Research Interests

***Undergraduates in Research***

I believe research should be understandable and attainable to all those who wish to participate. I therefore promote open access publication and collaborative work. I view students at all levels as indispensable to research. I attempt to incorporate undergraduates from diverse backgrounds in active roles in my projects. Providing opportunities to learn valuable skills, participate in data collection, analysis, and dissemination through peer reviewed publication and professional presentations. Let me know if you are interested in working with me on a project!

Genome Size Evolution Among Species

The amount of DNA in organisms varies widely from species to species (Up to 7,000 fold in animals!). However, more DNA does not make an organism more complex: Some grasshoppers have 6X the genome size as humans! Most of this variation in DNA content is actually due to highly repetitive non-coding regions and other things like transposable elements. So why does so much variation exists? How does this variation come to be? Are there adaptive patterns to any of this change? Are there consistent patterns of genome size change that exist between organisms? I use new and old genome size estimates in conjunction with comparative phylogenetic approaches to investigate these patterns of genome size change across a range of organisms. While most of my work has been in Drosophila species, I have been part of collaborative efforts to investigate these patterns of change across multiple families of beetles and other insects. I am working to sequence individuals that have unique patterns of change in order to investigate which mechanisms are driving these significant changes in size.
Figure: Genome size for all available insect data from local databases and plotted in color on an insect phylogeny. Darker colors represent smaller genomes

Genome Size Evolution Within Species

While genome size has been known to vary from species to species, genome size, like any other trait, can vary within a species. In fact, there was found to be about 30,000,000 more base pairs of DNA in the Drosophila DGRP with the largest genomes than the ones with the smallest! This within species variation has been shown to be correlated to other phenotypes, such as reproductive fitness, body size, and development time. I have utilized long running phenotype selection lines to evaluate genome size change in relatively short periods of time (Hjelmen et al 2020). I am working to investigate the evolutionary advantages (or disadvantages) to having more or less DNA. Does certain types of DNA assist in adaptation to new environments? What amount of variation in genome size is expected within a species? What contributes to this variation? And at what point does it lead to divergence/speciation?

scatterplot of drosophila genome size with cell count
Figure: Drosophila genome size and relative cell count ratio plotted for D. melanogaster lines selected for large or small body size. While genome size is not significantly different between large and smalle body sizes, there is a large difference in genome size variation between these body sizes (from Hjelmen et al. 2020)

Underreplication and Heterochromatin Content of the Genome

Underreplication is a fascinating phenomenon by which DNA replication is stalled before replicating the late replicating heterochromatin. This phenomenon has been noted for decades in the polytene salivary glands of Drosophila, but only recently was documented in the thoracic tissue of D. melanogaster. Recently, we showed (with the help of some expert dissection skills from an undergrad!) what thoracic tissues underreplication is occuring in (Johnston et al 2020). I also recently demonstrated underreplication in 132 species within the Drosophila genus (Hjelmen et al. 2020)! We know variation in genome size is largely due to repetetive and noncoding DNA (largely heterochromatic), and we findthat more of this "unreplicated" DNA occurs in species with larger genomes. We therefore use Underreplication to study the dynamics of Heterochromatin and Euchromatin change throughout time. We find dramatically different patterns of change between types of chromatin. Is this dependent on what group of species we look at? What is occuring in species that have significantly more heterochromatin? Why does this partial replication occur in thoracic tissue? And why in only Drosophila? Does it have something to due with adaptation to environments? What is the physiological benefit of more DNA in the thorax? I hope to answer these questions through long read sequencing, transcriptomics, and studies of phenotypes!

histogram of thoracic underreplication
Figure: Measurement of D. kepuluana thoracic nuclei with propidium iodide on a flow cytomter. Flow cytometric analysis demonstrates three peaks in thoraces, rather than the two peaks we see in neural nuclei. The peaks include the usual 2C and 4C peaks, but also includes a peak in which replication has stalled partway. For more information on underreplication, see Hjelmen et al. 2020 and Johnston et al. 2020.

Sex Chromosome Evolution

Sex chromosomes are often the first thing to which biologists attribute differences between sexes. While most of the DNA content in a genome is on the autosomes and therefore does not differ between the sexes, differences between sex chromosomes lead to highly differentiated gene expression and phenotypes between the sexes. In the an XY sex system, as the sex chromosomes differentiate, the Y chromosome becomes more and more sparse in the case of gene content and becomes highly heterochromatized and compacted. We have found that in many cases, not only does gene content decrease, but also the physical amount of DNA on the Y chromosome decreases (Hjelmen et al 2018, Hjelmen et al 2019). Hypothetically, the Y chromosome gets smaller and smaller throughout time, until it becomes so small it can be lost. Here we may see sex chromosome turnover and introduction of Neo-sex systems. So, how big can the differences between sexes become? How often are males in XY systems larger than females? Are those with larger male genomes indicative of neo-Sex chromosomes? Beyond just looking at physical size, I am interested in seeing what content is found on neo-sex chromosomes and investigating whether or not specific chromosomes are more likely to be selected to become sex chromosomes. To do this, I am sequencing males and females from species which I have identified as having prospective sex chromosome turnover events.

sex difference plot
Figure: Schematic of proposed sex chromosome degradation/evolution. Early in sex chromosome differentiation, it is expected increased transposable element activity will actually increase the size of the Y chromosome. Subsequent deletion bias will then reduce the size of the Y chromosome. This reduction may stall and results in equal sex chromosome sizes, continue until the Y chromosome disappears, or a neo-sex event may reset the sex chromosome pathway.