous species like salmon that migrate during summer. We used high-resolution remotely sensed water temperature data to characterize summer thermal heterogeneity patterns for 11,308 km of second–seventh-order rivers throughout the Pacific Northwest and northern California (USA). We evaluated (1) water temperature patterns at different spatial resolutions, (2) the frequency, size, and spacing of cool thermal patches suitable for Pacific salmon (i.e., contiguous stretches ≥ 0.25 km, ≤ 15 °C and ≥ 2 °C, aooler than adjacent water), and (3) potential influences of climate change on availability of cool patches. Thermal heterogeneity was nonlinearly related to the spatial resolution of water temperature data, and heterogeneity at fine resolution (< 1 km) would have been difficult to quantify without spatially continuous data. Cool patches were generally > 2.7 and < 13.0 km long, and spacing among patches was generally > 5.7 and < 49.4 km. Thermal heterogeneity varied among rivers, some of which had long uninterrupted stretches of warm water ≥ 20 °C, and others had many smaller cool patches. Our models predicted little change in future thermal heterogeneity among rivers, but within-river patterns sometimes changed markedly compared to contemporary patterns. These results can inform long-term monitoring programs as well as near-term climate-adaptation strategies.

Lampreys are jawless fishes (Cyclostomata) that are distributed antitropically around the world. Of the three extant lamprey clades (Petromyzontidae, Geotriidae, and Mordaciidae), Geotriidae and Mordaciidae are only found in the Southern Hemisphere. Geotriidae includes two anadromous species, G. australis and G. macrostoma, while Mordaciidae includes three species: Mordacia mordax (anadromous), M. lapicida (anadromous), and M. praecox (resident and non-feeding). Similar to several Northern Hemisphere species, Southern Hemisphere species are targeted by fisheries (G. australis), culturally significant (to Māori and Mapuche), key prey for many species (including endangered species), and regarded as crucial links for understanding the evolution of vertebrates. Prior to this work, key information on the Southern Hemisphere lampreys was dispersed throughout the literature, hindering attempts to synthesise critical information about these species. Here we provide detailed descriptions of the five Southern Hemisphere species to facilitate the identification efforts by technicians, managers, researchers, and other interested parties. We then review the taxonomy, distribution, biology, genetics, significance, and threats to these lampreys from over 100 years of written sources (e.g., peer-reviewed publications and agency reports), complemented by interviews and Indigenous knowledge, in order to synthesise and centralise key information. We conclude by identifying Western science knowledge gaps and offering suggestions for addressing them: this is critical as anthropogenic environmental changes are negatively affecting Southern Hemisphere lampreys, and will likely continue to do so into the future.

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) is a long-lived, anadromous species that is broadly distributed along the Atlantic coast of North America. Historic overharvest and habitat degradation resulted in significant declines to Atlantic sturgeon populations and, following decades of limited recovery, the species was listed under the Endangered Species Act of the United States in 2012. Given continued threats to recovery and limited information about population demography, there is a need for new tools to assist in Atlantic sturgeon conservation. Here, we present a range-wide microsatellite genetic baseline for North American Atlantic sturgeon that is comprised of 2510 individuals from 18 genetically distinct groups collected in 13 rivers and one estuary. Analysis of this baseline suggested that populations from the northern range of Atlantic sturgeon were more highly differentiated than those from the southern extent, where patterns of differentiation were complicated by rivers with genetically distinct spring and fall spawning runs and less geographic distance separating populations. Despite significant demographic bottleneck events, all populations showed at least moderate levels of genetic diversity across a suite of metrics. Additionally, individual-based assignment tests had over 80% accuracy for assigning individuals to their river of origin, highlighting the utility of this baseline for characterizing the composition of mixed-stock aggregations and understanding stock-specific vulnerability and recovery. The expanded spatial coverage of this baseline dataset enabled novel inferences about patterns of genetic differentiation and spawning phenology in Atlantic sturgeon which can be used to support conservation and management efforts.

Glaciers have shaped past and present habitats for Pacific salmon (Oncorhynchus spp.) in North America. During the last glacial maximum, approximately 45% of the current North American range of Pacific salmon was covered in ice. Currently, most salmon habitat occurs in watersheds in which glacier ice is present and retreating. This synthesis examines the multiple ways that glacier retreat can influence aquatic ecosystems through the lens of Pacific salmon life cycles. We predict that the coming decades will result in areas in which salmon populations will be challenged by diminished water flows and elevated water temperatures, areas in which salmon productivity will be enhanced as downstream habitat suitability increases, and areas in which new river and lake habitat will be formed that can be colonized by anadromous salmon. Effective conservation and management of salmon habitat and populations should consider the impacts of glacier retreat and other sources of ecosystem change.