Trait | GSM | α | r^{2} | (SD) | |
---|---|---|---|---|---|

Size | A | −0.5 | 0.073 | A 0.58 (0.14) | 11 |

A + A^{2} | −0.5 | 0.093 | A 0.57 (0.15) | 11 | |

A^{2} 0.21 (0.51) | |||||

Fertility | A | 1 | 0.012 | A 0.24 (0.24) | 0 |

A + A^{2} | 1 | 0.029 | A 0.36 (0.21) | 3 | |

A^{2} 1.24 (0.87) | |||||

(A + A^{2})_{rec} | 1 | 0.064 | A_{arm}0.44 (0.18) | 7 | |

A_{cen}0.02 (0.07) |

Results are shown for additive (A) and additive-by-additive (A

^{2}) 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. is improvement over the null model (likelihood ratio). 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.