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Development of genome-wide SNPs for population genetics and population assignment of Sebastiscus marmoratus. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0868-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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52
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Hendricks S, Anderson EC, Antao T, Bernatchez L, Forester BR, Garner B, Hand BK, Hohenlohe PA, Kardos M, Koop B, Sethuraman A, Waples RS, Luikart G. Recent advances in conservation and population genomics data analysis. Evol Appl 2018. [PMCID: PMC6099823 DOI: 10.1111/eva.12659] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.
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Affiliation(s)
- Sarah Hendricks
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Eric C. Anderson
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Santa Cruz California
- University of California Santa Cruz California
| | - Tiago Antao
- Division of Biological Sciences University of Montana Missoula Montana
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | | | - Brittany Garner
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
| | - Brian K. Hand
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Martin Kardos
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
| | - Ben Koop
- Department of Biology Centre for Biomedical Research University of Victoria Victoria British Columbia Canada
| | - Arun Sethuraman
- Department of Biological Sciences California State University San Marcos San Marcos California
| | - Robin S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington
| | - Gordon Luikart
- Flathead Lake Biological Station Montana Conservation Genomics Laboratory Division of Biological Science University of Montana Missoula Montana
- Wildlife Program Fish and Wildlife Genomics Group College of Forestry and Conservation University of Montana Missoula Montana
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Gaughran SJ, Quinzin MC, Miller JM, Garrick RC, Edwards DL, Russello MA, Poulakakis N, Ciofi C, Beheregaray LB, Caccone A. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evol Appl 2018; 11:1084-1093. [PMID: 30026799 PMCID: PMC6050186 DOI: 10.1111/eva.12551] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022] Open
Abstract
High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
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Affiliation(s)
| | - Maud C. Quinzin
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Joshua M. Miller
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | | | - Michael A. Russello
- Department of BiologyUniversity of British Columbia, Okanagan CampusKelownaBCCanada
| | - Nikos Poulakakis
- Department of BiologySchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
- Natural History Museum of CreteSchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto Fiorentino (FI)Italy
| | - Luciano B. Beheregaray
- Molecular Ecology LabSchool of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
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Bradbury IR, Wringe BF, Watson B, Paterson I, Horne J, Beiko R, Lehnert SJ, Clément M, Anderson EC, Jeffery NW, Duffy S, Sylvester E, Robertson M, Bentzen P. Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery. Evol Appl 2018; 11:918-930. [PMID: 29928300 PMCID: PMC5999200 DOI: 10.1111/eva.12606] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/20/2018] [Indexed: 12/12/2022] Open
Abstract
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.
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Affiliation(s)
- Ian R. Bradbury
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
- Department of BiologyDalhousie UniversityHalifaxNSCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Brendan F. Wringe
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
| | - Beth Watson
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Ian Paterson
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - John Horne
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - Robert Beiko
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Sarah J. Lehnert
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
| | - Marie Clément
- Center for Fisheries Ecosystems ResearchFisheries and Marine Institute of MemorialUniversity of NewfoundlandSt. John'sNLCanada
- Labrador Institute ofMemorial University of NewfoundlandHappy Valley‐Goose BayNLCanada
| | - Eric C. Anderson
- Fisheries Ecology DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSanta CruzCAUSA
| | | | - Steven Duffy
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
| | - Emma Sylvester
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Martha Robertson
- Science BranchDepartment of Fisheries and Oceans CanadaSt. John'sNLCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNSCanada
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55
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Crane NL, Tariel J, Caselle JE, Friedlander AM, Robertson DR, Bernardi G. Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size. PLoS One 2018; 13:e0198901. [PMID: 29949612 PMCID: PMC6021044 DOI: 10.1371/journal.pone.0198901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.
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Affiliation(s)
- Nicole L. Crane
- Department of Biology, Cabrillo College, Aptos, CA, United States of America
| | - Juliette Tariel
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer E. Caselle
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Alan M. Friedlander
- Pristine Seas, National Geographic Society, Washington, DC, United States of America
- Fisheries Ecology Research Lab, Department of Biology, University of Hawaii, Honolulu, HI, United States of America
| | | | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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56
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Pazmiño DA, Maes GE, Green ME, Simpfendorfer CA, Hoyos-Padilla EM, Duffy CJA, Meyer CG, Kerwath SE, Salinas-de-León P, van Herwerden L. Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers. Heredity (Edinb) 2018; 120:407-421. [PMID: 29321624 PMCID: PMC5889387 DOI: 10.1038/s41437-017-0025-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/15/2022] Open
Abstract
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.
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Affiliation(s)
- Diana A Pazmiño
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Universidad San Francisco de Quito - Galápagos Science Center, Quito, Ecuador.
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
- Laboratory for Cytogenetics and Genome Research, Center for Human Genetics, Genomics Core, KU Leuven, Leuven, Belgium
| | - Madeline E Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, Australia
- CSIRO Oceans & Atmosphere, Castray Esplanade, Battery Point, Hobart, TAS, Australia
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | | | - Clinton J A Duffy
- Auckland War Memorial Museum, The Domain, Auckland, New Zealand
- Department of Conservation, Private Bag 68908, Newton, Auckland, New Zealand
| | - Carl G Meyer
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Coconut Island, Kaneohe, HI, USA
| | - Sven E Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag × 3, Rondebosch, South Africa
- Department of Agriculture, Forestry and Fisheries: Fisheries Branch, Private Bag × 2, Vlaeberg, Cape Town, South Africa
| | - Pelayo Salinas-de-León
- Department of Marine Sciences, Charles Darwin Research Station. Av Charles Darwin s/n, Puerto Ayora, Galapagos Islands, Santa Cruz, Ecuador
- Pristine Seas, National Geographic Society, Washington, D. C., USA
| | - Lynne van Herwerden
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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57
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Yi S, Wang W, Zhou X. Genomic evidence for the population genetic differentiation of Misgurnus anguillicaudatus in the Yangtze River basin of China. Genomics 2018; 111:367-374. [PMID: 29474824 DOI: 10.1016/j.ygeno.2018.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/28/2018] [Accepted: 02/19/2018] [Indexed: 01/04/2023]
Abstract
Misgurnus anguillicaudatus, an important aquatic species, is mainly distributed in the Yangtze River basin. To reveal the population genetic structure of M. anguillicaudatus distributed in the Yangtze River basin, genotyping by sequencing (GBS) technique was employed to detect the genome wide genetic variations of M. anguillicaudatus. A total of 30.03 Gb raw data were yielded from 70 samples collected from 15 geographic sites located in the Yangtze River basin. Subsequently, 2092 high quality SNPs were genotyped across these samples and used for a series of genetic analysis. The results of genetic analysis showed that high levels of genetic diversity were observed and the populations from upper reaches (UR) were significantly differentiated from the middle and lower reaches (MLR) of Yangtze River basin. Meanwhile, no significant isolation by distance was detected among the populations. Ecological factors (e.g. complicated topography and climatic environment) and anthropogenic factors (e.g. aquaculture and agriculture cultivation) might account for the genetic disconnectivity between UR and MLR populations. This study provided valuable genetic data for the future breeding program and also for the conversation and scientific utilization of those abundant genetic resources stored in the Yangtze River basin.
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Affiliation(s)
- Shaokui Yi
- College of fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China; Fish Genetics and Breeding Laboratory, the Ohio State University South Centers, Piketon 45661, United States
| | - Weimin Wang
- College of fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaoyun Zhou
- College of fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.
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58
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Stobie CS, Oosthuizen CJ, Cunningham MJ, Bloomer P. Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing. Ecol Evol 2018; 8:2326-2342. [PMID: 29468047 PMCID: PMC5817159 DOI: 10.1002/ece3.3821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/17/2017] [Indexed: 12/12/2022] Open
Abstract
The KwaZulu‐Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu‐Natal Province, South Africa. In this study, we developed a single‐nucleotide polymorphism (SNP) dataset from double‐digest restriction site‐associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.
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Affiliation(s)
- Cora Sabriel Stobie
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Carel J Oosthuizen
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Michael J Cunningham
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa
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59
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Hohenlohe PA, Hand BK, Andrews KR, Luikart G. Population Genomics Provides Key Insights in Ecology and Evolution. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_20] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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60
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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61
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Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon. Proc Natl Acad Sci U S A 2017; 114:12964-12969. [PMID: 29162695 DOI: 10.1073/pnas.1711229114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.
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62
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Crossley MS, Chen YH, Groves RL, Schoville SD. Landscape genomics of Colorado potato beetle provides evidence of polygenic adaptation to insecticides. Mol Ecol 2017; 26:6284-6300. [DOI: 10.1111/mec.14339] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/21/2017] [Accepted: 08/21/2017] [Indexed: 12/13/2022]
Affiliation(s)
| | - Yolanda H. Chen
- Department of Plant and Soil Sciences University of Vermont Burlington VT USA
| | - Russell L. Groves
- Department of Entomology University of Wisconsin‐Madison Madison WI USA
| | - Sean D. Schoville
- Department of Entomology University of Wisconsin‐Madison Madison WI USA
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64
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Picq S, Keena M, Havill N, Stewart D, Pouliot E, Boyle B, Levesque RC, Hamelin RC, Cusson M. Assessing the potential of genotyping-by-sequencing-derived single nucleotide polymorphisms to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: A proof-of-concept study. Evol Appl 2017. [DOI: 10.1111/eva.12559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Sandrine Picq
- Laurentian Forestry Centre; Natural Resources Canada; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City QC Canada
| | - Melody Keena
- USDA Forest Service; Northern Research Station; Northeastern Center for Forest Health Research; Hamden CT USA
| | - Nathan Havill
- USDA Forest Service; Northern Research Station; Northeastern Center for Forest Health Research; Hamden CT USA
| | - Don Stewart
- Laurentian Forestry Centre; Natural Resources Canada; Quebec City QC Canada
| | - Esther Pouliot
- Laurentian Forestry Centre; Natural Resources Canada; Quebec City QC Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City QC Canada
| | - Richard C. Hamelin
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City QC Canada
- Department of Forest Sciences; Faculty of Forestry; The University of British Columbia; Vancouver BC Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City QC Canada
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65
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Veale AJ, Russello MA. Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka). Genome Biol Evol 2017; 9:2921-2939. [PMID: 29045601 PMCID: PMC5737441 DOI: 10.1093/gbe/evx215] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
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Affiliation(s)
- Andrew J. Veale
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
- Present address: Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand
| | - Michael A. Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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Sylvester EVA, Bentzen P, Bradbury IR, Clément M, Pearce J, Horne J, Beiko RG. Applications of random forest feature selection for fine-scale genetic population assignment. Evol Appl 2017; 11:153-165. [PMID: 29387152 PMCID: PMC5775496 DOI: 10.1111/eva.12524] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 07/11/2017] [Indexed: 01/10/2023] Open
Abstract
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than FST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using FST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.
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Affiliation(s)
| | - Paul Bentzen
- Marine Gene Probe Laboratory Department of Biology Dalhousie University Halifax NS Canada
| | | | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's NL Canada.,Labrador Institute Memorial University of Newfoundland Happy Valley-Goose Bay NL Canada
| | - Jon Pearce
- Northern SE Regional Aquaculture Association Hidden Falls Hatchery Sitka AK USA
| | - John Horne
- Marine Gene Probe Laboratory Department of Biology Dalhousie University Halifax NS Canada
| | - Robert G Beiko
- Faculty of Computer Science Dalhousie University Halifax NS Canada
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67
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Chan KO, Alexander AM, Grismer LL, Su YC, Grismer JL, Quah ESH, Brown RM. Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Mol Ecol 2017; 26:5435-5450. [DOI: 10.1111/mec.14296] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - Alana M. Alexander
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology; Kaohsiung Medical University; Kaohsiung City Taiwan
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; Auburn AL USA
- La Kretz Center for Californian Conservation Science; Institute of the Environment and Sustainability; University of California Los Angeles; Los Angeles CA USA
| | - Evan S. H. Quah
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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68
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Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
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69
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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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70
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Yu Y, Zhang X, Yuan J, Wang Q, Li S, Huang H, Li F, Xiang J. Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:277-286. [PMID: 28508952 DOI: 10.1007/s10126-017-9749-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The Pacific white shrimp Litopenaeus vannamei is a predominant aquaculture shrimp species in the world. Like other animals, the L. vannamei exhibited sexual dimorphism in growth trait. Mapping of the sex-determining locus will be very helpful to clarify the sex determination system and further benefit the shrimp aquaculture industry towards the production of mono-sex stocks. Based on the data used for high-density linkage map construction, linkage-mapping analysis was conducted. The sex determination region was mapped in linkage group (LG) 18. A large region from 0 to 21.205 cM in LG18 showed significant association with sex. However, none of the markers in this region showed complete association with sex in the other populations. So an association analysis was designed using the female parent, pool of female progenies, male parent, and pool of male progenies. Markers were de novo developed and those showing significant differences between female and male pools were identified. Among them, three sex-associated markers including one fully associated marker were identified. Integration of linkage and association analysis showed that the sex determination region was fine-mapped in a small region along LG18. The identified sex-associated marker can be used for the sex detection of this species at genetic level. The fine-mapped sex-determining region will contribute to the mapping of sex-determining gene and help to clarify sex determination system for L. vannamei.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Huang
- Hainan Guangtai Ocean Breeding Co., Ltd., Wenchang, 571300, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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71
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Xu S, Song N, Zhao L, Cai S, Han Z, Gao T. Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity. Sci Rep 2017; 7:1562. [PMID: 28484228 PMCID: PMC5431535 DOI: 10.1038/s41598-017-01742-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms.
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Affiliation(s)
- Shengyong Xu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5th Yushan Road, Qingdao, 266003, P.R. China
| | - Na Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5th Yushan Road, Qingdao, 266003, P.R. China
| | - Linlin Zhao
- The First Institute of Oceanography, State Oceanic Administration, 6th Xianxialing Road, Qingdao, 266061, P.R. China
| | - Shanshan Cai
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
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72
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Genome-wide SNPs reveal low effective population size within confined management units of the highly vagile Galapagos shark (Carcharhinus galapagensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0967-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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73
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A Dense Brown Trout ( Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3-GENES GENOMES GENETICS 2017; 7:1365-1376. [PMID: 28235829 PMCID: PMC5386884 DOI: 10.1534/g3.116.038497] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.
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74
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Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum. Sci Rep 2017; 7:229. [PMID: 28331182 PMCID: PMC5427961 DOI: 10.1038/s41598-017-00246-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926.98 cM were mapped to 18 sex-averaged linkage groups, with an average marker distance of 0.42 cM. Based on the high-density linkage map, ten QTLs for growth-related traits and shell color were detected. The coverage and density of the current map are sufficient for us to effectively detect QTL for segregating traits, and two QTL positions were all coincident with the closest markers. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of R. philippinarum and other bivalve molluscan species.
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75
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Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha
(Myrtaceae). Mol Ecol 2017; 26:1515-1532. [DOI: 10.1111/mec.14016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kanehiro Kitayama
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yusuke Onoda
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Tsujii
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Functional Genomics Center Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Atsushi J. Nagano
- Faculty of Agriculture; Ryukoku University; 1-5 Yokatani, Seta Ohe-cho Otsu Shiga 520-2194 Japan
- PRESTO, Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Mie N. Honjo
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
- Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
| | - Yuji Isagi
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
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76
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Walsh J, Lovette IJ, Winder V, Elphick CS, Olsen BJ, Shriver G, Kovach AI. Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird. Mol Ecol 2017; 26:1242-1255. [PMID: 28100017 DOI: 10.1111/mec.14010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 01/11/2023]
Abstract
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced-representation sequencing approach to generate a panel of 1929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish-water marsh habitats. These patterns support the current species-level recognition but do not match the subspecies-level taxonomy within each species-a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, 14850, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, NY, 14850, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Virginia Winder
- Department of Biology, Benedictine College, Atchison, KS, 66002, USA
| | - Chris S Elphick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, ME, 04469, USA
| | - Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, 19716, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
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77
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Larson WA, Limborg MT, McKinney GJ, Schindler DE, Seeb JE, Seeb LW. Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Mol Ecol 2016; 26:554-570. [PMID: 27864910 DOI: 10.1111/mec.13933] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 10/14/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with FST > 0.14 (average FST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80-402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Daniel E Schindler
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA
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78
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Aykanat T, Lindqvist M, Pritchard VL, Primmer CR. From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2016; 89:2658-2679. [PMID: 27709620 DOI: 10.1111/jfb.13149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.
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Affiliation(s)
- T Aykanat
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - M Lindqvist
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - V L Pritchard
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - C R Primmer
- Department of Biology, University of Turku, Turku, 20014, Finland
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79
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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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80
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McKinney GJ, Waples RK, Seeb LW, Seeb JE. Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations. Mol Ecol Resour 2016; 17:656-669. [DOI: 10.1111/1755-0998.12613] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Ryan K. Waples
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
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81
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Everett MV, Park LK, Berntson EA, Elz AE, Whitmire CE, Keller AA, Clarke ME. Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral Swiftia simplex (Nutting 1909) on the West Coast of the United States. PLoS One 2016; 11:e0165279. [PMID: 27798660 PMCID: PMC5087884 DOI: 10.1371/journal.pone.0165279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
Deep-sea corals are a critical component of habitat in the deep-sea, existing as regional hotspots for biodiversity, and are associated with increased assemblages of fish, including commercially important species. Because sampling these species is so difficult, little is known about the connectivity and life history of deep-sea octocoral populations. This study evaluates the genetic connectivity among 23 individuals of the deep-sea octocoral Swiftia simplex collected from Eastern Pacific waters along the west coast of the United States. We utilized high-throughput restriction-site associated DNA (RAD)-tag sequencing to develop the first molecular genetic resource for the deep-sea octocoral, Swiftia simplex. Using this technique we discovered thousands of putative genome-wide SNPs in this species, and after quality control, successfully genotyped 1,145 SNPs across individuals sampled from California to Washington. These SNPs were used to assess putative population structure across the region. A STRUCTURE analysis as well as a principal coordinates analysis both failed to detect any population differentiation across all geographic areas in these collections. Additionally, after assigning individuals to putative population groups geographically, no significant FST values could be detected (FST for the full data set 0.0056), and no significant isolation by distance could be detected (p = 0.999). Taken together, these results indicate a high degree of connectivity and potential panmixia in S. simplex along this portion of the continental shelf.
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Affiliation(s)
- Meredith V Everett
- National Research Council, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Linda K Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Ewann A Berntson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Anna E Elz
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Curt E Whitmire
- Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - Aimee A Keller
- Fishery Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
| | - M Elizabeth Clarke
- Office of the Science Director, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, United States of America
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82
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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83
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Waples RK, Larson WA, Waples RS. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity (Edinb) 2016; 117:233-40. [PMID: 27553452 PMCID: PMC5026758 DOI: 10.1038/hdy.2016.60] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 06/19/2016] [Accepted: 06/24/2016] [Indexed: 12/15/2022] Open
Abstract
Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates ([Ncirc ]e). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in [Ncirc ]e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of [Ncirc ]e is much lower than expected based on the assumption that each pair of loci provides completely independent information.
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Affiliation(s)
- R K Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - W A Larson
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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84
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Dussex N, Robertson BC, Salis AT, Kalinin A, Best H, Gemmell NJ. Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri. J Hered 2016; 107:581-592. [PMID: 27563072 DOI: 10.1093/jhered/esw056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/15/2016] [Indexed: 11/14/2022] Open
Abstract
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.
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Affiliation(s)
- Nicolas Dussex
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Bruce C Robertson
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Alexander T Salis
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Aleksandr Kalinin
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Hugh Best
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Neil J Gemmell
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
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85
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Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass. Sci Rep 2016; 6:32122. [PMID: 27555039 PMCID: PMC4995370 DOI: 10.1038/srep32122] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.
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86
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Torkamaneh D, Laroche J, Belzile F. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLoS One 2016; 11:e0161333. [PMID: 27547936 PMCID: PMC4993469 DOI: 10.1371/journal.pone.0161333] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method capable of producing thousands to millions of SNPs across a wide range of species. Undoubtedly, the greatest barrier to its broader use is the challenge of data analysis. Herein we describe a comprehensive comparison of seven GBS bioinformatics pipelines developed to process raw GBS sequence data into SNP genotypes. We compared five pipelines requiring a reference genome (TASSEL-GBS v1& v2, Stacks, IGST, and Fast-GBS) and two de novo pipelines that do not require a reference genome (UNEAK and Stacks). Using Illumina sequence data from a set of 24 re-sequenced soybean lines, we performed SNP calling with these pipelines and compared the GBS SNP calls with the re-sequencing data to assess their accuracy. The number of SNPs called without a reference genome was lower (13k to 24k) than with a reference genome (25k to 54k SNPs) while accuracy was high (92.3 to 98.7%) for all but one pipeline (TASSEL-GBSv1, 76.1%). Among pipelines offering a high accuracy (>95%), Fast-GBS called the greatest number of polymorphisms (close to 35,000 SNPs + Indels) and yielded the highest accuracy (98.7%). Using Ion Torrent sequence data for the same 24 lines, we compared the performance of Fast-GBS with that of TASSEL-GBSv2. It again called more polymorphisms (25.8K vs 22.9K) and these proved more accurate (95.2 vs 91.1%). Typically, SNP catalogues called from the same sequencing data using different pipelines resulted in highly overlapping SNP catalogues (79-92% overlap). In contrast, overlap between SNP catalogues obtained using the same pipeline but different sequencing technologies was less extensive (~50-70%).
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
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87
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Wang L, Wan ZY, Lim HS, Yue GH. Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass. Mol Ecol 2016; 25:3605-21. [PMID: 27262162 DOI: 10.1111/mec.13714] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/09/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022]
Abstract
Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Huan Sein Lim
- Marine Aquaculture Center, Agri-Food & Veterinary Authority of Singapore, 5 Maxwell Road, Singapore, 069110, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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88
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Wang J, Xue DX, Zhang BD, Li YL, Liu BJ, Liu JX. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus). PLoS One 2016; 11:e0157809. [PMID: 27336696 PMCID: PMC4919078 DOI: 10.1371/journal.pone.0157809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/06/2016] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dong-Xiu Xue
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bai-Dong Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing-Jian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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89
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Jahner JP, Gibson D, Weitzman CL, Blomberg EJ, Sedinger JS, Parchman TL. Fine-scale genetic structure among greater sage-grouse leks in central Nevada. BMC Evol Biol 2016; 16:127. [PMID: 27301494 PMCID: PMC4908695 DOI: 10.1186/s12862-016-0702-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/07/2016] [Indexed: 01/07/2023] Open
Abstract
Background Mating systems that reduce dispersal and lead to non-random mating might increase the potential for genetic structure to arise at fine geographic scales. Greater sage-grouse (Centrocercus urophasianus) have a lek-based mating system and exhibit high site fidelity and skewed mating ratios. We quantified population structure by analyzing variation at 27,866 single-nucleotide polymorphisms in 140 males from ten leks (within five lek complexes) occurring in a small geographic region in central Nevada. Results Lek complexes, and to a lesser extent individual leks, formed statistically identifiable clusters in ordination analyses, providing evidence for fine-scale geographic genetic differentiation. Lek geography predicted genetic differentiation even at a small geographic scale, which could be sharpened by strong site fidelity. Relatedness was also higher among individuals within lek complexes (and leks), suggesting that reproductive skew, where few males participate in most of the successful matings, could also potentially contribute to genetic differentiation. Models incorporating a habitat resistance surface as a proxy for potentially reduced movement due to landscape features indicated that both geographic distance and habitat suitability (i.e. preferred habitat) predicted genetic structure, with no significant effect of man-made barriers to movement (i.e. power lines and roads). Finally, we illustrate how data sets containing fewer loci (<4000) had less statistical precision and failed to detect the full degree of genetic structure. Conclusion Our results suggest that habitat features and lek site geography of sage-grouse shape fine scale genetic structure, and highlight how larger data sets can have increased precision and accuracy for quantifying ecologically relevant genetic structure over small geographic scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0702-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua P Jahner
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA. .,Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Daniel Gibson
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA
| | - Chava L Weitzman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | - Erik J Blomberg
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA.,Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, 04469, USA
| | - James S Sedinger
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, 89557, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.,Department of Biology, University of Nevada, Reno, NV, 89557, USA
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90
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Araneda C, Larraín MA, Hecht B, Narum S. Adaptive genetic variation distinguishes Chilean blue mussels ( Mytilus chilensis) from different marine environments. Ecol Evol 2016; 6:3632-3644. [PMID: 27195104 PMCID: PMC4851556 DOI: 10.1002/ece3.2110] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/24/2016] [Accepted: 03/03/2016] [Indexed: 01/06/2023] Open
Abstract
Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genomewide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1240 SNPs obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices, and low geographical distance. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.
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Affiliation(s)
- Cristián Araneda
- Departamento de Producción AnimalFacultad de Ciencias AgronómicasUniversidad de ChileAvda Santa Rosa 11315, La Pintana8820808SantiagoChile
| | - María Angélica Larraín
- Departamento de Ciencia de los Alimentos y Tecnología QuímicaFacultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSergio Livingstone 1007, Independencia8380492SantiagoChile
| | - Benjamin Hecht
- Columbia River Inter‐Tribal Fish Commission3059‐F National Fish Hatchery RoadHagermanID83332
| | - Shawn Narum
- Columbia River Inter‐Tribal Fish Commission3059‐F National Fish Hatchery RoadHagermanID83332
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91
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Benestan LM, Ferchaud A, Hohenlohe PA, Garner BA, Naylor GJP, Baums IB, Schwartz MK, Kelley JL, Luikart G. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol Ecol 2016; 25:2967-77. [DOI: 10.1111/mec.13647] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/12/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Laura Marilyn Benestan
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Anne‐Laure Ferchaud
- Departement de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec G1V 0A6 Canada
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow ID 83844 USA
| | - Brittany A. Garner
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
| | - Gavin J. P. Naylor
- Hollings Marine Lab College of Charleston and Medical University of South Carolina 331 Fort Johnson Rd. Charleston SC 29412 USA
| | - Iliana Brigitta Baums
- Department of Biology Pennsylvania State University 208 Mueller Lab University Park PA 1680 USA
| | - Michael K. Schwartz
- USDA Forest Service National Genomics Center for Wildlife and Fish Conservation 800 E. Beckwith Ave. Missoula MT 59801 USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA 99164 USA
| | - Gordon Luikart
- Flathead Lake Biological Station Fish and Wildlife Genomic Group Division of Biological Science University of Montana Missoula MT 59812 USA
- Wildlife Program Fish and Wildlife Genomic Group College of Forestry and Conservation University of Montana Missoula MT 59812 USA
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92
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A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity (Edinb) 2016; 117:207-16. [PMID: 27165767 DOI: 10.1038/hdy.2016.30] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 03/14/2016] [Accepted: 03/29/2016] [Indexed: 12/29/2022] Open
Abstract
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP data set are unlinked. The approach is applied to an empirical data set of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.
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93
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Rodríguez-Ezpeleta N, Bradbury IR, Mendibil I, Álvarez P, Cotano U, Irigoien X. Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection. Mol Ecol Resour 2016; 16:991-1001. [DOI: 10.1111/1755-0998.12518] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 01/31/2016] [Accepted: 02/26/2016] [Indexed: 12/20/2022]
Affiliation(s)
| | - Ian R. Bradbury
- Department of Fisheries and Oceans; St. John's NF A1C 5X1 Canada
| | - Iñaki Mendibil
- Marine Research Division; AZTI; Txatxarramend ugartea z/g Sukarrieta 48395 Bizkaia Spain
| | - Paula Álvarez
- Marine Research Division; AZTI; Txatxarramend ugartea z/g Sukarrieta 48395 Bizkaia Spain
| | - Unai Cotano
- Marine Research Division; AZTI; Txatxarramend ugartea z/g Sukarrieta 48395 Bizkaia Spain
| | - Xabier Irigoien
- Red Sea Research Center; King Abdullah University of Technology; Thuwal 23955 Saudi Arabia
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94
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Valenzuela-Quiñonez F. How fisheries management can benefit from genomics? Brief Funct Genomics 2016; 15:352-7. [DOI: 10.1093/bfgp/elw006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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95
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Larson WA, McKinney GJ, Limborg MT, Everett MV, Seeb LW, Seeb JE. Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map. J Hered 2015; 107:122-33. [PMID: 26712859 DOI: 10.1093/jhered/esv099] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/18/2015] [Indexed: 02/01/2023] Open
Abstract
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
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Affiliation(s)
- Wesley A Larson
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett).
| | - Garrett J McKinney
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Morten T Limborg
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Meredith V Everett
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - Lisa W Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
| | - James E Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195-5020 (Larson, McKinney, Limborg, LW Seeb, and JE Seeb); Morten T. Limborg is now at the Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen K, Denmark; Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA, 98112 (Everett)
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96
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Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Waples RS, Knudsen CM, Bosch WJ, Naish KA. Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding. Evol Appl 2015; 8:956-71. [PMID: 26640521 PMCID: PMC4662342 DOI: 10.1111/eva.12331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/02/2015] [Indexed: 12/28/2022] Open
Abstract
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | - Jeffrey J Hard
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | - Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | | | | | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
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97
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McKinney GJ, Seeb LW, Larson WA, Gomez‐Uchida D, Limborg MT, Brieuc MSO, Everett MV, Naish KA, Waples RK, Seeb JE. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (
Oncorhynchus tshawytscha
). Mol Ecol Resour 2015; 16:769-83. [DOI: 10.1111/1755-0998.12479] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/08/2015] [Accepted: 10/14/2015] [Indexed: 12/31/2022]
Affiliation(s)
- G. J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - L. W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - W. A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - D. Gomez‐Uchida
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. S. O. Brieuc
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - M. V. Everett
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - K. A. Naish
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - R. K. Waples
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
| | - J. E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA 98195‐5020 USA
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98
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Zhang BD, Xue DX, Wang J, Li YL, Liu BJ, Liu JX. Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis). Mol Ecol Resour 2015; 16:755-68. [PMID: 26439680 DOI: 10.1111/1755-0998.12476] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 01/30/2023]
Abstract
Recent advances in high-throughput sequencing technologies have offered the possibility to generate genomewide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters and to evaluate potential adaptive divergence. Here, we identified 27 556 single nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation were identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals, and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP data set of top quality score per contig or neutral loci. However, the two analysed populations were highly differentiated based on SNP data set of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST -based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. blast2go annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant blastx matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in this study provided a valuable tool for future population genetics and genomics studies of L. polyactis.
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Affiliation(s)
- Bai-Dong Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Xiu Xue
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Juan Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yu-Long Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing-Jian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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99
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Bradbury IR, Hamilton LC, Dempson B, Robertson MJ, Bourret V, Bernatchez L, Verspoor E. Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure. Mol Ecol 2015; 24:5130-44. [DOI: 10.1111/mec.13395] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Ian R. Bradbury
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory; Bedford Institute of Oceanography; Dartmouth Halifax Nova Scotia Canada B2Y 4A2
| | - Brian Dempson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Martha J. Robertson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Vincent Bourret
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec Canada G1V 0A6
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Louis Bernatchez
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Eric Verspoor
- Rivers and Lochs Institute; Inverness College University of the Highlands and Islands; Inverness IV2 5NA UK
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100
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Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0784-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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