Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

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dc.contributor.author Aykanat, Tutku
dc.contributor.author Johnston, Susan E.
dc.contributor.author Cotter, Deirdre
dc.contributor.author Cross, Thomas F.
dc.contributor.author Poole, Russell
dc.contributor.author Prodhl, Paulo A.
dc.contributor.author Reed, Thomas
dc.contributor.author Rogan, Ger
dc.contributor.author McGinnity, Philip
dc.contributor.author Primmer, Craig R.
dc.date.accessioned 2016-01-29T13:25:04Z
dc.date.available 2016-01-29T13:25:04Z
dc.date.issued 2014-03-31
dc.identifier.citation AYKANAT, T., JOHNSTON, S. E., COTTER, D., CROSS, T. F., POOLE, R., PRODŐHL, P. A., REED, T., ROGAN, G., MCGINNITY, P. & PRIMMER, C. R. 2014. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology, 14:68, 1-17. http://dx.doi.org/10.1186/1471-2148-14-68 en
dc.identifier.volume 14 en
dc.identifier.startpage 1 en
dc.identifier.endpage 17 en
dc.identifier.issn 1471-2148
dc.identifier.uri http://hdl.handle.net/10468/2234
dc.identifier.doi 10.1186/1471-2148-14-68
dc.description.abstract Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system. Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers. Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers. en
dc.description.sponsorship Suomalainen Tiedeakatemia, Finland (Grants 141231 and 137710 to Craig R. Primmer); Irish Government Sea Change Programme (Beaufort Marine Research Award in Fish Population Genetics to Philip McGinnity and Thomas Reed) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BioMed Central Ltd. en
dc.rights © Aykanat et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated. en
dc.rights.uri http://​creativecommons.​org/​licenses/​by/​2.​0 en
dc.subject Atlantic salmon en
dc.subject Heritability en
dc.subject Incomplete sampling en
dc.subject MasterBayes en
dc.subject Parentage assignment en
dc.subject Power analysis en
dc.subject Reproductive success en
dc.title Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Thomas Cross, School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland. +353-21-490-3000 Email: t.cross@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 271355272
dc.contributor.funder Suomalainen Tiedeakatemia, Finland
dc.contributor.funder Irish Government
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Evolutionary Biology en
dc.internal.IRISemailaddress t.cross@ucc.ie en
dc.identifier.articleid 68


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© Aykanat et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated. Except where otherwise noted, this item's license is described as © Aykanat et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.
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