Reverse evolution and gene expression studies on populations of drosophila melanogaster selected for rapid pre-adult development and early reproduction

Abstract

The fruit fly Drosophila melanogaster has been used in studies of genetics since the early 1900s, and is a powerful model system for both experimental evolution studies based on laboratory selection and studies focussing on the genetic control of developmental processes. It is, thus, an ideal system with which to address questions pertaining to the developmental and molecular biological underpinnings of adaptive evolutionary change in life-history related traits, an approach often termed developmental evolutionary biology. Laboratory selection experiments also provide an opportunity to address the reversibility, or lack thereof, of microevolutionary trajectories. In this thesis, I present results from two lines of investigation I carried out on a set of replicate D. melanogaster populations subjected to selection for rapid preadult development and early reproduction for over 250 generations. One one hand, I studied the evolutionary trajectories of several life-history related traits in these populations when subjected to 54 generations of reverse selection. In a separate set of experiments, I examined the expression levels of certain developmentally important genes in specific life-stages or tissues, as well as genome-wide expression levels in larvae, pupae and young adults of the selected populations and their ancestral controls. When I started my work, the four replicate selected populations of D. melanogaster (FEJ1-4) had already undergone 250 generations of selection for faster pre-adult development and early reproduction, and had diverged substantially for a variety of traits from the four matched ancestral control populations (JB1-4) that were maintained on a 21 day discrete generation cycle with no conscious selection on development time and early reproduction. Briefly, relative to the JBs, the FEJs showed reductions in the duration of all pre-adult life-stages, larval survivorship, body size and ix dry weight, lipid and glycogen content, adult lifespan and starvation and dessication resistance, and early life as well as lifetime fecundity. The FEJs also showed significantly reduced larval feeding rate and growth rate, foraging path length, digging propensity, pupation height and urea tolerance. Relative to the JBs, the FEJs had higher fecundity per unit dry weight early in life and took a longer time from eclosion to first mating. The reversibility of evolution has been debated extensively but rarely studied empirically except for a couple of studies on D. melanogaster and E. coli by M. R. Rose and R. E. Lenski, and colleagues, respectively. The reversibility of evolved phenotypes depends on different factors that could have changed during the course of forward selection, such as the availability of genetic variation, complexity and pattern of epistatic interactions, and accumulation of mutations. I derived four populations (RF1-4) from the FEJs, returned them to the ancestral JB maintenance regime and studied the trajectories of several traits over 54 generations of reverse selection. I found that larval and egg-to-adult survivorship, egg duration and early-life and middle-life fecundity converged back to ancestral control levels, whereas larval, pupal and egg-toadult duration and dry weight at eclosion did not converge completely. During the terminal few assays of the RFs, the correspondence between development time and dry weight at eclosion was parallel to that seen in the first 20 generations or so of forward selection in the FEJs, suggesting that despite incomplete convergence, the joint trajectory of these traits was similar under both forward and reverse selection. I also observed that the response to reverse selection with respect to durations of different pre-adult life stages was similar: the response was slow in the beginning up to generation 5 of reverse selection and hastened up thereafter and was fast till generation x 25, and after that again slowed down. My observations on development time and dry weight at eclosion are consistent with those of M. R. Rose and colleagues who used flies from the same ancestry and subjected them to selection for rapid development in much the same way as us. However, in their study, fecundity did not converge back to ancestral levels, and this difference in our results is probably due to the “early reproduction” part of the selection protocol being very different between the two sets of studies. Overall, the degree and mode of convergence I observed for the traits studied suggests (a) no erosion of genetic variation for these traits over 250 generations of forward selection in the FEJs, and (b) that it is unlikely that novel patterns of epistasis or new mutations have accumulated in the FEJs over the course of forward selection. My results also suggest that the broad contours of reverse evolution trajectories may be quite repeatable across studies if the past selection history and starting genetic material have been similar. Regulating gene expression is a key step by which an organism activates the information encoded in its genome to effect developmental changes, and differences in this regulation can cascade through development resulting in different morphological or physiological character states. Keeping this in view, I studied the gene expression through different methods in FEJs in comparison to the JB controls. Drosophila neuropeptide F (dnpf) is a homolog of mammalian NPY gene which is involved in food/foraging-related behaviors in mammals. dnpf is expressed in the central nervous system of Drosophila and plays a major role in the maintenance of foraging behavior. Its expression is high at foraging stage (early third instar) and low in the wandering stage (late third instar) in wild type larvae, and dnpf downregulation has been shown to act as a switch between foraging and pupation behavior in Drosophila. In a gene xi expression study done through semi-quantitative RT-PCR method, I found that dnpf expression in JBs was as expected (i.e. high at early third instar and low at late third instar), whereas dnpf expression in FEJs was low right from early third instar larva and it did not change till late third instar. This change in temporal pattern of dnpf expression could be an important causal factor underlying the huge reduction in larval third instar duration observed in the FEJs. Precise spatial and temporal expression of genes is important for proper pattern formation during development. In FEJs, some leg and wing malformations had been observed from about the 100th generation of selection. Therefore, to check if there was any change in the expression pattern of developmentally important proteins, I studied the expression patterns of some such proteins in the embryos as well as in the wing discs of third instar larvae by antibody staining technique. I observed no significant difference in the spatial expression pattern of these proteins in FEJs compared to their JB counterparts, suggesting that the expression patterns of these developmentally important proteins have not changed in FEJs over the course of selection. I also examined cell number and cell size in FEJs relative to the to JBs by staining wing discs of third instar larvae with antibody against the protein Armadillo, whereby one can mark the cell borders, count the cells and estimate their sizes. Using this technique, I found that FEJ wing discs had less number of bigger cells whereas JBs had more number of smaller cells. The reason for this is not clear at this time, but it may be that the FEJs have evolved a reduction in the number of cell divisions as part of a strategy to conserve energy. xii I further subjected one replicate population each of the FEJs and JBs to microarray analysis to examine differences in genome-wide patterns of gene expression between selected and control larvae, pupae and young adult males and females. I found that expression level of a few hundred genes was changed in FEJs in different lifestages used for the analysis. These changes were in both the directions i.e, many genes were up-regulated and many were down-regulated in FEJs in comparison to JBs, and many genes were consistently differentially expressed in FEJs across all life-stages studied. Genes related to epigenetic control were up-regulated in all the stages studied suggesting that changes in expression of many genes are possibly mediated by epigenetic mechanisms in the FEJs. Further, gene ontology (GO) term enrichment analysis using DAVID online bioinformatics tool showed that among the up-regulated genes were many eclusters of genes related to translation, developmental processes, phagocytosis etc., all of which are related to development. The down-regulated genes were related to glutathione metabolism which consist genes such as glutathione-Stransferase which is involved in oxidative stress mechanism. FEJs are less resistant to different stresses compared to JBs. This could be because of the down-regulation of the genes involved in glutathione metabolism. Further, it was observed that the genes involved in the insulin signaling pathway are down-regulated and that of ecdysone action were up-regulated in the FEJs. The final body size of Drosophila is known to be greatly affected by an antagonistic interaction of insulin signaling and ecdysone action, and these results suggest that the faster development of FEJS, and their smaller body size, could be mediated by the evolution of higher basal levels of ecdysone and reduced levels of insulin signalling. Though preliminary in nature, the gene expression results indicate several avenues of further research that are likely to enhance our understanding xiii of the molecular genetic and developmental underpinnings of the rapid development phenotype in the FEJs.