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FIGURE 7 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 7 Mean (S.E.; n = 30) relative gene transcription values for (a) Igf-I () Reference, and () Preline, (b) igf1ra () Reference, and () Preline, and (c) igf1bp1a () Reference, and () Preline using ef1α as standard in Salmo salar muscle, both in fresh water and during rearing in Preline semiclosed containment system (S-CCS;) and reference group (). Significant differences through time are denoted with capital letters within the reference group and lower-case letters within Preline S-CCS. SW, seawater

FIGURE 3 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

FIGURE 3 Mass–standard length (M–LS) relationships (MLR) determined for exercised () and control () Salmo trutta cohorts over 0–32 weeks from treatment initiation. Each cohort included LS00 individuals (n = 6) as a common origin

FIGURE 3 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 3 Mean [S.E.; n = 30; (a), (c), (d)] Salmo salar growth in mass (M) fork length (LF) and Fulton's condition factor (K) measured in freshwater (15 April 2016) and during the post-smolt phase (1–2 June; 1–2 June and 29–30 August 2016) (a) Measured mass () Preline, and () Reference, (b) estimated mean mass (Fishtalk calculations, CEF = 1.1) () Reference, and () Preline, (c) mean fork length () Preline, and () Reference and (d) condition factor (K) () Preline, and () Reference. Estimated mean mass covers both the post-smolt phase 5 May to 30 August, and the growth phase 31 August to 30 November. Changeover is indicated with a dot in the figure. SW, seawater. Significant difference between groups; *p <0.05; ***p <0.001

FIGURE 4 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 4 Accumulated mortality of Salmo salar in the Preline semiclosed containment system (S-CCS) 30 April to 30 August followed by the open pen growth phase (Buholmen) from 1 September to 30 November (;, changeover from S-CCS to open pen). The accumulated mortality in the reference group covers the period 5 May to 30 November ()

FIGURE 1 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

FIGURE 1 (a) Landmark positions () on Salmo trutta parr that were digitised twice and then averaged to minimize measurement error. (b) Shape changes associated with principal components (PCs) 1–3. PCs were derived from a between-group PC analysis of Procrustes superimposed landmarks., Consensus shape with numbered landmark positions;, Shape changes associated with each PC. Shape changes are scaled to observed PC scores: Left hand side shape changes (back outlines) are scaled to the minimum value observed across the sample on each respective PC (shown below the image) and right hand side shape changes (black outlines) are scaled to the maximum value observed across the sample on each respective PC. PC1 describes a change in head size, PC2 describes dorso-ventral arching of the body and PC3 describes changes in overall robustness and body depth

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

Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05) in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05)

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

F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis

F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site

FIGURE 3 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry

FIGURE 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent () Wood () No Wood

FIGURE 5 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry

FIGURE 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked

FIGURE 1 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry

FIGURE 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post

F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis

FIGURE 2 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry

FIGURE 2 Salmo trutta fry single-pass counts and associations with (a) D50, (b) depth and (c) velocity

FIGURE 2 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

FIGURE 2 (a) Principal component (PC) () C00, () C04, () C10, () C20, () C32, () E04, () E10, () E20, and () E32 and (b) linear discriminant (LD) scores for Salmo trutta treatment groups (C, control; E, exercise) across experimental weeks (i.e., age 00 (control sample before treatment initiation) to 32 (32 weeks of treatment); n = 6 individuals per group). PC1 and PC3, derived from a between-group PC analysis of Procrustes superimposed landmarks corrected for the arching artefact (PC2). LD1 and LD2, derived from a LD analysis on the corrected principal component scores. Ellipses demarcate 95% confidence intervals; O, group centroids. N.B. The change of direction for head size on LD1 resulting from a negative association with PC1 (see Table 2)

FIGURE 4 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr

FIGURE 4 Box plots showing median (), 25th–75th percentiles () and range () of Salmo trutta condition at length (KÞ for exercised () and control () Salmo trutta cohorts across the experimental period (i.e., age) weeks 4–32 after treatment initiation (n = 6 per group). *, significant differences of pairwise least-squares means between exercised and control cohorts; different lower-case letters (black, exercise; grey, control) denote significant differences of pairwise least-squares means within treatments across the experimental period

F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)