Glue genes are subjected to diverse selective forces in Drosophila during Drosophila development

Molecular evolutionary studies usually focus on genes with clear roles in adult fitness or on developmental genes expressed at multiple time points during the life of the organism. Here, we examine the evolutionary dynamics of Drosophila glue genes, a set of eight genes tasked with a singular primary function during a specific developmental stage: the production of glue that allows animal pupa to attach to a substrate for several days during metamorphosis. Using phenotypic assays and available data from transcriptomics, PacBio genomes, and genetic variation from global populations, we explore the selective forces acting on the glue genes within the cosmopolitan D. melanogaster species and its five closely related species, D. simulans, D. sechellia, D. mauritiana, D. yakuba, and D. teissieri. We observe a three-fold difference in glue adhesion between the least and the most adhesive D. melanogaster strain, indicating a strong genetic component to phenotypic variation. These eight glue genes are among the most highly expressed genes in salivary glands yet they display no notable codon bias. New copies of Sgs3 and Sgs7 are found in D. yakuba and D. teissieri with the Sgs3 coding sequence evolving rapidly after duplication in the D. yakuba branch. Multiple sites along the various glue genes appear to be constrained. Our population genetics analysis in D. melanogaster suggests signs of local adaptive evolution for Sgs3, Sgs5 and Sgs5bis and traces of recent selection for Sgs1, Sgs3, Sgs7 and Sgs8. Our work shows that stage-specific genes can be subjected to various dynamic evolutionary forces.Dataset1.ods: Raw data Sheet1: Stock_information: Information of the fly lines used for the analysis. Sheet2: adhesion_test: Results of the adhesion assay performed on pupae used in the analyses (including adhesion tests that were excluded from further analysis). Sheet3: glue_area: Pupa-substrate contact area measurements. Sheet4: codon_usage_and_expression: Expression level and codon adaptation index for genes expressed in salivary glands of wandering larva. Sheet5: PAML_dN_values: synonymous and non synonymous substitution rates obtained with PAML under M0 and free ratio models. Sheet6: FEL_results: raw results obtained by the Fixed Effect Likelihood method implemented in HyPhy via the datamonkey web platform. fasta_alignments.zip: Sequence alignments used for the different analyses. scripts.zip: folder containing scripts used to do the analyses. circos_plot_revised.R: R script to produce the revised circos plot figure 4. Fst_distribution.R: R script to analyze Fst between D. melanogaster populations. circos_raw_data.zip: data used to produce circos plot figures. glue_prints.zip: folder containing pictures of prints left by pupae after detachment. Funding provided by: Conseil National de la Recherche ScientifiqueCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100007175Award Number: MITI - AAP2020Funding provided by: European Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000781Award Number: FP7/2007-2013 Grant Agreement no. 33757