INV2 vs INV1, P = 0.0024; INV2 vs REC, P = 0.0002). Lack of differences in the test of negative gravitaxis also discards that the reduced odor attraction of strains INV1 and INV2 to some volatile compounds (Figure 3) could result from a somehow impaired motility. Error bars indicate 95% CI. (TIF) Figure S14 Average expression levels for the protein-coding genes encompassed in the ultraconserved region CG15121– CG16894 across six strains under study. (A) Males; (B) females. Statistically significant differences were assessed using a one-way ANOVA at FDR 0.01. *, statistically significant difference in the general ANOVA (Dataset S1); {, statistically significant difference in at least one of the planned contrasts (Table S17). No consistent differential expression between the strains carrying the disrupted ultraconserved region (INV1, INV2) and the strains with the standard arrangement (REC, SIM1, REV1, REV2) was found. For simplicity, gene order in the standard arrangement for this genomic region is shown. Expression units are arbitrary. Error bars, 95% CI. Note that the confidence interval of the geometric mean is not symmetrical. Green double arrowhead line, inner breakpoint of the inversion In(2R)51F11-56E2 that disrupts the ultraconserved region. Genes CG9218, CG11025, CG30128, and CG13873 are represented by several transcripts (Dataset S1). (PDF) Figure S15 Average expression levels for eight protein-coding genes flanking the outer breakpoint of the inversion In(2R)51F11- 56E2 across six strains under study. (A) Males; (B) females. Statistically significant differences were assessed using a one-way ANOVA at FDR 0.01 (Dataset S1). No statistically significant differential expression between the strains carrying the disrupted ultraconserved region (INV1, INV2) and the strains without the disruption (REC, SIM1, REV1, REV2) was found for the immediate flanking genes, thus ruling out any artifactual position effect incidentally generated by our procedure. Expression units are arbitrary. Error bars, 95% CI. Note that the confidence interval of the geometric mean is not symmetrical. Green double arrowhead line, outer inversion breakpoint. (TIF) Figure S16 Direction of expression change between males and females for the protein-coding genes encompassed in the ultra- conserved region CG15121–CG16894 across six strains. Expression change = 0, no sex bias; expression change.0, overexpression in males; expression change,0, overexpression in females. No consistent differences in the pattern of sex bias in gene expression were found between strains carrying the disrupted ultraconserved region (INV1, INV2) and those carrying the ultraconserved region in its intact form. For simplicity, gene order in the standard arrangement for this genomic region is shown. Statistical significance of the expression change between the sexes was assessed using a one-way ANOVA at FDR 0.01 for each strain separately (Dataset S3). The fold change in expression can be calculated as 2|direction of expression change|; the direction of expression change is provided in Dataset S3. Since each strain was analyzed separately, fold change across strains is not comparable. Green double arrowhead line, inner breakpoint disrupting the ultraconserved region CG15121–CG16894. Genes CG9218, CG11025, CG30128, and CG13873 are represented by several transcripts (Dataset S3). (TIF) Table S1 Phylogenetic organization of four gene neighborhoods of D. melanogaster in other Drosophila species according to recent reconstructions of their gene order. (PDF) Collinearity Conservation in Eukaryotes Table S2 Protein-coding genes present in the ultraconserved region CG15121–CG16894. (PDF) Table S3 Comparative organization of the ultraconserved region CG15121–CG16894 in A. gambiae. (PDF) Table S4 (PDF) Table S5 (PDF) Strains. Primers used. Table S6 Amplicons used to confirm the molecular organization of the genomic regions corresponding to the breakpoints of the inversion In(2R)51F11-56E2. (PDF) Table S7 Test for differences in progeny size among the strains generated in the course of the experiments using homozygous crosses. (PDF) Table S8 Test for differences in sex ratio among the strains generated in the course of the experiments using homozygous crosses. (PDF) Table S9 Evaluation of the effect of the disrupted ultraconserved region CG15121–CG16894 in heterozygosis on a variety of traits. (PDF) Table S10 Evaluation of the effect of the disrupted ultracon- served region CG15121–CG16894 on relative viability in compe- tition experiments prior to imago emergence. (PDF) Table S11 Fertility of males carrying the ultraconserved region CG15121–CG1689 in its disrupted or intact form. (PDF) Table S12 Sperm competence of males carrying the ultracon- served region CG15121–CG1689 in its disrupted or intact form in double mating experiments. (PDF) Table S13 Mating ability of flies carrying the ultraconserved region CG15121–CG1689 in its disrupted or intact form in three different timeframes. (PDF) Table S14 Response of flies carrying the ultraconserved region CG15121–CG1689 in its disrupted or intact form to a variety of volatile compounds. (PDF) Table S15 Performance of strains carrying the ultraconserved region CG15121–CG1689 in its disrupted or intact form based on four proxies of global homeostasis. (PDF) Table S16 Expression differences among strains using a one-way ANOVA at FDR 0.01. (PDF) Table S17 Expression differences detected in six planned contrasts using one-way ANOVA at FDR 0.01. (PDF) Table S18 Statistically significant enrichment for biological coherent patterns (GO term ontology, KEGG pathway, and PLoS Genetics | www.plosgenetics.org 12 February 2012 | Volume 8 | Issue 2 | e1002475