Computational protocol: Adaptive Evolution Is Substantially Impeded by Hill–Robertson Interference in Drosophila

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Protocol publication

[…] If immune and male-biased or testes specific genes tend to be overrepresented in specific recombination, mutation, or gene density regions then the correlations to the rate of adaptive evolution would not necessarily be a consequence of adaptive evolution being affected by recombination, mutation, or gene density. Thus, Gene Ontology (GO) terms for 6,141 genes were downloaded from Fruitfly release 78 using the R package biomaRt (). A list of GO terms related to immune response and testes was constructed using the EBI’s GO tool QuickGO (). When a given gene was associated to a GO term from this list it was labeled as “Immune&Testes genes,” the rest of genes were labelled as “Control genes.” The list of immune response and testes related GO terms and the lists of genes in each group can be consulted in the supplementary table S6, Supplementary Material online. A permutation test was applied to assess whether Ka+ are significantly higher as it has been reported before (; ; ) for immune response and testes related genes relative to the rest of control genes. We shuffled without replacement 1,000 times the complete list of genes by means of ad hoc Bash and Perl Scripting. Then, we estimated Ka+ using the DFE-alpha software (, see below) for each randomized group. Thus, we got the expected null distribution for the differences between Control genes minus the Immune&Testes genes for the statistic Ka+. Finally, the one-tailed P value was obtained by counting the number of replicates below the observed difference divided by the total number of replicates (1,000). The expected null distributions and the observed differences can be consulted in the supplementary figure S4, Supplementary Material online. […]

Pipeline specifications

Software tools BioMart, QuickGO
Application Genome annotation
Organisms Drosophila melanogaster, Drosophila yakuba
Chemicals Amino Acids