Table 1 Genomic heritability estimates
TraitGSMαr2Embedded Image (SD)Embedded Image
SizeA−0.50.073A 0.58 (0.14)11
A + A2−0.50.093A 0.57 (0.15)11
A2 0.21 (0.51)
FertilityA10.012A 0.24 (0.24)0
A + A210.029A 0.36 (0.21)3
A2 1.24 (0.87)
(A + A2)rec10.064Aarm 0.44 (0.18)7
Acen 0.02 (0.07)
  • Results are shown for additive (A) and additive-by-additive (A2) GSM, and for the most predictive model tested (if neither of the above), shown in bold. α is the scaling parameter from Speed et al. (2012), which determines the effect size expectation for markers as a function of allele frequency, where 0 is unweighted and smaller values assign greater weight to rare alleles (see Equations 1 and 2). Unconstrained REML estimates and SD are shown for components > 0 at convergence. Embedded Image is improvement over the null model (likelihood ratio). Embedded Image is additive and additive-by-additive similarity defined at the level of recombination rate domains (tips, arms and centers, merged across chromosomes). See Equation S4 and associated discussion in File S22. GSM, genetic similarity matrices; LR, log likelihood ratios; REML, restricted/residual maximum likelihood.