At northern latitudes, the most robust cue for assessing the onset of winter is the shortening of day lengths. Many species use day length as a cue to increase their cold tolerance and/or enter into diapause, but little is known about changes in gene expression that occur under different day lengths. We investigate the gene expression changes associated with differences in light/dark cycles in Drosophila montana, a northerly distributed species with a strong adult photoperiodic reproductive diapause. To examine gene expression changes induced by light both prior to and during diapause, we used both nondiapausing and diapausing flies. We found that the majority of genes that are differentially expressed between different day lengths in nondiapausing and diapausing flies differ. However, the biological processes involved were broadly similar. These included neuron development and metabolism, which are largely consistent with an increase in cold tolerance previously observed to occur in these flies. We also found that many genes associated with reproduction change in expression level between different day lengths, suggesting that D. montana use changes in day length to cue changes in reproduction both before and after entering into diapause. Finally, we also identified several interesting candidate genes for light-induced changes including Lsp2, para, and Ih.
