Genomic perspectives on the pathogenic chytrid fungus and persisting amphibian hosts

My dissertation research is focused on using molecular tools to advance amphibian conservation and better understand the drivers of amphibian declines. My work is centered around the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), which has been linked to catastrophic amphibian declines around the world. During my time as a PhD student I developed and implemented a new method to genotype Bd from noninvasive swab samples (Chapters 1 and 2). I also used genomic tools to understand how one critically endangered amphibian species is recovering after a Bd outbreak in Panama (Chapter 3)./nFirst, I developed a new molecular method to genotype noninvasive Bd DNA samples. The most common non-invasive method for sampling Bd from natural populations is to swab amphibian skin. As a result, hundreds of thousands of swabs have been collected from amphibians around the world. However, Bd DNA collected via swabs is often low in quality and/or quantity. Working with a team in the Rosenblum lab at UC Berkeley, I developed a custom Bd genotyping assay that uses microfluidic PCR technology to amplify many carefully selected regions of the Bd genome. Here I show that this new assay has the power to accurately discriminate among the major Bd clades. Additionally, I show that this method can genotype swabs taken from preserved museum specimens, opening the possibility of retrospective Bd surveys to investigate historic pathogen dynamics./nNext, I used this new genotyping method to unveil cryptic diversity of Bd to reveal new threats for amphibians. Bd consists of distinct genetic lineages that vary in geographic extent and virulence. Most surveys for Bd report only the presence or absence of the pathogen, but some regions of the world have endemic Bd lineages and simply testing for Bd presence is not particularly informative. Using the new genotyping method for Bd described above, we can elucidate the historic relationship between amphibian communities and Bd and document recent lineage spread. By forming an opportunistic, collaborative network with amphibian biologists around the world I was able to genotype 222 new Bd samples collected from 24 different countries. This study presents the discovery of a new divergent lineage of Bd, highlights areas where divergent Bd lineages are coming into secondary contact and advances our understanding of the global distribution of this pathogen./nFinally, I used whole exome sequencing to understand mechanisms of persistence in the variable Harlequin frogs of Panama (Atelopus varius, Atelopus zeteki). The Panamanian golden frog (Atelopus varius) declined precipitously in the early 2000’s due to an outbreak of Bd in Panama. Once thought to be extirpated from Panama, A. varius populations have recently been rediscovered in multiple locations across their historic range. Using tissue samples collected from A. varius before and after the Bd outbreak in Panama, I sequenced whole exomes with the goal of describing potential genetic mechanisms of persistence. In my study I document the genetic diversity of contemporary populations in the wild and in captivity and search for genes under positive selection in wild, persistent populations. My research aims to inform conservation and captive management of these species as well as evaluate the potential for genetic rescue in imperiled amphibians.

Advisor: Rosenblum, Erica B