1
|
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.
Collapse
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
| |
Collapse
|
2
|
Wierzbicki H, Zatoń-Dobrowolska M, Mucha A, Moska M. Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes. Genes (Basel) 2021; 12:genes12050637. [PMID: 33922932 PMCID: PMC8146073 DOI: 10.3390/genes12050637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species.
Collapse
|
3
|
Graham CF, Eberts RL, Goncin U, Somers CM. Spontaneous hybridization and introgression between walleye ( Sander vitreus) and sauger ( Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing. Evol Appl 2021; 14:965-982. [PMID: 33897814 PMCID: PMC8061268 DOI: 10.1111/eva.13174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022] Open
Abstract
Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) single nucleotide polymorphisms clearly resolved walleye and sauger, and classified hybrids with high confidence. F1, F2, and multigeneration hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F1 hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12 of 173 (7%) fish field identified as pure walleye, and one of 24 (4%) identified as pure sauger were actually hybrids. In addition, two of 15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without preidentification of informative loci, eliminating some of the key challenges associated with other marker types.
Collapse
Affiliation(s)
| | - Rebecca L. Eberts
- Fish, Wildlife, and Lands Branch, Ministry of EnvironmentGovernment of SaskatchewanPrince AlbertSKCanada
| | - Una Goncin
- Department of BiologyUniversity of ReginaReginaSKCanada
| | | |
Collapse
|
4
|
Genetic interactions among native and introduced stocks of Oncorhynchus mykiss in the upper Willamette River, Oregon. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
5
|
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
| |
Collapse
|
6
|
Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs. BMC Genomics 2020; 21:541. [PMID: 32758142 PMCID: PMC7430818 DOI: 10.1186/s12864-020-06960-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.
Collapse
|
7
|
von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020. [PMID: 31925943 DOI: 10.1111/1755-0998.13136.applying] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| |
Collapse
|
8
|
Taillebois L, Sabatino S, Manicki A, Daverat F, Nachón DJ, Lepais O. Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax. Evol Appl 2020; 13:636-651. [PMID: 32211057 PMCID: PMC7086104 DOI: 10.1111/eva.12889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Hybridization dynamics between co-occurring species in environments where human-mediated changes take place are important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations' abundance threatens its persistence. The main objective was to evaluate the extent of hybridization and introgression between those interacting species. We developed a set of 77 species-specific SNP loci that allowed a better resolution than morphological traits as they enabled the detection of hybrids up to the third generation. Variable rates of contemporary hybridization and introgression patterns were detected in 12 studied sites across the French Atlantic coast. Mitochondrial markers revealed a cyto-nuclear discordance almost invariably involving A. alosa individuals with an A. fallax mitochondrial DNA and provided evidence of historical asymmetric introgression. Overall, contemporary and historical introgression revealed by nuclear and mitochondrial markers strongly suggests that a transfer of genes occurs from A. fallax toward A. alosa genome since at least four generations. Moreover, the outcomes of introgression greatly depend on the catchments where local processes are thought to occur. Undoubtedly, interspecific interaction and gene flow should not be overlooked when considering the management of those species.
Collapse
Affiliation(s)
- Laura Taillebois
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
| | | | - Aurélie Manicki
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
| | | | - David José Nachón
- EABXIRSTEACestas CedexFrance
- Estación de Hidrobioloxía ‘Encoro do Con’Universidade de Santiago de CompostelaVilagarcía de ArousaSpain
| | - Olivier Lepais
- ECOBIOPINRAUniversité de Pau et Pays de l’AdourSaint‐Pée‐sur‐NivelleFrance
- BIOGECOINRA, Univ. BordeauxCestasFrance
| |
Collapse
|
9
|
von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| |
Collapse
|
10
|
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.
Collapse
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;
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar). Mar Genomics 2018; 39:26-38. [DOI: 10.1016/j.margen.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]
|
13
|
Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
| |
Collapse
|
14
|
Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG. A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits. Evol Appl 2016; 10:276-296. [PMID: 28250812 PMCID: PMC5322405 DOI: 10.1111/eva.12450] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
Collapse
Affiliation(s)
- Lei Liu
- Department of Integrative Biology University of Guelph Guelph ON Canada; Present address: School of Marine Sciences Ningbo University Ningbo China
| | | | | | - Matthew Peter Kent
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Danielle MacDonald
- Saint Andrews Biological Station Department of Fisheries and Oceans Canada Saint Andrews NB Canada
| | | |
Collapse
|