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Kokkonen AL, Searle PC, Shiozawa DK, Evans RP. Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies ( Oncorhynchus clarkii). Evol Appl 2024; 17:e13735. [PMID: 39006004 PMCID: PMC11239772 DOI: 10.1111/eva.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 07/16/2024] Open
Abstract
For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species-level consideration if other recent species elevations are retained.
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Affiliation(s)
- Andrea L. Kokkonen
- Department of Microbiology and Molecular BiologyBrigham Young UniversityProvoUtahUSA
| | - Peter C. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | | | - R. Paul Evans
- Department of Microbiology and Molecular BiologyBrigham Young UniversityProvoUtahUSA
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2
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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Harris AC, Oyler-McCance SJ, Fike JA, Fairchild MP, Kennedy CM, Crockett HJ, Winkelman DL, Kanno Y. Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Setzke C, Wong C, Russello MA. Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon. Sci Rep 2021; 11:22798. [PMID: 34815428 PMCID: PMC8611073 DOI: 10.1038/s41598-021-01958-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.
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Affiliation(s)
- Christopher Setzke
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Carmen Wong
- Parks Canada Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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Biermann C, Havlick D. Genetics and the question of purity in cutthroat trout restoration. Restor Ecol 2021. [DOI: 10.1111/rec.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christine Biermann
- Department of Geography and Environmental Studies University of Colorado Colorado Springs 1420 Austin Bluffs Parkway Colorado Springs CO 80918 U.S.A
| | - David Havlick
- Department of Geography and Environmental Studies University of Colorado Colorado Springs 1420 Austin Bluffs Parkway Colorado Springs CO 80918 U.S.A
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7
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Affiliation(s)
- Mark Henry Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103; or
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Love Stowell SM, Gagne RB, McWhirter D, Edwards W, Ernest HB. Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sierra M. Love Stowell
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Roderick B. Gagne
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Doug McWhirter
- Wyoming Game and Fish DepartmentJackson Regional Office 420 N Cache St Jackson WY 830001 USA
| | - William Edwards
- Wyoming Game and Fish DepartmentWildlife Health Laboratory 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Holly B. Ernest
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
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Landres P, Hahn BA, Biber E, Spencer DT. Protected area stewardship in the Anthropocene: integrating science, law, and ethics to evaluate proposals for ecological restoration in wilderness. Restor Ecol 2020. [DOI: 10.1111/rec.13104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Landres
- Aldo Leopold Wilderness Research Institute, USDA Forest ServiceRocky Mountain Research Station Missoula MT 59801 U.S.A
| | - Beth A. Hahn
- Aldo Leopold Wilderness Research Institute, USDA Forest ServiceRocky Mountain Research Station Missoula MT 59801 U.S.A
| | - Eric Biber
- Berkeley School of LawUniversity of California, Berkeley Berkeley CA 94720 U.S.A
| | - Daniel T. Spencer
- Environmental StudiesThe University of Montana Missoula MT 59812 U.S.A
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Hammer MP, Adams M, Thacker CE, Johnson JB, Unmack PJ. Comparison of genetic structure in co-occurring freshwater eleotrids (Actinopterygii: Philypnodon) reveals cryptic species, likely translocation and regional conservation hotspots. Mol Phylogenet Evol 2019; 139:106556. [DOI: 10.1016/j.ympev.2019.106556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 06/20/2019] [Accepted: 07/04/2019] [Indexed: 11/25/2022]
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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Eaton KR, Loxterman JL, Keeley ER. Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography. PLoS One 2018; 13:e0202043. [PMID: 30096159 PMCID: PMC6086439 DOI: 10.1371/journal.pone.0202043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Abstract
Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.
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Affiliation(s)
- Kendra R. Eaton
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Janet L. Loxterman
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - Ernest R. Keeley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
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Spatiotemporal genetic structure of anadromous Arctic char (Salvelinus alpinus) populations in a region experiencing pronounced climate change. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1047-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Peacock MM, Hekkala ER, Kirchoff VS, Heki LG. Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171253. [PMID: 29291110 PMCID: PMC5717685 DOI: 10.1098/rsos.171253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/13/2017] [Indexed: 05/05/2023]
Abstract
Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.
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Affiliation(s)
- Mary M. Peacock
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Ecology, Evolution, and Conservation Biology Interdisciplinary Program, University of Nevada, Reno, NV 89557, USA
| | - Evon R. Hekkala
- Department of Biological Sciences, Fordham University, New York, NY 10458, USA
| | - Veronica S. Kirchoff
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- United States Department of Agriculture, Agricultural Research Service, Reno, NV 89512, USA
| | - Lisa G. Heki
- United States Fish and Wildlife Service, Lahontan National Fish Hatchery Complex, 1340 Financial Blvd, Suite 234, Reno, NV 89502, USA
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Roberts JJ, Fausch KD, Schmidt TS, Walters DM. Thermal regimes of Rocky Mountain lakes warm with climate change. PLoS One 2017; 12:e0179498. [PMID: 28683083 PMCID: PMC5500263 DOI: 10.1371/journal.pone.0179498] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 05/31/2017] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic climate change is causing a wide range of stresses in aquatic ecosystems, primarily through warming thermal conditions. Lakes, in response to these changes, are experiencing increases in both summer temperatures and ice-free days. We used continuous records of lake surface temperature and air temperature to create statistical models of daily mean lake surface temperature to assess thermal changes in mountain lakes. These models were combined with downscaled climate projections to predict future thermal conditions for 27 high-elevation lakes in the southern Rocky Mountains. The models predict a 0.25°C·decade-1 increase in mean annual lake surface temperature through the 2080s, which is greater than warming rates of streams in this region. Most striking is that on average, ice-free days are predicted to increase by 5.9 days ·decade-1, and summer mean lake surface temperature is predicted to increase by 0.47°C·decade-1. Both could profoundly alter the length of the growing season and potentially change the structure and function of mountain lake ecosystems. These results highlight the changes expected of mountain lakes and stress the importance of incorporating climate-related adaptive strategies in the development of resource management plans.
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Affiliation(s)
- James J. Roberts
- Colorado Water Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
- * E-mail:
| | - Kurt D. Fausch
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Travis S. Schmidt
- Colorado Water Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
| | - David M. Walters
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States of America
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Houston DD, Evans RP, Crowley JM, Shiozawa DK. Genetic Characterization of Two Populations of Bonneville Cutthroat Trout in Great Basin National Park, USA. WEST N AM NATURALIST 2015. [DOI: 10.3398/064.075.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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DeHaan PW, Adams BA, Tabor RA, Hawkins DK, Thompson B. Historical and contemporary forces shape genetic variation in the Olympic mudminnow (Novumbra hubbsi), an endemic fish from Washington State, USA. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0627-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Valiquette E, Perrier C, Thibault I, Bernatchez L. Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada. Evol Appl 2014; 7:625-44. [PMID: 25067947 PMCID: PMC4105915 DOI: 10.1111/eva.12160] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/17/2014] [Indexed: 11/29/2022] Open
Abstract
Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations.
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Affiliation(s)
- Eliane Valiquette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Isabel Thibault
- Ministère du Développement durable, de l'Environnement de la Faune et des Parcs Québec, QC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
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Houston DD, Elzinga DB, Maughan PJ, Smith SM, Kauwe JSK, Evans RP, Stinger RB, Shiozawa DK. Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing. BMC Genomics 2012; 13:724. [PMID: 23259499 PMCID: PMC3549761 DOI: 10.1186/1471-2164-13-724] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/19/2012] [Indexed: 11/23/2022] Open
Abstract
Background Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations. Results Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses. Conclusions Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans.
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Affiliation(s)
- Derek D Houston
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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