Seasonality of Genomic Variation in Drosophila melanogaster

Abstract

Local adaptation is of fundamental importance in evolutionary biology and understanding the genetic basis of adaptation to new environments has gained importance in recent years. One of the most common organisms for these studies is Drosophila melanogaster. As is well known, Drosophila melanogaster is a cosmopolitan species and is spread almost all around the world. Although its whole genome has been known for many years, this organism has started to be used more in adaptation studies with the development of new generation sequencing technology. Adaptation is the primary mechanism that allows organisms to survive in different environments. Spatial and temporal environmental variation can lead to different selective pressures on populations. The direction of selection by spatial and temporal alteration, and the mechanism behind rapid adaptation are poorly understood. Seasons are one of the important temporal effects on populations in temperate regions, and Drosophila may respond through rapid adaptation to temporal changes in the environment. For this purpose, we analyzed genomic variation of D. melanogaster to determine seasonal single nucleotide polymorphisms (SNPs) by using Pool-Seq next generation sequencing method to understand mechanism underlying rapid adaptation to seasonal changes in this organism. Our results suggest that seasons cause genomic variation in Drosophila melanogaster. Tajima’s D values were mostly negative for 2014 samples, but we did not see this pattern for other years. Majority of FST values, the differentiation between the samples from different timepoints of the year, were not high, but at some regions it was as high as 0.45, yet this was not consistent through years. We also calculated allele frequencies and we found 982,000 common SNPs in three year samples which have sharing common positions. Almost half of these SNPs were intronic, 9.4% were exonic, and 8.7% were in the intergenic regions. We found a total of 6516 structural variants such as insertions and deletions. Most of these SNPs were not seasonal however, approximately 3.5% (32,428) of them were seasonally significant. Approximately 72% of these SNPs were in protein coding regions. We also identify genes that contain seasonal SNPs such as couch potato (cpo), sickie, and Insulin-like receptor (InR) which are involved in crucial signaling pathways in Drosophila melanogaster. These results suggest that seasons in temperate regions create a selection pressure on Drosophila melanogaster populations and local populations respond to this pressure with rapid adaptation