1
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Muller-Girard M, Fowles G, Duchamp J, Kouneski S, Mollohan C, Smyser TJ, Turner GG, Westrich B, Doyle JM. A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population. BMC Ecol Evol 2022; 22:137. [PMID: 36418951 PMCID: PMC9686018 DOI: 10.1186/s12862-022-02083-w] [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: 01/26/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. RESULTS We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. CONCLUSIONS Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
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Affiliation(s)
- Megan Muller-Girard
- grid.265122.00000 0001 0719 7561Department of Environmental Science and Studies, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | - Gretchen Fowles
- Endangered and Nongame Species Program, New Jersey DEP Fish and Wildlife, 1255 County Rd 629, Lebanon, NJ 08833 USA
| | - Joseph Duchamp
- grid.257427.10000000088740847Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, PA 15705-1081 USA
| | - Samantha Kouneski
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | | | - Timothy J. Smyser
- grid.413759.d0000 0001 0725 8379USDA-APHIS-WS National Wildlife Research Center, Fort Collins, CO USA
| | - Gregory G. Turner
- Pennsylvania Game Commission, 2001 Elmerton Avenue, Harrisburg, PA 17110 USA
| | - Bradford Westrich
- grid.448453.a0000 0004 1130 5264Indiana Department of Natural Resources, 5596 East State Road 46, Bloomington, IN 47401 USA
| | - Jacqueline M. Doyle
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
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2
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Sundaray JK, Dixit S, Rather A, Rasal KD, Sahoo L. Aquaculture omics: An update on the current status of research and data analysis. Mar Genomics 2022; 64:100967. [PMID: 35779450 DOI: 10.1016/j.margen.2022.100967] [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: 06/17/2021] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
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Affiliation(s)
- Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Ashraf Rather
- Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu and Kashmir, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
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3
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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4
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LeBlanc NM, Gahagan BI, Andrews SN, Avery TS, Puncher GN, Reading BJ, Buhariwalla CF, Curry RA, Whiteley AR, Pavey SA. Genomic population structure of Striped Bass ( Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River. Evol Appl 2020; 13:1468-1486. [PMID: 32684970 PMCID: PMC7359840 DOI: 10.1111/eva.12990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 11/28/2022] Open
Abstract
Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.
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Affiliation(s)
- Nathalie M. LeBlanc
- Department of Biological SciencesCanadian Rivers InstituteUniversity of New BrunswickSaint JohnNBCanada
| | - Benjamin I. Gahagan
- Massachusetts Division of Marine FisheriesAnnisquam River Marine Fisheries StationGloucesterMAUSA
| | - Samuel N. Andrews
- Department of BiologyCanadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
| | - Trevor S. Avery
- Departments of Biology and Mathematics & StatisticsAcadia UniversityWolfvilleNSCanada
| | - Gregory N. Puncher
- Department of Biological SciencesCanadian Rivers InstituteUniversity of New BrunswickSaint JohnNBCanada
- Molecular Biology LaboratoryMaurice Lamontagne Institute, Fisheries and Oceans CanadaMont‐JoliQCCanada
| | - Benjamin J. Reading
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
- Pamlico Aquaculture Field LaboratoryNorth Carolina State UniversityAuroraNCUSA
| | | | - R. Allen Curry
- Department of Biology and Faculty of Forestry and Environmental ManagementCanadian Rivers InstituteUniversity of New BrunswickFrederictonNBCanada
| | - Andrew R. Whiteley
- Department of Ecosystem and Conservation Sciences and Wildlife Biology ProgramW. A. Franke College of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
| | - Scott A. Pavey
- Department of Biological SciencesCanadian Rivers InstituteUniversity of New BrunswickSaint JohnNBCanada
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5
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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.
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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
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6
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Reid K, Carlos Garza J, Gephard SR, Caccone A, Post DM, Palkovacs EP. Restoration-mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial-era dam. Evol Appl 2020; 13:652-664. [PMID: 32211058 PMCID: PMC7086056 DOI: 10.1111/eva.12890] [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: 06/14/2019] [Revised: 08/30/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022] Open
Abstract
Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus ) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial-era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous juvenile production, the magnitude and direction of introgression, and the potential for competition between ecotypes. We obtained fin clips from all adult alewife stocked into the lake during the restoration and a sample of juveniles produced in the lake two years after the stocking began. We assessed the ancestry of juveniles using categorical assignment and pedigree reconstruction with newly developed microhaplotype genetic markers. Anadromous alewives successfully spawned in the lake and hybridized with the landlocked population. Parentage assignments revealed that male and female anadromous fish contributed equally to juvenile F1 hybrids. The presence of landlocked backcrosses shows that some hybrids were produced within the first two years of secondary contact, matured in the lake, and reproduced. Therefore, introgression appears directional, from anadromous into landlocked, in the lake environment. Differences in estimated abundance of juveniles of different ecotypes in different habitats were also detected, which may reduce competition between ecotypes as the restoration continues. Our results illustrate the utility of restoration projects to study the outcomes of secondary contact in real ecosystems.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
| | - John Carlos Garza
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCAUSA
| | - Steven R. Gephard
- Fisheries DivisionConnecticut Department of Energy and Environmental ProtectionOld LymeCTUSA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - David M. Post
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
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7
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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.
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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
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8
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Baetscher DS, Hasselman DJ, Reid K, Palkovacs EP, Garza JC. Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern. Ecol Evol 2017; 7:6638-6648. [PMID: 28904746 PMCID: PMC5587496 DOI: 10.1002/ece3.3215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/22/2017] [Accepted: 06/09/2017] [Indexed: 01/16/2023] Open
Abstract
Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and then developed molecular genetic assays for genotyping sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.
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Affiliation(s)
- Diana S. Baetscher
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCAUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
| | - Daniel J. Hasselman
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
- Present address:
Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Kerry Reid
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
| | - John Carlos Garza
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCAUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
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