Anthony Snead

Functional Genomics

Understanding how genomic variation scales to phenotypic variation, on which natural selection acts, is a central theme in evolutionary biology. Using the northern two-lined salamander (Eurycea bislineata) and the spotted lanternfly (Lycorma delicatula), I am currently using whole genome sequencing along with physiological and morphometric data to explicitly link genetic variants with traits potentially under selection in urban landscapes. However, a full understanding of genome-phenome relationship requires interrogating the intermediate steps between genomic change and phenotypic changes (i.e., transcription & translation). Hence, I employ transcriptomic methods like RNAseq to understand how gene expression regulates phenotypic change. I have been particularly interested in plastic changes in gene expression driven by both genotypic and environmental variation. I have been exploring the GxE interaction both in relation to developmental temperature in the mangrove rivulus fish (Kryptolebias marmoratus) and paternal predator exposure in three-spined stickleback (Gasterosteus aculeatus) with plan to extend this to the spotted lanternfly.

Species Distribution Modeling

A species range is dictated by abiotic and biotic factors that either limit species survival and reproduction in a given environment or limit the ability of a species to reach a given area. I use a combination of environmental data, occurrence/count data, and statistical modeling to model the ecological niche of species and predict future distributions. Using the mangrove rivulus fish (Kryptolebias marmoratus), I demonstrated that they are unlikely to shift their range along side their foundation species (mangrove trees) leaving them trapped in fragmented habitats with limited protection (Snead et al. 2022). While I am currently applying this to the brain-eating amoeba (Naegleria fowleri) and brook salamanders (Eurycea spp.), I am also extending this work in a phylogenetic context to understand niche evolution and predict past changes in habitat suitability using paleoclimatic data.

Adaptation Genomics

While my functional genomics work attempts to link genetic and phenotypic variation, my work on adaptation genomics attempts to link functional genomic variation with environmental variation and ecological context. My adaptation genomics work and functional genomics work goes hand in hand. Currently, I use cities as natural replicated experiments to identify genes potentially related to adaptive phenotypes under selection within urban landscapes. I am using the northern two-lined salamander (Eurycea bislineata) and the spotted lanternfly (Lycorma delicatula) as distantly related systems to understand the repeatability of adaptation to urban landscape. To better contextualize genotype by environment associations, I am also assembling and annotating these genomes while collecting critical phenotypic data across differentiated populations. Through collaborations with the Garroway lab, I am also venturing into genomic forecasting with artic whales.

Landscape Genetics

While understanding adaptive evolution is critical to predicting if and how species will respond to environmental change, neutral evolutionary processes such as gene flow and genetic drift dictate both local genetic diversity and the spread of potentially adaptive alleles which could dictate future evolutionary responses. Using the mangrove rivulus fish (Kryptolebias marmoratus), I have demonstrated that asymmetric ocean currents are associated with both genetic differentiation and estimates of directional gene flow between mangrove patches (Snead et al. 2023). Using graph theory, I also found that patch level genotypic and genetic diversity are impacted primarily by the population’s centrality to the metapopulation rather than measure of fragmentation or habitat area (Snead et al. in prep). I am extending this work with forward genetic simulations to evaluate how landscape and oceanic factors impact rates of evolutionary and genetic rescue. Similarly, I am using the northern two-lined salamander (Eurycea bislineata) and the spotted lanternfly (Lycorma delicatula) as model systems to evaluate how demographic history, land use, and the environment drives spatial patterns of genetic diversity across urban landscapes.

Environmental DNA

Environmental DNA (eDNA) is a rapidly growing field focused on utilizing DNA fragments shed into the environment through excrement, mucus, epithelial cells or other mechanisms. In my eDNA work with the mangrove rivulus fish (Kryptolebias marmoratus), I am combining laboratory experiments to quantify the impact of environmental factors and density on the accumulation and degradation of DNA with field studies attempting to predict relative abundance from eDNA concentration. I am also developing assays for terrestrial applications to understand microhabitat associations in reptiles and insects using metabarcoding approaches.

Research