Biology subjects

Fangue, N. A.

Publications and source records attributed to Fangue, N. A..

7 recordsLinked to original sources

bioRxiv2026

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15{degrees}C and 18{degrees}C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

evolutionary biology↗

bioRxiv2026

Quantifying catch inequality in recreational fisheries: a case study with California steelhead (Oncorhynchus mykiss)

Catch inequality --the disproportionate distribution of catch across anglers-- is a fundamental but overlooked driver of recreational fisheries dynamics. Here, we use 11 years (2012-2022) of compulsory angler report cards to characterize long-term catch dynamics in the specialized recreational steelhead (Oncorhynchus mykiss) fishery in California, U.S.A. Spatialized catch data reveal the fishery is principally supported by wild fish, despite evidence of widespread hatchery straying. California steelhead appear to represent the most catch-unequal recreational fishery studied yet, exhibiting a statewide Gini coefficient of 0.81. Across basins, inequality varies (range 0.74-0.86) but remains relatively stable over time and flow conditions; high inequality is primarily driven by significant proportions of zero-catch anglers. We find the relationship between sample size and inequality measures especially influential for fisheries data. Hence, we develop a three-prong approach for identifying minimal sample sizes required for robust Gini estimation. Across basins and years, an average minimum of 77 report cards were required for the present fishery. High catch inequality may complicate traditional management efficacy and catch-per-unit-effort data utilization, emphasizing its consideration in fisheries management.

ecology↗

bioRxiv2025

Highly and lowly domesticated endangered fish from a conservation hatchery diverge in their thermal physiology, transcriptome, and methylome

Conservation hatcheries aim to produce fish for supplementation of wild populations, but hatchery environments may drive phenotypic divergence from wild fish. These diverged traits may have reduced fitness in the wild, which could compromise wild population sustainability and evolutionary potential, such as in response to climate change. Delta smelt are a critically endangered fish species that are safeguarded against extinction with a hatchery refuge population. We investigated whether elevated rearing temperature through larval development adjusted upper thermal tolerance limits (acclimation) in Delta smelt, whether upper thermal tolerance and plasticity (acclimation ability) differed between fish with old or recent hatchery ancestry (high or low domestication index; DI), and temperature and DI effects on liver transcriptome and methylome patterns. We observed that elevated rearing temperatures induced higher thermal tolerance (acclimation). Individuals with higher DI also had higher upper thermal tolerances, but high DI families had reduced thermal plasticity between rearing temperatures. This is consistent with domestication causing heritable elevation of upper thermal tolerance but at the cost of reduced thermal plasticity. High and low DI fish were differentiated in both genetic variation and methylome variation, suggesting the influence of both during domestication. But methylome differences distinguishing high and low DI fish did not overlap with temperature-induced methylome changes, and do not appear to be stably inherited in the hatchery. We conclude that domestication selection has altered thermal physiology within the refuge hatchery despite careful genetic management, underpinned by shifts in the transcriptome and methylome. These changes could affect Delta smelt fitness upon reintroduction to habitats that continue to warm, and show that physiological traits can diverge even within carefully genetically managed hatchery populations.

evolutionary biology↗

bioRxiv2024

Air Pocket for a Non-Air-Breathing Fish: Developing Respirometry Methodology for the critically endangered Delta Smelt

Respirometry quantifies O2 consumption to estimate metabolic activity across stressor(s), and the resulting data is central for devising conservation strategies for fishes. Due to its rapid adoption and widespread utility, protocols have been established to foster quality control and increase consistency. However, the application of established respirometry protocols on the Delta Smelt (Hypomesus transpacificus) have been largely unsuccessful, with reports over the past 12 years documenting high mortality rates that can only be circumvented with very short measurement duration ([~]4 h). This prevents the measurement of standard metabolic rate (SMR) and critical O2 tension (Pcrit), and ultimately obstructed physiological research, management actions and conservation tools development. In this study, we detailed the anecdotal, behavioral and empirical evidence that culminated in successful measurements of Delta Smelt SMR and Pcrit at 10, 12, 15, 17 and 19{degrees}C. We discovered the Delta Smelt is physotomous and requires frequent refilling of its air bladder to maintain buoyancy. Inspired by air-breathing fish respirometry, the inclusion of an air pocket within their chamber led to considerably more robust respirometry measurements compared to past attempts. The influence of fasting and time of day on O2 consumption were also examined. Altogether, this methodology paves the way for acquiring critical knowledge needed to inform Delta Smelt research and conservation (e.g. the development of metabolic index). The lessons learned may also have implications for other aspects of Delta Smelt conservation such as decreasing conservation aquaculture operating costs and improving survival during fish transport and supplementation.

physiology↗

bioRxiv2024

Fish Blood Response to Ash-Induced Environmental Alkalinization, and their Implications to Wildfire-Scarred Watersheds

Changes in land use, warming climate and increased drought have amplified wildfire frequency and magnitude globally. Ash mixing into aquatic systems after wildfires rapidly increases water pH, creating an additional threat to wildlife, especially species that are already threatened, endangered and/or migratory. Here, Chinook salmon (Oncorhynchus tshawytscha) yearlings acclimated to 15 or 20{degrees}C were exposed to an environmentally relevant concentration of ash (0.25% w/v) which caused water pH to rapidly rise from [~]8.1 to [~]9.2. Mortalities occurred within the first 12 hours, and was higher at the higher temperature (33 versus 20 %). The greatest differences in blood chemistry between the two temperatures were dramatically greater ([~]7.5-fold) and very rapid (within 1 hour) spikes in both plasma total ammonia (to [~]1200 {micro}M) and lactate (to [~]6 mM) in warm-acclimated salmon, whereas cold-acclimated salmon experienced a much smaller and gradual rise in plasma total ammonia. Salmon at both temperatures experienced extracellular and intracellular alkalosis within 1 hour that recovered within 24 hours, but the alkalosis was smaller in magnitude in fish at warmer temperature. Impacts on plasma ion concentrations were relatively mild and plasma glucose increased by 2- to 4-fold at both temperatures. Notably, the increase in plasma total ammonia in fish at the warmer temperature was far faster and much greater than those reported in previous studies exposing fish despite higher water pH (9.4-10.5) induced without using ash. This suggests that ash has physiological impacts that cannot be explained by high water pH alone which may relate to the complex mixture of metals and organic compounds also released from ash. This demonstrates post-wildfire ash input can induce lethal yet previously unexplored physiological disturbances in fish and highlights the complex interaction with warmer temperatures typical of wildfire-scarred landscapes.

physiology↗

bioRxiv2022

Habitat use differences mediate anthropogenic threat exposure in white sturgeon

Understanding intraspecific variation in habitat use, particularly of long-lived fishes across multiple life history stages, is core to improved conservation management. Here, we present results from a synthesis of acoustic telemetry data for large juvenile and adult white sturgeon (Acipenser transmontanus) from 2010 to 2017 in the San Francisco Estuary and Sacramento River ecosystems. We focused primarily on uncovering spatial patterns of inferred habitat occupancy across life stages, and on linking habitat use to population threats. We found substantial differences in habitat use across individuals and over time that was related to fish age class. However, differences in habitat use were not explained by fish sex or water year flow conditions. We estimated an index of angling exposure, which showed that fish entering reproductive maturity, which historically were of harvestable size, were detected less often than other sizes in areas with high angler pressure, suggesting possible behavioral avoidance of areas of high angler pressure. Additionally, we used historical data to evaluate potential exposure of white sturgeon to a severe red tide event in late summer 2022. We found that >50% of reproductive-age fish may have been residing in areas affected by the red tide. Future monitoring and management of white sturgeon might benefit from examining multiple phases of white sturgeon life history. For example, additional tracking studies could improve understanding of juvenile habitat use, adult survival rates, patterns of anadromy, and cross-basin habitat utilization.

ecology↗

bioRxiv2021

Survival of a threatened salmon is linked to spatial variability in river conditions

Extirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

ecology↗