1
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Freedman MG, Kronforst MR. Migration genetics take flight: genetic and genomic insights into monarch butterfly migration. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101079. [PMID: 37385346 PMCID: PMC10592233 DOI: 10.1016/j.cois.2023.101079] [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: 03/30/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
Abstract
Monarch butterflies have emerged as a model system in migration genetics. Despite inherent challenges associated with studying the integrative phenotypes that characterize migration, recent research has highlighted genes and transcriptional networks underlying aspects of the monarch's migratory syndrome. Circadian clock genes and the vitamin A synthesis pathway regulate reproductive diapause initiation, while diapause termination appears to involve calcium and insulin signaling. Comparative approaches have highlighted genes that distinguish migratory and nonmigratory monarch populations, as well as genes associated with natural variation in propensity to initiate diapause. Population genetic techniques demonstrate that seasonal migration can collapse patterns of spatial structure at continental scales, whereas loss of migration can drive differentiation between even nearby populations. Finally, population genetics can be applied to reconstruct the monarch's evolutionary history and search for contemporary demographic changes, which can provide relevant context for understanding recently observed declines in overwintering North American monarch numbers.
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2
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Baerwald MR, Funk EC, Goodbla AM, Campbell MA, Thompson T, Meek MH, Schreier AD. Rapid CRISPR-Cas13a genetic identification enables new opportunities for listed Chinook salmon management. Mol Ecol Resour 2023. [PMID: 36847138 DOI: 10.1111/1755-0998.13777] [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: 11/21/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can fill an unoccupied niche between real-time, inexpensive, but error-prone visual identification and more expensive or time-consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR-based SHERLOCK assays capable of rapidly (<1 h), accurately (94%-98% concordance between phenotypic and genotypic assignments), and sensitively (detects 1-10 DNA copies/reaction) distinguishing ESA-listed Chinook salmon runs (winter- and spring-run) from each other and from unlisted runs (fall- and late fall-run) in California's Central Valley. The assays can be field deployable with minimally invasive mucus swabbing negating the need for DNA extraction (decreasing costs and labour), minimal and inexpensive equipment needs, and minimal training to conduct following assay development. This study provides a powerful genetic approach for a species of conservation concern that benefits from near real-time management decision-making but also serves as a precedent for transforming how conservation scientists and managers view genetic identification going forward. Once developed, CRISPR-based tools can provide accurate, sensitive, and rapid results, potentially without the prohibitive need for expensive specialty equipment or extensive molecular training. Further adoption of this technology will have widespread value for the monitoring and protection of our natural resources.
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Affiliation(s)
- Melinda R Baerwald
- Division of Integrated Science and Engineering, California Department of Water Resources, Sacramento, California, USA
| | - Emily C Funk
- Genomic Variation Laboratory, Department of Animal Sciences, University of California Davis, Davis, California, USA
| | - Alisha M Goodbla
- Genomic Variation Laboratory, Department of Animal Sciences, University of California Davis, Davis, California, USA
| | - Matthew A Campbell
- Genomic Variation Laboratory, Department of Animal Sciences, University of California Davis, Davis, California, USA
| | - Tasha Thompson
- Department of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Programme, Michigan State University, East Lansing, Michigan, USA.,Wild Salmon Center, Portland, OR, USA
| | - Mariah H Meek
- Department of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Programme, Michigan State University, East Lansing, Michigan, USA
| | - Andrea D Schreier
- Genomic Variation Laboratory, Department of Animal Sciences, University of California Davis, Davis, California, USA
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3
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023; 179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
| | - Jose M Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain; Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Josephine R Paris
- Department of Health, Life and Environmental Sciences, University of l'Aquila, Coppito, Italy; Department of Biosciences, University of Exeter, Exeter, UK
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, UK; Department of Biological Sciences, Faculty of Sciences, University of Calgary, Calgary, Canada
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
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4
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Biello R, Zampiglia M, Fuselli S, Fabbri G, Bisconti R, Chiocchio A, Mazzotti S, Trucchi E, Canestrelli D, Bertorelle G. From
STRs
to
SNPs
via
ddRAD
‐seq: geographic assignment of confiscated tortoises at reduced costs. Evol Appl 2022; 15:1344-1359. [PMID: 36187190 PMCID: PMC9488678 DOI: 10.1111/eva.13431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost‐effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD‐seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro‐area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re‐assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in‐situ of confiscated animals and their possible re‐allocation in the wild. Our methodological pipeline can easily be extended to other species.
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Affiliation(s)
- Roberto Biello
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park Norwich UK
| | - Mauro Zampiglia
- Department of Ecological and Biological Science Tuscia University Viterbo Italy
- Central Laboratory for the National DNA Database, Prison Administration Department, Ministry of Justice Rome Italy
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy
| | - Giulia Fabbri
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy
- Department of Veterinary Medicine University of Sassari Sassari Italy
| | - Roberta Bisconti
- Department of Ecological and Biological Science Tuscia University Viterbo Italy
| | - Andrea Chiocchio
- Department of Ecological and Biological Science Tuscia University Viterbo Italy
| | | | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy
- Department of Life and Environmental Sciences Marche Polytechnic University Ancona Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Science Tuscia University Viterbo Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology University of Ferrara Ferrara Italy
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5
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Guragain P, Båtnes AS, Zobolas J, Olsen Y, Bones AM, Winge P. IIb-RAD-sequencing coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice ( Lepeophtheirus salmonis). Ecol Evol 2022; 12:e8809. [PMID: 35414904 PMCID: PMC8986551 DOI: 10.1002/ece3.8809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.
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Affiliation(s)
- Prashanna Guragain
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Anna Solvang Båtnes
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - John Zobolas
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Yngvar Olsen
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Atle M. Bones
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Per Winge
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
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6
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Dallaire X, Normandeau É, Mainguy J, Tremblay J, Bernatchez L, Moore J. Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation. Evol Appl 2021; 14:1880-1897. [PMID: 34295370 PMCID: PMC8287999 DOI: 10.1111/eva.13248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice-free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation-by-distance reflecting contemporary gene flow. Results from three gene-environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.
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Affiliation(s)
- Xavier Dallaire
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Julien Mainguy
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Jean‐Éric Tremblay
- Département de Biologie, Université LavalQuébecQCCanada
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Jean‐Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
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7
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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8
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Jenkins TL, Ellis CD, Triantafyllidis A, Stevens JR. Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster. Evol Appl 2019; 12:1881-1899. [PMID: 31700533 PMCID: PMC6824076 DOI: 10.1111/eva.12849] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction-site-associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north-east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern-isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors-remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.
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Affiliation(s)
- Tom L. Jenkins
- Department of Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Charlie D. Ellis
- Department of Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
- National Lobster HatcherySouth QuayPadstowUK
| | | | - Jamie R. Stevens
- Department of Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
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9
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Population Genomics Applied to Fishery Management and Conservation. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_66] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Whitaker JM, Welsh AB, Hondorp DW, Boase JC, Merovich GT, Welsh S, Krueger C. Variation in DNA methylation is associated with migratory phenotypes of lake sturgeon Acipenser fulvescens in the St. Clair River, MI, USA. JOURNAL OF FISH BIOLOGY 2018; 93:942-951. [PMID: 30246341 DOI: 10.1111/jfb.13804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Lake sturgeon Acipenser fulvescens populations show a variety of movement patterns that are poorly understood. To compare two migratory phenotypes of A. fulvescens in the St. Clair River, MI, USA, multiple data types were analysed. Individual fish were classified into migratory phenotypes based on acoustic telemetry data collected 2012-2015. Acipenser fulvescens consistently showed movement from the St. Clair River upriver into Lake Huron or downriver into Lake St. Clair. The two migratory phenotypes were then compared for differences in morphometrics, genetics and epigenetics. Morphological differences based on linear measurements were not detected between phenotypes. Microsatellite data from 11 loci suggested one population with no genetic differentiation between migratory phenotypes. Our epigenetic results indicated that the migratory phenotypes are differentially methylated (P < 0.05), thus epigenetics may be associated with migratory differences in A. fulvescens. Only one restriction site was identified to be driving the differential methylation (P < 0.05). While little evidence at neutral loci occurred for genetic differentiation of A. fulvescens, DNA methylation may play a role in the observed movement pattern variation. When combined with microsatellite and morphometric analyses, our results suggested that different migratory patterns may reflect phenotypic plasticity, allowing A. fulvescens to acclimate to short-term environmental variability. Without an integrated approach, the role of epigenetics in the migratory phenotype of A. fulvescens may have been overlooked. Further characterization of migratory phenotypes could be important for management to conserve behavioural variation across the distribution of A. fulvescens and for design of stocking guidelines.
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Affiliation(s)
- Justine M Whitaker
- School of Natural Resources, West Virginia University, Morgantown, West Virginia
| | - Amy B Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia
| | - Darryl W Hondorp
- U.S. Geological Survey - Great Lakes Science Center, Ann Arbor, Michigan
| | - James C Boase
- U.S. Fish and Wildlife Service - Alpena Fish and Wildlife Conservation Office, Alpena, Michigan
| | - George T Merovich
- Department of Environmental Science, Fisheries and Aquatic Sciences Program, Juniata College, Huntingdon, Pennsylvania
| | - Stuart Welsh
- US Geological Survey, West Virginia Cooperative Fish and Wildlife Research Unit, School of Natural Resources, Morgantown, West Virginia
| | - Charles Krueger
- Department of Fisheries and Wildlife, Michigan State University, Center for Systems Integration and Sustainability, East Lansing, Michigan
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11
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Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B. Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon. Ecol Evol 2016; 6:7706-7716. [PMID: 30128122 PMCID: PMC6093154 DOI: 10.1002/ece3.2493] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 01/05/2023] Open
Abstract
Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large‐scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single‐nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well‐chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site‐associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.
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Affiliation(s)
- Mariah H Meek
- Department of Natural Resources Cornell University Ithaca NY USA.,Department of Animal Science University of California Davis Davis CA USA
| | - Melinda R Baerwald
- Department of Animal Science University of California Davis Davis CA USA
| | - Molly R Stephens
- Department of Animal Science University of California Davis Davis CA USA.,School of Natural Science University of California, Merced Merced CA USA
| | - Alisha Goodbla
- Department of Animal Science University of California Davis Davis CA USA
| | - Michael R Miller
- Department of Animal Science University of California Davis Davis CA USA
| | | | - Bernie May
- Department of Animal Science University of California Davis Davis CA USA
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