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

• Published in: BMC Evolutionary Biology
• Main Authors: Aykanat, T., Johnston, S., Cotter, D., Cross, T., Poole, R., Prodohl, P., Reed, T., Rogan, G., McGinnity, P., Primmer, C.
• Format: Report
• Language: English
• Published: BioMed Central 2014
• Subjects: Atlantic salmon; Heritability; Incomplete sampling; MasterBayes; Parentage assignment; Power analysis; Reproductive success; Salmo salar
• Online Access: http://hdl.handle.net/10793/961; https://doi.org/10.1186/1471-2148-14-68

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. This study was supported by the Finnish Academy (grants 141231 and 137710 to CRP). PMG, TR were supported by the Beaufort Marine Research Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme.