57 year experiment, Drosophila kept in dark for 1400 generations, many evolutionary changes (record longest postdoc!)
Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment
Minako Izutsu1,2#, Jun Zhou3, Yuzo Sugiyama1, Osamu Nishimura1, Tomoyuki Aizu4, Atsushi Toyoda4, Asao Fujiyama4, Kiyokazu Agata1,2, Naoyuki Fuse1#*
1 Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan, 2 Laboratory for Molecular Developmental Biology, Graduate School of Science, Kyoto University, Kyoto, Japan, 3 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America, 4 Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.
Amazing experiment by Izutsu et al. where they kept flies in the dark for 57 years and then sequenced them. Goes a long way in explaining evolution of traits under certain conditions: think cave dwelling animals. Score one for evolution.