Differentially expressed genes between the 0.1 MPa, 10 MPa, and 26 MPa growth conditions (adjusted P value<0.1).

<p>Log2-fold change is indicated <i>vs.</i> the average counts over all six samples.</p><p>Differentially expressed genes between the 0.1 MPa, 10 MPa, and 26 MPa growth conditions (adjusted P value<0.1).</p

Distribution of the differentially expressed genes according to the clusters of orthologous groups of proteins (COG) classification (in percentage).

<p>The numbers in parentheses indicate the numbers of differentially expressed genes for each COG.</p

Heatmap of <i>D. hydrothermalis</i> gene expression changes with pressure.

<p>Normalized counts obtained with DESeq, transformed into log2 (RPKM+1), were used to generate a heatmap showing over-expressed (red) and under-expressed (green) genes with 2 replicates for 3 pressure conditions (0.1, 10 and 26 MPa). Three clusters corresponding to DESeq pressure-regulated genes, with an adjusted P-value<0.1, are shown (A: 10 <i>vs.</i> 0.1 MPa; B: 26 <i>vs.</i> 10 MPa; C: 26 <i>vs.</i> 0.1 MPa). Functional annotation corresponding to pressure-regulated genes is displayed.</p

Genomic organization of <i>D. hydrothermalis</i> overlaid with differentially expressed genes and expression levels obtained from RNA-seq experiments.

<p>Moving from the outside inward, the circles represent 1, 2) CDS on the plus and minus strands of the genome; loci of differentially expressed genes in 3) 26 MPa <i>vs.</i> 0.1 MPa, 4) 10 MPa <i>vs.</i> 0.1 MPa, 5) 26 MPa <i>vs.</i> 10 MPa; coverage (from BAM format) for 6) 26 MPa, 7) 10 MPa, 8) 0.1 MPa; 9) GC skew.</p

Quantitation of glutamate levels (A) and intracellular ATP (B) in <i>D. hydrothermalis</i> cells grown under different pressure conditions.

<p>Quantitation of glutamate levels (A) and intracellular ATP (B) in <i>D. hydrothermalis</i> cells grown under different pressure conditions.</p

Venn diagram showing numbers of differentially expressed genes in <i>D. hydrothermalis</i> between the hydrostatic pressures of 0.1 MPa, 10 MPa and 26 MPa (adjusted P-value<0.1).

<p>Venn diagram showing numbers of differentially expressed genes in <i>D. hydrothermalis</i> between the hydrostatic pressures of 0.1 MPa, 10 MPa and 26 MPa (adjusted P-value<0.1).</p

Information about individuals included in the GBS VCF file

Morph and localities for each individual included in the GBS study

Supplementary Methods and TablesThis file includes details about methods and parameters used, as well as supplementary results on analyses ofphenotype and whole genome analyses. from A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the <i>Zosterops borbonicus</i> white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex <i>cis</i>-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection