Pipeline for determining Y-linked gene transfers. R script.

R script used to determine incipient Y-linked transfers using male/female pairs from two D. melanogaster strains. All data are publicly available. See supplementary materials for full description of pipeline, and description of data used in pipeline

Use polymorphism data to determine age of Y-linked transfer

R script for determining the age of a Y-linked transfers and perform statistical tests comparing age distribution of non-genic and genic transfers. See supplementary materials for more details, including description of datasets used

Dmel_AP1-AP2-RAP1-RAP2_novoalign.sync

Drosophila melanogaster SNP data. Reads were mapped using novoalign. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information)

Extract reads from bam file based on presence of specific allele

Python script that reads from bam file based on presence of alleles in text file (text file with three columns: 1. Chromsome, 2. Position, 3. alllele [A, T, C, G]). Returns a bam file with extracted reads. See script for more details. example: python get_male_spec_reads.py -b bam.file -s snp.fil

Dsim_AP1-AP2-RAP1-RAP2_novoalign.sync

Drosophila simulans SNP data. Reads were mapped using novoalign. Populations were sequenced as a single sample (e.g Pool-Seq). Their order in the sync file is as follows: AP1-AP2-RAP1-RAP2. The sync file only contains high-quality SNPs with downsampled allele counts (see main publication for additional information)

drift_expectations_pool-sampling_mated_females.R

R script simulating genetic drift in isofemale lines

Dmel_3reps_F0F59_majorChr_downsampled

Sync file of allele coverage for Drosophila melanogaster SNPs in major chromosome arms (X, 2L, 2R, 3L, 3R). Columns in this sync file correspond to chromosome, position, base, Dmel _A_F0, Dmel _B_F0, Dmel _C_F0, Dmel _A_F59_Hot, Dmel _B_F59_Hot, Dmel _C_F59_Hot. Nomenclature of the samples is as follows: e.g. species_replicate_generation_selection regime. Species: Dmel (Drosophila melanogaster), replicate: letters (A-Z), generation: F#, # indicating the number of generations, and selection regime: Hot. Format specification of sync file is described in Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436. See main publication for additional information about data processing, SNP calling and filtering

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