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Kobayashi KM, Bond RM, Reid K, Garza JC, Kiernan JD, Palkovacs EP. Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish. Evol Appl 2024; 17:e13712. [PMID: 38911264 PMCID: PMC11192968 DOI: 10.1111/eva.13712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/05/2024] [Accepted: 04/14/2024] [Indexed: 06/25/2024] Open
Abstract
Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.
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Affiliation(s)
- Katie M. Kobayashi
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Rosealea M. Bond
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological SciencesUniversity of Hong KongHong KongHong Kong, SAR
| | - J. Carlos Garza
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Joseph D. Kiernan
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
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2
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Raines C, Lovy J, Phelps N, Mor S, Ng TFF, Iwanowicz L. Discovery and Genomic Characterization of a Novel Hepadnavirus from Asymptomatic Anadromous Alewife ( Alosa pseudoharengus). Viruses 2024; 16:824. [PMID: 38932117 PMCID: PMC11209213 DOI: 10.3390/v16060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 06/28/2024] Open
Abstract
The alewife (Alosa pseudoharengus) is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015-2018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family: Hepadnaviridae; genus: Metahepadnavirus). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in this species, alewives are migratory interjurisdictional fishes of management concern. Identification of microbial agents using de novo sequencing and other advanced technologies is a critical aspect of understanding disease ecology for informed population management.
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Affiliation(s)
- Clayton Raines
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, 11649 Leetown Road, Kearneysville, WV 25430, USA;
- West Virginia Cooperative Fish and Wildlife Research Unit, Davis College of Agriculture, Natural Resources & Design, West Virginia University, 1 Waterfront Pl, Morgantown, WV 26506, USA
| | - Jan Lovy
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA;
- NJ Fish & Wildlife, Office of Fish and Wildlife Health and Forensics, 605 Pequest Rd, Oxford, NJ 07863, USA
| | - Nicolas Phelps
- Department of Fisheries, Wildlife, and Conservation Biology, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USA;
| | - Sunil Mor
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, 1155 North Campus Drive, Brookings, SD 570077, USA;
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55455, USA
| | - Terry Fei Fan Ng
- Department of Pathology, University of Georgia, Athens, GA 30602, USA;
| | - Luke Iwanowicz
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, 11649 Leetown Road, Kearneysville, WV 25430, USA;
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
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3
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Stahlke AR, Bitume EV, Özsoy ZA, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. Hybridization and range expansion in tamarisk beetles ( Diorhabda spp.) introduced to North America for classical biological control. Evol Appl 2022; 15:60-77. [PMID: 35126648 PMCID: PMC8792477 DOI: 10.1111/eva.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/31/2023] Open
Abstract
With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata × D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.
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Affiliation(s)
- Amanda R. Stahlke
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS)Beltsville Agricultural Research Center, Bee Research LaboratoryBeltsvilleMarylandUSA
| | - Ellyn V. Bitume
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
- U.S. Department of Agriculture, Forest Service (USDA‐FS), Pacific Southwest, Institute of Pacific Islands ForestryHiloHawaiiUSA
| | - Zeynep A. Özsoy
- Department of Biological SciencesColorado Mesa UniversityGrand JunctionColoradoUSA
| | - Dan W. Bean
- Colorado Department of AgriculturePalisadeColoradoUSA
| | - Anne Veillet
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Meaghan I. Clark
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eliza I. Clark
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Patrick Moran
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
| | - Ruth A. Hufbauer
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Paul A. Hohenlohe
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
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4
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Barker KJ, Xu W, Van Scoyoc A, Serota MW, Moravek JA, Shawler AL, Ryan RE, Middleton AD. Toward a new framework for restoring lost wildlife migrations. Conserv Lett 2021. [DOI: 10.1111/conl.12850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Kristin J. Barker
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Wenjing Xu
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Amy Van Scoyoc
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Mitchell W. Serota
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Jessie A. Moravek
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Avery L. Shawler
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Rachael E. Ryan
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
| | - Arthur D. Middleton
- Department of Environmental Science, Policy, and Management University of California—Berkeley Berkeley California
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5
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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6
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Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
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7
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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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8
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Smith SE, Palkovacs EP, Weidel BC, Bunnell DB, Jones AW, Bloom DD. A century of intermittent eco-evolutionary feedbacks resulted in novel trait combinations in invasive Great Lakes alewives ( Alosa pseudoharengus). Evol Appl 2020; 13:2630-2645. [PMID: 33294013 PMCID: PMC7691454 DOI: 10.1111/eva.13063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 01/17/2023] Open
Abstract
Species introductions provide opportunities to quantify rates and patterns of evolutionary change in response to novel environments. Alewives (Alosa pseudoharengus) are native to the East Coast of North America where they ascend coastal rivers to spawn in lakes and then return to the ocean. Some populations have become landlocked within the last 350 years and diverged phenotypically from their ancestral marine population. More recently, alewives were introduced to the Laurentian Great Lakes (~150 years ago), but these populations have not been compared to East Coast anadromous and landlocked populations. We quantified 95 years of evolution in foraging traits and overall body shape of Great Lakes alewives and compared patterns of phenotypic evolution of Great Lakes alewives to East Coast anadromous and landlocked populations. Our results suggest that gill raker spacing in Great Lakes alewives has evolved in a dynamic pattern that is consistent with responses to strong but intermittent eco-evolutionary feedbacks with zooplankton size. Following their initial colonization of Lakes Ontario and Michigan, dense alewife populations likely depleted large-bodied zooplankton, which drove a decrease in alewife gill raker spacing. However, the introduction of large, non-native zooplankton to the Great Lakes in later decades resulted in an increase in gill raker spacing, and present-day Great Lakes alewives have gill raker spacing patterns that are similar to the ancestral East Coast anadromous population. Conversely, contemporary Great Lakes alewife populations possess a gape width consistent with East Coast landlocked populations. Body shape showed remarkable parallel evolution with East Coast landlocked populations, likely due to a shared response to the loss of long-distance movement or migrations. Our results suggest the colonization of a new environment and cessation of migration can result in rapid parallel evolution in some traits, but contingency also plays a role, and a dynamic ecosystem can also yield novel trait combinations.
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Affiliation(s)
- Shelby E. Smith
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
| | - Eric P. Palkovacs
- Department of Ecology & Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
| | - Brian C. Weidel
- United States Geological Survey (USGS) at the Great Lakes Science CenterLake Ontario Biological StationOswegoNYUSA
| | - David B. Bunnell
- United States Geological Survey (USGS) at the Great Lakes Science CenterAnn ArborMIUSA
| | - Andrew W. Jones
- National Oceanic and Atmospheric Administration (NOAA) FisheriesNortheast Fisheries Science CenterNarragansettRIUSA
| | - Devin D. Bloom
- Department of Biological SciencesWestern Michigan UniversityKalamazooMIUSA
- Institute of the Environment and SustainabilityWestern Michigan UniversityKalamazooMIUSA
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9
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Bootsma ML, Gruenthal KM, McKinney GJ, Simmons L, Miller L, Sass GG, Larson WA. A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms. Mol Ecol Resour 2020; 20:1706-1722. [PMID: 32668508 DOI: 10.1111/1755-0998.13226] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022]
Abstract
Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye (Sander vitreus), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.
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Affiliation(s)
- Matthew L Bootsma
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA
| | - Kristen M Gruenthal
- Office of Applied Science, Wisconsin Department of Natural Resources, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, USA
| | - Garrett J McKinney
- NRC Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Levi Simmons
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA
| | - Loren Miller
- Minnesota Department of Natural Resources, University of Minnesota, St. Paul, MN, USA
| | - Greg G Sass
- Wisconsin Department of Natural Resources, Escanaba Lake Research Station, Office of Applied Science, WI, USA
| | - Wesley A Larson
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA.,Ted Stevens Marine Research Institute, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, USA
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