Genotypes_Carneiro_et_al

Genotypic data used in the study. The coordinates for the different populations and information on the different markers can be found in the Supplementary Material associated with the manuscript and main manucsript, respectively

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

Proportion of amino acid substitutions driven to fixation by positive selection (α) and divergence at nonsynonymous and synonymous sites (dN/dS) for genes within and outside differentiated regions.

a<p>Only includes genes located within sampled regions in our study and exclude genes located in regions of differentiation identified using only one of the statistics.</p>b<p>Method of Eyre-Walker and Keightley <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003519#pgen.1003519-EyreWalker1" target="_blank">[73]</a>. 95% confidence intervals of α estimates were obtained using 200 bootstrap replicates.</p>c<p>Only genes with one-to-one orthology relationships were considered. Standard deviation is shown in parenthesis.</p><p>Proportion of amino acid substitutions driven to fixation by positive selection (α) and divergence at nonsynonymous and synonymous sites (dN/dS) for genes within and outside differentiated regions.</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

Highly heterogeneous size of differentiated regions.

<p>Histogram summarizing the physical size (Kb) of independent regions of differentiation between rabbit subspecies.</p

Regions of high differentiation are enriched for regions undergoing low rates of gene exchange.

<p>Mean RND (A) and Fays and Wu's <i>H</i> values (B) for intronic fragments contained within and outside regions of differentiation. Regions of differentiated were defined both based on the proportion of fixed differences to shared polymorphisms and on a Z-score higher than three (three standard deviations departing from the median <i>F_ST</i> over all windows)). N.S. – non significant. Asterisks designate significant differences (t-test) for each comparison (*<i>P</i><0.05; **<i>P</i><0.01; ***<i>P</i><0.001).</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 differential expression.

1<p>variance explained by domestication/species, mean across expressed genes.</p>2<p>absolute fold change, mean across expressed genes.</p>3<p>Fraction of all possible permutations of the domestication factor where the respective statistic is matched or exceeded.</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