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Using a recently introduced replicated pooled genome wide association approach (Pool-GWAS) we compare the genomic regions contributing to natural variation in abdominal pigmentation in female European and South African Drosophila melanogaster. In both the European and the South African flies regions around the genes tan and bric-à-brac 1 (bab1) are found most closely associated with pigmentation. However, while in the European populations tan shows a much stronger association than bab1, the converse is true for the South African flies. Most of the sequencing data for the European flies (2 replicates from Vienna, Austria and 3 from Bolzano, Italy) have been deposited on the ENA under study ID ERP001827 (http://www.ebi.ac.uk/ena/data/view/ERP001827)All samples added to this study were aligned to to the combined genomes of D. melanogaster (v. 5.18), Wolbachia pipientis (AE017196.1), Lactobacillus brevis (CP000416.1), Acetobacter pasteurianus (AP011170), and phage phiX174 (NC_001422.1) using BWA aln v. 0.5.9 (Li and Durbin 2009) without seeding allowing for two gap openings (-o 2), an alignment distance threshold leading to loss of less than 1% of reads assuming a 2% error rate (-n 0.01), and up to 12bp gap extensions (-e 12 –d 12). |