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Moccetti P, Bolland JD, Adams CE, Rodger JR, Honkanen HM, Newton M, Lothian AJ, Nunn AD, Joyce DA. Genotype But Not Body Shape Predicts River Migration Success in Atlantic Salmon. Ecol Evol 2024; 14:e70682. [PMID: 39687579 PMCID: PMC11647181 DOI: 10.1002/ece3.70682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/18/2024] [Accepted: 11/20/2024] [Indexed: 12/18/2024] Open
Abstract
Migratory species typically undertake demanding long-distance journeys, across different habitat types during which they are exposed to multiple natural and anthropogenic stressors. Mortality during migration is typically high and may be human induced. Understanding individual responses to these selection pressures is rarely attempted because of the challenges of relating individual phenotypic and genetic data to migration success. Here, we show distinct single nucleotide polymorphism (SNP) sets significantly differentiated between Atlantic salmon smolts making successful migrations to sea and those that failed to migrate, in two different rivers. In contrast, morphological variation was not diagnostic of migration success. Populations from each river were genetically distinct, and while different genes were possibly implicated in migration success in each river, they related to common biological processes (e.g., osmoregulation and immune and stress response). Given that migration failure should quickly purge polymorphism at selected SNPs from a population, the question of how genetic diversity in these populations is maintained is an important one. Standing genetic variation could be maintained by different life history strategies and/or environmentally driven balancing selection. Our work highlights the importance of preserving genetic diversity to ensure evolutionary resilience at the population level and has practical implications for management.
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Affiliation(s)
- Paolo Moccetti
- Energy and Environment InstituteUniversity of HullHullUK
- Evolutionary and Ecological Genomics Group, School of Natural SciencesUniversity of HullHullUK
- Hull International Fisheries Institute, School of Natural SciencesUniversity of HullHullUK
- Institute of Earth SciencesUniversity of Applied Sciences and Arts of Southern SwitzerlandMendrisioSwitzerland
| | - Jonathan D. Bolland
- Evolutionary and Ecological Genomics Group, School of Natural SciencesUniversity of HullHullUK
| | - Colin E. Adams
- Scottish Centre for Ecology and the Natural Environment, School of Biodiversity One Health & Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Jessica R. Rodger
- Atlantic Salmon Trust Fellow, Scottish Centre for Ecology and the Natural Environment, School of Biodiversity One Health & Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Hannele M. Honkanen
- Scottish Centre for Ecology and the Natural Environment, School of Biodiversity One Health & Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Matthew Newton
- Scottish Centre for Ecology and the Natural Environment, School of Biodiversity One Health & Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Angus J. Lothian
- Atlantic Salmon Trust Fellow, Scottish Centre for Ecology and the Natural Environment, School of Biodiversity One Health & Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Andy D. Nunn
- Evolutionary and Ecological Genomics Group, School of Natural SciencesUniversity of HullHullUK
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2
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Flanagan SP, Alonzo SH. Supergenes are not necessary to explain the maintenance of complex alternative phenotypes. Proc Biol Sci 2024; 291:20241715. [PMID: 39406344 PMCID: PMC11479756 DOI: 10.1098/rspb.2024.1715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/04/2024] [Accepted: 09/17/2024] [Indexed: 10/20/2024] Open
Abstract
Evolutionary biology aims to explain the diversity seen in nature. Evolutionary theory provides frameworks to understand how simple polymorphisms or continuous variation are maintained, but phenotypes inherited as discrete suites of quantitative traits are difficult to fit into this framework. Supergenes have been proposed as a solution to this problem-if causal genes are co-located, they can be inherited as if a single gene, thus bridging the gap between simple polymorphisms and continuous traits. We develop models to ask: how are critical supergenes for maintaining phenotypic diversity? In our simplest model, without explicit genetic architectures, three alternative reproductive morphs are maintained in many of the parameter combinations we evaluated. For these same parameter values, models with demographic stochasticity, recombination and mutation (but without explicit genetic architecture) maintained only two of these three morphs, with stochasticity determining which morphs persisted. With explicit genetic architectures, regardless of whether causal loci were co-located in a supergene or distributed randomly, this stochasticity in which morphs are maintained was reduced. Even when phenotypic variation was lost, genetic diversity was maintained. Altogether, categorical traits with polygenic bases exhibited similar evolutionary dynamics to those determined by supergenes. Our work suggests that supergenes are not the only answer to the puzzle of how discrete polygenic phenotypic variation is maintained.
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Affiliation(s)
- Sarah P. Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Suzanne H. Alonzo
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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3
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Wang D, Abbott J, Brenninger FA, Klein K, Nava-Bolaños A, Yong L, Richter XYL. Female alternative reproductive tactics: diversity and drivers. Trends Ecol Evol 2024; 39:937-946. [PMID: 38955568 DOI: 10.1016/j.tree.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024]
Abstract
It is often argued that anisogamy causes alternative reproductive tactics (ARTs) to be more common in males than females. We challenge this view by pointing out logical flaws in the argument. We then review recent work on the diversity of female ARTs, listing several understudied types such as solitary versus communal breeding and facultative parthenogenesis. We highlight an important difference between male and female ARTs that caused female ARTs to be overlooked: male ARTs tend to focus on successful fertilization, whereas female ARTs occur at many stages of reproduction and often form complex networks of decision points. We propose to study correlated female ARTs as a whole to better understand their drivers and eco-evolutionary dynamics.
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Affiliation(s)
- Daiping Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, 100101 Beijing, China; University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Jessica Abbott
- Department of Biology, Lund University, 22362 Lund, Sweden
| | - Franziska A Brenninger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Kora Klein
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, 55122 Mainz, Germany
| | - Angela Nava-Bolaños
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Campus Juriquilla, Universidad Nacional Autónoma de México, Boulevard Juriquilla, Jurica La Mesa, Juriquilla, 76230 Querétaro, México
| | - Lengxob Yong
- Marine Resources Research Institute, South Carolina Department of Natural Resources, Charleston, SC 29412, USA
| | - Xiang-Yi Li Richter
- Institute of Ecology and Evolution, Baltzerstrasse 6, University of Bern, 3012 Bern, Switzerland.
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4
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Bekkevold D, Besnier F, Frank‐Gopolos T, Nielsen EE, Glover KA. Introgression affects Salmo trutta juvenile life-history traits generations after stocking with non-native strains. Evol Appl 2024; 17:e13725. [PMID: 38962360 PMCID: PMC11219512 DOI: 10.1111/eva.13725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 07/05/2024] Open
Abstract
Introgression of non-native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long-term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout (Salmo trutta, L.) population, subjected to intensive stocking with domesticated hatchery fish of non-native origin. We used wild-caught genetically wild and admixed trout as well as fish from the partly domesticated hatchery strain used for stocking the river up until ~15 years prior to this study, to produce 22 families varying in hatchery/wild admixture. Following a replicated common-garden experiment conducted in fish tanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a significant positive relationship between family admixture and fish size upon termination, an effect observed through all levels of admixture. Furthermore, the admixture effect was most distinct at the higher rearing temperatures. Although the hatchery strain used for stocking had been in culture for ~7 generations, it had not been deliberately selected for increased growth. These data thus demonstrate: (i) that growth had increased in the hatchery strain even in the absence of deliberate directional selection for this trait, (ii) that the increasing effect of admixture by temperature could represent inadvertent selection for performance in the hatchery strain at higher temperatures, and most significantly, (iii) that despite undergoing up to five generations of natural selection in the admixed wild population, the genetically increased growth potential was still detectable and thus persistent. Our findings suggest that altered growth patterns and potentially their cascading effects are of importance to the severity of hatchery/wild introgression, especially under changing-climate scenarios and are of general significance to conservation practitioners seeking to evaluate long-term effects of intra-specific hybridization including under recovery.
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Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Thomas Frank‐Gopolos
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Einar E. Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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5
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Brown MS, Carvalheiro R, Taylor RS, Mekkawy W, Luke TDW, Rands L, Nieuwesteeg D, Evans BS, Wade NM, Lind CE, Hilder PE. Probabilistic reaction norm reveals family-related variation in the association between size, condition, and sexual maturation onset in Atlantic salmon (Salmo salar). JOURNAL OF FISH BIOLOGY 2024; 104:939-949. [PMID: 37996984 DOI: 10.1111/jfb.15626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
This study investigated the relationship between the size, condition, year class, family, and sexual maturity of Atlantic salmon (Salmo salar) using data collected in an aquaculture selective breeding programme. Males that were sexually mature at 2 years of age (maiden spawn) have, on average, greater fork length and condition factor (K) at 1 year of age than their immature counterparts. For every 10-mm increase in fork length or 0.1 increase in K at 1 year of age, the odds of sexual maturity at 2 years of age increased by 1.48 or 1.22 times, respectively. Females that were sexually mature at 3 years of age (maiden spawn) have, on average, greater fork length and K at 2 years of age than their immature counterparts. For every 10-mm increase in fork length or 0.1 increase in K at 2 years of age, the odds of sexual maturity at 3 years of age increased by 1.06 or 1.44 times, respectively. The family explained 34.93% of the variation in sexual maturity among 2-year-old males that was not attributable to the average effects of fork length and K at 1 year of age and year class. The proportion of variation in sexual maturity among 3-year-old females explained by the family could not be investigated. These findings suggest that the onset of sexual maturation in Atlantic salmon is conditional on performance (with respect to energy availability) surpassing a threshold, the magnitude of which can vary between families and is determined by a genetic component. This could support the application of genetic selection to promote or inhibit the onset of sexual maturation in farmed stocks.
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Affiliation(s)
| | | | | | - Wagdy Mekkawy
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
| | | | - Lewis Rands
- Salmon Enterprises of Tasmania Pty. Ltd., Wayatinah, Tasmania, Australia
| | - Damien Nieuwesteeg
- Salmon Enterprises of Tasmania Pty. Ltd., Wayatinah, Tasmania, Australia
| | - Brad S Evans
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
| | - Nicholas M Wade
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, UK
| | - Curtis E Lind
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
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6
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Bernos TA, Chang SL, Giglio RM, Davenport K, Fisher J, Lowery E, Bearlin A, Simmons R, Fortin M, Day CC, Landguth EL. Evaluating the evolutionary mechanisms maintaining alternative mating strategies in a simulated bull trout ( Salvelinus confluentus) population. Ecol Evol 2023; 13:e9965. [PMID: 37038529 PMCID: PMC10082177 DOI: 10.1002/ece3.9965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
The coexistence of distinct alternative mating strategies (AMS) is often explained by mechanisms involving trade-offs between reproductive traits and lifetime fitness; yet their relative importance remains poorly understood. Here, we used an established individual-based, spatially explicit model to simulate bull trout (Salvelinus confluentus) in the Skagit River (Washington, USA) and investigated the influence of female mating preference, sneaker-specific mortality, and variation in age-at-maturity on AMS persistence using global sensitivity analyses and boosted regression trees. We assumed that two genetically fixed AMS coexisted within the population: sneaker males (characterized by younger age-at-maturity, greater AMS-specific mortality, and lower reproductive fitness) and territorial males. After 300 years, variation in relative sneaker success in the system was explained by sneaker males' reproductive fitness (72%) and, to a lesser extent, the length of their reproductive lifespan (21%) and their proportion in the initial population (8%). However, under a wide range of parameter values, our simulated scenarios predicted the extinction of territorial males or their persistence in small, declining populations. Although these results do not resolve the coexistence of AMS in salmonids, they reinforce the importance of mechanisms reducing sneaker's lifetime reproductive success in favoring AMS coexistence within salmonid populations but also limit the prediction that, without any other selective mechanisms at play, strong female preference for mating with territorial males and differences in reproductive lifespan allow the stable coexistence of distinct AMS.
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Affiliation(s)
- Thaïs A. Bernos
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
| | - Sarah L. Chang
- Department of BiologyUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
| | - Rachael M. Giglio
- Department of Ecology, Evolution, and Organismal BiologyOhio State UniversityColumbusOhioUSA
- United States Department of AgricultureNational Wildlife Research CenterOttawaOntarioUSA
| | - Kaeli Davenport
- Department of Wildlife BiologyUniversity of MontanaMissoulaMontanaUSA
| | | | | | | | | | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Casey C. Day
- School of Public and Community Health SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Erin L. Landguth
- School of Public and Community Health SciencesUniversity of MontanaMissoulaMontanaUSA
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7
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Gamble MM, Calsbeek RG. A potential role for restricted intertactical heritability in preventing intralocus conflict. Evol Appl 2021; 14:2576-2590. [PMID: 34815740 PMCID: PMC8591329 DOI: 10.1111/eva.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 11/29/2022] Open
Abstract
Intralocus sexual conflict, which arises when the same trait has different fitness optima in males and females, reduces population growth rates. Recently, evolutionary biologists have recognized that intralocus conflict can occur between morphs or reproductive tactics within a sex and that intralocus tactical conflict might constrain tactical dimorphism and population growth rates just as intralocus sexual conflict constrains sexual dimorphism and population growth rates. However, research has only recently focused on sexual and tactical intralocus conflict simultaneously, and there is no formal theory connecting the two. We present a graphical model of how tactical and sexual conflict over the same trait could constrain both sexual and tactical dimorphisms. We then use Coho salmon (Oncorhynchus kisutch), an important species currently protected under the Endangered Species Act, to investigate the possibility of simultaneous sexual and tactical conflict. Larger Coho males gain access to females through fighting while smaller males are favored through sneaking tactics, and female reproductive success is positively correlated with length. We tested for antagonistic selection on length at maturity among sexes and tactics and then used parent-offspring regression to calculate sex- and tactic-specific heritabilities to determine whether and where intralocus conflict exists. Selection on length varied in intensity and form among tactics and years. Length was heritable between dams and daughters (h 2 ± 95% CI = 0.361 ± 0.252) and between fighter males and their fighter sons (0.867 ± 0.312), but no other heritabilities differed significantly from zero. The lack of intertactical heritabilities in this system, combined with similar selection on length among tactics, suggests the absence of intralocus conflict between sexes and among tactics, allowing for the evolution of sexual and tactical dimorphisms. Our results suggest that Coho salmon populations are unlikely to be constrained by intralocus conflict or artificial selection on male tactic.
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Affiliation(s)
- Madilyn M. Gamble
- Graduate Program in Ecology, Evolution, Ecosystems, and SocietyDartmouth CollegeHanoverNHUSA
| | - Ryan G. Calsbeek
- Graduate Program in Ecology, Evolution, Ecosystems, and SocietyDartmouth CollegeHanoverNHUSA
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8
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Wacker S, Skaug HJ, Forseth T, Solem Ø, Ulvan EM, Fiske P, Karlsson S. Considering sampling bias in close-kin mark-recapture abundance estimates of Atlantic salmon. Ecol Evol 2021; 11:3917-3932. [PMID: 33976784 PMCID: PMC8093659 DOI: 10.1002/ece3.7279] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 12/04/2022] Open
Abstract
Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close-kin mark-recapture (CKMR) is based on the principles of conventional mark-recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out-migrating smolts PIT-tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV < 0.15), due to the detection of a high number of parent-offspring pairs. Sampling of adults was age- and size-biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT-tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT-tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.
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Affiliation(s)
| | - Hans J. Skaug
- Department of MathematicsUniversity of BergenBergenNorway
| | | | - Øyvind Solem
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Eva M. Ulvan
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Peder Fiske
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Sten Karlsson
- Norwegian Institute for Nature ResearchTrondheimNorway
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9
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Fjelldal PG, Hansen TJ, Wargelius A, Ayllon F, Glover KA, Schulz RW, Fraser TWK. Development of supermale and all-male Atlantic salmon to research the vgll3 allele - puberty link. BMC Genet 2020; 21:123. [PMID: 33183224 PMCID: PMC7664053 DOI: 10.1186/s12863-020-00927-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Farmed Atlantic salmon are one of the most economically significant global aquaculture products. Early sexual maturation of farmed males represents a significant challenge to this industry and has been linked with the vgll3 genotype. However, tools to aid research of this topic, such as all-male and clonal fish, are still lacking. The present 6-year study examined if all-male production is possible in Atlantic salmon, a species with heteromorphic sex chromosomes (males being XY, females XX), and if all-male fish can be applied to further explore the vgll3 contribution on the likelihood of early maturation. RESULTS Estrogen treatment of mixed sex yolk sac larvae gave rise to one sexually mature hermaphrodite with a male genotype (XY) that was used to produce both self-fertilized offspring and androgenetic double haploid (dh) offspring following egg activation with UV treated sperm and pressure shock to block the first mitotic division. There were YY supermales among both offspring types, which were crossed with dh females. Between 1 and 8% of the putative all-male offspring from the eight crosses with self-fertilized supermales were found to have ovaries, and 95% of these phenotypic females were also genetically female. None of the offspring from the one dh supermale cross had ovaries. When assessing the general contribution of the vgll3 locus on the likelihood of early post-smolt sexual maturation (jacking) in the all-male populations we found individuals that were homozygous for the early maturing genotype (97%) were more likely to enter puberty than individuals that were homozygous for the late maturing genotype (26%). However, the likelihood of jacking within individuals with an early/late heterozygous genotype was higher when the early allele came from the dam (94%) compared to the sire (45%). CONCLUSIONS The present results show that supermale Atlantic salmon are viable and fertile and can be used as a research tool to study important aspects of sexual maturation, such as to further explore the sex dependent parental genetic contribution to age at puberty in Atlantic salmon. In addition, we report the production of viable double haploid supermale fish.
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Affiliation(s)
- Per Gunnar Fjelldal
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Tom J. Hansen
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Anna Wargelius
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Fernando Ayllon
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Rüdiger W. Schulz
- Reproductive Biology Group, Division Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Thomas W. K. Fraser
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
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10
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Aykanat T, Rasmussen M, Ozerov M, Niemelä E, Paulin L, Vähä JP, Hindar K, Wennevik V, Pedersen T, Svenning MA, Primmer CR. Life-history genomic regions explain differences in Atlantic salmon marine diet specialization. J Anim Ecol 2020; 89:2677-2691. [PMID: 33460064 DOI: 10.1111/1365-2656.13324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 07/14/2020] [Indexed: 01/04/2023]
Abstract
Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction. We aimed to test the hypothesis that heritable resource acquisition variation that covaries with efficiency along the ontogeny would influence maturation timing of individuals. To test this hypothesis, we utilized Atlantic salmon as a model which exhibits a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as stomach fullness and composition) of individuals with different ages, and linked it with genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity. Consistent with the hypothesis, we demonstrated that one of the life-history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked to six6, and suggestively (but non-significantly) to vgll3 genomic regions. We further showed Atlantic salmon switched to the so-called 'feast and famine' strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often. These results suggest genetic variation underlying resource utilization may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food web structures.
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Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Martin Rasmussen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mikhail Ozerov
- Department of Biology, University of Turku, Turku, Finland.,Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Eero Niemelä
- Department of Biology, University of Turku, Turku, Finland.,Natural Resources Institute Finland (Luke), Oulu, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha-Pekka Vähä
- Association for Water and Environment of Western Uusimaa, Lohja, Finland
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | | | - Torstein Pedersen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Martin-A Svenning
- Arctic Ecology Department, Norwegian Institute for Nature Research (NINA), Tromsø, Norway
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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11
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Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L, Dutech C, Aissi A, Bacles CF, Daverat F, Launey S, Guichoux E. Fast sequence-based microsatellite genotyping development workflow. PeerJ 2020; 8:e9085. [PMID: 32411534 PMCID: PMC7204839 DOI: 10.7717/peerj.9085] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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Affiliation(s)
- Olivier Lepais
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | | | - Aurélie Manicki
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | - Laura Taillebois
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | - Cecile F.E. Bacles
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | - Sophie Launey
- INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France
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12
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Bouchard C, Lange F, Guéraud F, Rives J, Tentelier C. Sexual maturity increases mobility and heterogeneity in individual space use in Atlantic salmon (Salmo salar) parr. JOURNAL OF FISH BIOLOGY 2020; 96:925-938. [PMID: 32048290 DOI: 10.1111/jfb.14282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
We assessed the effects of sexual maturity on space use in Atlantic salmon (Salmo salar) parr as facultative early maturation enables us to work on individuals belonging to the same cohort. We monitored the space use of 40 1-year-old males in natura throughout a breeding season. First, mature individuals covered longer distances (absolute and upstream) and located within broader home ranges than immature parr. Second, sexual maturity also generated a higher interindividual variability in space use. Finally, mature individuals exhibited a higher probability of association with likely breeding sites on average. However, some mature individuals experienced a lower probability than immature individuals, suggesting that the space use of some mature individuals may not be optimal. Moreover, mature parr exploiting a broader home range or covering longer upstream distances had a higher probability of association with likely breeding sites. Covering longer upstream distances may therefore increase the reproductive success of mature parr, while involving higher energetic costs and a greater risk of predation.
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Affiliation(s)
- Colin Bouchard
- Université de Pau & des Pays de l'Adour, e2s, INRAE, UMR 1224 Ecobiop, Saint-Pée sur Nivelle, France
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, Arles, France
| | - Frédéric Lange
- Université de Pau & des Pays de l'Adour, e2s, INRAE, UMR 1224 Ecobiop, Saint-Pée sur Nivelle, France
| | - François Guéraud
- Université de Pau & des Pays de l'Adour, e2s, INRAE, UMR 1224 Ecobiop, Saint-Pée sur Nivelle, France
| | - Jacques Rives
- Université de Pau & des Pays de l'Adour, e2s, INRAE, UMR 1224 Ecobiop, Saint-Pée sur Nivelle, France
| | - Cédric Tentelier
- Université de Pau & des Pays de l'Adour, e2s, INRAE, UMR 1224 Ecobiop, Saint-Pée sur Nivelle, France
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13
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Ferguson A, Reed TE, Cross TF, McGinnity P, Prodöhl PA. Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. JOURNAL OF FISH BIOLOGY 2019; 95:692-718. [PMID: 31197849 PMCID: PMC6771713 DOI: 10.1111/jfb.14005] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/09/2019] [Indexed: 05/10/2023]
Abstract
Brown trout Salmo trutta is endemic to Europe, western Asia and north-western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river-resident, lake-resident) and three main facultative migratory life histories (downstream-upstream within a river system, fluvial-adfluvial potamodromous; to and from a lake, lacustrine-adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River-residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial-adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine-adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold-trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non-genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river-resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr-smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration-residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
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Affiliation(s)
- Andrew Ferguson
- School of Biological SciencesQueen's University BelfastBelfastUK
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Tom F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Paulo A. Prodöhl
- School of Biological SciencesQueen's University BelfastBelfastUK
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14
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O'Sullivan RJ, Aykanat T, Johnston SE, Kane A, Poole R, Rogan G, Prodöhl PA, Primmer CR, McGinnity P, Reed TE. Evolutionary stasis of a heritable morphological trait in a wild fish population despite apparent directional selection. Ecol Evol 2019; 9:7096-7111. [PMID: 31312431 PMCID: PMC6617767 DOI: 10.1002/ece3.5274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 12/14/2022] Open
Abstract
Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree-derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so-called "paradox of stasis." To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies-which have largely been limited to birds and mammals-to study evolutionary processes on contemporary timescales.
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Affiliation(s)
- Ronan James O'Sullivan
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Susan E. Johnston
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Adam Kane
- School of Biology and Environmental Science and Earth InstituteUniversity College DublinDublinIreland
| | | | - Ger Rogan
- Marine Institute, FurnaceNewportMayoIreland
| | - Paulo A. Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Medical Biology CentreQueen's University BelfastBelfastUK
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Philip McGinnity
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Thomas Eric Reed
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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15
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Fraser TW, Fjelldal PG, Schulz RW, Norberg B, Hansen TJ. Termination of puberty in out-of-season male Atlantic salmon smolts. Comp Biochem Physiol A Mol Integr Physiol 2019; 232:60-66. [DOI: 10.1016/j.cbpa.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/02/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]
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16
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Ayllon F, Solberg MF, Glover KA, Mohammadi F, Kjærner-Semb E, Fjelldal PG, Andersson E, Hansen T, Edvardsen RB, Wargelius A. The influence of vgll3 genotypes on sea age at maturity is altered in farmed mowi strain Atlantic salmon. BMC Genet 2019; 20:44. [PMID: 31060499 PMCID: PMC6501413 DOI: 10.1186/s12863-019-0745-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/25/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND In Atlantic salmon in the wild, age at maturity is strongly influenced by the vgll3 locus. Under farming conditions, light, temperature and feeding regimes are known significantly advance or delay age at maturity. However, the potential influence of the vgll3 locus on the maturation of salmon reared under farming conditions has been rarely investigated, especially in females. RESULTS Here, we reared domesticated salmon (mowi strain) with different vgll3 genotypes under standard farming conditions until they matured at either one, two or more than two sea winters. Interestingly, and in contrast to previous findings in the wild, we were not able to identify a link between vgll3 and age at maturity in females when reared under farming conditions. For males however, we found that the probability of delaying maturation from one to two sea winters was significantly lower in fish homozygous for the early allele compared to homozygous fish for the late allele, while the probability for heterozygous fish was intermediate. These data also contrast to previous findings in the wild where the early allele has been reported as dominant. However, we found that the probability of males delaying maturation from two to three sea winters was regulated in the same manner as the wild. CONCLUSIONS Collectively, our data suggest that increased growth rates in mowi salmon, caused by high feed intake and artificial light and temperature regimes together with other possible genetic/epigenetic components, may significantly influence the impact that the vgll3 locus has on age at maturity, especially in females. In turn, our results show that the vgll3 locus can only to a large extent be used in selective breeding to control age at maturation in mowi males. In summary, we here show that in contrast to the situation in wild salmon, under farming conditions vgll3 does not seem to influence age at maturity in mowi females whereas in mowi males, maturing as one or two sea winters it alters the early allele effect from dominant to intermediate.
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Affiliation(s)
- Fernando Ayllon
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Monica F Solberg
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Institute of Biology, University of Bergen, Bergen, Norway
| | - Faezeh Mohammadi
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Erik Kjærner-Semb
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Per Gunnar Fjelldal
- Institute of Marine research (IMR), Matre Aquaculture Research Station, 5984, Matredal, Norway
| | - Eva Andersson
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Tom Hansen
- Institute of Marine research (IMR), Matre Aquaculture Research Station, 5984, Matredal, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
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Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
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18
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Bacles CFE, Bouchard C, Lange F, Manicki A, Tentelier C, Lepais O. Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2018; 92:699-726. [PMID: 29377125 DOI: 10.1111/jfb.13537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
This study assesses whether the effective number of breeders (Nb ) can be estimated using a time and cost-effective protocol using genetic sibship reconstruction from a single sample of young-of-the-year (YOY) for the purposes of Atlantic salmon Salmo salar population monitoring. Nb was estimated for 10 consecutive reproductive seasons for S. salar in the River Nivelle, a small population located at the rear-edge of the species distribution area in France, chronically under its conservation limit and subjected to anthropogenic and environmental changes. Subsampling of real and simulated data showed that accurate estimates of Nb can be obtained from YOY genotypes, collected at moderate random sampling intensity, achievable using routine juvenile electrofishing protocols. Spatial bias and time elapsed since spawning were found to affect estimates, which must be accounted for in sampling designs. Nb estimated in autumn for S. salar in the River Nivelle was low and variable across years from 23 (95% C.I. 14-41) to 75 (53-101) and was not statistically correlated with the estimated number of returning adults, but it was positively correlated with the estimated number of YOY at age 9 months. Nb was found to be lower for intermediate levels of redd aggregation, suggesting that the strength of the competition between males to access females affects reproductive success variance depending on redd spatial configuration. Thus, environmental factors such as habitat availability and quality for spawning and YOY development predominate over demographic ones (number of returning adults) in driving long-term population viability for S. salar in the River Nivelle. This study showcases Nb as an integrated parameter, encompassing demographic and ecological information about a reproductive event, relevant to the assessment of both short-term effects of management practices and long-term population conservation status.
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Affiliation(s)
- C F E Bacles
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
| | - C Bouchard
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
| | - F Lange
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
| | - A Manicki
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
| | - C Tentelier
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
| | - O Lepais
- ECOBIOP, INRA, Université Pau & Pays Adour, 64310, Saint-Pée-Sur-Nivelle, France
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