Research

I use genomic tools to understand how species persist in a changing world, investigating the role that disease plays in shaping ecological communities, past and present. My work is centered around the pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), which has caused catastrophic amphibian declines around the world. Using Bd as a model system, I design and apply new molecular tools for uncovering historic disease dynamics to better predict future risks to wildlife populations. I prioritize collaboration, innovation, and reflexivity, carefully considering the larger ethical and political context in which I conduct my research. My research also provides immense opportunity for student-led research using field, lab, and experimental approaches.

Google Scholar Profile

1. Searching host genomes for signatures of rapid evolution in the face of disease

Resilience in wildlife affected by disease provides a natural experiment to uncover underlying mechanisms and predict future vulnerabilities in our changing world. There are a growing number of resilient amphibian species that persist despite past declines and ongoing Bd exposure. By leveraging the shared selective environments and subsequent bottlenecks experienced by different host species, I seek to uncover the genomic signatures of resilience and address key questions in conservation and global change biology.

Research Accomplishments:

Used whole exome sequencing to uncover unusual outbreeding in the largest remaining highland population and create a list of candidate genes under selection.

Paper published in Global Change Biology.

Revealed genes under selection in exome sequences of persisting populations of Mountain Yellow-Legged Frogs.

Paper in prep.

Synthesized insights gained from genomic studies of amphibian resilience (and reflected on resilience in academia).

Paper published in Integrative and Comparative Biology

2. Developing new molecular methods to reveal historical and contemporary disease dynamics

Disease outcomes are dependent on the complex interaction between hosts, pathogens, and their shared environment. Understanding the role that each of these factors plays in determining disease outcomes is a central question in disease ecology. Bd is present in almost all amphibian communities but does not always cause deadly disease outbreaks. One key factor influencing disease outcomes in amphibians is the Bd variant or variants that may be present in a population. The introduction of new disease variants into naïve populations can pose significant risks to wildlife. Therefore, tracking Bd variants across time and space is critical to understanding historical disease dynamics and identifying future risks.

Research Accomplishments:

Developed a custom Bd genotyping assay that uses microfluidic PCR to sequence 200 phylogenetically informative regions of the Bd genome.

Paper published in Molecular Ecology Resources.

Leveraged a global collaborative network to sequence archived skin swabs, identify a new, divergent Bd variant, and track the global spread of the hypervirulent Bd-GPL lineage.

Paper published in PNAS.

Revealed Bd genetic patterns consistent with a wave-like outbreak in Panama and a more complex outbreak pattern in the Sierra Nevada.

Paper published in Proc Roy Soc B

3. Experimental approaches to understanding host/pathogen evolutionary processes

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While field-based studies are important for informing management and understanding the ecological context of evolutionary processes, laboratory-based experimental approaches have tremendous power to reveal precise evolutionary mechanisms underlying larger processes. I have recently broadened my training and emerged as an experienced experimental biologist to complement my suite of field-based research projects. My current postdoc, focused on studying plant pathogens (Aspergillus sp.), has prepared me to implement a vigorous experimental research program as I start my own lab studying fungal pathogens of animals. Working with the USDA I have completed multiple experiments studying the transcriptomics of mycotoxin degradation and competition dynamics between different Aspergillus isolates and published whole genome sequences of new Aspergillus species. Combining insights gained working with Aspergillus with my previous experience working with Bd in the lab (Byrne et al. 2018, PLOS One) I will experimentally study the competitive dynamics in Bd to uncover how deadly, hybrid lineages arise in this system. This work can help reveal the origin of the global panzootic lineage of Bd and reveal the mechanism of host/pathogen co-evolutionary dynamics evidenced by molecular data (Byrne et al. 2022, PLOS One).

Research Accomplishments:

Revisited a discarded lab experiment to reveal new insights and offer best practices for working with Bd in the lab.

Paper published in PLOS One.

Published new whole genome sequences for Aspergillus toxicus and Aspergillus texensis.

Paper in review at Microbiology Resource Announcements.

Completed transcriptomic study of aflatoxin degredation by Aspergillus flavus.

Paper in prep.

Future Directions:

Applying new sequencing technologies to look at Bd genomes back in time and at high resolution in contemporary systems.
Compete Bd-GPL lineages against each other to reveal the mechanisms of host-genotype associations.
Whole genome Bd sequencing (see Voyles et al. 2018, Science) to investigate how host-pathogen specificity evolves using field and lab experiments.
Expanding our understanding of the genomics of amphibian resilience by sequencing more species from around the world as a part of the RIBBiTR team.
Integrating research goals and methods into undergraduate courses.