title: Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland. tutayk@utu.fi.
authors.forename: Tutku
authors.initials: T
authors.lastname: Aykanat
authors.forename: Susan E
authors.initials: SE
authors.lastname: Johnston
authors.forename: Deirdre
authors.initials: D
authors.lastname: Cotter
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Cross
authors.forename: Russell
authors.initials: R
authors.lastname: Poole
authors.forename: Paulo A
authors.initials: PA
authors.lastname: Prodőhl
authors.forename: Thomas
authors.initials: T
authors.lastname: Reed
authors.forename: Ger
authors.initials: G
authors.lastname: Rogan
authors.forename: Philip
authors.initials: P
authors.lastname: McGinnity
authors.forename: Craig R
authors.initials: CR
authors.lastname: Primmer
mesh_terms: D000483:Alleles; D000818:Animals; D005075:Biological Evolution; D003198:Computer Simulation; D005260:Female; D008297:Male; D018895:Microsatellite Repeats; D010375:Pedigree; D045483:Rivers; D020317:Salmo salar / Q000235:genetics*