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Two unconnected time-integrated tracers of niche use provided similar conclusions about individual foraging behaviour and niche adaptations (functional traits in head shape) within a subarctic lake population of Arctic charr ( Salvelinus alpinus). Zooplanktivorous individuals mainly from the pelagic zone were characterised by having low δ13C values, high infections of the parasites transmitted by pelagic copepods (especially Diphyllobothrium spp.) and slender heads with long snouts. In contrast, fish individuals that had consumed benthic prey in the littoral zone were enriched in δ13C and had high abundances of parasites transmitted by Gammarus lacustris ( Cyathocephalus truncatus and Cystidicola farionis) and a robust head shape. There were strong positive correlations between individual δ13C values and the abundance of the two parasite species transmitted by Gammarus, but a negative correlation between δ13C and the infection of copepod-borne parasites. The close relationships between diet variation (foraging behaviour), the time-integrated ecological tracers ( SI and parasites) and functional trophic morphology (niche adaptations) evidently reflect long-term temporally stable niche use of each individual predator. The two independent time-integrated tracers both gave valuable information of specialised trophic behaviour at the individual level, which is an important basis for studies related to ecological (e.g., resource partitioning) and evolutionary (e.g., polymorphism) topics within a population. [ABSTRACT FROM AUTHOR]

Ecological speciation mechanisms are widely assumed to play an important role in the early stages of divergence between incipient species, and this especially true of fishes. In the present study, we tested explicitly for post-zygotic barriers to gene flow between a sympatric, recently diverged lamprey species pair that likely arose through ecological divergence. Experimental in vitro hybridization between anadromous parasitic Lampetra fluviatilis and resident nonparasitic Lampetra planeri resulted in a high proportion of embryos capable of attaining the burrowing pro-larval stage, strongly indicating no post-zygotic barriers to gene flow between these species. A sympatric, locally-adapted resident parasitic form of L. fluviatilis was also found to successfully hybridize with both members of this species pair. The consequences of these findings are discussed in the context of lamprey speciation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108, 378-383. [ABSTRACT FROM AUTHOR]

1. We report on freshwater resident eel numbers in western Scotland based on two time series of data, independent of each other, spanning 28 years and that do not rely upon fisheries information. 2. Data from eel captures on trash screens of a pumping station (1982-2003) on Loch Lomond and electrofishing data from a stream in Lochaber, the Allt Coire nan Con (1989-2010), are compared with similar time series eel population data from elsewhere in the British Isles and more widely in Europe. 3. Over the period of the study, indices of eel numbers from across Europe declined by between 72 and 95%; in stark contrast, neither time series from western Scotland showed evidence for decline between 1982 and 2010. 4. We provisionally conclude that freshwater populations in western Scotland are being maintained by regional processes directly related to the proximity of the leading edge of the North Atlantic Drift and the Continental Shelf Current and the direction of prevailing winds. [ABSTRACT FROM AUTHOR]

1. The effect of a newly introduced population of signal crayfish (Pacifastacus leniusculus) on a riverine invertebrate community in the River Clyde, Scotland, is examined. Five hypotheses related to crayfish impact on the invertebrate community are tested by comparing sites containing signal crayfish with similar sites in the same river which have not yet been colonized. 2. The hypothesis that crayfish significantly reduce the total numbers of invertebrates in the community was supported by this study, with invertebrate density in areas containing signal crayfish around 60% of that with no observed crayfish. 3. The hypothesis that crayfish presence affects some groups more than others was also supported. Plecoptera, Chironomidae, Diptera and Hirudinea, in particular, showed evidence of reduced species numbers in areas containing crayfish, and Plecoptera, Hirudinea, Tricladida and Hydracarina showed evidence of reduced densities. Community diversity and richness was also lower at sites containing crayfish. 4. Neither the hypothesis that overall invertebrate biomass would be lower at sites with crayfish present nor the hypothesis that individual invertebrate size would be lower at sites with crayfish was supported. 5. Overall the study indicates that introduced signal crayfish can significantly and fundamentally modify fluvial macroinvertebrate community structure. [ABSTRACT FROM AUTHOR]

1. Although conceptually robust, it has proven difficult to find practical measures of niche width that are simple to obtain, yet provide an adequate descriptor of the ecological position of the population examined. 2. Trophic niche has proven more tractable than other niche dimensions. However, indices used as a proxy for trophic niche width often suffer from the following difficulties. Such indices rarely lie along a single scale making comparisons between populations or species difficult; have difficulty in combining dietary prey diversity and evenness in an ecologically meaningful way; and fail to integrate diet over ecological time-scales thus usually only comprise single snapshots of niche width. 3. We propose an alternative novel method for the comparison of trophic niche width: the use of variance of tissue stable isotope ratios, especially those of nitrogen and carbon. 4. This approach is a potentially powerful method of measuring trophic niche width, particularly if combined with conventional approaches, because: it provides a single measure on a continuous axis that is common to all species; it integrates information on only assimilated prey over time; the integration period changes with choice of tissue sampled; and data production is theoretically fast and testing among populations simple. 5. Empirical studies are now required to test the benefits of using isotopic variance as a measure of niche width, and in doing so help refine this approach. Journal of Animal Ecology (2004) 73, 1007–1012 [ABSTRACT FROM AUTHOR]

Migration is a high‐risk behavior. For the Atlantic salmon, Salmo salar, migrating from its river nursery area to marine feeding grounds, the magnitude of risk varies with habitat type. Passage through lakes, in particular, is associated with low rates of migration success. Downstream migrating salmon smolts are rheotactic when migrating in rivers, but lakes typically provide poorer directional currents for migrating salmon. In this study we tested if, in the absence of clear navigational cues in lakes, Atlantic salmon smolts switch to a random search strategy to find the outflowing river. We constructed random search simulations to test if lake basin shape has an effect on migration success. We also compared simulated migration characteristics with migrations of salmon smolts through five real lakes for which there are telemetry data for migrating salmon. Correlated random walk simulations showed that a random search strategy could be successful for all lake shapes tested but was more successful in curved (round and elliptical) than rectangular basin shapes. Rectangular basins with the migration start and stop points at the ends of the lake had a higher success than those where these points were perpendicular to the axis of the lake. In general, a random walk model predicted the migration success rate of fish tracked through real lakes. However, for two lakes the simulated migration success exceeded that of actual success, suggesting that fish passing through these lakes were not adopting a random search strategy. We speculate that this is the result of either conflicting navigational cues which inhibit smolts from finding the lake outlet or that they temporarily suspend migration (e.g., to feed). Modelling predicted that for small lakes, directional swimming in short steps (ca. 100 m) followed by turns with very low variation from the direction of travel resulted in the highest migration success. For larger lakes, longer step lengths but also with low turn variation (simulated turning angle drawn from distributions of standard deviation 2° and 5° around a mean of 0°) resulted in the highest migration success. We conclude that navigation in downstream migrating salmon smolts switches from rheotaxis in rivers to a random search tactic in lakes except where residual flow cues in some lakes prevent this, at times resulting in suboptimal navigation outcomes. [ABSTRACT FROM AUTHOR]

Trap and transport, the capture and subsequent translocation of fish during the freshwater phase of their migration, is becoming more common as a management intervention. Although the technique can be successful, it is costly and can have unintended effects on the fish being transported. This study investigates whether trap and transport can be used to increase the migration success of Atlantic salmon, Salmo salar, smolts in naturally flowing rivers. Seaward‐migrating S. salar (n = 294) from two UK rivers were tracked using acoustic telemetric techniques. Outmigration success and timing were compared between non‐transported (released at the original in‐river capture site) and transported (released ca. 23 km downstream of the capture site) individuals. Downstream translocation increased the proportion of fish that successfully migrated to marine waters, and there was no indication that transport reduced post‐release survival. The post‐release migration speed of transported fish was slower than expected but this was likely a function of their advanced migration timing rather than an inhibition of their capacity to migrate. These results suggest that trap and transport can increase the outmigration success of S. salar smolts, but the earlier river exit dates of transported fish could negatively affect their survival at sea. [ABSTRACT FROM AUTHOR]

ABSTRACT Riverine habitat fragmentation by barriers, including impoundments, is common and their effects on obligate aquatic organisms are manifold. Organisms, such as Atlantic salmon (Salmo salar), that make extensive river migrations are particularly vulnerable to the effects of impoundments. In this study, we use acoustic telemetry to examine the migratory behaviour of Atlantic salmon, as they migrate to sea for the first time as juvenile ‘smolts’, in a river with a series of dams that form a complex hydropower scheme. We demonstrate that overall migration success in the River Dee catchment and particularly through standing waters was remarkably high. We speculate that high migration success in standing waters could be due to relative current speeds providing good quality directional cues to migrants. Migration success past the two dams in this study, was relatively high, although the number of unsuccessful passage attempts before a successful passage was also very high. The vast majority of smolts passed the dams when the turbines were operational. At one dam, smolts did not use an available fish pass but migrated through the generating turbines. These findings provide several routes through which generation could be managed to enhance the success of downstream smolt migration in rivers where there are similar patterns of hydrogeneration in place. [ABSTRACT FROM AUTHOR]

Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout (Salmo trutta) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation. [ABSTRACT FROM AUTHOR]

Background: Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results: We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare completeness and annotation statistics of our new assemblies to available related species. Conclusion: New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species. [ABSTRACT FROM AUTHOR]

Partial migration, in which some individuals of a population migrate while other individuals remain resident, is generally associated with ontogenetic shifts to better feeding or as a response to adversity, but its underlying mechanisms remain relatively unknown. Brown trout ( Salmo trutta) exhibit partial migration, with some individuals remaining in fresh water (freshwater-resident) while others undertake an anadromous migration, gain most of their adult size at sea, and then return to fresh water to spawn. The option adopted by an individual trout is thought to be partly determined by its growth performance in early life, which in the stochastic and dynamic environment of freshwater streams may be dependent on its flexibility. To examine potential effects of parent type on phenotypic flexibility, we measured the metabolism, growth, and morphology of full-sibling groups of offspring from freshwater-resident and anadromous parents both before and after a switch in diet. We found that fry had a higher growth rate and a more rounded head and body shape when reared on chironomid larvae compared with when they were reared on Daphnia, but diet had no effect on standard metabolic rate. Interestingly, offspring of anadromous parents were less able to maintain their growth rate when fed on Daphnia than were those of freshwater-residents and showed a correspondingly greater increase in growth following a switch from Daphnia to chironomid larvae. Offspring of anadromous parents also showed less morphological flexibility in response to diet than did the offspring of freshwater-residents. We discuss how the migration history of the parents might interact with phenotypic flexibility in early life to influence the migration probability of the offspring. [ABSTRACT FROM AUTHOR]

Understanding the effects of trophic status and dissolved organic carbon concentration (DOC) on lake carbon cycling is essential for accurate ecosystem carbon models. Using isotopically labelled substrates we assessed spatial and temporal variability in bacterial respiration (BR) and algal primary production (PP) in two trophically, morphometrically and hydrologically different basins in Loch Lomond, a large temperate lake in Scotland. GIS modelling was used to construct a whole lake balance for bacterial production/respiration and PP, and from this the proportion of heterotrophy fuelled by allochthonous carbon was estimated. We tested the hypotheses that trophic status and DOC concentration affect the balance between PP and BR and examined which is the more significant driving factor. Additionally we estimated the percentage of BR that is fuelled by terrestrial carbon. PP varied seasonally and showed inter-basin homogeneity. BR was greatest in the mesotrophic south basin in autumn, which corresponded to measured peak DOC input, though over an annual cycle no relationship was observed between BR and DOC concentration. The PP:BR ratio was 0.37 ± 0.30 and 0.3 ± 0.45 in the north and south basins, respectively, assuming a bacterial growth efficiency of 0.1. We have found that allochthonous carbon potentially supports a substantial quantity of pelagic production, even during periods of high photosynthesis. Less productive systems are thought to be dominated by heterotrophic processes. However, we have found that the mesotrophic basin of a large lake to be as heterotrophic as its neighbouring oligotrophic basin, an observation that has implications for our understanding of modelling of the role of lakes in linking the terrestrial-atmospheric carbon cycle. [ABSTRACT FROM AUTHOR]

Atlantic salmon (Salmo salar) smolt migration through standing waters is generally known to be associated with slow migration speed and low success. Most previous studies have however been conducted on impounded waters. The bathymetry and specifically the flow dynamics around the outlets differ markedly between impounded lakes and naturally draining lakes. To date no study has attempted to disentangle the effects of the impoundment from that of standing water itself. This question was tested in a single naturally draining standing water and two impounded standing waters within a single catchment using fish tagged with acoustic and PIT tags (in three and two lakes, respectively). Overall migration success (river to estuary) was very low (10%); migration success through the lakes was also very low (total loss rates range: 31 to 55%; 16 to 53%.km−1) compared with migration in the river downstream of the lakes (range: 3.9 to 10.8%.km−1). Migration success was no lower in impounded lakes compared with the naturally draining lake. 49% of directional movements were in a direction opposite to the migration pathway, indicating that a lack of navigational cues may be in-part responsible for low migration success. We tentatively conclude that successful migration through standing waters without strong directional cues may be more stochastic than previously thought. We suggest that at least for some impoundments (as shown here), the impoundment per se may not reduce migration success, its greater effect being the creation of the standing water through which smolts are required to migrate. However, any impoundment effect is likely to be dependent upon a combination of lake basin shape, the exit route from the lake and the navigational cues available to smolts. [ABSTRACT FROM AUTHOR]

Fishways are commonly employed to improve river connectivity for fishes, but the extent to which they cater for natural phenotypic diversity has been insufficiently addressed. We measured differential upstream passage success of three wild brown trout (Salmo trutta) phenotypes (anadromous, freshwater-resident adult and parr-marked), encompassing a range of sizes and both sexes, at a Larinier superactive baffle fishway adjacent to a flow-gauging weir, using PIT telemetry (n = 160) and radio telemetry (n = 53, double tagged with PIT tags). Fish were captured and tagged downstream of the weir in the autumn pre-spawning period, 2017, in a tributary of the River Wear, England, where over 95% of tributary spawning habitat was available upstream of the weir. Of 57 trout that approached the weir-fishway complex, freshwater-resident adult and parr-marked phenotypes were less successful in passing than anadromous trout (25%, 36%, and 63% passage efficiency, respectively). Seventy-one percent of anadromous trout that passed upstream traversed the weir directly. Although the fishway facilitated upstream passage, it was poor in attracting fish of all phenotypes (overall attraction efficiency, 22.8%). A higher proportion (68.2%) of parr-marked trout that approached the weir were male and included sexually mature individuals, compared with that of freshwater-resident (37.8%) and anadromous trout (37.0%). The greater passage success of anadromous trout was likely due to their greater size and locomotory performance compared to the other phenotypes. Barriers and fishways can act as selection filters, likely the case in this study, and greater consideration needs to be given to supporting natural diversity in populations when proposing fishway designs to mitigate river connectivity problems. • Route choice and passage success was measured for three brown trout phenotypes. • Fishway entrance had low attraction efficiency for all phenotypes. • More fish traversed weir directly than utilised fishway. • Anadromous trout had greater chance of passing weir than other phenotypes. • Differential passage success between phenotypes may have evolutionary consequences. [ABSTRACT FROM AUTHOR]

Following the publication of this article [1], the authors noticed found that they incorrectly reported the BUSCO completeness for the PhyloFish brown trout and European whitefish transcriptomes. This was due to an error in their TransDecoder pipeline and restricted to those two datasets and their interpretation. They apologise for this misreported result and thank the authors of the PhyloFish database for bringing it to their attention. [ABSTRACT FROM AUTHOR]

There is some evidence that the river migration success of Atlantic salmon smolts, on their first migration to sea, varies both spatially and temporally. However, we have only a poor understanding of what may be driving this variation. In this study, we used acoustic telemetry to quantify the spatial and temporal variations in river migration success in Atlantic salmon smolts on their first migration to sea. In total 4120 Atlantic salmon smolts migrating through 22 rivers in Scotland, England, Ireland, and Northern Ireland over multiple years were included in the study. Individuals were defined as successful migrants if detected leaving the river to enter marine waters. The results show significant temporal (up to 4 years) and spatial (river) variations in migration success, with overall between-river migration success varying from 3.4% to 97.0% and between years from 3.4% and 61.0%. Temporal variation in migration success was river specific, with some rivers being more temporally stable (exhibiting little variation between years) than others. Across all rivers and years, individual migration success was predicted positively by body condition and negatively by tag burden. The rate of migration success for a population (migration success standardized to a common river distance [proportion km -1 ]) was predicted by a number of environmental factors. The proportion of river catchment that comprised wetland and woodland positively predicted migration success, whereas the proportion of grassland and peatland in a catchment negatively predicted the rate of migration success. Although the mechanisms through which these effects may be operating were not directly examined in this study, we discuss some potential routes through which they may occur., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea., (© 2024 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories., (© 2024 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Phenotypic plasticity has been presented as a potential rapid-response mechanism with which organisms may confront swift environmental change and increasing instability. Among the many difficulties potentially facing freshwater fishes in recently glaciated ecosystems is that of invertebrate prey communities becoming significantly altered in species composition and relative abundance. To test how the rapidity of diet resource change may affect phenotypic responses during development, we subjected juvenile brown trout to pelagic-type or littoral-type diets that alternated either daily, sub-seasonally, or not at all over a single growth season. The proportional intake of each diet was traced with stable isotopes of carbon and nitrogen and modelled with morphometric data on head and jaw shape. While those trout exposed to a single diet type developed predictable morphologies associated with pelagic or littoral foragers, those raised on alternating diets expressed more unpredictable morphologies. With extreme (daily) or even sub-seasonal (monthly) resource instability, the association of diet type with the phenotype was overwhelmed, calling into question the efficacy of plasticity as a means of adaptation to environments with rapidly fluctuating prey resources., Competing Interests: The authors declare no conflicts of or competing interests., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The freshwater phase of the first seaward migration of juvenile Atlantic salmon (Salmo salar) is relatively well understood when compared with our understanding of the marine phase of their migration. In 2021, 1008 wild and 60 ranched Atlantic salmon smolts were tagged with acoustic transmitters in 12 rivers in England, Scotland, Northern Ireland and Ireland. Large marine receiver arrays were deployed in the Irish Sea at two locations: at the transition of the Irish Sea into the North Atlantic between Ireland and Scotland, and between southern Scotland and Northern Ireland, to examine the early phase of the marine migration of Atlantic salmon smolts. After leaving their natal rivers' post-smolt migration through the Irish Sea was rapid with minimum speeds ranging from 14.03 to 38.56 km.day -1 for Atlantic salmon smolts that entered the Irish Sea directly from their natal river, to 9.69-39.94 km.day -1 for Atlantic salmon smolts that entered the Irish Sea directly from their natal estuary. Population minimum migration success through the study area was strongly correlated with the distance of travel, populations further away from the point of entry to the open North Atlantic exhibited lower migration success. Post-smolts from different populations experienced different water temperatures on entering the North Atlantic. This was largely driven by the timing of their migration and may have significant consequences for feeding and ultimately survivorship. The influence of water currents on post-smolt movement was investigated using data from previously constructed numerical hydrodynamic models. Modeled water current data in the northern Irish Sea showed that post-smolts had a strong preference for migrating when the current direction was at around 283° (west-north-west) but did not migrate when exposed to strong currents in other directions. This is the most favorable direction for onward passage from the Irish Sea to the continental shelf edge current, a known accumulation point for migrating post-smolts. These results strongly indicate that post-smolts migrating through the coastal marine environment are: (1) not simply migrating by current following (2) engage in active directional swimming (3) have an intrinsic sense of their migration direction and (4) can use cues other than water current direction to orientate during this part of their migration., (© 2023 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Geometric morphometrics is widely used to quantify morphological variation between biological specimens, but the fundamental influence of operator bias on data reproducibility is rarely considered, particularly in studies using photographs of live animals taken under field conditions. We examined this using four independent operators that applied an identical landmarking scheme to replicate photographs of 291 live Atlantic salmon ( Salmo salar L.) from two rivers. Using repeated measures tests, we found significant inter-operator differences in mean body shape, suggesting that the operators introduced a systematic error despite following the same landmarking scheme. No significant differences were detected when the landmarking process was repeated by the same operator on a random subset of photographs. Importantly, in spite of significant operator bias, small but statistically significant morphological differences between fish from the two rivers were found consistently by all operators. Pairwise tests of angles of vectors of shape change showed that these between-river differences in body shape were analogous across operator datasets, suggesting a general reproducibility of findings obtained by geometric morphometric studies. In contrast, merging landmark data when fish from each river are digitised by different operators had a significant impact on downstream analyses, highlighting an intrinsic risk of bias. Overall, we show that, even when significant inter-operator error is introduced during digitisation, following an identical landmarking scheme can identify morphological differences between populations. This study indicates that operators digitising at least a sub-set of all data groups of interest may be an effective way of mitigating inter-operator error and potentially enabling data sharing., Competing Interests: The authors declare there are no competing interests., (©2023 Moccetti et al.)

Polymorphic Arctic charr Salvelinus alpinus populations frequently display distinct differences in habitat use, diet, and parasite communities. Changes to the relative species densities and composition of the wider fish community have the potential to alter the habitat niche of sympatric Arctic charr populations. This study evaluated the temporal stability of the parasite community, diet, and stable isotopes (δ 13 C, δ 15 N) of three sympatric Arctic charr morphs (piscivore, benthivore, and planktivore) from Loch Rannoch, Scotland, in relation to changes to the fish community. All Arctic charr morphs displayed distinct differences in parasite communities, diet, and stable isotope signatures over time, despite the establishment of four new trophically transmitted parasite taxa, and increased fish and zooplankton consumption by the piscivorous and planktivore morphs, respectively. Native parasite prevalence also increased in all Arctic charr morphs. Overall, Loch Rannoch polymorphic Arctic charr morph populations have maintained their distinct trophic niches and parasite communities through time despite changes in the fish community. This result indicates that re-stocking a native fish species has the potential to induce shifts in the parasite community and diet of Arctic charr morphs., Competing Interests: None declared., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

It is thought that survival during migration is particularly poor for Atlantic salmon post-smolts immediately after entry into sea and particularly in the estuarine environment. Nonetheless, there is currently a lack of information on Atlantic salmon post-smolt movement behaviour in estuaries in the UK. This study used acoustic tagging to estimate loss rates and compare the behaviour of Atlantic salmon post-smolts migrating from two distinctly different rivers draining into the Clyde Estuary, the River Endrick (n = 145) and the Gryffe (n = 102). Contrary to most literature, post-smolts undertook rapid migrations through the estuary, potentially decreasing their exposure to predators/anthropogenic stressors and reducing their estimated loss rates (river: 1%-3% km -1 ; estuary: 0.20%-0.60% km -1 ). The low loss rates in the estuary occurred despite post-smolts engaging in passive reversal movements with the tide upon entering the estuary, possibly allowing them more time to adapt to the increased salinity. Atlantic salmon post-smolts from both the rivers used similar migration pathways exiting into the coastal marine zone during ebbing tide. This study provides novel information on the timing and migratory routes of Atlantic salmon post-smolts in the Clyde Estuary that can ultimately be used to inform management decisions on how to assess and reduce the potential impacts of current natural and anthropogenic stressors. Temporal repeatability of this study over multiple years is required to determine if there is variation in the factors driving the migratory patterns and loss rates of smolts in this system., (© 2022 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

There are strong signals that the selection forces favouring the expression of long-distance sea migration by Atlantic salmon (Salmo salar) are changing. Unlike many other behavioural traits, the costs of migration are incurred before any fitness benefits become apparent to the migrant. The expression of this behaviour has thus been shaped by selection forces over multiple generations and cannot respond to short interval (within a single generation) environmental change as many other behavioural traits can. Here we provide a framework to examine the evolutionary and ecological consequences of a sustained increase in migration cost. We argue that Atlantic salmon may have entered an evolutionary trap, where long-distance sea migration has become maladaptive because of shifting environmental conditions. We predict that if higher migration costs (affecting survivorship and ultimately fitness) persist, then shifting selection pressures will result in continuing declines in population size. We suggest, however, that in some populations there is demonstrable capacity for evolutionary rescue responses within the species which is to be found in the variation in the expression of migration. Under a scenario of low to moderate change in the selection forces that previously promoted migration, we argue that disruptive, sex-based selection would result in partial migration, where females retain sea migration but with anadromy loss predominantly in males. With more acute selection forces, anadromy may be strongly selected against, under these conditions both sexes may become freshwater resident. We suggest that as the migration costs appear to be higher in catchments with standing waters, then this outcome is more likely in such systems. We also speculate that as a result of the genetic structuring in this species, not all populations may have the capacity to respond adequately to change. The consequences of this for the species and its management are discussed., (© 2022 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

It has been suggested that a trade-off between cognitive capacity and developmental costs may drive brain size and morphology across fish species, but this pattern is less well explored at the intraspecific level. Physical habitat complexity has been proposed as a key selection pressure on cognitive capacity that shapes brain morphology of fishes. In this study, we compared brain morphology of brown trout, Salmo trutta , from stream, lake, and hatchery environments, which generally differ in physical complexity ranging from low habitat complexity in the hatchery to high habitat complexity in streams and intermediate complexity in lakes. We found that brain size, and the size of optic tectum and telencephalon differed across the three habitats, both being largest in lake fish with a tendency to be smaller in the stream compared to hatchery fish. Therefore, our findings do not support the hypothesis that in brown trout the volume of brain and its regions important for navigation and decision-making increases in physically complex habitats. We suggest that the observed differences in brain size might be associated with diet quality and habitat-specific behavioral adaptations rather than physical habitat complexity., Competing Interests: Authors have no conflict of interests to declare., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome-wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (F ST  = 0.433-0.712) from the English/Welsh and other European populations. Differentiation was elevated genome-wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto-nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre-glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum., (© 2021 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.)

Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially in the face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but the attendant small population sizes and new ecological pressures might affect phenotypic and genotypic variation and trajectories dramatically and in unknown ways. In Scotland, the European whitefish ( Coregonus lavaretus ) is native to only two lakes and vulnerable to extirpation. Six new refuge populations were established over the last 30 years as a conservation measure. In this study, we examined whether there is a predictable ecological and evolutionary response of these fishes to translocation. We found eco-morphological differences, as functional traits relating to body shape differed between source and refuge populations. Dual isotopic analyses suggested some ecological release, with the diets in refuge populations being more diverse than in source populations. Analyses of up to 9117 genome-mapped SNPs showed that refuge populations had reduced genetic diversity and elevated inbreeding and relatedness relative to source populations, though genomic differentiation was low ( F ST  = 0.002-0.030). We identified 14 genomic SNPs that showed shared signals of a selective response to translocations, including some located near or within genes involved in the immune system, nervous system and hepatic functions. Analysis of up to 120,897 epigenomic loci identified a component of consistent differential methylation between source and refuge populations. We found that epigenomic variation and genomic variation were associated with morphological variation, but we were not able to infer an effect of population age because the patterns were also linked with the methodology of the translocations. These results show that conservation-driven translocations affect evolutionary potential by impacting eco-morphological, genomic and epigenomic components of diversity, shedding light on acclimation and adaptation process in these contexts., Competing Interests: None declared., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Environmental conditions can impact the development of phenotypes and in turn the performance of individuals. Climate change, therefore, provides a pressing need to extend our understanding of how temperature will influence phenotypic variation. To address this, we assessed the impact of increased temperatures on ecologically significant phenotypic traits in Arctic charr (Salvelinus alpinus). We raised Arctic charr at 5°C and 9°C to simulate a predicted climate change scenario and examined temperature-induced variation in ossification, bone metabolism, skeletal morphology, and escape response. Fish reared at 9°C exhibited less cartilage and bone development at the same developmental stage, but also higher bone metabolism in localized regions. The higher temperature treatment also resulted in significant differences in craniofacial morphology, changes in the degree of variation, and fewer vertebrae. Both temperature regime and vertebral number affected escape response performance, with higher temperature leading to decreased latency. These findings demonstrate that climate change has the potential to impact development through multiple routes with the potential for plasticity and the release of cryptic genetic variation to have strong impacts on function through ecological performance and survival., (© 2021 The Authors. Evolution & Development Published by Wiley Periodicals LLC.)

Background: Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup., Results: All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling., Conclusions: Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.

It is well recognized that environmental degradation caused by human activities can result in dramatic losses of species and diversity. However, comparatively little is known about the ability of biodiversity to re-emerge following ecosystem recovery. Here, we show that a European whitefish subspecies, the gangfisch Coregonus lavaretus macrophthalmus, rapidly increased its ecologically functional diversity following the restoration of Lake Constance after anthropogenic eutrophication. In fewer than ten generations, gangfisch evolved a greater range of gill raker numbers (GRNs) to utilize a broader ecological niche. A sparse genetic architecture underlies this variation in GRN. Several co-expressed gene modules and genes showing signals of positive selection were associated with GRN and body shape. These were enriched for biological pathways related to trophic niche expansion in fishes. Our findings demonstrate the potential of functional diversity to expand following habitat restoration, given a fortuitous combination of genetic architecture, genetic diversity and selection.

Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Q lake-P  = 96.8%, F st  = 0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Q anad-P  = 37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations., (© 2018 John Wiley & Sons Ltd.)

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Sympatric speciation is thought to be strongly linked to resource specialization with alternative resource use acting as a fundamental agent driving divergence. However, sympatric speciation through niche expansion is dependent on foraging specialization being consistent over space and time. Standard metabolic rate is the minimal maintenance metabolic rate of an ectotherm in a post-absorptive and inactive state and can constitute a significant portion of an animal's energy budget; thus, standard metabolic rate and growth rate are two measures frequently used as an indication of the physiological performance of individuals. Physiological adaptations to a specific diet may increase the efficiency with which it is utilized, but may have an increased cost associated with switching diets, which may result in a reduced standard metabolic rate and growth rate. In this study, we use the diet specialization often seen in polymorphic Arctic charr (Salvelinus alpinus) populations to study the effects of different prey on standard metabolic rate and growth rate as well as the effects that early prey specialization may have on the ability to process other prey types efficiently. We found a significant effect of prey type on standard metabolic rate and growth rate. Furthermore, we found evidence of diet specialization with all fish maintaining a standard metabolic rate and growth rate lower than expected when fed on a diet different to which they were raised, possibly due to a maladaptation in digestion of alternative prey items. Our results show that early diet specialization may be reinforced by the elevated costs of prey switching, thus promoting the process of resource specialization during the incipient stages of sympatric divergence., (© 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.)