Two complementary depictions of the developmental architecture underlying the genotype–phenotype map for complex traits.

<p>A captures the idea that large amounts of genetic variation funnel to smaller numbers of pathways and processes. These processes then interact to produce structured and modulated phenotypic variation in a complex trait. B, which derives from Wagner <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004724#pgen.1004724-Wagner2" target="_blank">[20]</a>, shows the many-to-many mapping of genes to traits; while both Cs show the modular pattern of gene effects on processes and the effects of processes on sets of phenotypic traits. These depictions illustrate some of the complexity involved in constructing models of genotype–phenotype relations in complex traits.</p

Neonatal Skull Landmark Data

This file contains raw landmark coordinates for neonatal mouse skulls

Two-block partial least squares analysis (PLS) of the neonatal mouse basicranium and face.

<p>Wireframes depict singular warp deformations of shape along each PLS axis. Abbreviations: PLS = partial least squares axis; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models. Wireframe superimposition on skull renderings indicates approximate position of landmarks under consideration.</p

Two-block partial least squares analysis (PLS) of the adult mouse basicranium and face.

<p>Abbreviations: PC = principal component; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control; UG2 = Brachymorph undergrowth model; UG2c = brachymorph undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models. Wireframe superimposition on skull renderings indicates approximate position of landmarks under consideration.</p

Procrustes distances between neonatal mean shapes.

<p>All comparisons are significant at p < 0.0001 except UG1 -> UG1c, which is significant at p = 0.0102. Abbreviations: OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models.</p><p>Procrustes distances between neonatal mean shapes.</p

Principal components analysis (PCA) of neonatal mouse skulls.

<p>A) Scatter plot of PC1 and PC2 of neonatal whole-skull shape. B) Wireframe depictions of group mean shapes. Abbreviations: PC = principal component; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models.</p

Two-block partial least squares analysis (PLS) of the neonatal mouse basicranium and calvarium.

<p>Wireframes depict singular warp deformations of shape along each PLS axis. Abbreviations: PLS = partial least squares axis; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models. Wireframe superimposition on skull renderings indicates approximate position of landmarks under consideration.</p

Principal components analysis (PCA) of adult mouse skulls.

<p>A) Scatter plot of PC1 and PC2 of adult whole-skull shape. B) Wireframe depictions of group mean shapes. Abbreviations: PC = principal component; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control; UG2 = Brachymorph undergrowth model; UG2c = brachymorph undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models.</p

Two-block partial least squares analysis (PLS) of the adult mouse basicranium and calvarium.

<p>Abbreviations: PC = principal component; OG = Pten overgrowth model; OGc = overgrowth control, UG1 = Trsp undergrowth model; UG1c = Trsp undergrowth control; UG2 = Brachymorph undergrowth model; UG2c = brachymorph undergrowth control. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#sec002" target="_blank">Materials and Methods</a> for a full explanation of these models. Wireframe superimposition on skull renderings indicates approximate position of landmarks under consideration.</p

Neonatal (A) and adult (B) landmarks used in this study.

<p>Landmark descriptions and numbers are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118355#pone.0118355.t001" target="_blank">Table 1</a>.</p