DOI: 10.5061/dryad.hdr7sqvq2
title: Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila

description: Understanding how and when key novel adaptations evolved is a central goal
 of evolutionary biology. Within the immigrans-tripunctata radiation of
 Drosophila, many mushroom-feeding species are tolerant of host toxins,
 such as cyclopeptides, that are lethal to nearly all other eukaryotes. In
 this study, we used phylogenetic and functional approaches to investigate
 the evolution of cyclopeptide tolerance in the immigrans-tripunctata
 radiation of Drosophila. First, we inferred the evolutionary relationships
 among 48 species in this radiation using 978 single copy orthologs. Our
 results resolved previous incongruities within species groups across the
 phylogeny. Second, we expanded on previous studies of toxin tolerance by
 assaying 16 of these species for tolerance to α-amanitin and found that
 six of them could develop on diet with toxin. Finally, we asked how
 α-amanitin tolerance might have evolved across the immigrans-tripunctata
 radiation, and inferred that toxin tolerance was ancestral in
 mushroom-feeding Drosophila and subsequently lost multiple times. Our
 findings expand our understanding of toxin tolerance across the
 immigrans-tripunctata radiation and emphasize the uniqueness of toxin
 tolerance in this adaptive radiation and the complexity of biochemical
 adaptations.
description: # Investigating the phylogenetic history of toxin tolerance in
 mushroom-feeding <i>Drosophila</i>
 [https://doi.org/10.5061/dryad.hdr7sqvq2](https://doi.org/10.5061/dryad.hdr7sqvq2) This dataset contains all of the raw fastq files from the RNA sequencing done. The species that were sequenced are listed in Table 1 of the accompanying manuscript. These fastq files were filtered as described in the methods of the paper and assembled into transcriptomes for downstream phylogenetic analyses. ## Description of the data and file structure For each species, there are two files with either "\_1.fq.gz" or "\_2.fq.gz" following the species name. These are the corresponding forward and reverse reads for the paired-end RNA sequencing that was performed. These files have abbreviated names for each species which are listed below: | Species | Abbreviation | | ------- | ------------ | | acutilabella | acutila | | albomicans | albomic | | angularis | angular | | arawakana | arawak | | bizonata | bizonat | | brachynephros | brachy | | cardinoides | c\_noides | | cardini | cardini | | deflecta | deflecta | | dunni | dunni | | falleni | falleni | | funebris | funebris | | guarani | guarani | | guttifera | guttifera | | immigrans | immigran | | macroptera | mac | | macrospina | macrosp | | multispina | multisp | | munda | mun | | nigrodunni | n\_dunni | | nigromaculata | n\_macul | | neotestacea | neotest | | occidentalis | occiden | | orientacea | orient | | pallidipennis | pallidi | | palustris | palus | | parthenogenetica | partheno | | phalerata | phalerat | | polymorpha | polymor | | putrida | putrida | | quinaria | quinaria | | recens | recens | | suboccidentalis | s\_occid | | subpalustris | s\_palus | | subquinaria (Coastal) | s\_quin\_C | | subquinaria (Inland) | s\_quin\_I | | similis | similis | | subbadia | subbadia | | sulfurigaster | sulfur | | tenebrosa | tenebro | | testacea | testac | | transversa | transver | | tripunctata | tripunc | ## Code/Software Code to perform the analyses are found at https://github.com/trm76056/phylogenetic-tree.