Summary statistics of all quantitative trait loci (QTL) for scleral ossification detected in this study.

<p>LOD = logarithm of the odds. PVE = percent variance explained.</p

Recessive inheritance of scleral ossicles at all QTL positions.

<p>Effect plots displaying average scleral ossicle number for each genotypic class observed in the CF x SF F2 hybrids from all three analyses. In each case, F2 hybrids with two cavefish alleles have fewer scleral ossicles on average than those with either one or two surface fish alleles. This pattern is consistent with the recessive inheritance of scleral ossicle loss in CF [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref013" target="_blank">13</a>].</p

Chi-square (χ²) analysis of observed and expected ratios of the combined CF(Pa) x SF(Mx) F2 progeny from Gross <i>et al</i>. [15] and the CF(Pa) x SF(Tx) F2 progeny from O’Quin <i>et al</i>. [13] with and without scleral ossicles due to a genotypic threshold at 1–4 loci.

<p>Chi-square (χ²) analysis of observed and expected ratios of the combined CF(Pa) x SF(Mx) F2 progeny from Gross <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref015" target="_blank">15</a>] and the CF(Pa) x SF(Tx) F2 progeny from O’Quin <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref013" target="_blank">13</a>] with and without scleral ossicles due to a genotypic threshold at 1–4 loci.</p

Skewed distribution of scleral ossicles in CF x SF F2 hybrids.

<p>(<b>A</b>) Example CF(Pa) x SF(Mx) F2 progeny from Gross <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref015" target="_blank">15</a>] with 0, 1, and 2 scleral ossicles. (<b>B</b>) Distribution of scleral ossicles among CF(Pa) x SF(Tx) F2 originally published in O'Quin <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref013" target="_blank">13</a>], from CF(Pa) x SF(Mx) F2 from Gross <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171061#pone.0171061.ref015" target="_blank">15</a>], and the combined F2 from both analyses. In each case, the skewed distributions of F2 progeny with two scleral ossicles is consistent with hypothesis that multiple genes control scleral ossicle formation through an epistatic threshold model of inheritance.</p