The combination of experimental evolution with high-throughput sequencing of pooled individuals—i.e., evolve and resequence (E&R)—is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ∼60 generations in a novel hot environment for D. melanogaster and D. simulans. For D. simulans, the regions carrying putatively selected loci were far more distinct, and thus harbored fewer false positives, than those in D. melanogaster. We propose that species without segregating inversions and higher recombination rates, such as D. simulans, are better suited for E&R studies that aim to characterize the genetic variants underlying the adaptive response.
Dsim_3reps_F0F60_majorChr_downsampled
Sync file of allele coverage for Drosophila simulans SNPs in major chromosome arms (X, 2L, 2R, 3L, 3R). Columns in this sync file correspond to chromosome, position, base, Dsim_A_F0, Dsim_B_F0, Dsim_C_F0, Dsim_A_F60_Hot, Dsim_B_F60_Hot, Dsim_C_F60_Hot. Nomenclature of the samples is as follows: e.g. species_replicate_generation_selection regime. Species: Dsim (Drosophila simulans), replicate: letters (A-Z), generation: F#, # indicating the number of generations, and selection regime: Hot. Format specification of sync file is described in Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
Bioinformatics 2011;27:3435-3436. See main publication for additional information about data processing, SNP calling and filtering.
Dsim_baseF60_rep1-3-5_bam.sorted.rmdup.filter.mpileup.Q20.polymorphic_repeatIndelmaskedmincov5_Ytranslocremoved_majorChr_downsampled.sync
Dmel_3reps_F0F59_majorChr_downsampled
Sync file of allele coverage for Drosophila melanogaster SNPs in major chromosome arms (X, 2L, 2R, 3L, 3R). Columns in this sync file correspond to chromosome, position, base, Dmel _A_F0, Dmel _B_F0, Dmel _C_F0, Dmel _A_F59_Hot, Dmel _B_F59_Hot, Dmel _C_F59_Hot. Nomenclature of the samples is as follows: e.g. species_replicate_generation_selection regime. Species: Dmel (Drosophila melanogaster), replicate: letters (A-Z), generation: F#, # indicating the number of generations, and selection regime: Hot. Format specification of sync file is described in Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).
Bioinformatics 2011;27:3435-3436. See main publication for additional information about data processing, SNP calling and filtering.
Dmel_base_F59_reps_1_4_5_downsampled.mpileup.Q20.polymorphic_majorChr.sync