Research

I am an evolutionary biologist/ecologist working in Dr. Laura Reed's Lab who is interested in the evolution of novel biochemical adaptations, particularly when the adaptation is costly under some conditions. With my research, I aim to characterize such adaptations using genomic, transcriptomic, and metabolomic tools and also examine the evolution of these traits in a phylogenetic framework. Below are some of the projects I'm currently working on.

Cyclopeptide Tolerance in mushroom-feeding Drosophila

Drosophila flies exhibit a utilize a wide variety of food resources that include sap, fruits, flowers, cacti, and mushrooms. The mushroom-feeding species are generalists on fleshy Basidomycota mushrooms, and these hosts are critical to all of the flies life stages. The mushroom-feeding species are among a very limited number of eukaryotes that can tolerate cyclopeptide toxins (including the deadly alpha-amanitin), which are found in some species of Amanita mushrooms. While the toxic mushrooms make up only a small portion of their possible diet, all mushroom-feeding Drosophila that have been assayed can tolerate high concentrations of the toxins. My research is currently focused on elucidating our understanding of the novel biochemical adaptation that allows the flies to use toxic mushrooms as hosts.
Quantifying physiological mechanisms of toxin tolerance.

Cyclopeptide toxins act by binding to RNA polymerase II, which inhibits the production of messenger RNA and leads to cell death in most multi-cellular organisms. The physiological mechanism of toxin tolerance within mushroom-feeding Drosophila is poorly understood, but we do know the flies do not have mutations in their RNA polymerase II that would prevent the toxin from binding. To better characterize the physiological mechanism, we are using metabolomic and transcriptomic analyses of larvae after they are reared on diets with and without the toxin. We are analyzing the spectra generated by global NMR of two tolerant species (D. guttifera and D. recens) and one susceptible species (D. deflecta) to identify both the impact of the toxin on the larval metabolome and the manner in which the larvae metabolize it. In addition, we are comparing gene expression within D. guttifera and D. recens larvae after feeding on diets with and without toxin to identify genes that may contribute to toxin tolerance. We will expand both lines of inquiry to eight tolerant species and two or more susceptible species with our Dimensions of Biodiveristy Grant (DEB-1737869).
PLS of larval metabolomes
Results of NMR analysis: PLS comparing the spectra generated from analysis of larvae reared on diets with cyclopeptides.
Sequencing genomes to identify genetic signature of toxin tolerance.

Expanding on our characterization of the physiological mechanism of tolerance using transcriptomics and metabolomics, we are sequencing the genomes of seven species (toxin tolerant and susceptible). The evolution of novel adaptations including cyclopeptide tolerance can produce changes in the genomes of species in which they occur. These changes can include gene duplications and/or changes in the rates of molecular evolution.  We are sequencing the genomes of these species using a combination of long reads (Oxford Nanopore GridION) and short reads (Illumina HiSeq) and constructing a hybrid, de novo assembly for each species. We are getting ready to begin annotation of these assemblies using other Drosophila genomes and the RNAseq reads generated for each species. Once the genomes are annotated, we will examine them in a phylogenetic context to identify potential genomic signals of toxin tolerance, such as gene duplication events in detoxification gene families.
A plot comparing log transformed read length with average basecall Phred quality score for D. funebris GridION data.
A plot comparing plot comparing the log transformed read length with average basecall Phred quality score for the D. funebris sequence data generated by the GridION.
Examining intraspecific variation in toxin tolerance.

Within species, the genetic basis of novel adaptations can be a single gene or multiple genes. When intraspecific variation is observed within a population for a trait of interest this indicates a polygenic basis for the adaptation. We have examined variation of cyclopeptide tolerance in a population of D. tripunctata that occurs on the campus of the University of Alabama. When we reared larvae of nine, inbred D. tripunctata strains on a diet containing natural concentrations of alpha-amanitin, we found significant genetic variation in survival to pupation. These same strains also showed a variety of responses when two families of detoxification genes were inhibited, but did not lose tolerance. Examining differential gene expression in a line with higher fitness on a diet with a natural toxin concentration has produced a very exciting hypothesis of how the larvae detoxify the cyclopeptide alpha-amanitin (Stay tuned for the upcoming publication!). We will shortly begin selection experiments coupled with whole-genome sequencing of pooled population samples to identify alleles that contribute to cyclopeptide tolerance in D. tripunctata and three other mushroom-feeding species. We will also be sequencing the genome of four tolerant and one susceptible species to identify potential gene duplication events or changes in rates of molecular evolution that are unique to tolerant species.
Female Drosophila tripunctata
Drosophila tripunctata. Photo by Thomas Werner from the Drosophilids of the Midwest and Northeast 2017.
Characterizing the evolution of feeding behavior and toxin tolerance.

To examine the evolution of mushroom-feeding and cyclopeptide tolerance in Drosophila, a well resolved phylogeny is needed. Our current understanding of the evolutionary relationships among these flies. Previous studies were unable to resolve the relationships among species groups or focused on a single species group of mushroom-feeding flies. We reconstructed a phylogenetic hypothesis of the relationships within the quinaria species group based on 27 species and 40 protein-coding loci (Scott Chialvo et al. 2019). Our resulting tree supported the monophyly of the testacea but not the quinaria ​species group. Neither cyclopeptide tolerance nor responses to gene inhibition assays predicted the relationship recovered, and it appears there have been multiple losses/gains of cyclopepetide tolerance and mushroom feeding. With our recent award, we have begun expanding our taxon sampling to include 16 additional species from the already sampled groups and other closely related species groups. For this upcoming analysis, we will use transcriptomic data to reconstruct a phylogenetic hypothesis of the group and examine the evolution of cyclopeptide tolerance.
Phylogenetic tree illustrating evolution of feeding behavior
Reconstruction of feeding behavior in quinaria and testace groups (Scott Chialvo et al. 2019).