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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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Kitada S, Kishino H. Population structure of chum salmon and selection on the markers collected for stock identification. Ecol Evol 2021; 11:13972-13985. [PMID: 34707832 PMCID: PMC8525185 DOI: 10.1002/ece3.8102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/25/2022] Open
Abstract
Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single-nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH-3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2-dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.
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Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and TechnologyTokyoJapan
| | - Hirohisa Kishino
- Graduate School of Agriculture and Life SciencesThe University of TokyoTokyoJapan
- Present address:
The Research Institute of Evolutionary BiologyTokyoJapan
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May SA, McKinney GJ, Hilborn R, Hauser L, Naish KA. Power of a dual-use SNP panel for pedigree reconstruction and population assignment. Ecol Evol 2020; 10:9522-9531. [PMID: 32953080 PMCID: PMC7487233 DOI: 10.1002/ece3.6645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 11/28/2022] Open
Abstract
The use of high-throughput, low-density sequencing approaches has dramatically increased in recent years in studies of eco-evolutionary processes in wild populations and domestication in commercial aquaculture. Most of these studies focus on identifying panels of SNP loci for a single downstream application, whereas there have been few studies examining the trade-offs for selecting panels of markers for use in multiple applications. Here, we detail the use of a bioinformatic workflow for the development of a dual-purpose SNP panel for parentage and population assignment, which included identifying putative SNP loci, filtering for the most informative loci for the two tasks, designing effective multiplex PCR primers, optimizing the SNP panel for performance, and performing quality control steps for downstream applications. We applied this workflow to two adjacent Alaskan Sockeye Salmon populations and identified a GTseq panel of 142 SNP loci for parentage and 35 SNP loci for population assignment. Only 50-75 panel loci were necessary for >95% accurate parentage, whereas population assignment success, with all 172 panel loci, ranged from 93.9% to 96.2%. Finally, we discuss the trade-offs and complexities of the decision-making process that drives SNP panel development, optimization, and testing.
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Affiliation(s)
- Samuel A. May
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Garrett J. McKinney
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Ray Hilborn
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Kerry A. Naish
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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McKinney G, McPhee MV, Pascal C, Seeb JE, Seeb LW. Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon. G3 (BETHESDA, MD.) 2020; 10:1553-1561. [PMID: 32165371 PMCID: PMC7202013 DOI: 10.1534/g3.119.400972] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/28/2020] [Indexed: 11/26/2022]
Abstract
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
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Affiliation(s)
- Garrett McKinney
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Megan V McPhee
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
| | - Carita Pascal
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
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Sard NM, Smith SR, Homola JJ, Kanefsky J, Bravener G, Adams JV, Holbrook CM, Hrodey PJ, Tallon K, Scribner KT. RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecol Evol 2020; 10:1469-1488. [PMID: 32076528 PMCID: PMC7029094 DOI: 10.1002/ece3.6001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.
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Affiliation(s)
- Nicholas M. Sard
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Biology DepartmentSUNY OswegoOswegoNew York
| | - Seth R. Smith
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jeannette Kanefsky
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | | | - Jean V. Adams
- Great Lakes Science CenterU.S. Geological SurveyAnn ArborMichigan
| | - Christopher M. Holbrook
- Great Lakes Science CenterHammond Bay Biological StationU.S. Geological SurveyMillersburgMichigan
| | | | - Kevin Tallon
- Fisheries and Oceans CanadaSault Ste. MarieONCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Department of Integrative BiologyState UniversityEast LansingMichigan
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Sci Rep 2017; 7:10768. [PMID: 28883428 PMCID: PMC5589735 DOI: 10.1038/s41598-017-10647-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.
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Waples RK, Seeb JE, Seeb LW. Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta). Mol Ecol 2017; 26:4131-4144. [PMID: 28452089 DOI: 10.1111/mec.14163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
Whole-genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole-genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run-timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species.
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Affiliation(s)
- R K Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - L W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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Garvin MR, Templin WD, Gharrett AJ, DeCovich N, Kondzela CM, Guyon JR, McPhee MV. Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael R. Garvin
- Oregon State University Ringgold Standard Institution ‐ Integrative Biology 3029 Cordley Hall, 2701 SW Campus Way Corvallis OR 97331‐4501 USA
| | - William D. Templin
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Anthony J. Gharrett
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
| | - Nick DeCovich
- Alaska Department of Fish and Game Division of Commercial Fisheries 333 Raspberry Road Anchorage AK 99518 USA
| | - Christine M. Kondzela
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Jeffrey R. Guyon
- Auke Bay Laboratories Alaska Fisheries Science Center National Oceanic and Atmospheric Administration National Marine Fisheries Service 17109 Point Lena Loop Road Juneau AK 99801 USA
| | - Megan V. McPhee
- University of Alaska Fairbanks College Fisheries and Ocean Sciences Juneau AK 99821 USA
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9
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Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers. PLoS One 2016; 11:e0164327. [PMID: 27723810 PMCID: PMC5056707 DOI: 10.1371/journal.pone.0164327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/25/2016] [Indexed: 01/15/2023] Open
Abstract
Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.
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10
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The invasion of an Atlantic Ocean river basin in Patagonia by Chinook salmon: new insights from SNPs. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0928-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Characterization of sixteen polymorphic microsatellite DNA loci in the chum salmon (Oncorhynchus keta) isolated by next-generation sequencing. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-014-0322-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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McPhee MV, Whited DC, Kuzishchin KV, Stanford JA. The effects of riverine physical complexity on anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss around the Pacific Rim. JOURNAL OF FISH BIOLOGY 2014; 85:132-150. [PMID: 24766581 DOI: 10.1111/jfb.12286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/23/2013] [Indexed: 06/03/2023]
Abstract
This study explored the relationship between riverine physical complexity, as determined from remotely sensed metrics, and anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss. The proportion of anadromy (estimated fraction of individuals within a drainage that are anadromous) was correlated with riverine complexity, but this correlation appeared to be driven largely by a confounding negative relationship between drainage area and the proportion of anadromy. Genetic diversity decreased with latitude, was lower in rivers with only non-anadromous individuals and also decreased with an increasing ratio of floodplain area to total drainage area. Anadromy may be less frequent in larger drainages due to the higher cost of migration associated with reaches farther from the ocean, and the negative relationship between genetic diversity and floodplain area may be due to lower effective population size resulting from greater population fluctuations associated with higher rates of habitat turnover. Ultimately, the relationships between riverine physical complexity and migratory life history or genetic diversity probably depend on the spatial scale of analysis.
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Affiliation(s)
- M V McPhee
- Flathead Lake Biological Station, The University of Montana, 32125 Bio Station Lane, Polson, MT 56860, U.S.A
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Greminger MP, Stölting KN, Nater A, Goossens B, Arora N, Bruggmann R, Patrignani A, Nussberger B, Sharma R, Kraus RHS, Ambu LN, Singleton I, Chikhi L, van Schaik CP, Krützen M. Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms. BMC Genomics 2014; 15:16. [PMID: 24405840 PMCID: PMC3897891 DOI: 10.1186/1471-2164-15-16] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 12/21/2013] [Indexed: 12/30/2022] Open
Abstract
Background High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets. Results We present an improved RRL (iRRL) protocol that maximizes the generation of homologous DNA sequences, thus achieving improved genotyping-by-sequencing efficiency. Our modifications facilitate generation of single-sample libraries, enabling individual genotype assignments instead of pooled-sample analysis. We sequenced ~1% of the orangutan genome with 41-fold median coverage in 31 wild-born individuals from two populations. SNPs and genotypes were called using three different algorithms. We obtained substantially different SNP datasets depending on the SNP caller. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC Genomics Workbench (CLC). Of all conflicting genotype calls, CLC was only correct in 17% of the cases. Furthermore, conflicting genotypes between two algorithms showed a systematic bias in that one caller almost exclusively assigned heterozygotes, while the other one almost exclusively assigned homozygotes. Conclusions Our enhanced iRRL approach greatly facilitates genotyping-by-sequencing and thus direct estimates of allele frequencies. Our direct comparison of three commonly used SNP callers emphasizes the need to question the accuracy of SNP and genotype calling, as we obtained considerably different SNP datasets depending on caller algorithms, sequencing depths and filtering criteria. These differences affected scans for signatures of natural selection, but will also exert undue influences on demographic inferences. This study presents the first effort to generate a population genomic dataset for wild-born orangutans with known population provenance.
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Affiliation(s)
- Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, Zurich, Switzerland.
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Petrou EL, Hauser L, Waples RS, Seeb JE, Templin WD, Gomez-Uchida D, Seeb LW. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta). Mol Ecol 2013; 22:5848-60. [PMID: 24118255 PMCID: PMC4265302 DOI: 10.1111/mec.12543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 02/03/2023]
Abstract
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.
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Affiliation(s)
- E L Petrou
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, 98112, USA
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15
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Petrou EL, Seeb JE, Hauser L, Witteveen MJ, Templin WD, Seeb LW. Fine-scale sampling reveals distinct isolation by distance patterns in chum salmon (Oncorhynchus keta) populations occupying a glacially dynamic environment. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0534-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Perrier C, Bourret V, Kent MP, Bernatchez L. Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon. Mol Ecol 2013; 22:5577-93. [DOI: 10.1111/mec.12500] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
| | - Matthew P. Kent
- Department of Animal and Aquaculture Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003 Aas 1432 Norway
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
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Miyakoshi Y, Nagata M, Kitada S, Kaeriyama M. Historical and Current Hatchery Programs and Management of Chum Salmon in Hokkaido, Northern Japan. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/10641262.2013.836446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Bradic M, Teotónio H, Borowsky RL. The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus. Mol Biol Evol 2013; 30:2383-400. [PMID: 23927992 PMCID: PMC3808867 DOI: 10.1093/molbev/mst136] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment.
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Garvin MR, Kondzela CM, Martin PC, Finney B, Guyon J, Templin WD, Decovich N, Gilk-Baumer S, Gharrett AJ. Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations. Ecol Evol 2013; 3:2362-77. [PMID: 23919176 PMCID: PMC3728971 DOI: 10.1002/ece3.628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 11/18/2022] Open
Abstract
Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations.
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Affiliation(s)
- Michael R Garvin
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks 17101 Point Lena Loop Road, Juneau, Alaska, 99801
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Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array. Mar Genomics 2013; 9:25-32. [DOI: 10.1016/j.margen.2012.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
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Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol 2013; 22:3002-13. [PMID: 23432212 DOI: 10.1111/mec.12239] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 12/14/2022]
Abstract
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300-400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA.
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Limborg MT, Blankenship SM, Young SF, Utter FM, Seeb LW, Hansen MHH, Seeb JE. Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss. Ecol Evol 2012; 2:1-18. [PMID: 22408722 PMCID: PMC3297173 DOI: 10.1002/ece3.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 12/21/2022] Open
Abstract
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies
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Nielsen EE, Bekkevold D. The memory remains: application of historical DNA for scaling biodiversity loss. Mol Ecol 2012; 21:1539-41. [PMID: 22443424 DOI: 10.1111/j.1365-294x.2012.05498.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Few species worldwide have attracted as much attention in relation to conservation and sustainable management as Pacific salmon. Most populations have suffered significant reductions, many have disappeared, and even entire evolutionary significant units (ESUs) are believed to have been lost. Until now, no 'smoking gun' in terms of direct genetic evidence of the loss of a salmon ESU has been produced. In this issue of Molecular Ecology, Iwamoto et al. (2012) use microsatellite analysis of historical scale samples of Columbia River sockeye salmon (Oncorhynchus nerka) from 1924 (Fig. 1) to ask the pertinent question: Do the historical samples contain salmon from extirpated populations or ESUs? They identified four genetic groups in the historical samples of which two were almost genetically identical to contemporary ESUs in the river, one showed genetic relationship with a third ESU, but one group was not related to any of the contemporary populations. In association with ecological data, the genetic results suggest that an early migrating Columbia River headwater sockeye salmon ESU has been extirpated. The study has significant importance for conservation and reestablishment of sockeye populations in the Columbia River, but also underpins the general significance of shifting baselines in conservation biology, and how to assess loss of genetic biodiversity. The results clearly illustrate the huge and versatile potential of using historical DNA in population and conservation genetics. Because of the extraordinarily plentiful historical samples and rapid advances in fish genomics, fishes are likely to spearhead future studies of temporal ecological and population genomics in non-model organisms. [Figure: see text].
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Affiliation(s)
- Einar E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark.
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Van Bers NEM, Crooijmans RPMA, Groenen MAM, Dibbits BW, Komen J. SNP marker detection and genotyping in tilapia. Mol Ecol Resour 2012; 12:932-41. [PMID: 22524158 DOI: 10.1111/j.1755-0998.2012.03144.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.
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Affiliation(s)
- N E M Van Bers
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, Wageningen, 6700 AH, The Netherlands
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Wang Y, Nielsen R. Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias. Mol Ecol 2012; 21:974-86. [PMID: 22211450 PMCID: PMC3951478 DOI: 10.1111/j.1365-294x.2011.05413.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The inference of population divergence times and branching patterns is of fundamental importance in many population genetic analyses. Many methods have been developed for estimating population divergence times, and recently, there has been particular attention towards genome-wide single-nucleotide polymorphisms (SNP) data. However, most SNP data have been affected by an ascertainment bias caused by the SNP selection and discovery protocols. Here, we present a modification of an existing maximum likelihood method that will allow approximately unbiased inferences when ascertainment is based on a set of outgroup populations. We also present a method for estimating trees from the asymmetric dissimilarity measures arising from pairwise divergence time estimation in population genetics. We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations.
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Affiliation(s)
- Yong Wang
- Department of Integrative Biology, University of California, 3060 VLSB, Berkeley, CA 94720, USA.
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Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 2010; 11:335-48. [PMID: 21429141 DOI: 10.1111/j.1755-0998.2010.02936.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Until recently, single nucleotide polymorphism (SNP) discovery in nonmodel organisms faced many challenges, often depending upon a targeted-gene approach and Sanger sequencing of many individuals. The advent of next-generation sequencing technologies has dramatically improved discovery, but validating and testing SNPs for use in population studies remain labour intensive. Here, we detail a SNP discovery and validation pipeline that incorporates 454 pyrosequencing, high-resolution melt analysis (HRMA) and 5' nuclease genotyping. We generated 4.59×10(8) bp of redundant sequence from transcriptomes of two individual chum salmon, a highly valued species across the Pacific Rim. Nearly 26000 putative SNPs were identified--some as heterozygotes and some as homozygous for different nucleotides in the two individuals. For validation, we selected 202 templates containing single putative SNPs and conducted HRMA on 10 individuals from each of 19 populations from across the species range. Finally, 5' nuclease genotyping validated 37 SNPs that conformed to Hardy-Weinberg equilibrium expectations. Putative SNPs expressed as heterozygotes in an ascertainment individual had more than twice the validation rate of those homozygous for different alleles in the two fish, suggesting that many of the latter may have been paralogous sequence variants. Overall, this validation rate of 37/202 suggests that we have found more than 4500 templates containing SNPs for use in this population set. We anticipate using this pipeline to significantly expand the number of SNPs available for the studies of population structure and mixture analyses as well as for the studies of adaptive genetic variation in nonmodel organisms.
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Affiliation(s)
- J E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020, USA
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