DOI: 10.5061/dryad.w0vt4b8p2
title: Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

description: Background Insect pest control programs often use periods of insecticide
 treatment with intermittent breaks, to prevent fixing of mutations
 conferring insecticide resistance. Such mutations are typically costly in
 an insecticide free environment, and their frequency is determined by the
 balance between insecticide treatment and cost of resistance. Ace, a key
 gene in neuronal signaling, is a prominent target of many insecticides and
 across several species three amino acid replacements (I161V, G265A and
 F330Y) provide resistance against several insecticides. Because
 temperature disturbs neuronal signaling homeostasis, we reasoned that the
 cost of insecticide resistance could be modulated by ambient temperature.
 Results Experimental evolution of a natural Drosophila simulans population
 at hot and cold temperature regimes uncovered a surprisingly strong effect
 of ambient temperature. In the cold temperature regime, the resistance
 mutations were strongly counter selected (s= -0.055), but in a hot
 environment the fitness costs of resistance mutations were reduced by
 almost 50% (s=-0.031). We attribute this unexpected observation to the
 advantage of the reduced enzymatic activity of resistance mutations in hot
 environments. Conclusion We show that fitness costs of insecticide
 resistance genes are temperature-dependent, and suggest that duration of
 insecticide-free periods need to be adjusted for different climatic
 regions to reflect these costs. We suggest that such environment-dependent
 fitness effects may be more common than previously assumed and pose a
 major challenge for modeling climate change.
description: PHENOTYPIC ANALYSIS <strong>Fecundity_stats.R:
 </strong>Statistical analysis of the fecundity phenotypic
 assay 
 <strong>Insecticides_stats.R:</strong> Statistical analysis of
 the insecticide resistance phenotypic assay 
 <strong>Viability_stats.R:</strong> Statistical analysis of
 the viability phenotypic assay GENOMIC
 ANALYSIS 
 <strong>HaplotypeStructure.R: </strong>Analysis of the
 ancestral haplotypes (structure, resistance mutation status, marker SNPs,
 and diversity measurements); output = marker SNPs between haplotype class
 1, and 2 (n=166) 
 <strong>Pool-seq.R:</strong> Analysis of the experimental
 population in the hot and cold regime (raw allele frequency trajectories,
 resistance mutation trajectories, haplotype class frequency trajectories,
 selection coefficients (with poolSeq v0.3.2;
 https://github.com/popgenvienna)); output = replicate-specific haplotype
 class frequencies (1a, 1b, and 2) for hot, and cold regime
 AVAILABLE DATA 
 <strong>AF-DsimPort-ColdRegime-Ace.txt: </strong>allele
 frequencies of SNPs (+/- 200 kb around the Ace locus) in the experimental
 D.simulans Portugal populations evolving in the cold regime; frequency is
 polarised for the rising allele; used in Pool-seq.R 
 <strong>AF-DsimPort-HotRegime-Ace.txt:</strong> allele
 frequencies of SNPs (+/- 200 kb around the Ace locus) in the experimental
 D.simulans Portugal populations evolving in the hot regime; frequency is
 polarised for the rising allele; used in Pool-seq.R 
 <strong>Class-Markers.txt:</strong> output of
 HaplotypeStructure.R ; Chromosome/Postition/Allele information of the
 marker SNPs distinguishing class 1 from class 2 
 <strong>CMH-DsimPort-ColdRegime-Ace.txt:</strong> CMH test
 results (+/- 200 kb around the Ace locus) of generation 51 vs. generation
 0 of the experimental D.simulans Portugal populations evolving in the cold
 regime; used in Figure 4 
 <strong>CMH-DsimPort-HotRegime-Ace.txt: </strong>CMH test
 results (+/- 200 kb around the Ace locus) of generation 59 vs. generation
 0 of the experimental D.simulans Portugal populations evolving in the hot
 regime; used in Figure 4 
 <strong>dsimM252.1.1.exon_CDS_utr.clean.gtf:</strong> genome
 annotation D.simulans (M252 reference strain); used in
 HaplotypeStructure.R <strong>dsimPort*:
 </strong>SNP calls of the ancestral haplotypes; used in
 HaplotypeStructure.R 
 <strong>Fecundity.txt:</strong> raw Fecundity data
 
 <strong>HaploClasses-DsimPort-ColdRegime-Ace.txt:
 </strong>output of Pool-seq.R; haplotype class trajectories in the
 experimental D.simulans Portugal populations evolving in the cold
 regime 
 <strong>HaploClasses-DsimPort-HotRegime-Ace.txt:
 </strong>output of Pool-seq.R; haplotype class trajectories in the
 experimental D.simulans Portugal populations evolving in the hot
 regime 
 <strong>Malathion.txt: </strong>raw Insecticide resistance
 data, Malathion 
 <strong>Ne-DsimPort-ColdRegime.txt: </strong>used in
 Pool-seq.R; replicate-specific effective population size estimates between
 generation 0 and generation 51 for the experimental D.simulans populations
 evolving in the cold regime 
 <strong>Ne-DsimPort-HotRegime.txt: </strong>used in
 Pool-seq.R; replicate-specific effective population size estimates between
 generation 0 and generation 59 for the experimental D.simulans populations
 evolving in the hot regime <strong>Propoxur.txt:
 </strong>raw insecticide resistance data, Propoxur <strong>Viability.txt:
 </strong>raw Viability data