Expression levels of four genes with common expression in domesticated dogs, pigs, rabbits, and guinea pigs.

<p>Blue: domesticated animals, red: wild animals. Shown are the four genes with the lowest p-values for the domestication factor across dogs, pigs and rabbits, and with expression change in the same direction in these three species as well as guinea pigs. Expression levels are from variance stabilized data, separately normalized to the median in each species pair.</p

Gene expression in domesticated and wild animals.

<p>Cortical gene expression in four domesticated animal species is compared to their wild relatives (blue arrows), followed by comparisons between the four domestication events (red arrows). Next to each domesticated/wild pair, a heatmap shows expression levels of all respective DE genes (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen-1002962-t001" target="_blank">Table 1</a>). Genes were individually normalized and sorted by DE p-value, separately for genes up- and downregulated in domestication. Red (blue): lower (higher) expression. Due to the high number of DE genes, gene names are omitted for the guinea pig comparison. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen.1002962.s002" target="_blank">Dataset S2</a> for details on the DE genes.</p

Expression differences between tame and aggressive rats.

<p>A. Heatmap showing expression levels of DE genes. Genes were individually normalized and sorted by DE p-value, separately for genes up- and downregulated in domestication. Red (blue): lower (higher) expression. B. A QTL for tameness is located on chromosome one <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen.1002962-Albert2" target="_blank">[25]</a>. The x-axis shows the genetic position along chromosome one in centiMorgan (cM). The F-value is a measure of the likelihood of the presence of a QTL. The dashed horizontal line is the genome-wide significance threshold. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen.1002962-Albert2" target="_blank">[25]</a> for details. C. Expression differences in the tameness QTL region. Top panel: significance and location for each gene. P-values were signed so that positive (negative) values correspond to genes with higher expression in aggressive (tame) rats. Dashed lines: genome-wide 10% FDR threshold, dotted lines: p = 0.05. Lower panel: fold changes. Red: genes with FDR<10%, orange: genes with p<0.05. D: positions of <i>Dll3</i> and <i>Dhdh</i> (green vertical lines) compared to patterns of DNA polymorphism in the founder animals of the QTL pedigree used to identify the tameness QTL <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#pgen.1002962-Albert3" target="_blank">[49]</a>. Blue (red) line: nucleotide diversity in the tame (aggressive) founder animals.</p

Expression differences between domesticated and wild animals.

<p>A. Pairwise expression differences. Plotted for each comparison is in black on the left the mean variance explained by domestication, along with 95% confidence intervals (box whiskers) based on 10,000 bootstraps across genes. On the right in light blue is the null distribution of mean variance explained by domestication based on permutations of the domestication factor (box whiskers comprise 95% of the distribution, central horizontal bar is the median). B. For each comparison, the mean variance explained by domestication across genes is plotted as a function of sequence divergence expressed as the median fraction of nucleotides that differ between any two domesticated and wild animals in that comparison.</p

Pairwise overlap of DE genes among domestication events.

<p>Above diagonal: number of genes that are DE in both species, with Fisher's exact test p-values.</p><p>Below diagonal: Odds ratios of FET testing if DE genes in the one species predict expression direction in the other species, with Fisher's exact test p-values. Only the more significant direction is shown (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002962#s4" target="_blank">Materials and Methods</a> for details).</p