title: Dynamics of Dark-Fly Genome Under Environmental Selections.
abstract: Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize "Dark-fly", a Drosophila melanogaster line maintained in constant dark conditions for more than 60 years. Our previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. We found here that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination we designed an experiment for genome reselection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. We thereby detected condition-dependent selections toward approximately 6% of the genome. In addition, we observed the time-course trajectory of SNP frequency in the mixed populations through generations 0, 22, and 49, which resulted in notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
authors.forename: Minako
authors.initials: M
authors.lastname: Izutsu
authors.affiliation: Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan Department of Genetics, Graduate University for Advanced Studies, Mishima 411-8540, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan nfuse@gcoe.biol.sci.kyoto-u.ac.jp.
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Fuse
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics*; D004777:Environment; D005787:Gene Frequency; D059647:Gene-Environment Interaction; D056726:Genetic Association Studies; D049750:Genome, Insect; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D008126:Lod Score; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Drosophila; environmental adaptation; experimental evolution; genome-wide analysis; reselection experiment