Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila
Data files
Nov 09, 2023 version files 149.36 GB
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acutila_1.fq.gz
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acutila_2.fq.gz
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albomic_1.fq.gz
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albomic_2.fq.gz
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angular_1.fq.gz
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angular_2.fq.gz
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arawak_1.fq.gz
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arawak_2.fq.gz
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bizonat_1.fq.gz
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bizonat_2.fq.gz
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brachy_1.fq.gz
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brachy_2.fq.gz
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c_noides_1.fq.gz
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c_noides_2.fq.gz
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cardini_1.fq.gz
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cardini_2.fq.gz
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deflecta_1.fq.gz
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deflecta_2.fq.gz
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dunni_1.fq.gz
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dunni_2.fq.gz
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falleni_1.fq.gz
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falleni_2.fq.gz
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funebris_1.fq.gz
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funebris_2.fq.gz
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guarani_1.fq.gz
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guarani_2.fq.gz
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guttifer_1.fq.gz
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guttifer_2.fq.gz
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immigran_1.fq.gz
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immigran_2.fq.gz
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mac_R1.fastq.gz
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mac_R2.fastq.gz
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macrosp_1.fq.gz
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macrosp_2.fq.gz
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multisp_1.fq.gz
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multisp_2.fq.gz
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mun_R1.fastq.gz
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mun_R2.fastq.gz
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n_dunni_1.fq.gz
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n_dunni_2.fq.gz
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n_macul_1.fq.gz
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n_macul_2.fq.gz
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neotest_1.fq.gz
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neotest_2.fq.gz
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occiden_1.fq.gz
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occiden_2.fq.gz
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orient_1.fq.gz
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orient_2.fq.gz
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pallidi_1.fq.gz
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pallidi_2.fq.gz
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palust_1.fq.gz
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palust_2.fq.gz
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partheno_1.fq.gz
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partheno_2.fq.gz
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phalerat_1.fq.gz
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phalerat_2.fq.gz
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polymor_1.fq.gz
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polymor_2.fq.gz
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putrida_1.fq.gz
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putrida_2.fq.gz
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quinaria_1.fq.gz
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quinaria_2.fq.gz
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README.md
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recens_1.fq.gz
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recens_2.fq.gz
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s_occid_1.fq.gz
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s_occid_2.fq.gz
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s_palus_1.fq.gz
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s_palus_2.fq.gz
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s_quin_C_1.fq.gz
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s_quin_C_2.fq.gz
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s_quin_I_1.fq.gz
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s_quin_I_2.fq.gz
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similis_1.fq.gz
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similis_2.fq.gz
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subbadia_1.fq.gz
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subbadia_2.fq.gz
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sulfur_1.fq.gz
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sulfur_2.fq.gz
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tenebro_1.fq.gz
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tenebro_2.fq.gz
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testac_1.fq.gz
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testac_2.fq.gz
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transver_1.fq.gz
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transver_2.fq.gz
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tripunc_1.fq.gz
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tripunc_2.fq.gz
Abstract
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.
README: Investigating the phylogenetic history of toxin tolerance in mushroom-feeding <i>Drosophila</i>
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 |
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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.