Things change. This is a universal truth for all living things. Despite that, we humans try to impede the relentless force of change whenever we can. But in nature, organisms have to “roll with the punches.”
One of the most successful adaptive strategies that have evolved over the course of natural history in the response to changing biotic and abiotic factors across development is the complex life cycle. Simply put, complex life cycles are those that have distinct life history phases that differ morphologically, behaviorally, and physiologically. Probably one of the most well known examples is that of the butterfly where the caterpillar becomes a beautiful butterfly, but there are many, many more examples. In fact, the majority of multicellular animals undergo complex life cycles, regardless if we are tallying organisms, species, or phyla (Moran, 1994). This may come to a shock to us vertebrates as many of us do not have complex life cycles.
In humans, we do change significantly over our lifetimes. Morphologically, we get larger, become more proportional, and gain physically strength as our muscles grow. Of course, we also change in other ways, both behaviorally and physiologically. But our overall body plan and organs remain the same and function in similar ways. From these facts, it is acceptable to make the assumption that the genes that control certain traits when we are young are, for the most part, the same genes that control those same traits when get older. However, we can’t make the same assumption in organism that change so drastically over their life cycles.
It is easily apparent to even the unskilled observer that larvae and adults of most species look and behave very differently – this is usually due to the process of metamorphosis. For example, in holometabolous insects, that is, insects that go through a pupal phase, the overall body plan is reorganized and reconstructed during pupal metamorphosis. Butterflies are an example of these types of insects. It is theorized that metamorphosis evolved for a number of reasons. The first is that it limits competition between each life stage, allowing them to eat different things and live in different environments so that they do not take resources away from the other life stage. Another is that metamorphosis allows each life stage to specialize in different things (i.e. feeding for larvae and dispersal and mating for adults). These theories beg the question: what occurs at the genomic level during these drastic changes? And do the same genes that control a trait in larvae also control that same trait in adults?
We know that the genome does not edit itself over development. In other words, the A’s, C’s, G’s, and T’s largely remain where they are supposed to in most cells. However, the way the genome is expressed could change. There could be changes in the way genes are expressed via shifts in DNA methylation, and alterations to transcription factors and regulatory regions. Also, natural selection could act on different parts of the genome at certain developmental periods. In order to explore this possibility further, I use isogenic lines of Drosophila melanogaster (the common vinegar fly) from a collection known as the Drosophila Genetic Reference Panel, or the DGRP. Because these lines are isogenic (all individuals of a line have the same genetic makeup), and have their genomes sequenced, I can pinpoint what genes are associated with a trait in either life stage. I do this with a process known as Genome-Wide Association (GWA) mapping, which associations certain SNPs (alleles) that segregate within the DGRP population to some trait value that we are studying. In other words, it allows me to determine what alleles either confer high trait values or low trait values in my flies. Then I determine what genes those SNPs are located in, using genomic data available, to identify candidate loci for further study. I also use next-gen sequencing technology, specifically RNA-seq, to determine if changes in gene expression also occur in response to some stress across development.
The trait that I study is thermal hardiness, or the ability to maintain fitness despite acute exposure to temperature extremes. This is essentially the organisms ability to remain able to conduct normal bodily functions and behaviors despite a stressful environmental temperature. I study this because it is something that most organisms experience in most climates across the globe. Organisms usually have to deal with extreme cold, extreme heat or both at some point during the year and/or their life time. Moreover, it is directly related to fitness. If an organism cannot handle harsh temperatures, it won’t be able to ultimately reproduce. Since larvae and adults of Drosophila melanogaster used in this study are from a temperate climate in North Carolina, it is conceivable that ample amounts of genetic variation exists for thermal hardiness in the DGRP. Also, larvae and adults of D. melanogaster are subject to unique thermal habitats, making the system an excellent crucible for exploring the potential of genetic independence in thermal strategy across development.
My first chapter of my Ph.D. dissertation, published in the scientific literature as “Genetic Decoupling of Thermal Hardiness across Metamorphosis in Drosophila melanogaster” reports our findings that thermal hardiness, specifically cold hardiness, is decoupled across the metamorphic boundary. On average, their is no relationship between a larvae’s thermal hardiness and an adults, within isogenic lines. In other words, one cannot accurately predict the thermal hardiness of a larvae from the value of an adults and vice-versa. Also, using GWA, we found that the vast majority of SNPs found to have a high inclusion probability (statistical association) with the thermal hardiness of one life stage did not in the other. This provides evidence that the genetic architectures for thermal hardiness in larvae and adults are distinct. Evolutionarily, these findings provide evidence that each life stage can respond to natural selection independently, achieving their own fitness peaks without affecting the other life stage.
These findings have more broad-reaching implications as both significant crop pests and medically-relevant insects (i.e. mosquitoes) undergo complex life cycles. The way each life stage responds to thermal shifts in temperatures could dictate their global distributions. Therefore, accurate population modeling should take into account that each life stage could respond to climate differently.
I am currently in the process of finished two more chapters which are in some way follow-ups to this study. The first explores how developmental acclimation may affect the lack of correlation we see between life stages. Also, I am interested to see if a similar relationship exists for heat hardiness.
The third chapter explores gene expression between larvae and adults of lines that expressed the most drastic shifts in hardiness across metamorphosis. There are two main questions I aim to answer with this study: Do adults and larvae employ similar or different gene expression pathways to achieve thermal hardiness and what are the differences in gene expression pathways between flies with high thermal hardiness and low thermal hardiness within life stages?
Other Projects and Previous Research
I have also worked on ovarian development and reproductive arrest in an invasive fruit pest to North America and Europe known as Drosophila suzukii. This is not my first project with D. suzukii as I also worked on it during my masters looking at levels of genetic variation in the northeastern U.S. However, this work, a collaborative work with Elizabeth Everman, Ph.D., investigates how harsh cold temperature affect ovarian development in these flies at different points of development. Our findings show that, at least in the midwest, D. suzukii ovarian development responds to both low temperature and short photoperiod, indicated that some form of reproductive development exists in the species. Additionally, we also provide evidence that D. suzukii males and females have large capacity for short-term acclimation through Rapid Cold Hardening (RCH), which was not observed by researchers in more northern latitudes. Taken together, these results provide evidence that this invasive pest is able to adapt to fluctuating climates despite probable genetic bottlenecks incurred during its invasions of North America and Europe.
I am also passionate about cataloging genetic variation in natural populations over time. For my master’s thesis, I sequenced a number of microsatellite loci in wild populations of Drosophila simulans in Philadelphia and Lower Merion, Pennsylvania over two years (2011 – 2012).
Using pairwise tests of genic differentiation, I discovered significantly different allelic distributions at a number of loci with most significant results resulting in pairwise comparisons with dates at the end of the 2011 collection season and the beginning of the 2012 collection season. In addition, there were significant deviations from Hardy-Weinberg Equilibrium at a number of loci on several collection dates with most occurring at the end or beginning of a collection season. Finally, observed heterozygosity was lowest, on average, at the end of the 2011 collection season. Taken together, these results indicate a population bottleneck and reductions in population size and genetic variation at the end of a collection season followed by a rebound of the population, genetically distinct at several loci, the following year. It is unclear whether this was due to neutral processes, selection, migration, or a combination of all three forces. It would be interesting to perform a more detailed study in the future.