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 E.
dc.contributor.author	Rogan, Ger
dc.contributor.author	McGinnity, Philip
dc.contributor.author	Primmer, Craig R.
dc.contributor.funder	Suomalainen Tiedeakatemia, Finland
dc.contributor.funder	Irish Government
dc.date.accessioned	2016-01-29T13:25:04Z
dc.date.available	2016-01-29T13:25:04Z
dc.date.issued	2014-03-31
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.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	68
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.doi	10.1186/1471-2148-14-68
dc.identifier.endpage	17	en
dc.identifier.issn	1471-2148
dc.identifier.journaltitle	BMC Evolutionary Biology	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/2234
dc.identifier.volume	14	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

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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