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Carbonneau A, April J, Normandeau E, Ferchaud A, Nadeau V, Bernatchez L. Population genomics, life-history tactics, and mixed-stock subsistence fisheries in the northernmost American Atlantic salmon populations. Evol Appl 2024; 17:e13654. [PMID: 38405338 PMCID: PMC10883791 DOI: 10.1111/eva.13654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/27/2024] Open
Abstract
While Atlantic salmon (Salmo salar) of the northernmost American populations is alimentary, economically, and culturally important for Ungava Inuit communities (Nunavik, Canada) and might play a key role in the persistence of the species in a global warming context, many mysteries remain about those remote and atypical populations. Thus, our first aim was to document the genomic structure of the Nunavik populations. The second objective was to determine whether salmon only migrating to the estuary without reaching the sea, apparently unique to those populations, represent distinct populations from the typical anadromous salmons and subsequently explore the genetic basis of migratory life-history tactics in the species. Finally, the third goal was to quantify the contribution of each genetically distinct population and life-history tactic in the mixed-stock subsistence fishery of the Koksoak R. estuary. We used Genotyping-by-Sequencing to genotype 14,061 single nucleotide polymorphisms in the genome of 248 individuals from 8 source populations and 280 individuals from the Koksoak estuary mixed-stock fishery. Life-history tactics were identified by a visual assessment of scales. Results show a hierarchical structure mainly influenced by isolation-by-distance with 7 populations out of the 8 studied rivers. While no obvious structure was detected between marine and estuarine salmon within the population, we have identified genomic regions putatively associated with those migration tactics. Finally, all salmon captured in the Koksoak estuary originated from the Koksoak drainage and mostly from 2 tributaries, but no inter-annual variation in the contribution of these tributaries was found. Our results indicate, however, that both marine and estuarine salmon contribute substantially to estuarine fisheries and that there is inter-annual variation in this contribution. These findings provide crucial information for the conservation of salmon populations in a rapidly changing ecosystem, as well as for fishery management to improve the food security of Inuit communities.
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Affiliation(s)
- Alexandre Carbonneau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Julien April
- Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP)QuébecQuebecCanada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Anne‐Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas EstablishmentQuébecQuebecCanada
| | - Véronique Nadeau
- Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP)QuébecQuebecCanada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
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Subramanian S, Kumar M. Genomic footprints of bottleneck in landlocked salmon population. Sci Rep 2023; 13:6706. [PMID: 37185620 PMCID: PMC10130149 DOI: 10.1038/s41598-023-34076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and ponds of the Northern Hemisphere. Occasionally, the populations also got locked when the flow of rivers terminated from reaching the sea due to land upheaval. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers. According to the theories of population genetics, the effect of genetic drift is expected to be more pronounced in the former compared to the latter. Here we examined this using the whole genome data of landlocked and anadromous salmon populations of Norway. Our results showed a 50-80% reduction in the genomic heterozygosity in the landlocked compared to anadromous salmon populations. The number and total size of the runs of homozygosity (RoH) segments of landlocked salmons were two to eightfold higher than those of their anadromous counterparts. We found the former had a higher ratio of nonsynonymous-to-synonymous diversities than the latter. The investigation also revealed a significant elevation of homozygous deleterious Single Nucleotide Variants (SNVs) in the landlocked salmon compared to the anadromous populations. All these results point to a significant reduction in the population size of the landlocked salmons. This process of reduction might have started recently as the phylogeny revealed a recent separation of the landlocked from the anadromous population. Previous studies on terrestrial vertebrates observed similar signatures of a bottleneck when the populations from Island and the mainland were compared. Since landlocked waterbody such as ponds and lakes are geographically analogous to Islands for fish populations, the findings of this study suggest the similarity in the patterns of evolution between the two.
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Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia.
| | - Manoharan Kumar
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia
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Adams CE, Chavarie L, Rodger JR, Honkanen HM, Thambithurai D, Newton MP. An opinion piece: the evolutionary and ecological consequences of changing selection pressures on marine migration in Atlantic salmon. JOURNAL OF FISH BIOLOGY 2022; 100:860-867. [PMID: 35212396 PMCID: PMC9311443 DOI: 10.1111/jfb.15024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
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.
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Affiliation(s)
- Colin E. Adams
- Scottish Centre for Ecology & the Natural EnvironmentInstitute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
| | - Louise Chavarie
- Scottish Centre for Ecology & the Natural EnvironmentInstitute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
- Faculty of Environmental Sciences and Natural Resource ManagementThe Norwegian University of Life SciencesÅsNorway
| | - Jessica R. Rodger
- Atlantic Salmon Trust FellowScottish Centre for Ecology & the Natural Environment, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
| | - Hannele M. Honkanen
- Scottish Centre for Ecology & the Natural EnvironmentInstitute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
| | - Davide Thambithurai
- Atlantic Salmon Trust FellowScottish Centre for Ecology & the Natural Environment, Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
| | - Matthew P. Newton
- Scottish Centre for Ecology & the Natural EnvironmentInstitute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, RowardennanGlasgowUK
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Genetic Structure and Population Demography of White-Spotted Charr in the Upstream Watershed of a Large Dam. WATER 2020. [DOI: 10.3390/w12092406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
White-spotted charr (Salvelinus leucomaenis leucomaenis) is an anadromous fish that has been severely harmed by human land-use development, particularly through habitat fragmentation. However, the anthropogenic impacts on populations of this species have not been evaluated, except those on small dammed-off populations. Using multiplexed ISSR genotyping by sequencing, we investigated the genetic structure of white-spotted charr in four tributaries in the upper section of the Kanayama Dam in the Sorachi River, Hokkaido Island, Japan. There were no distinct genetic structures (FST = 0.014), probably because some active individuals migrate frequently among tributaries. By model-flexible demographic simulation, historical changes in the effective population size were inferred. The result indicates that the population size has decreased since the end of the last glacial period, with three major population decline events, including recent declines that were probably associated with recent human activities. Nevertheless, populations in the watershed upstream of the Kanayama Dam are still expected to be at low risk of immediate extinction, owing to the large watershed size and the limited number of small check dams. An effective conservation measure for sustaining the white-spotted charr population is to maintain high connectivity between tributaries, such as by providing fishways in check dams during construction.
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Andersen Ø, Vieira V, Dessen JE, Johnston IA. Influence of feed ration size on somatic and muscle growth in landlocked dwarf and farmed Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2019; 94:614-620. [PMID: 30810225 DOI: 10.1111/jfb.13942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
We examined the possible adaptation of the dwarf Bleke population of Atlantic salmon Salmo salar from Lake Byglandsfjord in southern Norway to limited food resources. The growth performance and muscle development in juvenile Bleke and farmed S. salar under satiated or restricted (50%) feeding were examined for 10 months, starting 3 weeks after first-feeding stage. Four-thousand fish were divided into four replicated groups and random samples of 16-40 fish per group were measured six times during the experiment. The two strains showed no significant difference in mean body mass when fed restricted ration, but the individual variation was considerably higher in the farmed fish. Both Bleke and farmed S. salar grew significantly faster when fed to satiation, but the farmed S. salar showed much higher gain in mass and were three times heavier (201.5 g vs 66.7 g) and possessed twice as many fast muscle fibres (179,682 vs 84,779) compared with landlocked S. salar after 10 months. Farmed fish fed full ration displayed both hypertrophic and hyperplasic muscle growth, while the increased growth in Bleke S. salar was entirely associated with a larger fibre diameter. The landlocked Bleke strain has apparently adapted to low food availability by minimising the metabolic costs of maintenance and growth through reduced dominance hierarchies and by an increase in average muscle fibre diameter relative to the ancestral condition.
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Affiliation(s)
- Øivind Andersen
- Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima AS), Aas, Norway
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Vera Vieira
- Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | - Jens-Erik Dessen
- Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima AS), Aas, Norway
| | - Ian A Johnston
- Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Scotland, UK
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Wright RF, Couture RM, Christiansen AB, Guerrero JL, Kaste Ø, Barlaup BT. Effects of multiple stresses hydropower, acid deposition and climate change on water chemistry and salmon populations in the River Otra, Norway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 574:128-138. [PMID: 27627688 DOI: 10.1016/j.scitotenv.2016.09.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Many surface waters in Europe suffer from the adverse effects of multiple stresses. The Otra River, southernmost Norway, is impacted by acid deposition, hydropower development and increasingly by climate change. The river holds a unique population of land-locked salmon and anadromous salmon in the lower reaches. Both populations have been severely affected by acidification. The decrease in acid deposition since the 1980s has led to partial recovery of both populations. Climate change with higher temperatures and altered precipitation can potentially further impact fish populations. We used a linked set of process-oriented models to simulate future climate, discharge, and water chemistry at five sub-catchments in the Otra river basin. Projections to year 2100 indicate that future climate change will give a small but measureable improvement in water quality, but that additional reductions in acid deposition are needed to promote full restoration of the fish communities. These results can help guide management decisions to sustain key salmon habitats and carry out effective long-term mitigation strategies such as liming. The Otra River is typical of many rivers in Europe in that it fails to achieve the good ecological status target of the EU Water Framework Directive. The programme of measures needed in the river basin management plan necessarily must consider the multiple stressors of acid deposition, hydropower, and climate change. This is difficult, however, as the synergistic and antagonistic effects are complex and challenging to address with modelling tools currently available.
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Affiliation(s)
- Richard F Wright
- Norwegian Institute for Water Research-NIVA, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Raoul-Marie Couture
- Norwegian Institute for Water Research-NIVA, Gaustadalléen 21, N-0349 Oslo, Norway; Ecohydrology Group, University of Waterloo, 200 University Ave, N2L 3G1 Waterloo, Canada.
| | - Anne B Christiansen
- Norwegian Institute for Water Research-NIVA, Region South, Jon Lilletuns vei 3, N-4879 Grimstad, Norway
| | - José-Luis Guerrero
- Norwegian Institute for Water Research-NIVA, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Øyvind Kaste
- Norwegian Institute for Water Research-NIVA, Region South, Jon Lilletuns vei 3, N-4879 Grimstad, Norway
| | - Bjørn T Barlaup
- Uni Research, Uni Environment, LFI, Thormøhlensgt. 49 B, 5006 Bergen, Norway
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Sundqvist L, Keenan K, Zackrisson M, Prodöhl P, Kleinhans D. Directional genetic differentiation and relative migration. Ecol Evol 2016; 6:3461-3475. [PMID: 27127613 PMCID: PMC4842207 DOI: 10.1002/ece3.2096] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum-likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.
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Affiliation(s)
- Lisa Sundqvist
- Department of Marine SciencesUniversity of GothenburgSE‐405 30GothenburgSweden
| | - Kevin Keenan
- School of Biological SciencesInstitute for Global Food SecurityQueen's University BelfastBelfastBT9 7BLUK
| | - Martin Zackrisson
- Department for Chemistry and Molecular BiologyUniversity of GothenburgSE‐405 30GothenburgSweden
| | - Paulo Prodöhl
- School of Biological SciencesInstitute for Global Food SecurityQueen's University BelfastBelfastBT9 7BLUK
| | - David Kleinhans
- ForWind Center for Wind Energy ResearchInstitute of PhysicsCarl von Ossietzky UniversityDE‐26129OldenburgGermany
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Wenne R, Drywa A, Kent M, Sundsaasen KK, Lien S. SNP Arrays for Species Identification in Salmonids. Methods Mol Biol 2016; 1452:97-111. [PMID: 27460372 DOI: 10.1007/978-1-4939-3774-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland.
| | - Agata Drywa
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Kristil Kindem Sundsaasen
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
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