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Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C, Kent M, Nugent CM, Bradbury IR. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecol Evol 2024; 14:e11068. [PMID: 38584771 PMCID: PMC10995719 DOI: 10.1002/ece3.11068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/31/2024] [Indexed: 04/09/2024] Open
Abstract
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
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Affiliation(s)
- Tony Kess
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Steven Duffy
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Amber Messmer
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - J. Brian Dempson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Jason Newport
- Marine Environmental Research Infrastructure for Data Integration and Application NetworkHalifaxNova ScotiaCanada
| | | | - Martha J. Robertson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Gerald Chaput
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Cindy Breau
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Julien April
- Ministère des Forêts de la Faune et des ParcsQuebecQuebecCanada
| | - Carole‐Anne Gillis
- Gespe'gewa'gi, Mi'gma'qi, ListugujGespe'gewa'gi Institute of Natural UnderstandingQuebecQuebecCanada
| | - Matthew Kent
- Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Cameron M. Nugent
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
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2
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Lehnert SJ, Bradbury IR, Wringe BF, Van Wyngaarden M, Bentzen P. Multifaceted framework for defining conservation units: An example from Atlantic salmon ( Salmo salar) in Canada. Evol Appl 2023; 16:1568-1585. [PMID: 37752960 PMCID: PMC10519414 DOI: 10.1111/eva.13587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 09/28/2023] Open
Abstract
Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed "designatable units"; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to "big data" is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in-depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.
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Affiliation(s)
- Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | | | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNova ScotiaCanada
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3
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Gao G, Waldbieser GC, Youngblood RC, Zhao D, Pietrak MR, Allen MS, Stannard JA, Buchanan JT, Long RL, Milligan M, Burr G, Mejía-Guerra K, Sheehan MJ, Scheffler BE, Rexroad CE, Peterson BC, Palti Y. The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon. G3 (BETHESDA, MD.) 2023; 13:jkad138. [PMID: 37335943 PMCID: PMC10468304 DOI: 10.1093/g3journal/jkad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species.
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Affiliation(s)
- Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
| | - Geoffrey C Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Dongyan Zhao
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Michael R Pietrak
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Melissa S Allen
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - Jason A Stannard
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - John T Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - Roseanna L Long
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
| | - Melissa Milligan
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Gary Burr
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Katherine Mejía-Guerra
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Moira J Sheehan
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Brian E Scheffler
- USDA-ARS Genomics and Bioinformatics Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA
| | - Caird E Rexroad
- USDA-ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
| | - Brian C Peterson
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
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Lantiegne TH, Purchase CF. Can cryptic female choice prevent invasive hybridization in external fertilizing fish? Evol Appl 2023; 16:1412-1421. [PMID: 37622094 PMCID: PMC10445091 DOI: 10.1111/eva.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/08/2023] [Indexed: 08/26/2023] Open
Abstract
Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre-mating and post-mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid in general had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation between the native North American species.
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Affiliation(s)
- Tyler H. Lantiegne
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland & LabradorCanada
| | - Craig F. Purchase
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland & LabradorCanada
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5
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Nugent CM, Kess T, Brachmann MK, Langille BL, Holborn MK, Beck SV, Smith N, Duffy SJ, Lehnert SJ, Wringe BF, Bentzen P, Bradbury IR. Genomic and machine learning-based screening of aquaculture-associated introgression into at-risk wild North American Atlantic salmon (Salmo salar) populations. Mol Ecol Resour 2023. [PMID: 37246351 DOI: 10.1111/1755-0998.13811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
Abstract
The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at-risk wild North American salmon populations. Here, we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7-SSR, 100-SSR and 220K-SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three datasets showed that the 100-SSR panel and 7-SSR panels replicated the full 220K-SNP-based admixture estimates with low accuracy (r2 of .64 and .49, respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K-SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301-SNP) for European admixture detection in future monitoring work and then developed and tested a python package, salmoneuadmix (https://github.com/CNuge/SalmonEuAdmix), which uses a deep neural network to make de novo estimates of individuals' European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at-risk species conservation and management.
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Affiliation(s)
- Cameron M Nugent
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Matthew K Brachmann
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Barbara L Langille
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Melissa K Holborn
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Samantha V Beck
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Biodiversity and Freshwater Conservation, University of the Highlands and Islands, Inverness, UK
| | - Nicole Smith
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Steven J Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
| | - Brendan F Wringe
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Paul Bentzen
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, Newfoundland and Labrador, Canada
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6
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Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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7
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Bradbury IR, Lehnert SJ, Kess T, Van Wyngaarden M, Duffy S, Messmer A, Wringe B, Karoliussen S, Dempson JB, Fleming IA, Solberg MF, Glover KA, Bentzen P. Genomic evidence of recent European introgression into North American farmed and wild Atlantic Salmon. Evol Appl 2022; 15:1436-1448. [PMID: 36187183 PMCID: PMC9488674 DOI: 10.1111/eva.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/10/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar, used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon (n = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon (n = 403) and escapees (n = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals (p < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild.
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Affiliation(s)
- I. R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - 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
| | - M. Van Wyngaarden
- Biology Department Dalhousie University 1355 Oxford Street Halifax Nova Scotia
| | - S. Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - A. Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - B. Wringe
- Bedford Institute of Oceanography Fisheries and Oceans Canada Dartmouth NS Canada
| | - S. Karoliussen
- Centre for Integrative Genetics Norwegian University of Life Sciences Ås Norway
| | - J. B. Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - I. A. Fleming
- Department of Ocean Sciences, Ocean Sciences Centre Memorial University of Newfoundland St John’s, NL, A1C 5S7 Canada
| | - M. F. Solberg
- Institute of Marine Research Population Genetics Research Group PO Box 1870, Nordnes, N‐5817 Bergen Norway
| | - K. A. Glover
- Institute of Marine Research Population Genetics Research Group PO Box 1870, Nordnes, N‐5817 Bergen Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
| | - P. Bentzen
- Biology Department Dalhousie University 1355 Oxford Street Halifax Nova Scotia
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8
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Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. BIOLOGY 2022; 11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.
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Affiliation(s)
- María Gabián
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - Paloma Morán
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain;
| | - Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
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9
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Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
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Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
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10
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Crotti M, Bean CW, Gowans ARD, Winfield IJ, Butowska M, Wanzenböck J, Bondarencko G, Praebel K, Adams CE, Elmer KR. Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus). J Evol Biol 2021; 34:1954-1969. [PMID: 34653264 PMCID: PMC9251650 DOI: 10.1111/jeb.13948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome‐wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (FST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome‐wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto‐nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre‐glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.
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Affiliation(s)
- Marco Crotti
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK.,NatureScot, Clydebank, UK
| | | | - Ian J Winfield
- Lake Ecosystems Group, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Magdalena Butowska
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Josef Wanzenböck
- Research Institute for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | | | - Kim Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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11
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Zueva KJ, Lumme J, Veselov AE, Primmer CR, Pritchard VL. Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of north‐eastern Europe. J Evol Biol 2020; 34:866-878. [DOI: 10.1111/jeb.13732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Affiliation(s)
| | - Jaakko Lumme
- Department of Biology University of Oulu Oulu Finland
| | | | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Victoria L. Pritchard
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Rivers and Lochs Institute Inverness College University of Highlands and Islands Inverness UK
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12
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Kess T, Brachmann M, Boulding EG. Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly dispersing snail. J Evol Biol 2020; 34:193-207. [PMID: 33108001 DOI: 10.1111/jeb.13724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Littorina saxatilis is becoming a model system for understanding the genomic basis of ecological speciation. The parallel formation of crab-adapted ecotypes that exhibit partial reproductive isolation from wave-adapted ecotypes has enabled genomic investigation of conspicuous shell traits. Recent genomic studies suggest that chromosomal rearrangements may enable ecotype divergence by reducing gene flow. However, the genomic architecture of traits that are divergent between ecotypes remains poorly understood. Here, we use 11,504 single nucleotide polymorphism (SNP) markers called using the recently released L. saxatilis genome to genotype 462 crab ecotype, wave ecotype and phenotypically intermediate Spanish L. saxatilis individuals with scored phenotypes. We used redundancy analysis to study the genetic architecture of loci associated with shell shape, shape corrected for size, shell size and shell ornamentation, and to compare levels of co-association among different traits. We discovered 341 SNPs associated with shell traits. Loci associated with trait divergence between ecotypes were often located inside putative chromosomal rearrangements recently characterized in Swedish L. saxatilis. In contrast, we found that shell shape corrected for size varied primarily by geographic site rather than by ecotype and showed little association with these putative rearrangements. We conclude that genomic regions of elevated divergence inside putative rearrangements were associated with divergence of L. saxatilis ecotypes along steep environmental axes-consistent with models of adaptation with gene flow-but were not associated with divergence among the three geographical sites. Our findings support predictions from models indicating the importance of genomic regions of reduced recombination allowing co-association of loci during ecological speciation with ongoing gene flow.
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Affiliation(s)
- Tony Kess
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Matthew Brachmann
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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