DOI: 10.5061/dryad.k25qf
title: Data from: Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups

description: Accurate estimates of heritability (h²) are necessary to assess adaptive
 responses of populations and evolution of fitness-related traits in
 changing environments. For plants, h² estimates generally rely on maternal
 progeny designs, assuming that offspring are either half-sibs or
 unrelated. However, plant mating systems often depart from half-sib
 assumptions, this can bias h² estimates. Here, we investigate how to
 accurately estimate h² in non-model species through the analysis of
 sibling designs with a moderate genotyping effort. We performed
 simulations to investigate how microsatellite marker information available
 for only a subset of offspring can improve h² estimates based on maternal
 progeny designs in presence of non-random mating, inbreeding in the
 parental population or maternal effects. We compared the basic family
 method, considering or not adjustments based on average relatedness
 coefficients, and methods based on the animal model. The animal model was
 used with average relatedness information, or with hybrid relatedness
 information: associating one-generation pedigree and family assumptions,
 or associating one-generation pedigree and average relatedness
 coefficients. Our results highlighted that methods using marker-based
 relatedness coefficients performed as well as pedigree-based methods in
 presence of non-random mating (i.e. unequal male reproductive
 contributions, selfing), offering promising prospects to investigate in
 situ heritabilities in natural populations. In presence of maternal
 effects, only the use of pairwise relatednesses through pedigree
 information improved the accuracy of h² estimates. In that case the amount
 of father-related offspring in the sibling design is the most critical.
 Overall, we showed that the method using both one-generation pedigree and
 average relatedness coefficients was the most robust to various ecological
 scenarios.
description: AdditiveValuesUntreated file generated by the simulation model that contains the additive genetic values and phenotypic values of the simulated parental population. First column = ID; second column = additive value; third column = phenotypic valueGenotypeFileUntreated file generated by the simulation model that contains the genotype of the individuals at the Nl neutral loci simulated (Nl columns)PhiACoefficientsUntreated file generated by the simulation model that contains the pairwise individual kinship coefficients estimated based on the simulated pedigree (matrix format)LoisellePaternalCoefficientsUntreated file generated by the simulation model that contains the pairwise individual paternal relatedness coefficients estimated based on the Loiselle approach (matrix format)PhenotypeUntreated file generated by the simulation model that contains the phenotypic values of the simulated offspring population at the AsREML format (2 columns: ID, PHENO)InputParameter_AllelicFrequenciesText file generated by the simulation model that resumes the information about the simulation parameters (VA, VE, Ng, Nfam, Noff...) and the drew allelic frequenciesHSFS_MatrixRelatedness matrix used by the "HSFS" method at the AsREML format (.grm). Matrix generated a posteriori with a R script.Hybrid_MatrixRelatedness matrix used by the "Hybrid" method at the AsREML format (.grm). Matrix generated a posteriori with a R script.PhiA_MatrixRelatedness matrix used by the reference method "PhiA" at the AsREML format (.grm). Matrix generated a posteriori with a R script.Relatedness_MatrixRelatedness matrix used by the "Relatedness" method at the AsREML format (.grm). Matrix generated a posteriori with a R script.SimulatedPedigreeUntreated file generated by the simulation model that contains the pedigree of the simulated offspring population (Firts column = Individual identity, second column = Dam identity, third column = Sire identity)