Environmental change influences the life history of salmon Salmo salar in the North Atlantic Ocean

Annual mean total length (L_T) of wild one‐sea‐winter (1SW) Atlantic salmon Salmo salar of the Norwegian River Imsa decreased from 63 to 54 cm with a corresponding decrease in condition factor (K) for cohorts migrating to sea from 1976 to 2010. The reduction in L_T is associated with a 40% decline in mean individual mass, from 2 to 1·2 kg. Hatchery fish reared from parental fish of the same population exhibited similar changes from 1981 onwards. The decrease in L_T correlated negatively with near‐surface temperatures in the eastern Norwegian Sea, thought to be the main feeding area of the present stock. Furthermore, S. salar exhibited significant variations in the proportion of cohorts attaining maturity after only one winter in the ocean. The proportion of S. salar spawning as 1SW fish was lower both in the 1970s and after 2000 than in the 1980s and 1990s associated with a gradual decline in post‐smolt growth and smaller amounts of reserve energy in the fish. In wild S. salar, there was a positive association between post‐smolt growth and the sea survival back to the River Imsa for spawning. In addition, among smolt year‐classes, there were significant positive correlations between wild and hatchery S. salar in L_T, K and age at maturity. The present changes may be caused by ecosystem changes following the collapse and rebuilding of the pelagic fish abundance in the North Atlantic Ocean, a gradual decrease in zooplankton abundance and climate change with increasing surface temperature in the Norwegian Sea. Thus, the observed variation in the life‐history traits of S. salar appears primarily associated with major changes in the pelagic food web in the ocean.     

Whole body elemental and proximate composition of Atlantic salmon (Salmo salar) during the life cycle

Atlantic salmon ( Salmo salar ) raised under production conditions were sampled periodically during their life cycle, in fresh and salt water, to determine their proximate and elemental composition. The parameters changed in relation to life cycle stage and fish size, and were influenced by whether the fish were in salt or freshwater. Measurements presented can be used to assist in the formulation of feeds, and to determine the health and nutritional status of commercially reared Atlantic salmon.     

Thiamin dynamics during the adult life cycle of Atlantic salmon (Salmo salar)

Thiamin is an essential water-soluble B vitamin known for its wide range of metabolic functions and antioxidant properties. Over the past decades, reproductive failures induced by thiamin deficiency have been observed in several salmonid species worldwide, but it is unclear why this micronutrient deficiency arises. Few studies have compared thiamin concentrations in systems of salmonid populations with or without documented thiamin deficiency. Moreover, it is not well known whether and how thiamin concentration changes during the marine feeding phase and the spawning migration. Therefore, samples of Atlantic salmon (Salmo salar) were collected when actively feeding in the open Baltic Sea, after the sea migration to natal rivers, after river migration, and during the spawning period. To compare populations of Baltic salmon with systems without documented thiamin deficiency, a population of landlocked salmon located in Lake Vänern (Sweden) was sampled as well as salmon from Norwegian rivers draining into the North Atlantic Ocean. Results showed the highest mean thiamin concentrations in Lake Vänern salmon, followed by North Atlantic, and the lowest in Baltic populations. Therefore, salmon in the Baltic Sea seem to be consistently more constrained by thiamin than those in other systems. Condition factor and body length had little to no effect on thiamin concentrations in all systems, suggesting that there is no relation between the body condition of salmon and thiamin deficiency. In our large spatiotemporal comparison of salmon populations, thiamin concentrations declined toward spawning in all studied systems, suggesting that the reduction in thiamin concentration arises as a natural consequence of starvation rather than to be related to thiamin deficiency in the system. These results suggest that factors affecting accumulation during the marine feeding phase are key for understanding the thiamin deficiency in salmonids.     

Distributional range shifts of Western Atlantic benthic Sargassum species (Fucales,Phaeophyceae) under future climate change scenarios

Climate change is altering the world’s marine biota, in particular, their geographic distribution. Sargassum species are foundation species that play critical ecological roles in tropical benthic communities, providing food, habitat heterogeneity and shelter for a wide range of marine organisms. To understand how future changes in abiotic variables could affect the distribution of Sargassum species along the Western Atlantic Ocean, we performed Ecological Niche Models (ENM) for 12 benthic Sargassum species. We projected present and future habitat suitability distributions under the RCP 4.5 and RCP 8.5 IPCC scenarios. We fit ENM and created ensembles from different algorithms. Our results predict changes in species latitudinal range (niche suitability) in the order of 0.5˚ to 8.1˚ northward, and 0˚ to 5.5˚ southward. Six species are likely to reduce their suitability area from 10% to 80%, while other six species are likely to expand their suitability area from 4% to 168%. Overall, changes in suitability area and latitudinal ranges will increase at larger latitudes for most species while suitability areas will decrease at lower latitudes for half of the species. This pattern is consistent with the expected tropicalization of temperate latitudes following global warming. Such changes can produce considerable losses in ecosystem services maintained by healthy Sargassum beds, particularly at lower latitudes. Our findings highlight the need to improve Sargassum conservation policies and management strategies to avoid the negative effects caused by losses in Sargassum forests.     

Hierarchical analysis of wild Atlantic salmon (Salmo salar) fecundity in relation to body size and developmental traits

Using data from wild Atlantic salmon Salmo salar returning to spawn in seven Scottish rivers, we developed a model of fecundity based on individual body size and key developmental traits. We used a novel approach to model selection which maximises predictive accuracy for application to target river stocks to select the best from a suite of Bayesian hierarchical models. This approach aims to ensure the optimal model within the candidate set includes covariates that best predict out-of-sample data to estimate fecundity in areas where no direct observations are available. In addition to body size, the final model included the developmental characteristics of age at smolting and years spent at sea. Using two independent long-term monitoring datasets, the consequences of ignoring these characteristics was revealed by comparing predictions from the best model with models that omitted them.     

Spatial and temporal genetic structure of a river‐resident Atlantic salmon (Salmo salar) after millennia of isolation

The river‐resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (F_ST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size N_e of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta‐population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.     

Inclusion of water temperature in a fuzzy logic Atlantic salmon (Salmo salar) parr habitat model

As water temperature is projected to increase in the next decades and its rise is clearly identified as a threat for cold water fish species, it is necessary to adapt and optimize the tools allowing to assess the quantity and quality of habitats with the inclusion of temperature. In this paper, a fuzzy logic habitat model was improved by adding water temperature as a key determinant of juvenile Atlantic salmon parr habitat quality. First, salmon experts were consulted to gather their knowledge of salmon parr habitat, then the model was validated with juvenile salmon electrofishing data collected on the Sainte-Marguerite, Matapedia and Petite-Cascapedia rivers (Québec, Canada). The model indicates that when thermal contrasts exist at a site, cooler temperature offered better quality of habitat. Our field data show that when offered the choice, salmon parr significantly preferred to avoid both cold areas (<15 °C) and warm areas (>20.5 °C). Because such thermal contrasts were not consistently present among the sites sampled, the model was only validated for less than 60% of the sites. The results nevertheless indicate a significant correlation between median Habitat Quality Index and parr density for the Sainte-Marguerite River (R² = 0.38). A less important, albeit significant (F-test; p = 0.036) relationship was observed for the Petite-Cascapedia river (R² = 0.14). In all instances, the four-variable (depth, velocity, substrate size and temperature) model provided a better explanation of parr density than a similar model excluding water temperature.     

Evidence of changing migratory patterns of wild Atlantic salmon Salmo salar smolts in the River Bush,Northern Ireland,and possible associations with climate change

The migration patterns, timing and biological characteristics of wild Atlantic salmon Salmo salar smolts in the River Bush, Northern Ireland, were examined over the period 1978–2008. A distinct change in the timing of the smolt run was detected with progressively earlier emigration periods evident across the time series. The shift in run timing ranged from 3·6 to 4·8 days 10 years^?1 for a range of standard migratory audit points. The timing of smolt emigration has been linked to ambient river temperature patterns. Distinct seasonal patterns were evident for biological characteristics of River Bush smolts with mean age and fork length decreasing throughout the emigration period. Marine survival patterns in 1 sea winter River Bush S. salar were strongly influenced by the run timing of the preceding smolt year such that later emigrating cohorts demonstrated increased survival. Possible mechanisms for this relationship based on local climatic variation have been explored, including the effect of potential thermal mismatch between freshwater and marine environments.     

An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin-biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half-sibs in nature most probably reduce the opportunity and advantage of kin-biased behaviour, in contrast to laboratory studies conducted in artificial, high-density conditions.     

An evaluation of the quality of fall-fingerling Atlantic salmon (Salmo salar L.) released to natural lacustrine nursery areas in Newfoundland,Canada

Results of experiments on controlled releases of fall-fingerling Atlantic salmon to lacustrine habitats in Newfoundland are reviewed in terms of survival during freshwater residence and smolt yield per unit of standing water habitat. Average survival from parr to smolt in three consecutive annual releases was 12.9% and we conclude that the quality of fall-fingerling salmon, produced from our semi-natural rearing techniques, was satisfactory. Year-class survival decreased progressively with consecutive releases. Rate of increase in juvenile salmon biomass remained stable over the duration of the study, suggesting that the average annual biomass of 1.6 kg ha^–1 of juvenile salmon released did not exceed habitat carrying capacity. Precocity did not appear to represent a significant deterrent to fall-fingerling survival. Annual smolt yield (by year-class) from stocking ranged from 53 to 130 ha^–1 (mean = 77 smolts ha^–1).     

Multi‐decadal range changes vs. thermal adaptation for north east Atlantic oceanic copepods in the face of climate change

Populations may potentially respond to climate change in various ways including moving to new areas or alternatively staying where they are and adapting as conditions shift. Traditional laboratory and mesocosm experiments last days to weeks and thus only give a limited picture of thermal adaptation, whereas ocean warming occurring over decades allows the potential for selection of new strains better adapted to warmer conditions. Evidence for adaptation in natural systems is equivocal. We used a 50‐year time series comprising of 117 056 samples in the NE Atlantic, to quantify the abundance and distribution of two particularly important and abundant members of the ocean plankton (copepods of the genus Calanus) that play a key trophic role for fisheries. Abundance of C. finmarchicus, a cold‐water species, and C. helgolandicus, a warm‐water species, were negatively and positively related to sea surface temperature (SST) respectively. However, the abundance vs. SST relationships for neither species changed over time in a manner consistent with thermal adaptation. Accompanying the lack of evidence for thermal adaptation there has been an unabated range contraction for C. finmarchicus and range expansion for C. helgolandicus. Our evidence suggests that thermal adaptation has not mitigated the impacts of ocean warming for dramatic range changes of these key species and points to continued dramatic climate induced changes in the biology of the oceans.     

A review of the likely effects of climate change on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta,with particular reference to water temperature and flow

The present paper reviews the effects of water temperature and flow on migrations, embryonic development, hatching, emergence, growth and life‐history traits in light of the ongoing climate change with emphasis on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta. The expected climate change in the Atlantic is for milder and wetter winters, with more precipitation falling as rain and less as snow, decrease in ice‐covered periods and frequent periods with extreme weather. Overall, thermal limits for salmonids are species specific. Scope for activity and growth and optimal temperature for growth increase with temperature to an optimal point before constrain by the oxygen content of the water. The optimal temperature for growth decreases with increasing fish size and varies little among populations within species, whereas the growth efficiency may be locally adapted to the temperature conditions of the home stream during the growth season. Indirectly, temperature influences age and size at smolting through its effect on growth. Time of spawning, egg hatching and emergence of the larvae vary with temperature and selective effects on time of first feeding. Traits such as age at first maturity, longevity and fecundity decrease with increasing temperature whilst egg size increases with temperature. Water flow influences the accessibility of rivers for returning adults and speed of both upstream and downstream migration. Extremes in water flow and temperature can decrease recruitment and survival. There is reason to expect a northward movement of the thermal niche of anadromous salmonids with decreased production and population extinction in the southern part of the distribution areas, migrations earlier in the season, later spawning, younger age at smolting and sexual maturity and increased disease susceptibility and mortality. Future research challenges are summarized at the end of the paper.     

Challenging claims in the study of migratory birds and climate change

Recent shifts in phenology in response to climate change are well established but often poorly understood. Many animals integrate climate change across a spatially and temporally dispersed annual life cycle, and effects are modulated by ecological interactions, evolutionary change and endogenous control mechanisms. Here we assess and discuss key statements emerging from the rapidly developing study of changing spring phenology in migratory birds. These well‐studied organisms have been instrumental for understanding climate‐change effects, but research is developing rapidly and there is a need to attack the big issues rather than risking affirmative science. Although we agree poorly on the support for most claims, agreement regarding the knowledge basis enables consensus regarding broad patterns and likely causes. Empirical data needed for disentangling mechanisms are still scarce, and consequences at a population level and on community composition remain unclear. With increasing knowledge, the overall support (‘consensus view’) for a claim increased and between‐researcher variability in support (‘expert opinions') decreased, indicating the importance of assessing and communicating the knowledge basis. A proper integration across biological disciplines seems essential for the field's transition from affirming patterns to understanding mechanisms and making robust predictions regarding future consequences of shifting phenologies.     

Comparision of a serological potency assay for furunculosis vaccines (Aeromonas salmonicida subsp. salmonicida) to intraperitoneal challenge in Atlantic salmon (Salmo salar L.)

Batch potency testing of salmonid vaccines is mainly performed by in vivo challenge, which requires a lot of animals and causes severe pain. Due to the animal welfare concerns associated with in vivo immunization challenge tests, methods which could refine, reduce or replace (3Rs) these tests are needed.The aim of this study was to assess the use of serological assay (immunization & antibody estimation with an enzyme-linked immunosorbent assay (ELISA) for batch potency testing of oil adjuvanted, inactivated commercial furunculosis vaccines. In total ten vaccines were included in the study: two commercial multi-component vaccines and two experimental single-component furunculosis vaccines with 5% and 20% antigen content (relative to the commercial vaccine), from two manufacturers. In addition two experimental single component vaccines based on A-layer positive and A-layer negative Aeromonas salmonicida respectively were included. Challenge and blood sampling were conducted 9 weeks post vaccination.There was a correlation between antibody response against A. salmonicida as measured by ELISA and protection in i.p. challenge.This study shows that the ELISA assay can be used for testing different vaccine formulations and can potentially replace in vivo challenge tests for batch potency testing of furunculosis vaccines.     

Signals of large scale climate drivers,hatchery enhancement,and marine factors in Yukon River Chinook salmon survival revealed with a Bayesian life history model

Understanding how species might respond to climate change involves disentangling the influence of co‐occurring environmental factors on population dynamics, and is especially problematic for migratory species like Pacific salmon that move between ecosystems. To date, debate surrounding the causes of recent declines in Yukon River Chinook salmon (Oncorhynchus tshawytscha) abundance has centered on whether factors in freshwater or marine environments control variation in survival, and how these populations at the northern extremity of the species range will respond to climate change. To estimate the effect of factors in marine and freshwater environments on Chinook salmon survival, we constructed a stage‐structured assessment model that incorporates the best available data, estimates incidental marine bycatch mortality in trawl fisheries, and uses Bayesian model selection methods to quantify support for alternative hypotheses. Models fitted to two index populations of Yukon River Chinook salmon indicate that processes in the nearshore and marine environments are the most important determinants of survival. Specifically, survival declines when ice leaves the Yukon River later in the spring, increases with wintertime temperature in the Bering Sea, and declines with the abundance of globally enhanced salmon species consistent with competition at sea. In addition, we found support for density‐dependent survival limitations in freshwater but not marine portions of the life cycle, increasing average survival with ocean age, and age‐specific selectivity of bycatch mortality in the Bering Sea. This study underscores the utility of flexible estimation models capable of fitting multiple data types and evaluating mortality from both natural and anthropogenic sources in multiple habitats. Overall, these analyses suggest that mortality at sea is the primary driver of population dynamics, yet under warming climate Chinook salmon populations at the northern extent of the species’ range may be expected to fare better than southern populations, but are influenced by foreign salmon production.     

Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out‐migrating smolt and post‐spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (N_b) and the generational effective population size (N_e) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed N_e estimates, suggesting that mature male parr are significantly increasing N_b and N_e over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.     

Induction of vitellogenin synthesis in an Atlantic salmon (Salmo salar) hepatocyte culture: a sensitive in vitro bioassay for the oestrogenic and anti-oestrogenic activity of chemicals

A variety of organic compounds have been documented to bind to the oestrogen receptor and induce oestrogenic effects in different vertebrates. The presence of these environmental oestrogens or oestrogen mimics in the aquatic environment has been suspected of disrupting the normal endocrinology of wild populations of fish. In this study, induction of vitellogenin synthesis in primary hepatocytes from Atlantic salmon (Salmo salar) was optimized and validated as an oestrogenic in vitro bioassay using a sensitive capture vitellogenin enzyme-linked immunosorbent assay. After proper optimization (cell media supplements, cell density, temperature and exposure time), this assay gave a sensitive and reproducible response to both endogenous steroids (relative potency: 17β-oestradiol?oestriol>oestrone>17α-oestradiol) and a range of common oestrogen mimics (relative potency: ethynyloestradiol and diethylstilboestrol?genistein and zearalenone?bisphenol A and 4-t-octylphenol>4-n-nonylphenol and 2′-chloro,4-chloro-diphenyltrichloroethane (o,p′-DDT). However, the androgen testosterone and the putative oestrogen mimics dieldrin and toxaphene were not shown to be oestrogenic using this hepatocyte bioassay. Oestrogen-induced vitellogenin synthesis was efficiently inhibited by the anti-oestrogen ZM 189.154, suggesting that this bioassay may be used for testing both the oestrogenic and the anti-oestrogenic properties of chemicals.     

Length measurement accuracy of adaptive resolution imaging sonar and a predictive model to assess adult Atlantic salmon (Salmo salar) into two size categories with long-range data in a river

Imaging sonars are used around the world for fish population monitoring. The accuracy of the length measurements has been reported in multiple studies for relatively short (<15 m) ranges and high image resolution. However, imaging sonars are often used at longer ranges (i.e., >15 m) where the images produced from sonar returns become less detailed. The accuracy of the length measurements from the Adaptive Resolution Imaging Sonar (ARIS) was tested by releasing n = 69 known-sized adult Atlantic salmon (Salmo salar) directly into the sonar field at ranges between 15 and 29 m, and measuring their echoes manually by four users and semi-automatically using a computer workflow in Echoview software. Overall, the length measurements were very variable: compared to true (fork) lengths, the mean of differences varied between −9.9 cm and 7.8 cm in the human-generated datasets, and between −42.8 cm and −20 cm in the computer-generated dataset. In addition, the length measurements in different datasets were only in poor or moderate agreement with each other (intraclass correlation <0.61). Contrary to our expectations, the distance from the transducer or the subjectively assessed echo quality did not have an effect on the measurement accuracy in most of the datasets and when it did, the effect was not systematic between the datasets. Therefore, a size class and length prediction model was implemented in a Bayesian framework to group salmon into two size categories: One-Sea-Winter (<63 cm) and Multi-Sea-Winter (≥63 cm) groups. The model correctly predicted the size category in 83% of the fish in the computer-generated dataset and ranged from 68% to 74% in the human-generated datasets. We conclude that fish length measurements derived from long-range imaging sonar data should be used with caution, but post-processing can improve the usefulness of the data for specific purposes, such as adult Atlantic salmon population monitoring.     

Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests,Brazil

Aim Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species. Location Atlantic forests of south‐eastern Brazil. Methods The historical distribution of 21 bird species was estimated using Maxent . After superimposing the present‐day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre‐ and post‐deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre‐ and post‐deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis. Results Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change. Main conclusions The changes in environmental conditions that have occurred with large‐scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra‐specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present‐day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra‐specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.     

Ontogeny constrains phenology: opportunities for activity and reproduction interact to dictate potential phenologies in a changing climate

As global warming has lengthened the active seasons of many species, we need a framework for predicting how advances in phenology shape the life history and the resulting fitness of organisms. Using an individual‐based model, we show how warming differently affects annual cycles of development, growth, reproduction and activity in a group of North American lizards. Populations in cold regions can grow and reproduce more when warming lengthens their active season. However, future warming of currently warm regions advances the reproductive season but reduces the survival of embryos and juveniles. Hence, stressful temperatures during summer can offset predicted gains from extended growth seasons and select for lizards that reproduce after the warm summer months. Understanding these cascading effects of climate change may be crucial to predict shifts in the life history and demography of species.