Additional file 4: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

Fasta file of TE sequences generated in the TE annotation, with basic description of each TE sequence. (TXT 892 kb

Additional file 2: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

Table S1. D. pseudoobscura species group lines used in this study. Table S2. TEs found in D. obscura group. Sorted by if they are previously discovered or novel, then by Order and super family. Transmission states if the TE family is found to transfer between species. Table S3. Diagonal table showing the total number of TE families found in each species for comparison. In brackets, the number of novel TE families found shared between species. Table S4. Comparisons of dN/dS between TEs and nuclear genes. The dS values presented here are compared to the dS values of nuclear genes between the given species calculated previously. We considered a transfer event between two species to have occurred if the TE dS value is less than the 2.5th percentile for nuclear genes. For instances where no dS for nuclear comparisons are available, we used the dS between D. pseudoobscura and the species of interest. Table S5. Number of unique and shared polymorphic sites for each species comparison, for each TE family, used in the boxplots in Fig. 2e. (XLSX 153 kb

Additional file 3: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

TE insertion density per megabase (estimated from PopoolationTE2 output) for each TE order and each species analysed here. (TXT 166 kb

Additional file 9: Figure S6. of A novel method for quantifying the rate of embryogenesis uncovers considerable genetic variation for the duration of embryonic development in Drosophila melanogaster

Inversion polymorphisms and their effect on DOE (PDF 170 kb

Overview of the experimental design.

<p>Wild <i>D. melanogaster</i> flies were collected from Vienna, Austria, and Bolzano, Italy, brought into a controlled environment in the laboratory, and treated as shown in the figure. The same procedure was used for all five replicates, with each replicate resulting in 1,500 females for phenotyping, and with 100 light and dark flies from each replicate sequenced.</p

Genome-wide association study of female abdominal pigmentation.

<p>A) Manhattan plot for abdominal pigmentation in the full data set (including all five replicates). The–log₁₀<i>p</i>-values are plotted against the position on each chromosome. The horizontal dashed line indicates the genome-wide significance threshold at an FDR of 0.05. The red bars indicate candidate genes previously shown to affect pigmentation. B) Detailed view of the <i>tan</i> (left), <i>bab1</i> (middle) and <i>ebony</i> (right) regions. The positions on the x-axis are indicated in kb. The red bars indicate regulatory regions previously shown to affect pigmentation. C) Detailed view of top ranked polymorphisms located within or close to the three pigmentation genes. For every gene, the most significant SNPs fall in regulatory regions.</p