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FIGURE 5 in Comparison between Atlantic salmon Salmo salar post-smolts reared in open sea cages and in the Preline raceway semi-closed containment aquaculture system

FIGURE 5 Mean (+S.E.) Salmo salar skeletal muscle fibre diameter frequency distribution reared in Preline semi-closed containment system () and reference S. salar () after 4 months in seawater. Significant difference between groups; *p <0.05; ***p <0.001

FIGURE 2 in Comparison between Atlantic salmon Salmo salar post-smolts reared in open sea cages and in the Preline raceway semi-closed containment aquaculture system

FIGURE 2 (a) Alternate day mean water temperature and (b) salinity at the Salmo salar post- smolt Preline semi-closed containment system () and reference group () rearing systems between 5 May and 30 November 2016. Data from Preline S-CCS represents the Buholmen open-pen between 31 August and 30 November 2016

FIGURE 1 in Comparison between Atlantic salmon Salmo salar post-smolts reared in open sea cages and in the Preline raceway semi-closed containment aquaculture system

FIGURE 1 (a) Location of experiment area in Norway and (b) locations of the Preline semi-closed containment system (S-CCS), reference, freshwater and growing phase groups of Salmo salar post-smolts in Hordaland region; (c) schematic of the S-CCS; (d) standard open sea cages for S. salar production in Norway; (e) drawing of an open conical pen used to hold the reference group of fish

FIGURE 6 in Comparison between Atlantic salmon Salmo salar post-smolts reared in open sea cages and in the Preline raceway semi-closed containment aquaculture system

FIGURE 6 Mean (S.E.; n = 30) plasma IGF-I concentration of Salmo salar in both fresh water and during rearing in Preline S- semi-closed containment system (S-CCS;) and reference group (). Significant differences trough time are denoted with capital letters within the reference group, lower-case letters within the Preline S-CCS group and significant differences between rearing systems are shown: **p <0.01; ***p <0.001. SW, seawater

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Figures 2 and 3 in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean

Figures 2 and 3 summarize the under/over-representation of the more common growth patterns and years, respectively, amongst the k = 20 clusters. The SF growth pattern was over-represented for four of the five clusters of sub-branch A, in association with general underrepresentation of patterns showing an initial Fast (F) sequence (Figure 2). Sub-branch B revealed an essentially inverse structure to sub-branch A, with sporadic over-representation of patterns commencing with a Fast sequence and under-representation of those with an initial Slow sequence. Sub-branches C and D were heterogeneous

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F I G U R E 3 in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean

F I G U R E 3 Tabulation of significant under- and overrepresentation of the 20 dendrogram clusters amongst years of capture of return adult Salmo salar. Details as for Figure 2

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Figure 4b in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean

Figure 4b shows that there was (a) a decrease in the frequency of fish showing consistently Fast growth throughout the post-smolt period, (b) an increase in the frequency of the SF growth pattern and (c) an increase in the frequency of growth patterns including one or more Check sequences. Furthermore, these time-series changes in circulus pattern were linked significantly to contemporaneous and anomalous warming of the Norwegian Sea (Figure 5). As shown in Figure 6, one proximate consequence of these changes is manifest in the backcalculated mean length of fish at the midpoint of the winter annulus, following the completion of the post-smolt growth season. This showed a marked and significant decrease across the final six capture years of the time series.

F I G U R E 2 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 2 Mahers River study reach, Newfoundland, showing the habitat conditions before (riffle run) and after (pool) annual flooding.

F I G U R E 1 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 1 Mahers River and North Arm River, Newfoundland, Canada. The seasonally created pool (Flooded Pool reach) is located within Mahers River. Two control reaches were located in Mahers River; one immediately upriver of the created pool habitat (Riffle Above Pool reach) and another approximate 3 km upstream (Mahers Control reach) and two additional control reaches were located in the nearby North Arm River (North Arm 1 and 2).

F I G U R E 3 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments

F I G U R E 3 (a) Posterior distribution of the difference between the true value and posterior distribution estimates (in percentage of the true value) of annual total smolt abundance obtained from DM (Dirichlet-multinomial) model M5 (simulation exercise). Each line is a year, and the 10 (one for each replicate) distributions are overlaid. The overall average difference is indicated in the left corner of the panel and represented by a red dashed vertical line. (b) C.V. of the posterior distributions of total abundance obtained from DM model M5. Each blue dot corresponds to the C.V. of a unique year/replicate, and each dashed blue horizontal line corresponds to the average C.V. of a replicate across years. The average C.V. across years and replicates (red dashed line) is also indicated in the top-right corner of the panel.

F I G U R E 4 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments

F I G U R E 4 (a–c) Posterior distribution of the relative contribution of the smolt abundance associated with each upstream rotary screw trap (RST) and (d) posterior distribution of the relative contribution of the "rest" of the smolt abundance in relation to the total abundance for the DM (Dirichletmultinomial) model M5 (simulation exercise). The red dots correspond to the true values in the simulated dataset.

F I G U R E 1 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments

F I G U R E 1 Restigouche River catchment map with main streams and lakes. Red dots indicate the location of the rotary screw traps (RST). Black polygons indicate subcatchments draining into upstream RSTs. Top-right panels: zoom on the location of the two downstream RSTs and example of a smolt with a streamer tag. Photo credit: Marie-Camille St-Amour.

F I G U R E 5 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments

F I G U R E 5 (left panels, a–e) Posterior distributions of the estimated annual catchability θt,k at each rotary screw trap (RST), (middle panels, f– h) posterior distributions of the annual smolt abundance estimates associated with each upstream RST (Nmt,i), (i) the total smolt abundance for the Restigouche catchment (Nmtot), and (right panels, j–m) posterior distributions of the annual relative proportions of the total smolt abundance t of the Restigouche catchment estimated for each upstream RST and for the unsampled areas (rest, bottom-right panel) using the Restigouche dataset. In the catchability panels (a–e), the dashed gray line is the median, and the light and dark gray areas indicate the 2.5th–97.5th and 25th– 75th interquantile ranges, respectively, of the hyperparameter μθ, that is, the average catchability of each RST of the time series. In the relative k proportions panels (f–i) the thick dashed colored line in the top three panels indicates the average proportion of the total catchment abundance estimated at the upstream RST. The thick dashed gray lines indicate the proportions of the Restigouche catchment wetted areas of the subbasins sampled at the upstream RST(j–l) and the wetted area for the remainder of the Restigouche catchment not sampled by any upstream RST (m); the proportions for the rest of the catchment area change over years based on the specific upstream RSTs that operated in a given year. For all panels, the colored dot is the median, and the thin and thick vertical segments indicate the 2.5th–97.5th and 25th–75th interquantile ranges, respectively.

F I G U R E 7 in Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

F I G U R E 7 Model prediction of the proportion of juvenile Atlantic salmon choosing to smolt as 1-year-olds (full saturation, black = historical, green = SSP1-RCP2.6, orange = SSP3-RCP7.0, and red = SSP5-RCP8.5), 2-year-olds (medium saturation, black = historical, green = SSP1-RCP2.6, orange = SSP3-RCP7.0, and red = SSP5-RCP8.5), and 3-year-olds (low saturation, black = historical, green = SSP1-RCP2.6, orange = SSP3-RCP7.0, and red = SSP5-RCP8.5). The red line is the point of reaction norm calibration to Piggins and Mills (1985).

F I G U R E 5 in Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

F I G U R E 5 Ensemble average daily water temperature by day of year for the future projections under the three shared socioeconomic pathways and representative concentration pathways (SSP1-RCP2.6 left, SSP5-RCP7.0 middle, and SSP5-RCP8.5 right). Each line represents the day of year average temperature for the climate forcing ensemble with colors transitioning from blue to red toward the end of the century (starting with 2020 and ending with 2100). The lower dashed line represents the lower growth threshold temperature of 7 C, and the upper dashed line represents the upper growth threshold temperature for 23 C (Elliott & Hurley, 1997).

F I G U R E 6 Projected change between 1960 and 2100 in Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

F I G U R E 6 Projected change between 1960 and 2100 in length-at-smoltification decision (a, b, and c), length-at-smoltification as 1-year-olds (d, e, and f), and length-at-smoltification as 2-year-olds (g, h, and i) under the three shared socioeconomic pathways and representative concentration pathways: SSP1-RCP2.6 (green), SSP3-RCP7.0 (orange), and SSP5-RCP8.5 (red) for juvenile Atlantic salmon in the Burrishoole. The gray-shaded area represents the historical reference (2000 to 2020), and the red vertical line represents the historical average.

F I G U R E 4 in Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

F I G U R E 4 Generalized linear model of body length (mm) as a function of cumulative growing degree days (CGDD, C day) for the 23 observed cohorts of juvenile Atlantic salmon in the Burrishoole watershed. The solid line represents the mean length, and the gray bands represent the 95% prediction interval. The outer lines represent the sample density.

F I G U R E 3 in Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

F I G U R E 3 The residual error between observed and predicted water temperature (top panel), and the in-situ water temperature (black line) and long short-term memory neural network water temperature prediction (red crosses) for the training (1961–1994) and validation (1995–2019) dataset in the Mill Race (bottom panel). Years excluded due to accumulation of internal sate (green), prolonged periods of missing data (blue shaded), and measurement error (red shaded) are shown in the top panel, and the delineation of the training and validation period is shown by the vertical dashed line in both panels.

F I G U R E 5 in Migration patterns and navigation cues of Atlantic salmon post-smolts migrating from 12 rivers through the coastal zones around the Irish Sea

F I G U R E 5 Rose diagrams depicting (a) the hour of the day and (b) the direction of currents () when Atlantic salmon (Salmo salar) post-smolts were initially detected at a unique acoustic receiver on monitoring line B. The green and blue arrows show the mean hour (a) and mean current direction (b) when post-smolts were initially detected respectively (Lilly et al., 2022). The orange and yellow bands (a) show the variation in sunrise and sunset times for the total period over which any post-smolts were detected on monitoring line B (ie. April 21st–June 20th).

F I G U R E 4 in Migration patterns and navigation cues of Atlantic salmon post-smolts migrating from 12 rivers through the coastal zones around the Irish Sea

F I G U R E 4 Heatmaps displaying the number of Atlantic salmon (Salmo salar) post-smolts detected at each acoustic receiver on monitoring lines A and B (Figure 1) during the period of this study. The black stars show the location of each river (n = 11) where Atlantic salmon post-smolts originated. Rivers are grouped by coastal region where they entered the Irish Sea (Figure 1, (a) Region 1: Rivers Derwent, Nith, Bladnoch; (b) Region 2: Rivers Endrick, Gryffe; (c) Region 3: Rivers Bann, Bush, Carey, Glendun; (d) Region 4: Rivers Roe, Faughan).