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Sudbrack V, Mullon C. Fixation times of de novo and standing beneficial variants in subdivided populations. Genetics 2024; 227:iyae043. [PMID: 38527860 DOI: 10.1093/genetics/iyae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/17/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs from de novo recessive mutations, and dispersal is not too limited (such that approximately FST<0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of metapopulation dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, while de novo mutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
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Affiliation(s)
- Vitor Sudbrack
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Vaud, Switzerland
| | - Charles Mullon
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Vaud, Switzerland
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2
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Salvat-Leal I, Ortega A, Blanco E, García J, Romero D. Elemental composition in soft tissues as a model for identifying batches of juvenile Atlantic Bluefin Tuna (Thunnus thynnus). J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2023.105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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3
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F. L A, K. O S, E A, L K, R. B E, B N, P. G F, T. J H, R. W S, A W. The Piwil1 N domain is required for germ cell survival in Atlantic salmon. Front Cell Dev Biol 2022; 10:977779. [PMID: 36200047 PMCID: PMC9527287 DOI: 10.3389/fcell.2022.977779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic introgression of farmed salmon into wild populations can damage the genetic integrity of wild stocks and is therefore considered as an environmental threat. One possible solution is to induce sterility in farmed salmon. We have searched for proteins potentially essential for germline survival in Atlantic salmon. One of these is the argonaute protein Piwil1, known to be required for germ cell survival. To examine Piwil1 function in salmon, we induced indels in the N domain by CRISPR-Cas9. The encoded domain is present in all vertebrate Piwi proteins and has been linked to Tdrd1 protein interaction and PAZ lobe structure. The F0 founder generation of piwil1 crispant males and females displayed a mosaic pattern of piwil1 mutations, exhibiting highly mutated alleles (53%–97%) in their fin gDNA samples. In general, piwil1 crispants carried germ cells, went through puberty and became fertile, although a transient and partial germ cell loss and delays during the spermatogenic process were observed in many male crispants, suggesting that Piwil1 functions during salmon spermatogenesis. By crossing highly mutated F0 founders, we produced F1 fish with a mixture of: loss-of-function alleles (−); functional in frame mutated alleles (+) and wt alleles (+). In F1, all piwil1−/− fish lacked germ cells, while piwil1+/+ siblings showed normal ovaries and testes. Yet, most juvenile F1 piwil1+/−males and females displayed an intermediate phenotype with a higher somatic/germ cell ratio without an increase in germ cell apoptosis, suggestive of a gene dose effect on the number of germ cells and/or insufficient replacement of lost germ cells in heterozygous fish. Interestingly, the two longest in-frame indels in the N domain also ensured germ cell loss. Hence, the loss of 4–6 aa in this region Phe130-Ser136 may result in crucial changes of the protein structure, potentially affecting piRNA binding of the PAZ lobe, and/or affecting the binding of Piwil1 interacting proteins such as Tdrd protein, with critical consequences for the survival of primordial germ cells. In conclusion, we show that loss of piwil1 leads to loss of germ cells in salmon and that part of the N domain of Piwil1 is crucial for its function.
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Affiliation(s)
- Almeida F. L
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
- Embrapa Amazonia Ocidental, Manaus, Brazil
- *Correspondence: Almeida F. L,
| | - Skaftnesmo K. O
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Andersson E
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Kleppe L
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Edvardsen R. B
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Norberg B
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Fjelldal P. G
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Hansen T. J
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
| | - Schulz R. W
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
- Reproductive Biology Group, Department Biology, Science Faculty, Utrecht University, Utrecht, Netherlands
| | - Wargelius A
- Research Group Reproduction and Developmental Biology, Institute of Marine Research, Bergen, Norway
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4
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Harvey A, Skaala Ø, Borgstrøm R, Fjeldheim PT, Christine Andersen K, Rong Utne K, Askeland Johnsen I, Fiske P, Winterthun S, Knutar S, Sægrov H, Urdal K, Alan Glover K. Time series covering up to four decades reveals major changes and drivers of marine growth and proportion of repeat spawners in an Atlantic salmon population. Ecol Evol 2022; 12:e8780. [PMID: 35386868 PMCID: PMC8976282 DOI: 10.1002/ece3.8780] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 11/10/2022] Open
Abstract
Wild Atlantic salmon populations have declined in many regions and are affected by diverse natural and anthropogenic factors. To facilitate management guidelines, precise knowledge of mechanisms driving population changes in demographics and life history traits is needed. Our analyses were conducted on (a) age and growth data from scales of salmon caught by angling in the river Etneelva, Norway, covering smolt year classes from 1980 to 2018, (b) extensive sampling of the whole spawning run in the fish trap from 2013 onwards, and (c) time series of sea surface temperature, zooplankton biomass, and salmon lice infestation intensity. Marine growth during the first year at sea displayed a distinct stepwise decline across the four decades. Simultaneously, the population shifted from predominantly 1SW to 2SW salmon, and the proportion of repeat spawners increased from 3 to 7%. The latter observation is most evident in females and likely due to decreased marine exploitation. Female repeat spawners tended to be less catchable than males by anglers. Depending on the time period analyzed, marine growth rate during the first year at sea was both positively and negatively associated with sea surface temperature. Zooplankton biomass was positively associated with growth, while salmon lice infestation intensity was negatively associated with growth. Collectively, these results are likely to be linked with both changes in oceanic conditions and harvest regimes. Our conflicting results regarding the influence of sea surface temperature on marine growth are likely to be caused by long‐term increases in temperature, which may have triggered (or coincided with) ecosystem shifts creating generally poorer growth conditions over time, but within shorter datasets warmer years gave generally higher growth. We encourage management authorities to expand the use of permanently monitored reference rivers with complete trapping facilities, like the river Etneelva, generating valuable long‐term data for future analyses.
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Affiliation(s)
| | | | - Reidar Borgstrøm
- Faculty of Environmental Sciences and Natural Resource Management Ås Norway
| | | | | | | | | | - Peder Fiske
- Norwegian Institute for Nature Research Trondheim Norway
| | | | | | | | | | - Kevin Alan Glover
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
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5
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Besnier F, Ayllon F, Skaala Ø, Solberg MF, Fjeldheim PT, Anderson K, Knutar S, Glover KA. Introgression of domesticated salmon changes life history and phenology of a wild salmon population. Evol Appl 2022; 15:853-864. [PMID: 35603027 PMCID: PMC9108307 DOI: 10.1111/eva.13375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- F. Besnier
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - F. Ayllon
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - Ø. Skaala
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - M. F. Solberg
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | | | - K. Anderson
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - S. Knutar
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - K. A. Glover
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
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6
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Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Perry WB, Kaufmann J, Solberg MF, Brodie C, Coral Medina AM, Pillay K, Egerton A, Harvey A, Phillips KP, Coughlan J, Egan F, Grealis R, Hutton S, Leseur F, Ryan S, Poole R, Rogan G, Ryder E, Schaal P, Waters C, Wynne R, Taylor M, Prodöhl P, Creer S, Llewellyn M, McGinnity P, Carvalho G, Glover KA. Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon ( Salmo salar L.). Evol Appl 2021; 14:2319-2332. [PMID: 34603501 PMCID: PMC8477603 DOI: 10.1111/eva.13297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022] Open
Abstract
Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
- Water Research InstituteSchool of BiosciencesCardiff UniversityCardiffUK
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
| | - Joshka Kaufmann
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | | | - Christopher Brodie
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
| | | | - Kirthana Pillay
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Anna Egerton
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Alison Harvey
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
| | - Karl P. Phillips
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Fintan Egan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Ronan Grealis
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Steve Hutton
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Floriane Leseur
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Sarah Ryan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | | | - Ger Rogan
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Elizabeth Ryder
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Patrick Schaal
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
- Institute of BiodiversityAnimal Health & Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Catherine Waters
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Robert Wynne
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Martin Taylor
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Paulo Prodöhl
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen’s UniversityBelfastUK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Martin Llewellyn
- Institute of BiodiversityAnimal Health & Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Kevin Alan Glover
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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8
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How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq. BMC Genom Data 2021; 22:22. [PMID: 34182923 PMCID: PMC8237422 DOI: 10.1186/s12863-021-00974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers. Results Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations. Conclusions The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00974-3.
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9
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Wacker S, Aronsen T, Karlsson S, Ugedal O, Diserud OH, Ulvan EM, Hindar K, Næsje TF. Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon. Evol Appl 2021; 14:1450-1460. [PMID: 34025778 PMCID: PMC8127704 DOI: 10.1111/eva.13213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/14/2021] [Accepted: 02/26/2021] [Indexed: 11/27/2022] Open
Abstract
The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.
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Affiliation(s)
| | - Tonje Aronsen
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Sten Karlsson
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ola Ugedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | - Eva M. Ulvan
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Kjetil Hindar
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Tor F. Næsje
- Norwegian Institute for Nature ResearchTrondheimNorway
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10
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Van Eenennaam AL, De Figueiredo Silva F, Trott JF, Zilberman D. Genetic Engineering of Livestock: The Opportunity Cost of Regulatory Delay. Annu Rev Anim Biosci 2020; 9:453-478. [PMID: 33186503 DOI: 10.1146/annurev-animal-061220-023052] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically engineered (GE) livestock were first reported in 1985, and yet only a single GE food animal, the fast-growing AquAdvantage salmon, has been commercialized. There are myriad interconnected reasons for the slow progress in this once-promising field, including technical issues, the structure of livestock industries, lack of public research funding and investment, regulatory obstacles, and concern about public opinion. This review focuses on GE livestock that have been produced and documents the difficulties that researchers and developers have encountered en route. Additionally, the costs associated with delayed commercialization of GE livestock were modeled using three case studies: GE mastitis-resistant dairy cattle, genome-edited porcine reproductive and respiratory syndrome virus-resistant pigs, and the AquAdvantage salmon. Delays of 5 or 10 years in the commercialization of GE livestock beyond the normative 10-year GE product evaluation period were associated with billions of dollars in opportunity costs and reduced global food security.
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Affiliation(s)
| | | | - Josephine F Trott
- Department of Animal Science, University of California, Davis, California 95616, USA; ,
| | - David Zilberman
- Department of Agricultural and Resource Economics, University of California, Berkeley, California 94720, USA;
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11
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Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR. Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus) in Egypt. Front Genet 2020; 11:567969. [PMID: 33193660 PMCID: PMC7593532 DOI: 10.3389/fgene.2020.567969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A H Benzie
- WorldFish, Penang, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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12
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Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
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13
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Wu Z, Xu S, Wang L, Wu Q, Li J, Liu H, You F. Transcription profiles and fatty acid composition of the artificial induced triploid alevin in Atlantic salmon Salmo salar. Theriogenology 2020; 155:49-59. [DOI: 10.1016/j.theriogenology.2020.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
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14
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Abhinav KA, Collu M, Benjamins S, Cai H, Hughes A, Jiang B, Jude S, Leithead W, Lin C, Liu H, Recalde-Camacho L, Serpetti N, Sun K, Wilson B, Yue H, Zhou BZ. Offshore multi-purpose platforms for a Blue Growth: A technological, environmental and socio-economic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:138256. [PMID: 32470664 DOI: 10.1016/j.scitotenv.2020.138256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
"Blue Growth" and "Blue Economy" is defined by the World Bank as: "the sustainable use of ocean resources for economic growth, improved livelihoods and jobs, while preserving the health of ocean ecosystem". Multi-purpose platforms (MPPs) can be defined as offshore platforms serving the needs of multiple offshore industries (energy and aquaculture), aim at exploiting the synergies and managing the tensions arising when closely co-locating systems from these industries. Despite a number of previous projects aimed at assessing, from a multidisciplinary point of view, the feasibility of multipurpose platforms, it is here shown that the state-of-the-art has focused mainly on single-purpose devices, and adopting a single discipline (either economic, or social, or technological, or environmental) approach. Therefore, the aim of the present study is to provide a multidisciplinary state of the art review on, whenever possible, multi-purpose platforms, complementing it with single-purpose and/or single discipline literature reviews when not possible. Synoptic tables are provided, giving an overview of the multi-purpose platform concepts investigated, the numerical approaches adopted, and a comprehensive snapshot classifying the references discussed by industry (offshore renewables, aquaculture, both) and by aspect (technological, environmental, socio-economic). The majority of the multi-purpose platform concepts proposed are integrating only multiple offshore renewable energy devices (e.g. hybrid wind-wave), with only few integrating also aquaculture systems. MPPs have significant potential in economizing CAPEX and operational costs for the offshore energy and aquaculture industry by means of concerted spatial planning and sharing of infrastructure.
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Affiliation(s)
- K A Abhinav
- Naval Architecture, Ocean & Marine Engineering, University of Strathclyde, Glasgow, UK
| | - Maurizio Collu
- Naval Architecture, Ocean & Marine Engineering, University of Strathclyde, Glasgow, UK.
| | - Steven Benjamins
- Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, UK
| | - Huiwen Cai
- Zhejiang Ocean University, Changzhi Island, Zhoushan, Zhejiang, China
| | - Adam Hughes
- Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, UK
| | - Bo Jiang
- National Ocean Technology Center, No. 219, West Jieyuan Road, Tianjin, China
| | | | - William Leithead
- Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
| | - Cui Lin
- National Ocean Technology Center, No. 219, West Jieyuan Road, Tianjin, China
| | - Hongda Liu
- College of Automation, Harbin Engineering University, Harbin 150001, China
| | | | - Natalia Serpetti
- Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, UK
| | - Ke Sun
- College of Shipbuilding Engineering, Harbin Engineering University, Harbin 150001, China
| | - Ben Wilson
- Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, UK
| | - Hong Yue
- Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
| | - Bin-Zhen Zhou
- College of Shipbuilding Engineering, Harbin Engineering University, Harbin 150001, China
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15
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Islam SS, Wringe BF, Bradbury IR, Fleming IA. Behavioural variation among divergent European and North American farmed and wild Atlantic salmon (Salmo salar) populations. Appl Anim Behav Sci 2020. [DOI: 10.1016/j.applanim.2020.105029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8060471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.
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17
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Bicskei B, Taggart JB, Bron JE, Glover KA. Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions. BMC Genet 2020; 21:57. [PMID: 32471356 PMCID: PMC7257211 DOI: 10.1186/s12863-020-00858-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Domestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor. RESULTS Transcriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects. CONCLUSION We conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.
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Affiliation(s)
- Beatrix Bicskei
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - John B. Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - James E. Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - Kevin A. Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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18
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Naval-Sanchez M, McWilliam S, Evans B, Yáñez JM, Houston RD, Kijas JW. Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Front Genet 2020; 11:264. [PMID: 32318091 PMCID: PMC7147387 DOI: 10.3389/fgene.2020.00264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to versican, a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include arcvf, sema6, errb4, id2-like, and 6n1-like genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.
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Affiliation(s)
| | | | - Bradley Evans
- Salmon Enterprises of Tasmania Pty. Limited, Wayatinah, TAS, Australia
| | - José M Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - James W Kijas
- CSIRO Agriculture and Food, Brisbane, QLD, Australia
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19
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Besnier F, Solberg MF, Harvey AC, Carvalho GR, Bekkevold D, Taylor MI, Creer S, Nielsen EE, Skaala Ø, Ayllon F, Dahle G, Glover KA. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface. BMC Genet 2020; 21:13. [PMID: 32033538 PMCID: PMC7006396 DOI: 10.1186/s12863-020-0816-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
Background Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Results After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets. Discussion The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
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Affiliation(s)
- Francois Besnier
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - Monica F Solberg
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Alison C Harvey
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Einar E Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Øystein Skaala
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Geir Dahle
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| | - Kevin A Glover
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
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20
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Solberg MF, Robertsen G, Sundt-Hansen LE, Hindar K, Glover KA. Domestication leads to increased predation susceptibility. Sci Rep 2020; 10:1929. [PMID: 32029847 PMCID: PMC7005312 DOI: 10.1038/s41598-020-58661-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2020] [Indexed: 12/18/2022] Open
Abstract
Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.
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Affiliation(s)
- Monica F Solberg
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.
| | - Grethe Robertsen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Line E Sundt-Hansen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kevin A Glover
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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21
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Bekkevold D, Höjesjö J, Nielsen EE, Aldvén D, Als TD, Sodeland M, Kent MP, Lien S, Hansen MM. Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients. Evol Appl 2020; 13:400-416. [PMID: 31993085 PMCID: PMC6976966 DOI: 10.1111/eva.12877] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/22/2019] [Indexed: 12/19/2022] Open
Abstract
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.
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Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Johan Höjesjö
- Department of Biological & Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | - Marte Sodeland
- Department of Natural SciencesUniversity of AgderKristiansandNorway
| | | | - Sigbjørn Lien
- Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Michael Møller Hansen
- Department of Bioscience – Genetics, Ecology and EvolutionAarhus UniversityAarhusDenmark
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22
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Kleppe L, Edvardsen RB, Furmanek T, Andersson E, Skaftnesmo KO, Thyri Segafredo F, Wargelius A. Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon. BMC Genomics 2020; 21:99. [PMID: 32000659 PMCID: PMC6993523 DOI: 10.1186/s12864-020-6513-4] [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: 07/04/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Background Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be applied to inhibit Dnd function, including gene knockout, knockdown or immunization. Since it is challenging to develop a successful treatment against a gene product already existing in the body, alternative targets are being explored. Germ cells are surrounded by, and dependent on, gonadal somatic cells. Targeting genes essential for the survival of gonadal somatic cells may be good alternative targets for sterility treatments. Our aim was to identify and characterize novel germ cell and gonadal somatic factors in Atlantic salmon. Results We have for the first time analysed RNA-sequencing data from germ cell-free (GCF)/dnd knockout and wild type (WT) salmon testis and searched for genes preferentially expressed in either germ cells or gonadal somatic cells. To exclude genes with extra-gonadal expression, our dataset was merged with available multi-tissue transcriptome data. We identified 389 gonad specific genes, of which 194 were preferentially expressed within germ cells, and 11 were confined to gonadal somatic cells. Interestingly, 5 of the 11 gonadal somatic transcripts represented genes encoding secreted TGF-β factors; gsdf, inha, nodal and two bmp6-like genes, all representative vaccine targets. Of these, gsdf and inha had the highest transcript levels. Expression of gsdf and inha was further confirmed to be gonad specific, and their spatial expression was restricted to granulosa and Sertoli cells of the ovary and testis, respectively. Finally, we show that inha expression increases with puberty in both ovary and testis tissue, while gsdf expression does not change or decreases during puberty in ovary and testis tissue, respectively. Conclusions This study contributes with transcriptome data on salmon testis tissue with and without germ cells. We provide a list of novel and known germ cell- and gonad somatic specific transcripts, and show that the expression of two highly active gonadal somatic secreted TGF-β factors, gsdf and inha, are located within granulosa and Sertoli cells.
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Affiliation(s)
- Lene Kleppe
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | | | - Tomasz Furmanek
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Eva Andersson
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kai Ove Skaftnesmo
- 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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23
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Rodriguez Barreto D, Garcia de Leaniz C, Verspoor E, Sobolewska H, Coulson M, Consuegra S. DNA Methylation Changes in the Sperm of Captive-Reared Fish: A Route to Epigenetic Introgression in Wild Populations. Mol Biol Evol 2020; 36:2205-2211. [PMID: 31180510 PMCID: PMC6759066 DOI: 10.1093/molbev/msz135] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or transgenerational epigenetic modifications in Atlantic salmon. We found that the sperm of wild and captive-reared males differed in methylated regions consistent with early epigenetic signatures of domestication. Some of the epigenetic marks that differed between hatchery and wild males affected genes related to transcription, neural development, olfaction, and aggression, and were maintained in the offspring beyond developmental reprogramming. Our findings suggest that rearing in captivity may trigger epigenetic modifications in the sperm of hatchery fish that could explain the rapid phenotypic and genetic changes observed among hybrid fish. Epigenetic introgression via fish sperm represents a previously unappreciated mechanism that could compromise locally adapted fish populations.
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Affiliation(s)
| | | | - Eric Verspoor
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Halina Sobolewska
- Noahgene Ltd, The e-Centre, Cooperage Way Business Village, Alloa, United Kingdom
| | - Mark Coulson
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, United Kingdom
| | - Sofia Consuegra
- Biosciences Department, College of Science, Swansea University, Swansea, United Kingdom
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Abstract
Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 104-106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA;
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195-5020, USA;
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program and Biotechnology Institute, University of Helsinki, 00014 Helsinki, Finland;
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25
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Žužul I, Šegvić-Bubić T, Talijančić I, Džoić T, Lepen Pleić I, Beg Paklar G, Ivatek-Šahdan S, Katavić I, Grubišić L. Spatial connectivity pattern of expanding gilthead seabream populations and its interactions with aquaculture sites: a combined population genetic and physical modelling approach. Sci Rep 2019; 9:14718. [PMID: 31604982 PMCID: PMC6788985 DOI: 10.1038/s41598-019-51256-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/28/2019] [Indexed: 11/24/2022] Open
Abstract
In gilthead seabream the number of domesticated individuals increased annually, and escape events occur regularly in the Adriatic Sea. Still there is a lack of population genetic characteristics and evidence of the extent and geographic scale of interbreeding resulting from fish-farm escapees. We screened 1586 individuals using a panel of 21 neutral microsatellite loci in several consecutive years and here report on the medium-scale detection of hybrid and farmed seabream in the natural environment. Wild adults showed a lack of genetic structure within basin and sampling years and reduced connectivity with wild offspring collection, suggesting their temporal residency within the Adriatic. On the contrary, by linking the results of multiannual genetic analyses with the results of coupled hydrodynamic and individual based models (IBM-Ichthyop), we observed a strong connection of wild seabream associated with tuna-aquaculture sites and offspring from the nursery grounds, indicating that the surroundings of tuna sea-cage farms can function as a spawning grounds. The study results present the genetic baseline of wild and farmed strains from the eastern Adriatic Sea, as a first step toward development of a mitigation strategy for fish escapees aimed at controlling further erosion of genetic integrity.
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Affiliation(s)
- Iva Žužul
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Tanja Šegvić-Bubić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia.
| | - Igor Talijančić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Tomislav Džoić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Gordana Beg Paklar
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | | | - Ivan Katavić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
| | - Leon Grubišić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, 21000, Split, Croatia
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26
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Harvey AC, Quintela M, Glover KA, Karlsen Ø, Nilsen R, Skaala Ø, Sægrov H, Kålås S, Knutar S, Wennevik V. Inferring Atlantic salmon post-smolt migration patterns using genetic assignment. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190426. [PMID: 31824688 PMCID: PMC6837218 DOI: 10.1098/rsos.190426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Understanding migratory patterns is important for predicting and mitigating unwanted consequences of environmental change or anthropogenic challenges on vulnerable species. Wild Atlantic salmon undergo challenging migrations between freshwater and marine environments, and the numbers of salmon returning to their natal rivers to reproduce have declined over several decades. Mortality from sea lice linked to fish farms within their seaward migration routes is proposed as a contributing factor to these declines. Here, we used 31 microsatellite markers to establish a genetic baseline for the main rivers in the Hardangerfjord, western Norway. Mixed stock analysis was used to assign Atlantic salmon post-smolts caught in trawls in 2013-2017 back to regional reporting units. Analyses demonstrated that individuals originating from rivers located in the inner region of the fjord arrived at the outer fjord later than individuals from middle and outer fjord rivers. Therefore, as post-smolts originating from inner rivers also have to migrate longer distances to exit the fjord, these data suggest that inner fjord populations are more likely to be at risk of mortality through aquaculture-produced sea lice, and other natural factors such as predation, than middle or outer fjord populations with earlier exit times and shorter journeys. These results will be used to calibrate models estimating mortality from sea lice on wild salmon for the regulation of the Norwegian aquaculture industry.
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Affiliation(s)
- A. C. Harvey
- Institute of Marine Research (IMR), Bergen, Norway
| | - M. Quintela
- Institute of Marine Research (IMR), Bergen, Norway
| | - K. A. Glover
- Institute of Marine Research (IMR), Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Ø. Karlsen
- Institute of Marine Research (IMR), Bergen, Norway
| | - R. Nilsen
- Institute of Marine Research (IMR), Tromsø, Norway
| | - Ø. Skaala
- Institute of Marine Research (IMR), Bergen, Norway
| | - H. Sægrov
- Rådgivende Biologer AS, Bergen, Norway
| | - S. Kålås
- Rådgivende Biologer AS, Bergen, Norway
| | - S. Knutar
- Institute of Marine Research (IMR), Bergen, Norway
| | - V. Wennevik
- Institute of Marine Research (IMR), Bergen, Norway
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27
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Lehnert SJ, Kess T, Bentzen P, Kent MP, Lien S, Gilbey J, Clément M, Jeffery NW, Waples RS, Bradbury IR. Genomic signatures and correlates of widespread population declines in salmon. Nat Commun 2019; 10:2996. [PMID: 31278264 PMCID: PMC6611788 DOI: 10.1038/s41467-019-10972-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.
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Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada.
| | - T Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
| | - P Bentzen
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - M P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - S Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - J Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, UK
| | - M Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, 155 Ridge Rd, St. John's, NL, A1C 5R3, Canada
- Labrador Institute, Memorial University of Newfoundland, 219 Hamilton River Rd, Happy Valley-Goose Bay, NL, A0P 1E0, Canada
| | - N W Jeffery
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Dr, Dartmouth, NS, B2Y 4A2, Canada
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, 98112, USA
| | - I R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
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28
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Bruce SA, Daniel PC, Krause MK, Henson FG, Pershyn CE, Wright JJ. A methodological approach to the genetic identification of native Brook Trout (Salvelinus fontinalis) populations for conservation purposes. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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29
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Wennevik V, Quintela M, Skaala Ø, Verspoor E, Prusov S, Glover KA. Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway. Ecol Evol 2019; 9:6901-6921. [PMID: 31380023 PMCID: PMC6662299 DOI: 10.1002/ece3.5258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.
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Affiliation(s)
| | | | | | - Eric Verspoor
- Rivers and Lochs Institute, Inverness CollegeUniversity of the Highlands and IslandsInvernessUK
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO)MurmanskRussia
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30
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Skaala Ø, Besnier F, Borgstrøm R, Barlaup B, Sørvik AG, Normann E, Østebø BI, Hansen MM, Glover KA. An extensive common-garden study with domesticated and wild Atlantic salmon in the wild reveals impact on smolt production and shifts in fitness traits. Evol Appl 2019; 12:1001-1016. [PMID: 31080511 PMCID: PMC6503829 DOI: 10.1111/eva.12777] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/15/2023] Open
Abstract
Interactions between domesticated escapees and wild conspecifics represent a threat to the genetic integrity and fitness of native populations. For Atlantic salmon, the recurrent presence of large numbers of domesticated escapees in the wild makes it necessary to better understand their impacts on native populations. We planted 254,400 eggs from 75 families of domesticated, F1-hybrid, and wild salmon in a river containing up- and downstream traps. Additionally, 41,630 hatchery smolts of the same pedigrees were released into the river. Over 8 years, 6,669 out-migrating smolts and 356 returning adults were recaptured and identified to their families of origin with DNA. In comparison with wild salmon, domesticated fish had substantially lower egg to smolt survival (1.8% vs. 3.8% across cohorts), they migrated earlier in the year (11.8 days earlier across years), but they only displayed marginally larger smolt sizes and marginally lower smolt ages. Upon return to freshwater, domesticated salmon were substantially larger at age than wild salmon (2.4 vs. 2.0, 4.8 vs. 3.2, and 8.5 vs. 5.6 kg across sexes for 1, 2, and 3 sea-winter fish) and displayed substantially lower released smolt to adult survival (0.41% vs. 0.94% across releases). Overall, egg-to-returning adult survival ratios were 1:0.76:0.30 and 1:0.44:0.21 for wild:F1-hybrid:domesticated salmon, respectively, using two different types of data. This study represents the most updated and extensive analysis of domesticated, hybrid, and wild salmon in the wild and provides the first documentation of a clear genetic difference in the timing of smolt migration-an adaptive trait presumed to be linked with optimal timing of entry to seawater. We conclude that spawning and hybridization of domesticated escapees can lead to (i) reduced wild smolt output and therefore wild adult abundance, through resource competition in freshwater, (ii) reduced total adult abundance due to freshwater competition and reduced marine survival of domesticated salmon, and (iii) maladaptive changes in phenotypic traits.
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Affiliation(s)
| | | | - Reidar Borgstrøm
- Faculty of Environmental Sciences and Natural Resource ManagementÅsNorway
| | | | | | | | | | - Michael Møller Hansen
- Institute of Marine ResearchNordnes, BergenNorway
- Department of BioscienceAarhus UniversityAarhus CDenmark
| | - Kevin Alan Glover
- Institute of Marine ResearchNordnes, BergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
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31
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Vandeputte M, Gagnaire PA, Allal F. The European sea bass: a key marine fish model in the wild and in aquaculture. Anim Genet 2019; 50:195-206. [PMID: 30883830 PMCID: PMC6593706 DOI: 10.1111/age.12779] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2019] [Indexed: 01/13/2023]
Abstract
The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.
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Affiliation(s)
- M Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
| | - P-A Gagnaire
- Institut des Sciences de l'Evolution de Montpellier, UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - F Allal
- MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
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32
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Hagen IJ, Jensen AJ, Bolstad GH, Diserud OH, Hindar K, Lo H, Karlsson S. Supplementary stocking selects for domesticated genotypes. Nat Commun 2019; 10:199. [PMID: 30643117 PMCID: PMC6331577 DOI: 10.1038/s41467-018-08021-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023] Open
Abstract
Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.
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Affiliation(s)
- Ingerid J Hagen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway.
| | - Arne J Jensen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Geir H Bolstad
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Ola H Diserud
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Håvard Lo
- Norwegian Veterinary Institute, P.O. Box 5695 Torgarden, 7485, Trondheim, Norway
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
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33
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Robertsen G, Reid D, Einum S, Aronsen T, Fleming IA, Sundt‐Hansen LE, Karlsson S, Kvingedal E, Ugedal O, Hindar K. Can variation in standard metabolic rate explain context-dependent performance of farmed Atlantic salmon offspring? Ecol Evol 2019; 9:212-222. [PMID: 30680108 PMCID: PMC6342125 DOI: 10.1002/ece3.4716] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 01/13/2023] Open
Abstract
Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild-type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self-maintenance) during domestication. Fitness-related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy-demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed-wild hybrids and pure wild offspring. Next, we test early-life performance (in terms of survival and growth) of hybrids relative to that of their wild half-siblings, as well as their competitive abilities, in semi-natural conditions of high and low food availability. Finally, we test how SMR affects early-life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi-natural streams. Yet, the presence of hybrids led to decreased survival of their wild half-siblings. Contrary to our hypothesis about context-dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.
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Affiliation(s)
| | - Donald Reid
- School of Life Sciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Sigurd Einum
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Tonje Aronsen
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ian A. Fleming
- Department of Ocean SciencesMemorial University of NewfoundlandSt John’sNewfoundlandCanada
| | | | - Sten Karlsson
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Eli Kvingedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ola Ugedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Kjetil Hindar
- Norwegian Institute for Nature ResearchTrondheimNorway
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34
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Harvey AC, Skilbrei OT, Besnier F, Solberg MF, Sørvik AGE, Glover KA. Implications for introgression: has selection for fast growth altered the size threshold for precocious male maturation in domesticated Atlantic salmon? BMC Evol Biol 2018; 18:188. [PMID: 30558529 PMCID: PMC6298023 DOI: 10.1186/s12862-018-1294-y] [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: 07/09/2017] [Accepted: 11/16/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Mature male parr (MMP) represent an important alternative life-history strategy in Atlantic salmon populations. Previous studies indicate that the maturation size threshold for male parr varies among wild populations and is influenced by individual growth, environmental conditions, and genetics. More than ten generations of breeding have resulted in domesticated salmon displaying many genetic differences to wild salmon, including greatly increased growth rates. This may have resulted in domesticated fish with the potential to outgrow the size threshold for early maturation, or evolution of the size threshold of the trait itself. To investigate this, we performed a common-garden experiment under farming conditions using 4680 salmon from 39 families representing four wild, two wild-domesticated hybrid, and two domesticated strains. RESULTS Domesticated salmon outgrew wild salmon 2-5-fold, and hybrids displayed intermediate growth. Overall, the numbers of MMP varied greatly among families and strains: averaging 4-12% in domesticated, 18-25% in hybrid, and 43-74% in the wild populations. However, when the influence of growth was accounted for, by dividing fish into lower and upper size modes, no difference in the incidence of MMP was detected among domesticated and wild strains in either size mode. In the lower size mode, hybrids displayed significantly lower incidences of mature males than their wild parental strains. No consistent differences in the body size of MMP, connected to domestication, was detected. CONCLUSIONS Our data demonstrate: 1- no evidence for the evolution of the size threshold for MMP in domesticated salmon, 2- the vastly lower incidence of MMP in domesticated strains under aquaculture conditions is primarily due to their genetically increased growth rate causing them to outgrow the size threshold for early maturation, 3- the incidence of MMP is likely to overlap among domesticated and wild salmon in the natural habitat where they typically display overlapping growth, although hybrid offspring may display lower incidences of mature male parr. These results have implications for wild salmon populations that are exposed to introgression from domesticated escapees.
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Affiliation(s)
- A C Harvey
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - O T Skilbrei
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - F Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - A-G E Sørvik
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Department of Biology, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
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35
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White SL, Miller WL, Dowell SA, Bartron ML, Wagner T. Limited hatchery introgression into wild brook trout ( Salvelinus fontinalis) populations despite reoccurring stocking. Evol Appl 2018; 11:1567-1581. [PMID: 30344628 PMCID: PMC6183464 DOI: 10.1111/eva.12646] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 01/17/2023] Open
Abstract
Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive-raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long-term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential and contribute to local population extirpation. However, low survival and fitness of captive-raised individuals can minimize the long-term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive-raised) for 1,742 wild-caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild-caught individuals probabilistically assigned to wild origin, and only 5.6% of wild-caught fish assigned to introgressed. Models examining environmental drivers of introgression explained <3% of the among-population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery-derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known.
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Affiliation(s)
- Shannon L. White
- Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
- Department of Ecosystem Science and ManagementPennsylvania State UniversityUniversity ParkPennsylvania
| | - William L. Miller
- Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
- Department of Ecosystem Science and ManagementPennsylvania State UniversityUniversity ParkPennsylvania
| | | | | | - Tyler Wagner
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvania
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Glover KA, Solberg MF, Besnier F, Skaala Ø. Cryptic introgression: evidence that selection and plasticity mask the full phenotypic potential of domesticated Atlantic salmon in the wild. Sci Rep 2018; 8:13966. [PMID: 30228303 PMCID: PMC6143624 DOI: 10.1038/s41598-018-32467-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/03/2018] [Indexed: 01/13/2023] Open
Abstract
Domesticated Atlantic salmon grow much faster than wild salmon when reared together in fish tanks under farming conditions (size ratios typically 1:2-3). In contrast, domesticated salmon only display marginally higher growth than wild salmon when reared together in rivers (size ratios typically 1:1-1.2). This begs the question why? Is this a difference in the plastic response driven by divergent energy budgets between the two environments, or is it a result of selection, whereby domesticated salmon that display the greatest growth-potential are those at greatest risk of mortality in the wild? We reared domesticated, hybrid and wild salmon in a river until they smoltified at age 2 or 4, and thereafter in fish tanks for a further 2 years. In the river, there was no difference in the mean size between the groups. In contrast, after being transferred from the river to fish tanks, the domesticated salmon significantly outgrew the wild salmon (maximum size ratio of ~1:1.8). This demonstrates that selection alone cannot be responsible for the lack of growth differences observed between domesticated and wild salmon in rivers. Nevertheless, the final size ratios observed after rearing in tanks were lower than expected in that environment, thus suggesting that plasticity, as for selection, cannot be the sole mechanism. We therefore conclude that a combination of energy-budget plasticity, and selection via growth-potential mortality, cause the differences in growth reaction norms between domesticated and wild salmon across these contrasting environments. Our results imply that if phenotypic changes are not observed in wild populations following introgression of domesticated conspecifics, it does not mean that functional genetic changes have not occurred in the admixed population. Clearly, under the right environmental conditions, the underlying genetic changes will manifest themselves in the phenotype.
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Affiliation(s)
- Kevin A Glover
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway. .,University of Bergen, Department of Biology, P.O. Box 7803, N-5020, Bergen, Norway.
| | - Monica F Solberg
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
| | - Øystein Skaala
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
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Wringe BF, Jeffery NW, Stanley RRE, Hamilton LC, Anderson EC, Fleming IA, Grant C, Dempson JB, Veinott G, Duffy SJ, Bradbury IR. Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic. Commun Biol 2018; 1:108. [PMID: 30271988 PMCID: PMC6123692 DOI: 10.1038/s42003-018-0112-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreeding resulting from individual escape events is lacking. We screened juvenile Atlantic salmon using 95 single nucleotide polymorphisms following a single, large aquaculture escape in the Northwest Atlantic and report the landscape-scale detection of hybrid and feral salmon (27.1%, 17/18 rivers). Hybrids were reproductively viable, and observed at higher frequency in smaller wild populations. Repeated annual sampling of this cohort revealed decreases in the presence of hybrid and feral offspring over time. These results link previous observations of escaped salmon in rivers with reports of population genetic change, and demonstrate the potential negative consequences of escapes from net-pen aquaculture on wild populations.
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Affiliation(s)
- Brendan F Wringe
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Nicholas W Jeffery
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Ryan R E Stanley
- Science Branch, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Lorraine C Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, 95060, USA
| | - Ian A Fleming
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Carole Grant
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - J Brian Dempson
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Geoff Veinott
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Steven J Duffy
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Ian R Bradbury
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada.
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada.
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Castellani M, Heino M, Gilbey J, Araki H, Svåsand T, Glover KA. Modeling fitness changes in wild Atlantic salmon populations faced by spawning intrusion of domesticated escapees. Evol Appl 2018; 11:1010-1025. [PMID: 29928306 PMCID: PMC5999203 DOI: 10.1111/eva.12615] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/11/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco-genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%-10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%-50% escapees) were clear changes visible in this period. Our modeling also revealed that genetic changes in phenotypic and demographic characteristics were greater in situations where strayers originating from a neighboring wild population were domestication-admixed and changed in parallel with the focal wild population, as opposed to nonadmixed. While recovery in the phenotypic and demographic characteristics was observed in many instances after domesticated salmon intrusion was halted, in the most extreme intrusion scenario, the population went extinct. Based upon results from these simulations, together with existing knowledge, we suggest that a combination of reduced spawning success of domesticated escapees, natural selection purging maladapted phenotypes/genotypes from the wild population, and phenotypic plasticity, buffer the rate and magnitude of change in phenotypic and demographic characteristics of wild populations subject to spawning intrusion of domesticated escapees. The results of our simulations also suggest that under specific conditions, natural straying among wild populations may buffer genetic changes in phenotypic and demographic characteristics resulting from introgression of domesticated escapees and that variation in straying in time and space may contribute to observed differences in domestication-driven introgression among native populations.
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Affiliation(s)
| | - Mikko Heino
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
- International Institute for Applied Systems Analysis (IIASA)LaxenburgAustria
| | - John Gilbey
- Freshwater Fisheries LaboratoryMarine ScotlandPitlochryUK
| | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | | | - Kevin A. Glover
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
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Judging a salmon by its spots: environmental variation is the primary determinant of spot patterns in Salmo salar. BMC Ecol 2018; 18:14. [PMID: 29650003 PMCID: PMC5897946 DOI: 10.1186/s12898-018-0170-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fish, morphological colour changes occur from variations in pigment concentrations and in the morphology, density, and distribution of chromatophores in the skin. However, the underlying mechanisms remain unresolved in most species. Here, we describe the first investigation into the genetic and environmental basis of spot pattern development in one of the world's most studied fishes, the Atlantic salmon. We reared 920 salmon from 64 families of domesticated, F1-hybrid and wild origin in two contrasting environments (Hatchery; tanks for the freshwater stage and sea cages for the marine stage, and River; a natural river for the freshwater stage and tanks for the marine stage). Fish were measured, photographed and spot patterns evaluated. RESULTS In the Hatchery experiment, significant but modest differences in spot density were observed among domesticated, F1-hybrid (1.4-fold spottier than domesticated) and wild salmon (1.7-fold spottier than domesticated). A heritability of 6% was calculated for spot density, and a significant QTL on linkage group SSA014 was detected. In the River experiment, significant but modest differences in spot density were also observed among domesticated, F1-hybrid (1.2-fold spottier than domesticated) and wild salmon (1.8-fold spottier than domesticated). Domesticated salmon were sevenfold spottier in the Hatchery vs. River experiment. While different wild populations were used for the two experiments, on average, these were 6.2-fold spottier in the Hatchery vs. River experiment. Fish in the Hatchery experiment displayed scattered to random spot patterns while fish in the River experiment displayed clustered spot patterns. CONCLUSIONS These data demonstrate that while genetics plays an underlying role, environmental variation represents the primary determinant of spot pattern development in Atlantic salmon.
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Smedley M, Migaud H, McStay E, Clarkson M, Bozzolla P, Campbell P, Taylor J. Impact of dietary phosphorous in diploid and triploid Atlantic salmon ( Salmo salar L.) with reference to early skeletal development in freshwater. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2018; 490:329-343. [PMID: 29681666 PMCID: PMC5905282 DOI: 10.1016/j.aquaculture.2018.02.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 05/28/2023]
Abstract
In order to assess the effect of dietary phosphorus (P) in reducing vertebral malformations and improving freshwater (FW) performance in triploid Atlantic salmon (Salmo salar), both triploid and diploid Atlantic salmon were fed three different dietary P inclusion levels (low: 4.9, medium: 7.7, and high: 9.7 g available P kg-1) from first feeding until smolt. Somatic and skeletal response was assessed at fry (~0.5 g), parr (~5 g) and smolt (~45 g) stages. Triploid parr initially grew faster on the high P diet, while groups fed low P resulted in a significantly higher weight at smolt. Image analysis of double stained Alcian blue and Alizarin red S fry revealed that low P fed triploid fish presented less well mineralised vertebrae, and significantly more malformed vertebrae in both parr and smolt stages following x-ray radiographic assessment. Triploid parr fed high and medium P had similar numbers of malformed vertebrae relative to their diploid counterparts but greater numbers than at smolt. Low P fed triploids had the highest prevalence of jaw and vertebral malformations as well as the highest number of deformed vertebrae in the central caudal vertebral region, which was more pronounced at parr than at smolt. Shorter vertebrae dorso-ventral lengths were observed throughout the spinal column (R1-R4) in parr fed low P and only in the caudal region (R3) at smolt. In parr, both ploidies showed reduced phosphate homeostasis protein fgf23 gene expression in vertebrae when fed low P diets, while triploids showed greater down-regulation of osteogenic factors (alp, opn and igf1r) between diets relative to diploids, suggesting possible greater active suppression of mineralisation and reduced osteogenic potential in triploids. No effects of diet or ploidy on gene expression were evident at smolt. Comparisons between development stages suggest early P supplementation in triploids is crucial for skeletal development. Ultimately, reducing vertebral deformities observed at smolt with higher P supplementation in triploids could contribute towards improving skeletal performance and welfare of the stocks in the marine phase.
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Affiliation(s)
- M.A. Smedley
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - H. Migaud
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - E.L. McStay
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - M. Clarkson
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - P. Bozzolla
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | | | - J.F. Taylor
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
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Robinson NA, Timmerhaus G, Baranski M, Andersen Ø, Takle H, Krasnov A. Training the salmon's genes: influence of aerobic exercise, swimming performance and selection on gene expression in Atlantic salmon. BMC Genomics 2017; 18:971. [PMID: 29246115 PMCID: PMC5731093 DOI: 10.1186/s12864-017-4361-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/01/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and genetic origin. Eggs from the selectively bred Bolaks salmon and wild Lærdal River salmon strains were reared until parr in a common environment. Swimming performance was assessed by subjecting the fish to either continuous hard exercise or control conditions for 18 days. Heart was sampled for examination of gene expression using RNA-seq (~60 fish/treatment). RESULTS Lower expression of genes affecting immune function was found in domesticated than wild parr. Among wild parr under control exercise the expression of a large number of genes involved in general metabolism, stress and immune response was lower in superior swimmers suggesting that minimisation of energy expenditure during periods of low activity makes parr better able to sustain bursts of swimming for predator avoidance. A similar set of genes were down-regulated with training among wild parr with inferior swimming performance. These parr react to training in a way that their cardiac expression patterns become like the superior performing wild parr under control exercise conditions. Diversifying selection caused by breeding of domesticated stock, and adaptive pressures in wild stock, has affected the expression and frequency of single nucleotide polymorphisms (SNPs) for multiple functional groups of genes affecting diverse processes. SNPs associated with swimming performance in wild parr map to genes involved in energetic processes, coding for contractile filaments in the muscle and controlling cell proliferation. CONCLUSIONS Domesticated parr have less phenotypic plasticity in response to training and lower expression of genes with functions affecting immune response. The genetic response to training is complex and depends on the background of parr and their swimming ability. Exercise should be tailored to the genetics and swimming performance of fish.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima, Osloveien 1, 1430 Ås, Norway
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, Vic 3010 Australia
- Nofima, PO Box 210, 1431 Ås, Norway
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Harvey AC, Tang Y, Wennevik V, Skaala Ø, Glover KA. Timing is everything: Fishing-season placement may represent the most important angling-induced evolutionary pressure on Atlantic salmon populations. Ecol Evol 2017; 7:7490-7502. [PMID: 28944033 PMCID: PMC5606871 DOI: 10.1002/ece3.3304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/01/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023] Open
Abstract
Fisheries‐induced evolution can change the trajectory of wild fish populations by selectively targeting certain phenotypes. For important fish species like Atlantic salmon, this could have large implications for their conservation and management. Most salmon rivers are managed by specifying an angling season of predetermined length based on population demography, which is typically established from catch statistics. Given the circularity of using catch statistics to estimate demographic parameters, it may be difficult to quantify the selective nature of angling and its evolutionary impact. In the River Etne in Norway, a recently installed trap permits daily sampling of fish entering the river, some of which are subsequently captured by anglers upstream. Here, we used 31 microsatellites to establish an individual DNA profile for salmon entering the trap, and for many of those subsequently captured by anglers. These data permitted us to investigate time of rod capture relative to river entry, potential body size‐selective harvest, and environmental variables associated with river entry. Larger, older fish entered the river earlier than smaller, younger fish of both sexes, and larger, older females were more abundant than males and vice versa. There was good agreement between the sizes of fish harvested by angling, and the size distribution of the population sampled on the trap. These results demonstrate that at least in this river, and with the current timing of the season, the angling catch reflects the population's demographics and there is no evidence of size‐selective harvest. We also demonstrated that the probability of being caught by angling declines quickly after river entry. Collectively, these data indicate that that the timing of the fishing season, in relation to the upstream migration patterns of the different demographics of the population, likely represents the most significant directional evolutionary force imposed by angling.
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Affiliation(s)
| | - Yongkai Tang
- Freshwater Fisheries Research Center Chinese Academy of Fishery Sciences Wuxi China
| | | | | | - Kevin A Glover
- Institute of Marine Research Bergen Norway.,Department of Biology Sea Lice Research Centre University of Bergen Bergen Norway
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A comparison of disease susceptibility and innate immune response between diploid and triploid Atlantic salmon (Salmo salar) siblings following experimental infection with Neoparamoeba perurans, causative agent of amoebic gill disease. Parasitology 2017; 144:1229-1242. [PMID: 28492111 PMCID: PMC5647666 DOI: 10.1017/s0031182017000622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Few studies have focussed on the health and immunity of triploid Atlantic salmon and therefore much is still unknown about their response to commercially significant pathogens. This is important if triploid stocks are to be considered for full-scale commercial production. This study aimed to investigate and compare the response of triploid and diploid Atlantic salmon to an experimental challenge with Neoparamoeba perurans, causative agent of amoebic gill disease (AGD). This disease is economically significant for the aquaculture industry. The results indicated that ploidy had no significant effect on gross gill score or gill filaments affected, while infection and time had significant effects. Ploidy, infection and time did not affect complement or anti-protease activities. Ploidy had a significant effect on lysozyme activity at 21 days post-infection (while infection and time did not), although activity was within the ranges previously recorded for salmonids. Stock did not significantly affect any of the parameters measured. Based on the study results, it can be suggested that ploidy does not affect the manifestation or severity of AGD pathology or the serum innate immune response. Additionally, the serum immune response of diploid and triploid Atlantic salmon may not be significantly affected by amoebic gill disease.
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45
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Triploid atlantic salmon (Salmo salar L.) post-smolts accumulate prevalence more slowly than diploid salmon following bath challenge with salmonid alphavirus subtype 3. PLoS One 2017; 12:e0175468. [PMID: 28403165 PMCID: PMC5389816 DOI: 10.1371/journal.pone.0175468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/27/2017] [Indexed: 01/15/2023] Open
Abstract
Triploid Atlantic salmon (Salmo salar L.) may play an important role in the sustainable expansion of the Norwegian aquaculture industry. Therefore, the susceptibility of triploid salmon to common infections such as salmonid alphavirus (SAV), the causative agent of pancreas disease (PD), requires investigation. In this study, shortly after seawater transfer, diploid and triploid post-smolts were exposed to SAV type 3 (SAV3) using a bath challenge model where the infectious dose was 48 TCID50 ml-1 of tank water. Copy number analysis of SAV3 RNA in heart tissue showed that there was no difference in viral loads between the diploids and triploids. Prevalence reached 100% by the end of the 35-day experimental period in both infected groups. However, prevalence accumulated more slowly in the triploid group reaching 19% and 56% at 14 and 21 days post exposure (dpe) respectively. Whereas prevalence in the diploid group was 82% and 100% at the same time points indicating some differences between diploid and triploid fish. Both heart and pancreas from infected groups at 14 dpe showed typical histopathological changes associated with pancreas disease. Observation of this slower accumulation of prevalence following a natural infection route was possible due to the early sampling points and the exposure to a relatively low dose of virus. The triploid salmon in this study were not more susceptible to SAV3 than diploid salmon indicating that they could be used commercially to reduce the environmental impact of escaped farmed fish interbreeding with wild salmon. This is important information regarding the future use of triploid fish in large scale aquaculture where SAV3 is a financial threat to increased production.
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46
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Harvey AC, Fjelldal PG, Solberg MF, Hansen T, Glover KA. Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set. BMC Genet 2017; 18:34. [PMID: 28399816 PMCID: PMC5387229 DOI: 10.1186/s12863-017-0502-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
Abstract
Background The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid performance often show contrasting results. Studies have identified dosage and dosage-compensation effects for gene expression between triploid and diploid salmonids, but no study has investigated how ploidy and parent-origin effects interact on a polygenic trait in divergent lines of Atlantic salmon (i.e. slow growing wild versus fast growing domesticated phenotype). This study utilised two experiments relating to the freshwater growth of diploid and triploid groups of pure wild (0% domesticated genome), pure domesticated (100% domesticated genome), and F1 reciprocal hybrid (33%, 50% or 66% domesticated genome) salmon where triploidy was either artificially induced (experiment 1) or naturally developed/spontaneous (experiment 2). Results In both experiments, reciprocal hybrid growth was influenced by the dosage effect of the second maternal chromosome, with growth increasing as ploidy level increased in individuals with a domesticated dam (from 50% to 66% domesticated genome), and the inverse in individuals with a wild dam (from 50% to 33% domesticated genome). Conclusions We demonstrate that the combined effect of ploidy and parent-origin on growth, a polygenic trait, is regulated in an additive pattern. Therefore, in order to maximise growth potential, the aquaculture industry should consider placing more emphasis on the breeding value of the dam than the sire when producing triploid families for commercial production. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0502-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A C Harvey
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - P G Fjelldal
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - T Hansen
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Department of Biology, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
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47
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Bolstad GH, Hindar K, Robertsen G, Jonsson B, Sægrov H, Diserud OH, Fiske P, Jensen AJ, Urdal K, Næsje TF, Barlaup BT, Florø-Larsen B, Lo H, Niemelä E, Karlsson S. Gene flow from domesticated escapes alters the life history of wild Atlantic salmon. Nat Ecol Evol 2017; 1:124. [PMID: 28812692 DOI: 10.1038/s41559-017-0124] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022]
Abstract
Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals.
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Affiliation(s)
- Geir H Bolstad
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Grethe Robertsen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Bror Jonsson
- Norwegian Institute for Nature Research (NINA), NO-0349 Oslo, Norway
| | | | - Ola H Diserud
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Peder Fiske
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Arne J Jensen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kurt Urdal
- Radgivende Biologer, NO-5003 Bergen, Norway
| | - Tor F Næsje
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | | | | | - Håvard Lo
- Norwegian Veterinary Institute, NO-7485 Trondheim, Norway
| | - Eero Niemelä
- Natural Resources Institute Finland, FI-90014 Oulu, Finland
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
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48
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Béres B, Kánainé Sipos D, Müller T, Staszny Á, Farkas M, Bakos K, Orbán L, Urbányi B, Kovács B. Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary. PeerJ 2017; 5:e2804. [PMID: 28265489 PMCID: PMC5333548 DOI: 10.7717/peerj.2804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/19/2016] [Indexed: 12/19/2022] Open
Abstract
Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation.
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Affiliation(s)
- Beatrix Béres
- Department of Aquaculture, Szent István University , Gödöllő , Hungary
| | - Dóra Kánainé Sipos
- Department of Aquaculture, Szent István University, Gödöllő, Hungary; Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - Tamás Müller
- Department of Aquaculture, Szent István University , Gödöllő , Hungary
| | - Ádám Staszny
- Department of Aquaculture, Szent István University , Gödöllő , Hungary
| | - Milán Farkas
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary; Department of Environmental Safety and Ecotoxicology, Szent István University, Gödöllő, Hungary
| | - Katalin Bakos
- Department of Aquaculture, Szent István University, Gödöllő, Hungary; Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - László Orbán
- Department of Aquaculture, Szent István University, Gödöllő, Hungary; Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore; Centre for Comparative Genomics, Murdoch University, Murdoch, Australia
| | - Béla Urbányi
- Department of Aquaculture, Szent István University , Gödöllő , Hungary
| | - Balázs Kovács
- Department of Aquaculture, Szent István University, Gödöllő, Hungary; Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
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49
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Verspoor E, Knox D, Marshall S. Assessment of interbreeding and introgression of farm genes into a small Scottish Atlantic salmon Salmo salar stock: ad hoc samples - ad hoc results? JOURNAL OF FISH BIOLOGY 2016; 89:2680-2696. [PMID: 27730636 DOI: 10.1111/jfb.13173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
An eclectic set of tissues and existing data, including purposely collected samples, spanning 1997-2006, was used in an ad hoc assessment of hybridization and introgression of farmed wild Atlantic salmon Salmo salar in the small Loch na Thull (LnT) catchment in north-west Scotland. The catchment is in an area of marine farm production and contains freshwater smolt rearing cages. The LnT S. salar stock was found to be genetically distinctive from stocks in neighbouring rivers and, despite regular reports of feral farm S. salar, there was no evidence of physical or genetic mixing. This cannot be completely ruled out, however, and low level mixing with other local wild stocks has been suggested. The LnT population appeared underpinned by relatively smaller effective number of breeders (Neb ) and showed relatively low levels of genetic diversity, consistent with a small effective population size. Small sample sizes, an incomplete farm baseline and the use of non-diagnostic molecular markers, constrain the power of the analysis but the findings strongly support the LnT catchment having a genetically distinct wild S. salar population little affected by interbreeding with feral farm escapes.
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Affiliation(s)
- E Verspoor
- Rivers and Lochs Institute, University of the Highlands and Islands, Inverness College, Inverness, Scotland IV2 5NA, U.K
| | - D Knox
- Ardblair, St Andrews Crescent, Bridge of Tilt, Scotland PH18 5TA, U.K
| | - S Marshall
- West Sutherland Fisheries Trust, Scourie, Scotland IV27 4SX, U.K
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50
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Harvey AC, Solberg MF, Troianou E, Carvalho GR, Taylor MI, Creer S, Dyrhovden L, Matre IH, Glover KA. Plasticity in growth of farmed and wild Atlantic salmon: is the increased growth rate of farmed salmon caused by evolutionary adaptations to the commercial diet? BMC Evol Biol 2016; 16:264. [PMID: 27905882 PMCID: PMC5134087 DOI: 10.1186/s12862-016-0841-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of Atlantic salmon for commercial aquaculture has resulted in farmed salmon displaying substantially higher growth rates than wild salmon under farming conditions. In contrast, growth differences between farmed and wild salmon are much smaller when compared in the wild. The mechanisms underlying this contrast between environments remain largely unknown. It is possible that farmed salmon have adapted to the high-energy pellets developed specifically for aquaculture, contributing to inflated growth differences when fed on this diet. We studied growth and survival of 15 families of farmed, wild and F1 hybrid salmon fed three contrasting diets under hatchery conditions; a commercial salmon pellet diet, a commercial carp pellet diet, and a mixed natural diet consisting of preserved invertebrates commonly found in Norwegian rivers. Results For all groups, despite equal numbers of calories presented by all diets, overall growth reductions as high 68 and 83%, relative to the salmon diet was observed in the carp and natural diet treatments, respectively. Farmed salmon outgrew hybrid (intermediate) and wild salmon in all treatments. The relative growth difference between wild and farmed fish was highest in the carp diet (1: 2.1), intermediate in the salmon diet (1:1.9) and lowest in the natural diet (1:1.6). However, this trend was non-significant, and all groups displayed similar growth reaction norms and plasticity towards differing diets across the treatments. Conclusions No indication of genetic-based adaptation to the form or nutritional content of commercial salmon diets was detected in the farmed salmon. Therefore, we conclude that diet alone, at least in the absence of other environmental stressors, is not the primary cause for the large contrast in growth differences between farmed and wild salmon in the hatchery and wild. Additionally, we conclude that genetically-increased appetite is likely to be the primary reason why farmed salmon display higher growth rates than wild salmon when fed ad lib rations under hatchery conditions. Our results contribute towards an understanding of the potential genetic changes that have occurred in farmed salmon in response to domestication, and the potential mechanisms underpinning genetic and ecological interactions between farmed escapees and wild salmonids. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0841-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alison Catherine Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Deiniol Road, Bangor University, Bangor, LL57 2UW, UK
| | | | - Eva Troianou
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Gary Robert Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Deiniol Road, Bangor University, Bangor, LL57 2UW, UK
| | - Martin Ian Taylor
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Deiniol Road, Bangor University, Bangor, LL57 2UW, UK
| | - Lise Dyrhovden
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Ivar Helge Matre
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kevin Alan Glover
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
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