Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds

Age at release affects developmental physiology and sex-specific phenotypic diversity of hatchery steelhead trout (Oncorhynchus mykiss)

Most steelhead trout hatcheries increase growth rate during rearing to produce and release yearling smolts for harvest augmentation, but natural steelhead exhibit variable age of smoltification, so this common rearing practice may not be ideal for programs focused on recovering imperiled wild stocks; therefore, it is important to investigate and compare alternative hatchery rearing methods that promote life history diversity. Over six consecutive years, the Winthrop National Fish Hatchery on the Methow River, WA reared and released paired groups of age-1 (S1) and age-2 (S2) steelhead smolts. To understand how the two rearing methods affected developmental ontogeny and life-history, fish were sampled prior to hatchery release for factors associated with smoltification (size, gill Na+/K+ ATPase activity, and a qualitative smolt phenotype) and sexual maturation (sex, pituitary and testis mRNA transcripts, gonadosomatic index, and plasma 11-ketotestosterone). Our objectives were to quantify levels of smoltification and male maturation during hatchery rearing, combine metrics to estimate residualism (failure to migrate upon release), and compare the treatments by sex. Overall, S2 rearing produced 7.8% more smolts and 44-fold (4.4 vs. 0.1%) more precociously mature males than S1 rearing. Conversely, S1 rearing produced 31.6% more residuals than S2 rearing. While the proportion of total male residuals was comparable between treatments, the S1 treatment produced approximately five-fold more female residuals (20.6 vs. 4.2%). Because residuals contribute minimally to adult returns and the number of returning adult females is critical to the success of salmonid supplementation efforts, developing rearing techniques that maximize migration in females is a management priority. Physiological assessments are useful for characterizing and quantifying the effects and risks of different hatchery rearing regimes on steelhead life-history, in addition to providing sex-specific guidance to inform and optimize conservation management goals in supplementation programs.

Food-web dynamics of a floodplain mosaic overshadow the effects of engineered logjams for Pacific salmon and steelhead

Food webs vary in space and time. The structure and spatial arrangement of food webs are theorized to mediate temporal dynamics of energy flow, but empirical corroboration in intermediate-scale landscapes is scarce. River-floodplain landscapes encompass a mosaic of aquatic habitat patches and food webs, supporting a variety of aquatic consumers of conservation concern. How the structure and productivity of these patch-scale food webs change through time, and how floodplain restoration influences their dynamics, are unevaluated. We measured productivity and food-web dynamics across a mosaic of main-channel and side-channel habitats of the Methow River, WA, USA, during two study years (2009-2010; 2015-2016) and examined how food webs that sustained juvenile anadromous salmonids responded to habitat manipulation. By quantifying temporal variation in secondary production and organic matter flow across nontreated river-floodplain habitats and comparing that variation to a side channel treated with engineered logjams, we jointly confronted spatial food-web theory and assessed whether food-web dynamics in the treated side channel exceeded natural variation exhibited in nontreated habitats. We observed that organic matter flow through the more complex, main-channel food web was similar between study years, whereas organic matter flow through the simpler, side-channel food webs changed up to ~4-fold. In the side channel treated with engineered logjams, production of benthic invertebrates and juvenile salmonids increased between study years by 2× and 4×, respectively; however, these changes did not surpass the temporal variation observed in untreated habitats. For instance, juvenile salmonid production rose 17-fold in one untreated side-channel habitat, and natural aggregation of large wood in another coincided with a shift to community and food-web dominance by juvenile salmonids. Our findings suggest that interannual dynamism in material flux across floodplain habitat mosaics is interrelated with patchiness in food-web complexity and may overshadow the ecological responses to localized river restoration. Although this dynamism may inhibit detection of the ecological effects of river restoration, it may also act to stabilize aquatic ecosystems and buffer salmon and other species of conservation concern in the long term. As such, natural, landscape-level patchiness and dynamism in food webs should be integrated into conceptual foundations of process-based, river restoration.

Spatial and temporal variability of movements among sympatric salmonids in an unfragmented inland watershed

We determined the movement patterns of three abundant salmonids-Brown Trout (Salmo trutta), Mountain Whitefish (Prosopium williamsoni), and Rainbow Trout (Oncorhynchus mykiss)-in the Smith River watershed of Montana. We tagged 7,172 fish with passive integrated transponder (PIT) tags, monitored their movements past 15 stationary PIT arrays over four years, and located tagged fish between arrays by conducting mobile surveys. Movement patterns varied seasonally, among species, and among locations. Movement was greatest in the middle portion of the watershed, which included a pristine main-stem canyon and lower reaches of major tributaries. Fish rarely left the canyon, but movement into the canyon from other regions was common. Mountain Whitefish were most likely to move, and Brown Trout were least likely to move. Most fish travelled < 10 km, but some fish travelled over 100 km. Distinct movement patterns were not evident; rather, a continuous spectrum of movement behaviors was apparent. Movements by Mountain Whitefish and Rainbow Trout increased during their spawning periods. Movements peaked when mean daily water temperatures were between 11.3-17.1°C. Movements were diverse and probably contributed to metapopulation dynamics, population resiliency, and species diversity. Fish movements along stream networks connect populations across diverse landscapes, and therefore protecting and restoring stream connectivity along inland streams such as the Smith River is critical to maintaining productive fish assemblages.

Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.

Factors influencing migration of short-finned eels (Anguilla australis) over 3 years from a wetland system, Lake Condah, south-east Australia, downstream to the sea

Anguillid eel populations are under threat globally. A particularly vulnerable life-cycle stage is the migration of mature adult eels downstream from freshwater habitats through estuaries into the sea to spawn. This study investigated the factors associated with downstream migration of the short-finned eel Anguilla australis (Richardson 1841) from a coastal wetland (Lake Condah) in south-east Australia, using acoustic telemetry. Migration was associated with time of the year, higher water level and river flows, decreasing water temperature, and darker moon phases. Larger individuals and those in better condition were more likely to migrate from the wetland. Downstream migration peaked in spring, in contrast to the typical autumn migration period for other temperate anguillids. Variable responses, in comparison to other studies, highlight how migration cues may not be universal. In south-east Australia, short-finned eels may have evolved to migrate in multiple phases by first migrating to the estuary during typical seasonal spring flow pulses (e.g., to avoid being stranded in upland reaches during dry summer periods) and then migrating into the ocean in autumn. More research is needed to unravel these processes and causes, especially considering that the relationship between migration and hydrology may be complex and confounded (e.g., by human-induced disruptions to migratory pathways).

Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish

Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (Salvelinus fontinalis), understanding the drivers of asynchrony in population dynamics can improve the predictions of range-wide climate impacts. We analyzed the demographic time series from mark-recapture surveys of 11 natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km2 ) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of the five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrated that population demographics and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.

A genomic region associated with iteroparous spawning phenology is linked with age-at-maturity in female steelhead trout

Age-at-maturity and iteroparity are two life history variations of steelhead trout (Oncorhynchus mykiss) that are believed to increase population resilience and stability. While repeat-spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat-spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either "consecutive" (reproduce immediately the following season) or "skip" (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta (ERβ) and glycoprotein hormone beta-5 (GPHB5), which, in mammals, are estrogen-sensitive and expressed in reproductive tissues. Allele frequencies in this ERβ/GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age-at-maturity. These observations contribute to growing evidence that age-at-maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Using social-ecological models to explore stream connectivity outcomes for stakeholders and Yellowstone cutthroat trout

Despite growing interest in conservation and re-establishment of ecological connectivity, few studies have explored its context-specific social-ecological outcomes. We aimed to explore social and ecological outcomes to changing stream connectivity for both stakeholders and native fish species impacted by habitat fragmentation and nonnative species. We (1) investigated stakeholder perceptions of the drivers and outcomes of stream connectivity, and (2) evaluated the effects of stakeholder-identified connectivity and nonnative species scenarios on Yellowstone cutthroat trout (YCT) populations. Our study was conducted in the Teton River, Idaho, USA. We integrated two modeling approaches, mental modeling and individual-based ecological modeling, to explore social-ecological outcomes for stakeholders and YCT populations. Aggregation of mental models revealed an emergent pattern of increasing complexity as more types of stakeholders were considered, as well as gaps and linkages among different stakeholder knowledge areas. These results highlight the importance of knowledge sharing among stakeholders when making decisions about connectivity. Additionally, the results from the individual-based models suggested that the potential for a large, migratory life history form of YCT, in addition to self-preference mating where they overlap with rainbow trout, had the strongest effects on outcomes for YCT. Exploring social and ecological drivers and outcomes to changing connectivity is useful for anticipating and adapting to unintended outcomes, as well as making decisions for desirable outcomes. The results from this study can contribute to the management dialogue surrounding stream connectivity in the Teton River, as well as to our understanding of connectivity conservation and its outcomes more broadly.

Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population

Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.

Sex-specific heritabilities for length at maturity among Pacific salmonids and their consequences for evolution in response to artificial selection

Artificial selection, whether intentional or coincidental, is a common result of conservation policies and natural resource management. To reduce unintended consequences of artificial selection, conservation practitioners must understand both artificial selection gradients on traits of interest and how those traits are correlated with others that may affect population growth and resilience. We investigate how artificial selection on male body size in Pacific salmon (Oncorhynchus spp.) may influence the evolution of female body size and female fitness. While salmon hatchery managers often assume that selection for large males will also produce large females, this may not be the case-in fact, because the fastest-growing males mature earliest and at the smallest size, and because female age at maturity varies little, small males may produce larger females if the genetic architecture of growth rate is the same in both sexes. We explored this possibility by estimating sex-specific heritability values of and natural and artificial selection gradients on length at maturity in four populations representing three species of Pacific salmon. We then used the multivariate breeder's equation to project how artificial selection against small males may affect the evolution of female length and fecundity. Our results indicate that the heritability of length at maturity is greater within than between the sexes and that sire-daughter heritability values are especially small. Salmon hatchery policies should consider these sex-specific quantitative genetic parameters to avoid potential unintended consequences of artificial selection.

Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.

Graphical abstract

Diversity of life history and population connectivity of threadfin fish Eleutheronema tetradactylum along the coastal waters of Southern China

Understanding the diversity of life history, life stage connectivity and population is essential to determine the spatial scale over which fish populations operate. Otolith microchemistry analysis is a powerful tool to elucidate the life history and population connectivity of fish, providing important insights to the natal origin and population structure. In this study, we used laser ablation inductively coupled plasma mass spectrometry to analyze the chemical composition of otoliths throughout the entire lifetime of endangered fourfinger threadfin species, Eleutheronema tetradactylum. We reconstructed the life history of E. tetradactylum from Southern China collected from different locations over a spatial scale of 1200 km. Sr:Ca and Ba:Ca ratios profiles from otolith core-to-edge analysis suggested two contrasting life history patterns. Based on the differences in early life stages, we identified some fish spending their first year in an estuarine environment with subsequent movement to marine coastal systems, while some fish remaining in the coastal systems throughout their entire early life history stages. The non-metric multi-dimensional scaling showed a strong overlap in otolith core elemental composition, indicating a large-scale connectivity in the life history of E. tetradactylum. The immature fish from different natal origins mixed to a large extent when they fed and overwintered in the extensive offshore waters. Clustering of near core chemistry pointed to three possible sources of nursery for the threadfin fish. This study demonstrated the diversity of life history patterns of E. tetradactylum in Southern Chinese waters. Restoration in egg and larvae densities in coastal waters and estuaries may enhance their population abundances.

Feeding after spawning and energy balance at spawning are associated with repeat spawning interval in steelhead trout

Consecutive and skip repeat spawning (1- or ≥2-year spawning interval) life histories commonly occur in seasonally breeding iteroparous fishes. Spawning interval variation is driven by energetic status and impacts fisheries management. In salmonids, energetic status (either absolute level of energy reserves or the rate of change of energy reserves, i.e., energy balance) is thought to determine reproductive trajectory during a critical period ∼1 year prior to initial spawning. However, information on repeat spawners is lacking. To examine the timing and the aspects of energetic status that regulate repeat spawning interval, female steelhead trout (Oncorhynchus mykiss) were fasted for 10 weeks after spawning and then fed ad libitum and compared to ad libitum fed controls. Plasma growth hormone (GH) and insulin-like growth factor-I (IGF-I) levels were measured to assess long-term energy balance. Plasma estradiol levels showed that some fish in both groups initiated a consecutive spawning cycle. In fasted fish, GH was lower at spawning in consecutive versus skip spawners. In consecutive spawners, GH was higher at spawning in fed versus fasted fish. These results suggest that fish with a less negative energy balance at spawning initiated reproductive development in the absence of feeding, but that feeding during the post-spawning period enabled initiation of reproduction in some fish with a more negative energy balance at spawning. Thus, both energy balance at spawning and feeding after spawning regulated reproductive schedules. These results show that the critical period model of salmonid maturation applies to regulation of repeat spawning, and that the reproductive decision window extends into the first 10 weeks after spawning.

Tough places and safe spaces: Can refuges save salmon from a warming climate?

The importance of thermal refuges in a rapidly warming world is particularly evident for migratory species, where individuals encounter a wide range of conditions throughout their lives. In this study, we used a spatially explicit, individual-based simulation model to evaluate the buffering potential of cold-water thermal refuges for anadromous salmon and trout (Oncorhynchus spp.) migrating upstream through a warm river corridor that can expose individuals to physiologically stressful temperatures. We considered upstream migration in relation to migratory phenotypes that were defined in terms of migration timing, spawn timing, swim speed, and use of cold-water thermal refuges. Individuals with different migratory phenotypes migrated upstream through riverine corridors with variable availability of cold-water thermal refuges and mainstem temperatures. Use of cold-water refuges (CWRs) decreased accumulated sublethal exposures to physiologically stressful temperatures when measured in degree-days above 20, 21, and 22°C. The availability of CWRs was an order of magnitude more effective in lowering accumulated sublethal exposures under current and future mainstem temperatures for summer steelhead than fall Chinook Salmon. We considered two emergent model outcomes, survival and percent of available energy used, in relation to thermal heterogeneity and migratory phenotype. Mean percent energy loss attributed to future warmer mainstem temperatures was at least two times larger than the difference in energy used in simulations without CWRs for steelhead and salmon. We also found that loss of CWRs reduced the diversity of energy-conserving migratory phenotypes when we examined the variability in entry timing and travel time outside of CWRs in relation to energy loss. Energy-conserving phenotypic space contracted by 7%-23% when CWRs were unavailable under the current thermal regime. Our simulations suggest that, while CWRs do not entirely mitigate for stressful thermal exposures in mainstem rivers, these features are important for maintaining a diversity of migration phenotypes. Our study suggests that the maintenance of diverse portfolios of migratory phenotypes and cool- and cold-water refuges might be added to the suite of policies and management actions presently being deployed to improve the likelihood of Pacific salmonid persistence into a future characterized by climate change.

Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient

Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state-space models using age-0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4- to 3.5-fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6-fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity-life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function.

Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries

Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.

A melting cryosphere constrains fish growth by synchronizing the seasonal phenology of river food webs

Mountain watersheds often contain a mosaic of glacier-, snow-, and rain-fed streams that have distinct hydrologic, temperature, and biogeochemical regimes. However, as glaciers diminish and precipitation shifts from snow to rain, the physical and chemical characteristics that make glacial or snowmelt streams distinct from rain-fed streams will fade. Among the unforeseen consequences of this hydrologic homogenization could be the loss of unique food webs that sustain aquatic consumers. To explore the impacts of a melting cryosphere on stream food webs, we parameterized an aquatic food web model with empirical physicochemical data from glacier-, snow-, and rain-fed streams in southeast Alaska and used the model to simulate the seasonal biomass dynamics of aquatic primary producers and consumers and the growth of juvenile salmon. Model results suggest that glacier-, snow-, and rain-fed streams exhibit seasonal asynchronies in the timing of biofilm and aquatic invertebrate abundance. Although warmer rain-fed streams were more productive during the summer (June through September), colder glacial and snowmelt streams provided enhanced foraging and growth opportunities throughout the remainder of the year. For juvenile salmon that can track peaks in resource abundance within river networks, the loss of meltwater streams strongly constrained modeled growth opportunities by removing spatially and temporally distinct foraging habitats within a watershed. These findings suggest that climate change induced homogenization of high latitude river networks may result in the loss of unique food web dynamics, which could diminish the capacity of watersheds to sustain mobile consumers.

Strontium isotopes reveal diverse life history variations, migration patterns, and habitat use for Broad Whitefish (Coregonus nasus) in Arctic, Alaska

Conservation of Arctic fish species is challenging partly due to our limited ability to track fish through time and space, which constrains our understanding of life history diversity and lifelong habitat use. Broad Whitefish (Coregonus nasus) is an important subsistence species for Alaska's Arctic Indigenous communities, yet little is known about life history diversity, migration patterns, and freshwater habitat use. Using laser ablation Sr isotope otolith microchemistry, we analyzed Colville River Broad Whitefish 87Sr/86Sr chronologies (n = 61) to reconstruct movements and habitat use across the lives of individual fish. We found evidence of at least six life history types, including three anadromous types, one semi-anadromous type, and two nonanadromous types. Anadromous life history types comprised a large proportion of individuals sampled (collectively, 59%) and most of these (59%) migrated to sea between ages 0-2 and spent varying durations at sea. The semi-anadromous life history type comprised 28% of samples and entered marine habitat as larvae. Nonanadromous life history types comprised the remainder (collectively, 13%). Otolith 87Sr/86Sr data from juvenile and adult freshwater stages suggest that habitat use changed in association with age, seasons, and life history strategies. This information on Broad Whitefish life histories and habitat use across time and space will help managers and conservation planners better understand the risks of anthropogenic impacts and help conserve this vital subsistence resource.

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

Anadromous red-spotted masu salmon (Oncorhynchus masou ishikawae), a southernmost sea-migration form of salmonid, displays low variation in both age at seaward migration and sea age

We examined variations in age at seaward migration and sea age for the anadromous form of red-spotted masu salmon (Oncorhynchus masou ishikawae) in two Japanese rivers. The anadromous form of red-spotted masu salmon expressed only two sea migration patterns in the two rivers: (a) the majority of the salmon (95%, n = 81) were of age-0, and age-1 migrants were rare (n = 4); and (b) all the salmon examined (n = 22) made a return migration within a year, with 23% of the salmon exhibiting potamodromy in the river. Owing to low variation in their sea migratory patterns, the anadromous form of red-spotted masu salmon is likely vulnerable to environmental fluctuations.

Genomic region associated with run timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Conserving life-history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early- and late-migrating forms of Chinook salmon (Oncorhynchus tshawytscha) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high-throughput genotyping (GT-seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream-type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream-type and interior ocean-type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River.

Steelhead (Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139-0.170; females R 2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock-specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

On the Ecology and Distribution of Steelhead (Oncorhynchus mykiss) in California's Eel River

The preservation of life history and other phenotypic complexity is central to the resilience of Pacific salmon stocks. Steelhead (Oncorhynchus mykiss) express a diversity of life-history strategies such as the propensity to migrate (anadromy/residency) and the timing and state of maturation upon return to freshwater (run-timing), providing an opportunity to study adaptive phenotypic complexity. Historically, the Eel River supported upwards of 1 million salmon and steelhead, but the past century has seen dramatic declines of all salmonids in the watershed. Here we investigate life-history variation in Eel River steelhead by using Rapture sequencing, on thousands of individuals, to genotype the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy (OMY5) in the Eel River and other locations, as well as determine patterns of overall genetic differentiation. Our results provide insight into many conservation-related issues. For example, we found that distinct segregation between winter and summer-run steelhead correlated with flow-dependent barriers in major forks of the Eel, that summer-run steelhead inhabited the upper Eel prior to construction of an impassable dam, and that both life history and overall genetic diversity have been maintained in the resident trout population above; and we found no evidence of the summer-run allele in the South Fork Eel, indicating that summer run-timing cannot be expected to arise from standing genetic variation in this and other populations that lack the summer-run phenotype. The results presented in this study provide valuable information for designing future restoration and management strategies for O. mykiss in Northern California and beyond.

Documentation of en route mortality of summer chum salmon in the Koyukuk River, Alaska and its potential linkage to the heatwave of 2019

This paper documents a mass en route mortality event of adult summer chum salmon (Oncorhynchus keta) returning to the Koyukuk River, Alaska in the Yukon River basin. In response to reports from local communities, a small team of researchers (including the author) surveyed ca. 275 km of river on July 26 and 27, 2019 and counted 1,364 dead salmon. Although the total magnitude of mortality is unknown, counts from the survey certainly represent only a small fraction of the true number of fish that died. We sampled 73 carcasses to confirm death occurred prematurely prior to complete maturation and spawning, and to quantify sex and length. Visual inspection revealed a substantial fraction exhibited patterns of fungal growth consistent with secondary infections of skin lesions caused by the ubiquitous natural bacterial pathogen Flavobacterium columnare. Water temperatures during the survey averaged 17.1°C and the water was approximately 85% saturated with oxygen (ca. 8.5 mg/L), which likely contributed to the stress for upstream migrants. Evidence suggests size-selective en route mortality as female migrants that died were 2% and male migrants 5% shorter than individuals that survived to their spawning grounds on Henshaw Creek. This translates to very strong estimates of natural selection using standardized selection differentials, yet it is unclear whether selection acts on body size directly or indirectly through correlated phenotypic traits such as run timing. The mortality event likely underpins the below average returns of summer chum salmon to the Koyukuk River in 2019, suggesting an impact on spawner abundance. The future consequences of this, or potentially increasingly frequent, en route mortality events for population productivity and the extent to which genetic adaptation or adaptive phenotypic plasticity of migration behavior may facilitate persistence of these populations is unknown.

Indirect genetic control of migration in a salmonid fish

Migration is a complex trait that often has genetic underpinnings. However, it is unclear if migratory behaviour itself is inherited (direct genetic control), or if the decision to migrate is instead the outcome of a set of physiological traits (indirect genetic control). For steelhead/rainbow trout (Oncorhynchus mykiss), migration is strongly linked to a large genomic region across their range. Here, we demonstrate a shared allelic basis between early life growth rate and migratory behaviour. Next, we demonstrate that early life growth differs among resident/migratory genotypes in wild juveniles several months prior to migration, with resident genotypes achieving a larger size in their first few months of life than migratory genotypes. We suggest that the genetic basis of migration is likely indirect and mediated by physiological traits such as growth rate. Evolutionary benefits of this indirect genetic mechanism likely include flexibility among individuals and persistence of life-history diversity within and among populations.

Chronic exposure to a pervasive pharmaceutical pollutant erodes among-individual phenotypic variation in a fish

Pharmaceutical pollution is now recognised as a major emerging agent of global change. Increasingly, pharmaceutical pollutants are documented to disrupt ecologically important physiological and behavioural traits in exposed wildlife. However, little is known about potential impacts of pharmaceutical exposure on among-individual variation in these traits, despite phenotypic diversity being critical for population resilience to environmental change. Furthermore, although wildlife commonly experience multiple stressors contemporaneously, potential interactive effects between pharmaceuticals and biological stressors-such as predation threat-remain poorly understood. To redress this, we investigated the impacts of long-term exposure to the pervasive pharmaceutical pollutant fluoxetine (Prozac®) on among-individual variation in metabolic and behavioural traits, and the combined impacts of fluoxetine exposure and predation threat on mean metabolic and behavioural traits in a freshwater fish, the guppy (Poecilia reticulata). Using a mesocosm system, guppy populations were exposed for 15 months to one of two field-realistic levels of fluoxetine (nominal concentrations: 30 and 300 ng/L) or a solvent control. Fish from these populations were then tested for metabolic rate (oxygen uptake) and behaviour (activity), both before and after experiencing one of three levels of a predation treatment: an empty tank, a non-predatory fish (Melanotaenia splendida) or a predatory fish (Leiopotherapon unicolor). Guppies from both fluoxetine treatments had ∼70% lower among-individual variation in their activity levels, compared to unexposed fish. Similarly, fluoxetine exposure at the higher dosage was associated with a significant (26%) reduction in individual-level variation in oxygen uptake relative to unexposed fish. In addition, mean baseline metabolic rate was disrupted in low-fluoxetine exposed fish, although mean metabolic and behavioural responses to predation threat were not affected. Overall, our study demonstrates that long-term exposure to a pervasive pharmaceutical pollutant alters ecologically relevant traits in fish and erodes among-individual variability, which may be detrimental to the stability of contaminated populations globally.

Population and size-specific distribution of Atlantic salmon Salmo salar in the Baltic Sea over five decades

Population-specific assessment and management of anadromous fish at sea requires detailed information about the distribution at sea over ontogeny for each population. However, despite a long history of mixed-stock sea fisheries on Atlantic salmon, Salmo salar, migration studies showing that some salmon populations feed in different regions of the Baltic Sea and variation in dynamics occurs among populations feeding in the Baltic Sea, such information is often lacking. Also, current assessment of Baltic salmon assumes equal distribution at sea and therefore equal responses to changes in off-shore sea fisheries. Here, we test for differences in distribution at sea among and within ten Atlantic salmon Salmo salar populations originating from ten river-specific hatcheries along the Swedish Baltic Sea coast, using individual data from >125,000 tagged salmon, recaptured over five decades. We show strong population and size-specific differences in distribution at sea, varying between year classes and between individuals within year classes. This suggests that Atlantic salmon in the Baltic Sea experience great variation in environmental conditions and exploitation rates over ontogeny depending on origin and that current assessment assumptions about equal exploitation rates in the offshore fisheries and a shared environment at sea are not valid. Thus, our results provide additional arguments and necessary information for implementing population-specific management of salmon, also when targeting life stages at sea.

Scaling the risk landscape drives optimal life-history strategies and the evolution of grazing

Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure communities. Here we develop a theoretical framework that explicitly accounts for stochastic fluctuations of an individual consumer's energetic reserves while foraging and reproducing on a landscape with resources that range from uniformly distributed to highly clustered. First, we show that the selection of alternative life histories depends on both the mean and variance of resource availability, where depleted and more stochastic environments promote investment in each reproductive event at the expense of future fitness as well as more investment per offspring. We then show that if resource variance scales with body size due to landscape clustering, consumers that forage for clustered foods are susceptible to strong Allee effects, increasing extinction risk. Finally, we show that the proposed relationship between resource distributions, consumer body size, and emergent demographic risk offers key ecological insights into the evolution of large-bodied grazing herbivores from small-bodied browsing ancestors.

Evaluation of endocrine and transcriptomic markers of male maturation in winter-run Steelhead Trout (Oncorhynchus mykiss)

Steelhead Trout (Oncorhynchus mykiss) display a varied life-history, including precocious male maturation at age-1 or age-2. In wild fish, precocious male maturation represents an important component of a diverse life-history portfolio. In hatchery programs, however, it is undesirable if rearing practices increase rates of early male maturation and reduce numbers of anadromous male adults. Our study aimed to develop endocrine and molecular markers for identifying males at early stages of maturation in the spring (prior to smolt release) and evaluated the potential use of these markers for quantifying early male maturation rates at a hatchery scale. In a laboratory study, Skookumchuck winter-run Steelhead Trout were reared at a high growth rate in order to increase the occurrence of precocious male maturation. Fish were lethally sub-sampled in February, prior to the time of smolt release; in May, at the time of smolt release; and in September, when 1+ age maturing males that would spawn the following spring were clearly identifiable based solely on gonadosomatic index (GSI). In February and May samples, we measured GSI, plasma 11-ketotestosterone (11KT), mRNAs for pituitary follicle stimulating hormone (fshb) and luteinizing hormone (lhb) beta subunits, and analyzed stage of spermatogenesis by testis histology. Additionally, in May, we measured testis anti-Müllerian hormone (amh) and insulin-like growth factor 3 (igf3) mRNA. Our primary goal was to evaluate the aforementioned maturation indices for their efficacy in forecasting the proportion of fish initiating early male maturation in the spring (approximately 1 year prior to spermiation), compared to the proportion that actually matured. Combining measures of GSI, plasma 11KT, and pituitary fshb and lhb mRNA expression provided a useful, but conservative, estimate of the proportion of males initiating maturation in the spring (21%) compared to the proportion that were ultimately destined to mature (37%) the following spring. These results suggest that maturation may be less synchronous than previously appreciated and some males may have initiated maturation after our census in May.

Elevated plasma triglycerides and growth rate are early indicators of reproductive status in post-spawning female steelhead trout (Oncorhynchus mykiss)

Many iteroparous fishes spawn after skipping one or more yearly cycles, which impacts recruitment estimates used for fisheries management and conservation. The physiological mechanisms underlying the development of consecutive and skip spawning life histories in fishes are not well understood. In salmonids, lipid energy reserves and/or growth are thought to regulate the initiation of reproductive maturation during a critical period ~1 year prior to spawning. The fasting spawning migration of summer-run steelhead trout (Oncorhynchus mykiss) results in significant depletion of energy reserves during the proposed critical period for repeat spawning. To determine whether and when lipid energy reserves and growth influence repeat spawning, measures of lipid energy reserves, growth rate and reproductive development were tracked in female steelhead trout from first to second spawning as a consecutive or skip spawner in captivity. Plasma triglyceride (TG) levels and growth rate were elevated by 10 weeks after spawning in reproductive (i.e. consecutive spawning) versus non-reproductive (i.e. skip spawning) individuals. Muscle lipid (ML) levels, condition factor and plasma estradiol levels increased at later time points. The early differences in plasma TG levels and increases in growth rate are attributable to differential rates of feeding and assimilation between the groups following spawning. A year after spawning, plasma TG levels, MLs and growth rate decreased in consecutive spawners, attributable to transfer of lipid reserves into the ovary. During the year prior to second spawning, energy reserves and plasma estradiol levels were higher in reproductive skip spawners versus consecutive spawners, reflecting the energy deficit after first spawning. These results suggest that the decision to initiate ovarian recrudescence occurs by 10 weeks after first spawning and are consistent with the differences in energy reserves acquired following spawning being a consequence of that decision. This information will increase the success of conservation projects reconditioning post-spawning summer-run steelhead trout.

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Quantifying partial migration with sex-ratio balancing

Partial migration, the phenomenon in which animal populations are composed of both migratory and nonmigratory individuals, is widespread among migrating animals. The proportion of migrants in these populations has direct influences on population genetics and dynamics, ecosystem dynamics, mating systems, evolution, and responses to environmental change, yet there are very few studies that measure the proportion of migrants. This is because existing methods to estimate the proportion of migrants are time-consuming and expensive. In this paper, we demonstrate a new method for estimating the proportion of migrants in a population based on sex ratio measurements. Many partially migratory taxa exhibit sex-biased migration or residency, and in these cases, the sex ratios of migrants and nonmigrants are fundamentally related to the proportion of migrants in the population. We define this relationship quantitatively and show how it can be used to infer the proportion of migrants in a population through a process we term “sex-ratio balancing”. We obtain Bayesian estimates of proportion of migrants and quantify the uncertainty in these estimates with highest posterior density intervals. Lastly, we validate the sex-ratio balancing approach with a Chinook salmon (Oncorhynchus tshawytscha Walbaum in Artedi, 1792) data set. Sex-ratio balancing holds promise as a tool for quantifying partial migration and filling a key data gap about partially migratory taxa.

A comparison of stable and fluctuating resources with respect to evolutionary adaptation and life-history traits using individual-based modeling and machine learning

There are three non-mutually-exclusive key strategies evolved by gene pools to cope with fluctuating food resource availability, including evolutionary adaptation, phenotypic plasticity, and migration. We focus primarily on evolutionary adaptation and behavioral plasticity, which is a type of phenotypic plasticity, resulting in life-history changes as ways of dealing with fluctuations in food resource availability. Using EcoSim, a predator-prey individual-based model, we compare individuals with stable food resources with those in environments where there are fluctuating food resources in terms of adaptation through behavioral plasticity and evolution. The purpose of our study is to determine whether evolution and behavioral plasticity truly play a role in adapting to an environment with fluctuating food resources, as well as to determine whether there are specific gene divergences between gene pools in fluctuating food resource environments versus gene pools where food resources are relatively stable. An important result of our study is that individuals in environments that are unstable with respect to food resource availability exhibited significant differences in behaviors versus those in environments with stable food resources. Although behavioral plasticity facilitates a rapid response to unstable food conditions, our study revealed the evolution of perceptual traits such as vision range in reaction to fluctuating food resources, indicating the importance of evolution in adapting to unstable resource environments in the long run. Moreover, using decision trees, we found that there were significant behavioral gene divergences between individuals in environments with fluctuating food resources as opposed to individuals in environments with stable food resources.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations

Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.

Effects of loss of lateral hydrological connectivity on fish functional diversity

Loss of lateral hydrological connectivity (LHC) is a major cause of biodiversity decline in river floodplains, yet little is known about its effects on aquatic functional diversity in these ecosystems. We quantified functional alpha and beta diversity of fish assemblages in Yangtze River floodplain lakes and explored their responses to loss of LHC with generalized linear mixed models. Functional richness was much lower in lakes that were not connected to the Yangtze River (i.e., disconnected lakes), where functional evenness and divergence were higher. LHC was the most important factor shaping fish diversity patterns in this region. Predicted reductions in functional richness and taxonomic richness due to LHC loss were higher for functional richness (0.47-0.82) than taxonomic richness (0.32) for all species assemblages except nonmigratory species. The distribution of functional strategies of migratory and nonmigratory fishes was highly uneven throughout the floodplain. Taxonomic beta diversity was much higher than functional beta diversity. The former was due mainly to spatial turnover (73.6-83.8%), which suggested that dissimilarity of diversity among fish assemblages was largely induced by species replacement. The latter was induced by the nestedness-resultant component of overall beta diversity (70.7-86.0%), which indicated a high degree of function loss without replacement. Both taxonomic and functional beta diversity were higher in disconnected lakes, where they were significantly correlated with fishing activity and water quality, than in river-connected lakes. We showed for the first time the effects of loss of LHC on fish functional diversity in large river floodplains. We found a serious decline of fish functional richness in the Yangtze floodplain, and functional diversity remained highly vulnerable to loss of LHC even though this is a species-rich ecosystem.

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

It is now routinely possible to generate genomics-scale datasets for nonmodel species; however, many questions remain about how best to use these data for conservation and management. Some recent genomics studies of anadromous Pacific salmonids have reported a strong association between alleles at one or a very few genes and a key life history trait (adult migration timing) that has played an important role in defining conservation units. Publication of these results has already spurred a legal challenge to the existing framework for managing these species, which was developed under the paradigm that most phenotypic traits are controlled by many genes of small effect, and that parallel evolution of life history traits is common. But what if a key life history trait can only be expressed if a specific allele is present? Does the current framework need to be modified to account for the new genomics results, as some now propose? Although this real-world example focuses on Pacific salmonids, the issues regarding how genomics can inform us about the genetic basis of phenotypic traits, and what that means for applied conservation, are much more general. In this perspective, we consider these issues and outline a general process that can be used to help generate the types of additional information that would be needed to make informed decisions about the adequacy of existing conservation and management frameworks.

Criteria for a good catch: A conceptual framework to guide sourcing of sustainable salmon fisheries

The identification of sustainably managed fisheries is problematic for marketers and consumers of Pacific salmon food products owing to lack of well-defined and robust criteria that take into account current ecosystem science of salmon. We present the rationale for an alternative conceptual framework for salmon management that supports the development of sustainable sourcing criteria. Our approach contrasts with current large-scale fisheries certification programs such as that of the Marine Stewardship Council (MSC) and general consumer recommendation services such as Monterey Bay Aquarium’s Seafood Watch (SFW) program. Our framework is based on the “place-based” character of salmon populations and recognition of fundamental aspects of salmon ecology, particularly the evolution of population life histories that are locally adapted to freshwater spawning and rearing habitats. We describe how this framework underpins development of science-based sourcing criteria and how it differs in important respects from the industrial approach that historically and currently is the basis for most salmon management. We conclude with a discussion of how the framework and its application may provide a model for redirecting salmon management, in general, towards a more science- and place-based approach and why that is likely to be sustainable in the long term in a way that most contemporary salmon management is not.