101
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Benestan L, Gosselin T, Perrier C, Sainte-Marie B, Rochette R, Bernatchez L. RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus). Mol Ecol 2015; 24:3299-315. [DOI: 10.1111/mec.13245] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 05/09/2015] [Accepted: 05/12/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Laura Benestan
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Thierry Gosselin
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Charles Perrier
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
| | - Bernard Sainte-Marie
- Pêches et Océans Canada; Institut Maurice-Lamontagne; CP 1000 Mont-Joli Quebec Canada G5H 3Z4
| | - Rémy Rochette
- Department of Biology; University of New Brunswick; PO Box 5050 Saint John New Brunswick Canada E2L 4L5
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS); Université Laval; Québec Quebec Canada G1V0A6
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102
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Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM. Impacts of degraded
DNA
on restriction enzyme associated
DNA
sequencing (
RADS
eq). Mol Ecol Resour 2015; 15:1304-15. [DOI: 10.1111/1755-0998.12404] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Carly F. Graham
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Travis C. Glenn
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Andrew G. McArthur
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Douglas R. Boreham
- Medical Sciences Northern Ontario School of Medicine Greater Sudbury Ontario P0M Canada
| | - Troy Kieran
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Stacey Lance
- Savannah River Ecology Laboratory University of Georgia Athens GA 30602 USA
| | - Richard G. Manzon
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Jessica A. Martino
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Todd Pierson
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Sean M. Rogers
- Department of Biological Sciences University of Calgary Calgary Alberta T2N 1N4 Canada
| | - Joanna Y. Wilson
- Department of Biology McMaster University Hamilton Ontario L8S 4M1 Canada
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103
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Mason NA, Taylor SA. Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Mol Ecol 2015; 24:3009-25. [DOI: 10.1111/mec.13140] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/27/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
| | - Scott A. Taylor
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Rd. Ithaca NY 14853 USA
- Fuller Evolutionary Biology Program; Laboratory of Ornithology; Cornell University; 159 Sapsucker Woods Road Ithaca NY 14850 USA
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104
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Candy JR, Campbell NR, Grinnell MH, Beacham TD, Larson WA, Narum SR. Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (
Thaleichthys pacificus
, Osmeridae), an anadromous Pacific smelt. Mol Ecol Resour 2015; 15:1421-34. [DOI: 10.1111/1755-0998.12400] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/30/2015] [Accepted: 02/07/2015] [Indexed: 11/30/2022]
Affiliation(s)
- John R. Candy
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Nathan R. Campbell
- Columbia River Inter‐Tribal Fish Commission 3059‐F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Matthew H. Grinnell
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Terry D. Beacham
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Wesley A. Larson
- School of Aquatic and Fishery Science University of Washington 1122 NE Boat Street, Box 355020 Seattle WA 98195 USA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission 3059‐F National Fish Hatchery Road Hagerman ID 83332 USA
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105
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Waples RK, Seeb LW, Seeb JE. Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta). Mol Ecol Resour 2015; 16:17-28. [DOI: 10.1111/1755-0998.12394] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- R. K. Waples
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
| | - L. W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
| | - J. E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
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106
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Kristensen TN, Hoffmann AA, Pertoldi C, Stronen AV. What can livestock breeders learn from conservation genetics and vice versa? Front Genet 2015; 6:38. [PMID: 25713584 PMCID: PMC4322732 DOI: 10.3389/fgene.2015.00038] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/26/2015] [Indexed: 11/17/2022] Open
Abstract
The management of livestock breeds and threatened natural population share common challenges, including small effective population sizes, high risk of inbreeding, and the potential benefits and costs associated with mixing disparate gene pools. Here, we consider what has been learnt about these issues, the ways in which the knowledge gained from one area might be applied to the other, and the potential of genomics to provide new insights. Although there are key differences stemming from the importance of artificial versus natural selection and the decreased level of environmental heterogeneity experienced by many livestock populations, we suspect that information from genetic rescue in natural populations could be usefully applied to livestock. This includes an increased emphasis on maintaining substantial population sizes at the expense of genetic uniqueness in ensuring future adaptability, and on emphasizing the way that environmental changes can influence the relative fitness of deleterious alleles and genotypes in small populations. We also suspect that information gained from cross-breeding and the maintenance of unique breeds will be increasingly important for the preservation of genetic variation in small natural populations. In particular, selected genes identified in domestic populations provide genetic markers for exploring adaptive evolution in threatened natural populations. Genomic technologies in the two disciplines will be important in the future in realizing genetic gains in livestock and maximizing adaptive capacity in wildlife, and particularly in understanding how parts of the genome may respond differently when exposed to population processes and selection.
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Affiliation(s)
- Torsten N. Kristensen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
| | - Ary A. Hoffmann
- Department of Zoology and Department of Genetics, Bio21 Institute, The University of MelbourneMelbourne, VIC, Australia
| | - Cino Pertoldi
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
- Aalborg ZooAalborg, Denmark
| | - Astrid V. Stronen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg UniversityAalborg, Denmark
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107
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Shafer AB, Wolf JB, Alves PC, Bergström L, Bruford MW, Brännström I, Colling G, Dalén L, De Meester L, Ekblom R, Fawcett KD, Fior S, Hajibabaei M, Hill JA, Hoezel AR, Höglund J, Jensen EL, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popović D, Primmer CR, Reed FA, Roumet M, Salmona J, Schenekar T, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M, Veale A, Vergeer P, Vijay N, Vilà C, Weissensteiner M, Wennerström L, Wheat CW, Zieliński P. Genomics and the challenging translation into conservation practice. Trends Ecol Evol 2015; 30:78-87. [DOI: 10.1016/j.tree.2014.11.009] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
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108
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Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW. Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 2015; 24:328-45. [DOI: 10.1111/mec.13034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/29/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Lucie M. Gattepaille
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Robert E. A. Stewart
- Fisheries and Oceans Canada; Freshwater Institute; 501 University Crescent Winnipeg Manitoba R3T 2N6 Canada
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
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109
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Carlson BM, Onusko SW, Gross JB. A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology. G3 (BETHESDA, MD.) 2014; 5:241-51. [PMID: 25520037 PMCID: PMC4321032 DOI: 10.1534/g3.114.015438] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ~150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes.
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Affiliation(s)
- Brian M Carlson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
| | - Samuel W Onusko
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221
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110
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Abstract
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
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Affiliation(s)
- Atul Grover
- a Biotechnology Division , Defence Institute of Bio Energy Research , Goraparao, P.O. Arjunpur , Haldwani , Uttarakhand , India and
| | - P C Sharma
- b University School of Biotechnology, Guru Gobind Singh Indraprastha University , Dwarka Sec. 16C , New Delhi , India
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111
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Gray MM, St Amand P, Bello NM, Galliart MB, Knapp M, Garrett KA, Morgan TJ, Baer SG, Maricle BR, Akhunov ED, Johnson LC. Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient. Mol Ecol 2014; 23:6011-28. [PMID: 25370460 DOI: 10.1111/mec.12993] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 01/11/2023]
Abstract
Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour-joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within-prairie genetic diversity (92%). Using Bayenv2, 14 top-ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScanFST outliers were in common with Bayenv2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.
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Affiliation(s)
- Miranda M Gray
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
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112
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Moore JS, Bourret V, Dionne M, Bradbury I, O'Reilly P, Kent M, Chaput G, Bernatchez L. Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol 2014; 23:5680-97. [DOI: 10.1111/mec.12972] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
- Direction de la Protection de la Faune; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Mélanie Dionne
- Direction de la Faune Aquatique; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Ian Bradbury
- Science Branch; Fisheries and Oceans Canada; 80 East White Road St. John's Newfoundland A1C 5X1 Canada
| | - Patrick O'Reilly
- Science Branch; Fisheries and Oceans Canada; Bedford Institute of Oceanography; 1 Challenger Drive Dartmouth Nova Scotia B2Y 4A2 Canada
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE); Department of Animal and Aquacultural Sciences (IHA); Norwegian University of Life Sciences; PO Box 5003 1432 Aas Norway
| | - Gérald Chaput
- Fisheries and Oceans Canada; PO Box 5030 Moncton New Brunswick E1C 9B6 Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
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113
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Brodersen J, Seehausen O. Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs. Evol Appl 2014; 7:968-83. [PMID: 25553061 PMCID: PMC4231589 DOI: 10.1111/eva.12215] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/17/2014] [Indexed: 01/10/2023] Open
Abstract
While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys.
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Affiliation(s)
- Jakob Brodersen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and BiogeochemistryKastanienbaum, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and BiogeochemistryKastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of BernBern, Switzerland
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114
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Limborg MT, Waples RK, Seeb JE, Seeb LW. Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation. J Hered 2014; 105:741-51. [PMID: 25292170 DOI: 10.1093/jhered/esu063] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.
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Affiliation(s)
- Morten T Limborg
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg).
| | - Ryan K Waples
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
| | - James E Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
| | - Lisa W Seeb
- From the School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA 98195 (Limborg, Waples, Seeb, Seeb); and the National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark (Limborg)
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115
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Comparative mapping between Coho Salmon (Oncorhynchus kisutch) and three other salmonids suggests a role for chromosomal rearrangements in the retention of duplicated regions following a whole genome duplication event. G3-GENES GENOMES GENETICS 2014; 4:1717-30. [PMID: 25053705 PMCID: PMC4169165 DOI: 10.1534/g3.114.012294] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole genome duplication has been implicated in evolutionary innovation and rapid diversification. In salmonid fishes, however, whole genome duplication significantly pre-dates major transitions across the family, and re-diploidization has been a gradual process between genomes that have remained essentially collinear. Nevertheless, pairs of duplicated chromosome arms have diverged at different rates from each other, suggesting that the retention of duplicated regions through occasional pairing between homeologous chromosomes may have played an evolutionary role across species pairs. Extensive chromosomal arm rearrangements have been a key mechanism involved in re-dipliodization of the salmonid genome; therefore, we investigated their influence on degree of differentiation between homeologs across salmon species. We derived a linkage map for coho salmon and performed comparative mapping across syntenic arms within the genus Oncorhynchus, and with the genus Salmo, to determine the phylogenetic relationship between chromosome arrangements and the retention of undifferentiated duplicated regions. A 6596.7 cM female coho salmon map, comprising 30 linkage groups with 7415 and 1266 nonduplicated and duplicated loci, respectively, revealed uneven distribution of duplicated loci along and between chromosome arms. These duplicated regions were conserved across syntenic arms across Oncorhynchus species and were identified in metacentric chromosomes likely formed ancestrally to the divergence of Oncorhynchus from Salmo. These findings support previous studies in which observed pairings involved at least one metacentric chromosome. Re-diploidization in salmon may have been prevented or retarded by the formation of metacentric chromosomes after the whole genome duplication event and may explain lineage-specific innovations in salmon species if functional genes are found in these regions.
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116
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Everett MV, Seeb JE. Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing. Evol Appl 2014; 7:480-92. [PMID: 24822082 PMCID: PMC4001446 DOI: 10.1111/eva.12147] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/16/2013] [Indexed: 01/07/2023] Open
Abstract
Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome.
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Affiliation(s)
- Meredith V Everett
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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