List of protein coding genes found in regions of differentiation containing a single annotated gene.

<p>List of protein coding genes found in regions of differentiation containing a single annotated gene.</p

Low to moderate overall genetic differentiation between the two subspecies of rabbits.

<p>A) Histogram of <i>F_ST</i> values for all SNPs and SNPs showing a minor allele frequency (MAF) of 10%. B) Pie chart summarizing the proportion of fixed, shared and exclusive polymorphisms.</p

Levels of differentiation between subspecies varied greatly across the genome.

<p>Chromosomal distribution of genetic differentiation for all rabbit chromosomes. Each data point is based on a sliding window analysis using 100 kb windows with 10 kb steps. The solid black line denotes a Z-score of three (three standard deviations departing from the median <i>F_ST</i> over all windows). The relative proportion of fixed (red) versus shared (gray) polymorphism for each window is indicated below the graph (F/S).</p

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

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