DOI: 10.5061/dryad.dz08kps2p
title: Data from: Ecology-relevant bacteria drive the evolution of host antimicrobial peptides in Drosophila

description: Antimicrobial peptides are host-encoded immune effectors that combat
 pathogens and shape the microbiome in plants and animals. However, little
 is known about how the host antimicrobial peptide repertoire is adapted to
 its microbiome. Here we characterize the function and evolution of the
 Diptericin antimicrobial peptide family of Diptera. Using mutations
 affecting the two Diptericins (Dpt) of Drosophila melanogaster, we reveal
 the specific role of DptA for the pathogen Providencia rettgeri and DptB
 for the gut mutualist Acetobacter. Strikingly, presence of DptA- or
 DptB-like genes across Diptera correlates with the presence of Providencia
 and Acetobacter in their environment. Moreover, DptA- and DptB-like
 sequence predicts host resistance against infection by these bacteria
 across the genus Drosophila. Our study explains the evolutionary logic
 behind the bursts of rapid evolution of an antimicrobial peptide family
 and reveals how the host immune repertoire adapts to changing microbial
 environments.
description: The dataset was collected through wet lab experimentation and
 literature review, as described in the manuscript. In brief, bacterial
 infections were performed with immune mutant
 <em>Drosophila</em> flies. Immune evolution of fly defence
 genes was collected from previous studies and newly-published genomic data
 through sequence-based searches, and the host gene evolution was manually
 curated with a focus on specific residues of a priori interest.
description: The data are saved in excel file formats, csv file formats, and
 alignment and phylogeny data are provided in both Geneious proprietary
 software format, and either .nexus or .genbank as a non-proprietary
 alternative. Any Geneious files can be viewed with the free version of the
 software available from the company.
description: # Title of DatasetEcology-relevant bacteria drive the evolution of host
 antimicrobial peptides in Drosophila --- Fly infection experiment data
 alongside bioinformatic analyses (alignment, phylogeny, codon-based
 assessment of evolution) related to the evolution of the Diptera
 antimicrobial peptide family Diptericin, with a focus on Drosophila fruit
 flies. ## Description of the data and file structure The data are provided
 in folders that relate to the main figures as per the preprint version of
 the article. In this way, we hope the hierarchical structure of the
 folders is more intuitive to help readers find the specific data they are
 interested in related to a specific figure. The figures are titled per the
 preprint manuscript as this is the published text at time of writing. In
 the future, the supplementary figure naming format is likely to change
 from "Figure XsuppY", so we encourage users to view the latest
 version of the open access preprint to sort out any confusion. see:
 [https://doi.org/10.1101/2022.12.23.521774](https://doi.org/10.1101/2022.12.23.521774) Bioinformatic analyses were performed in Geneious, and we provide both the Geneious files (version R7 and later) to ensure ease of visualization. However we also have endeavoured to provide Nexus (.nex) or Genbank (.gb) files when possible to ensure users have access to data with their preferred software. User annotations to sequences we made in Geneious will not show up in .nexus files, and we cannot ensure that all software will read these annotations the same in GenBank files using other software. ## Sharing/Access information All data generated in this manuscript are free to access and re-use in future studies, and users are encouraged to cite with appropriate credit (specifically citation to the manuscript published in Science). ## Code/Software Statistics were run using a mix of R and Prism as was convenient for our purposes throughout the manuscript. The model for Figure 5 data was run in R and the output from our code is stored as a Text Document in the data folders pertaining to Figure 5 for full transparency.