Cycles, stochasticity and density dependence in pink salmon population dynamics

Synthesis of 6-bromo-7-arylaminoisoquinoline-5,8-quinones and its effects on Piscirickettsia salmonis infection in vitro

Among the most important aquaculture resources for our country, salmon and trout stand out. Their production has increased significantly in recent decades, making them two of the most valuable resources in economic terms. However, high aquaculture production has allowed many pathogens to proliferate, causing infectious diseases and significant production losses. Piscirickettsia salmonis is a gram-negative, facultative intracellular bacterium that is responsible for causing severe disease in a variety of salmonid fish species. Despite the significant impact of P. salmonis on aquaculture, effective treatments for this disease remain limited. Current prevention and control strategies often include antibiotics and vaccines. However, these treatments have shown varying degrees of efficacy. A promising approach involves synthesizing bioactive analog compounds with antibacterial properties. Quinones, secondary metabolites that are abundant in nature, have become a focal point of interest due to their diverse physiological activities, including antibiotic, insecticidal, antifungal, and anticancer properties. In this study, it is shown the synthesis of series 6-bromo-7-arylaminoisoquinoline-5,8-quinones, the characterization of these compounds using classical spectroscopic methods such as one-dimensional nuclear magnetic resonance (NMR), FT-IR (infrared), mass spectrometry, and the biological activity against Piscirickettsia salmonis. The brominated derivative compounds showed no cytotoxicity at any concentration evaluated. Furthermore, the infectivity of P. salmonis after treatment with the analog compounds indicated that derivatives methyl 6-bromo-7-((4-methoxyphenyl)amino)-1,3-dimethy-5,8-dioxo-5,8-dihydroisoquinoline-4-carboxylate (4b) and methyl 7-((4'-amino-[1,1'-biphenyl]-4-yl)amino)-6-bromo-1,3-dimethy-5,8-dioxo-5,8-dihydroisoquinoline-4-carboxylate (4g) reduced the bacterial load at 25 μg/mL concentration.

Marine reserves promote cycles in fish populations on ecological and evolutionary time scales

Marine reserves are considered essential for sustainable fisheries, although their effectiveness compared to traditional fisheries management is debated. The effect of marine reserves is mostly studied on short ecological time scales, whereas fisheries-induced evolution is a well-established consequence of harvesting. Using a size-structured population model for an exploited fish population of which individuals spend their early life stages in a nursery habitat, we show that marine reserves will shift the mode of population regulation from low size-selective survival late in life to low, early-life survival due to strong resource competition. This shift promotes the occurrence of rapid ecological cycles driven by density-dependent recruitment as well as much slower evolutionary cycles driven by selection for the optimal body to leave the nursery grounds, especially with larger marine reserves. The evolutionary changes increase harvesting yields in terms of total biomass but cause disproportionately large decreases in yields of larger, adult fish. Our findings highlight the importance of carefully considering the size of marine reserves and the individual life history of fish when managing eco-evolutionary marine systems to ensure both population persistence as well as stable fisheries yields.

Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations and non-linearity

Theory and analyses of fisheries data sets indicate that harvesting can alter population structure and destabilise non-linear processes, which increases population fluctuations. We conducted a factorial experiment on the population dynamics of Daphnia magna in relation to size-selective harvesting and stochasticity of food supply. Harvesting and stochasticity treatments both increased population fluctuations. Timeseries analysis indicated that fluctuations in control populations were non-linear, and non-linearity increased substantially in response to harvesting. Both harvesting and stochasticity induced population juvenescence, but harvesting did so via the depletion of adults, whereas stochasticity increased the abundance of juveniles. A fitted fisheries model indicated that harvesting shifted populations towards higher reproductive rates and larger-magnitude damped oscillations that amplify demographic noise. These findings provide experimental evidence that harvesting increases the non-linearity of population fluctuations and that both harvesting and stochasticity increase population variability and juvenescence.

Non-stationary and interactive effects of climate and competition on pink salmon productivity

Pacific salmon (Oncorhynchus spp.) are exposed to increased environmental change and multiple human stressors. To anticipate future impacts of global change and to improve sustainable resource management, it is critical to understand how wild salmon populations respond to stressors associated with human-caused changes such as climate warming and ocean acidification, as well as competition in the ocean, which is intensified by the large-scale production and release of hatchery reared salmon. Pink salmon (O. gorbuscha) are a keystone species in the North Pacific Ocean and support highly valuable commercial fisheries. We investigated the joint effects of changes in ocean conditions and salmon abundances on the productivity of wild pink salmon. Our analysis focused on Prince William Sound in Alaska, because the region accounts for ~50% of the global production of hatchery pink salmon with local hatcheries releasing 600-700 million pink salmon fry annually. Using 60 years of data on wild pink salmon abundances, hatchery releases, and ecological conditions in the ocean, we find evidence that hatchery pink salmon releases negatively affect wild pink salmon productivity, likely through competition between wild and hatchery juveniles in nearshore marine habitats. We find no evidence for effects of ocean acidification on pink salmon productivity. However, a change in the leading mode of North Pacific climate in 1988-1989 weakened the temperature-productivity relationship and altered the strength of intraspecific density dependence. Therefore, our results suggest non-stationary (i.e., time varying) and interactive effects of ocean climate and competition on pink salmon productivity. Our findings further highlight the need for salmon management to consider potential adverse effects of large-scale hatchery production within the context of ocean change.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Impact of stochastic migration on species diversity in meta-food webs consisting of several patches

The structure of space has an appreciable influence on the diversity and stability of ecosystems. So far, there are only few theoretical studies investigating the population dynamics of food webs consisting of many species that can migrate between several patches, and in most of these models migration is a continuous, deterministic process. However, when migration events are rare (for instance because the patches are far apart), migration is a stochastic process and should be modeled accordingly. We present computer simulations of a food web model of many species on a spatial network of several patches, combining deterministic local population dynamics with stochastic migration. We evaluate the influence of the migration rate and other model parameters on local and regional species diversity and on stability. We find that migration increases the number of surviving and coexisting populations by two effects. These are the rescue effect, which restores local populations that have gone extinct, and dynamical coexistence, which sustains local populations that could not persist in the absence of immigration. Both effects occur even when migration events are rare. Species diversity increases on local and regional scales with the frequency of migration events. Furthermore, we investigate the adiabatic limit in which population dynamics always reaches an equilibrium before the next migration event, and we investigate the possible long-term scenarios. While the final state often contains the same food web on all patches, we also find instances where two slightly different food webs coexist on different patches, even when initially each patch contained the same food web.

Large-scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern

Sex-specific diet information is important in the determination of predator impacts on prey populations. Unfortunately, the diet of males and females can be difficult to describe, particularly when they are marine predators. We combined two molecular techniques to describe haul-out use and prey preferences of male and female harbor seals (Phoca vitulina) from Comox and Cowichan Bay (Canada) during 2012-2013. DNA metabarcoding quantified the diet proportions comprised of prey species in harbor seal scat, and qPCR determined the sex of the individual that deposited each scat. Using 287 female and 260 male samples, we compared the monthly sex ratio with GLMs and analyzed prey consumption relative to sex, season, site, and year with PERMANOVA. The sex ratio between monthly samples differed widely in both years (range = 12%-79% males) and showed different patterns at each haul-out site. Male and female diet differed across both years and sites: Females consumed a high proportion of demersal fish species while males consumed more salmonid species. Diet composition was related to both sex and season (PERMANOVA: R 2 = 27%, p < 0.001; R 2 = 24%, p < 0.001, respectively) and their interaction (PERMANOVA: R 2 = 11%, p < 0.001). Diet differences between males and females were consistent across site and year, suggesting fundamental foraging differences, including that males may have a larger impact on salmonids than females. Our novel combination of techniques allowed for both prey taxonomic and spatiotemporal resolution unprecedented in marine predators.

Graph-facilitated resonant mode counting in stochastic interaction networks

Oscillations in dynamical systems are widely reported in multiple branches of applied mathematics. Critically, even a non-oscillatory deterministic system can produce cyclic trajectories when it is in a low copy number, stochastic regime. Common methods of finding parameter ranges for stochastically driven resonances, such as direct calculation, are cumbersome for any but the smallest networks. In this paper, we provide a systematic framework to efficiently determine the number of resonant modes and parameter ranges for stochastic oscillations relying on real root counting algorithms and graph theoretic methods. We argue that stochastic resonance is a network property by showing that resonant modes only depend on the squared Jacobian matrix J2, unlike deterministic oscillations which are determined by J By using graph theoretic tools, analysis of stochastic behaviour for larger interaction networks is simplified and stochastic dynamical systems with multiple resonant modes can be identified easily.

Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation

A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.

On signals of phase transitions in salmon population dynamics

Critical slowing down (CSD) reflects the decline in resilience of equilibria near a bifurcation and may reveal early warning signals (EWS) of ecological phase transitions. We studied CSD in the recruitment dynamics of 120 stocks of three Pacific salmon (Oncorhynchus spp.) species in relation to critical transitions in fishery models. Pink salmon (Oncorhynchus gorbuscha) exhibited increased variability and autocorrelation in populations that had a growth parameter, r, close to zero, consistent with EWS of extinction. However, models and data for sockeye salmon (Oncorhynchus nerka) indicate that portfolio effects from heterogeneity in age-at-maturity may obscure EWS. Chum salmon (Oncorhynchus keta) show intermediate results. The data do not reveal EWS of Ricker-type bifurcations that cause oscillations and chaos at high r. These results not only provide empirical support for CSD in some ecological systems, but also indicate that portfolio effects of age structure may conceal EWS of some critical transitions.

On signals of phase transitions in salmon population dynamics

Critical slowing down (CSD) reflects the decline in resilience of equilibria near a bifurcation and may reveal early warning signals (EWS) of ecological phase transitions. We studied CSD in the recruitment dynamics of 120 stocks of three Pacific salmon (Oncorhynchus spp.) species in relation to critical transitions in fishery models. Pink salmon (Oncorhynchus gorbuscha) exhibited increased variability and autocorrelation in populations that had a growth parameter, r, close to zero, consistent with EWS of extinction. However, models and data for sockeye salmon (Oncorhynchus nerka) indicate that portfolio effects from heterogeneity in age-at-maturity may obscure EWS. Chum salmon (Oncorhynchus keta) show intermediate results. The data do not reveal EWS of Ricker-type bifurcations that cause oscillations and chaos at high r. These results not only provide empirical support for CSD in some ecological systems, but also indicate that portfolio effects of age structure may conceal EWS of some critical transitions.

Climate change, pink salmon, and the nexus between bottom-up and top-down forcing in the subarctic Pacific Ocean and Bering Sea

Climate change in the last century was associated with spectacular growth of many wild Pacific salmon stocks in the North Pacific Ocean and Bering Sea, apparently through bottom-up forcing linking meteorology to ocean physics, water temperature, and plankton production. One species in particular, pink salmon, became so numerous by the 1990s that they began to dominate other species of salmon for prey resources and to exert top-down control in the open ocean ecosystem. Information from long-term monitoring of seabirds in the Aleutian Islands and Bering Sea reveals that the sphere of influence of pink salmon is much larger than previously known. Seabirds, pink salmon, other species of salmon, and by extension other higher-order predators, are tightly linked ecologically and must be included in international management and conservation policies for sustaining all species that compete for common, finite resource pools. These data further emphasize that the unique 2-y cycle in abundance of pink salmon drives interannual shifts between two alternate states of a complex marine ecosystem.

Complex population dynamics in mussels arising from density-linked stochasticity

Population fluctuations are generally attributed to the deterministic consequences of strong non-linear interactions among organisms, or the effects of random stochastic environmental variation superimposed upon the deterministic skeleton describing population change. Analysis of the population dynamics of the mussel Mytilus californianus taken in 16 plots over 18-years found no evidence that these processes explained observed strong fluctuations. Instead, population fluctuations arose because environmental stochasticity varied with abundance, which we term density-linked stochasticity. This phenomenon arises from biologically relevant mechanisms: recruitment variation and transmission of disturbance among neighboring individuals. Density-linked stochasticity is probably present frequently in populations, as it arises naturally from several general ecological processes, including stage structure variation with density, ontogenetic niche shifts, and local transmission of stochastic perturbations. More thoroughly characterizing and interpreting deviations from the mean behavior of a system will lead to better ecological prediction and improved insight into the important processes affecting populations and ecosystems.

Stochastic formulation of ecological models and their applications

The increasing use of computer simulation by theoretical ecologists started a move away from models formulated at the population level towards individual-based models. However, many of the models studied at the individual level are not analysed mathematically and remain defined in terms of a computer algorithm. This is not surprising, given that they are intrinsically stochastic and require tools and techniques for their study that may be unfamiliar to ecologists. Here, we argue that the construction of ecological models at the individual level and their subsequent analysis is, in many cases, straightforward and leads to important insights. We discuss recent work that highlights the importance of stochastic effects for parameter ranges and systems where it was previously thought that such effects would be negligible.