Tricia Rubi


Museum epigenomics

Ancient and historic DNA methods have opened up a wide range of new directions for research using paleontological specimens and natural history collections. Recently, researchers discovered that ancient and historic DNA retains patterns of in vivo cytosine methylation, an important modulator of gene expression. The implications of this discovery are compelling; these epigenetic markers may allow us to infer gene expression in past populations and observe how epigenetic effects change over time. Such studies may yield key insights into the role of epigenetic processes in adaptation and evolution.

In this project, I developed and tested methods for characterizing DNA methylation in museum specimens. I focused on traditionally-prepared bone tissues, which are among the oldest and most abundant specimen types found in museum collections. I used a combination of double digest restriction site-associated DNA sequencing (ddRAD-seq) and bisulfite sequencing to characterize genome-wide patterns in cytosine methylation in specimens dating back to 1940.

Epigenetic drivers of range expansion in Peromyscus

Colonist populations must rapidly adapt to novel environments, often under conditions of limited genetic diversity. In such populations, epigenetic mechanisms (processes that modulate gene expression) may facilitate rapid adaptation by generating phenotypic plasticity. In this research, I investigate the hypothesis that methylation-mediated plasticity acts as an adaptive buffer in colonist populations at the leading edge of a range expansion, focusing on the well-documented northward expansion of the white-footed mouse (Peromyscus leucopus). Using historic museum specimens collected over the past several decades, I am characterizing spatial and temporal patterns in DNA methylation over the course of a range expansion.

Complex signals and receiver behavior

Animal communication is often remarkably complex, incorporating many different behaviors, colors, patterns, sounds, odors, etc. My dissertation research investigated how signal complexity impacts the behavior of receivers – the individuals toward whom communication is directed. While signal complexity has been hypothesized to improve receiver performance, complexity can also pose cognitive challenges for receivers. In these experiments, I tested captive blue jays (Cyanocitta cristata) in lab-based, operant-style signaling games. I used this approach to characterize how attributes of the signaling system (signal reliability, multimodality, and environmental uncertainty) influence the signal following strategies adopted by receivers.

Sexual signaling in wolf spiders (Schizocosa) and predation risk

This project is a collaboration with Professors George Uetz (University of Cincinnati) and Dave Clark (Alma College). Wolf spider males perform elaborate courtship displays to woo potential mates. While these complex displays function to catch the attention of females, they are also exploited by a diverse suite of predators. This communication network shapes signal design through competing selective pressures. In this experiment, we used tools from signal detection theory to quantitatively describe eavesdropping on courting males spiders by avian predators (blue jays – Cyanocitta cristata).

Photo credits: P. leucopus – Charles Homler, C. cristata – Tricia Rubi, S. vulgaris – Virginia Heinen