Global distribution of Chytrid lineages
The amphibian chytrid fungus – Batrachochytrium dendrobatidis (Bd) – is one of the most devastating wildlife pathogens ever documented. 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. However, by using a new genotyping method for Bd (see research below) we can elucidate the historic relationship between the amphibian community and the pathogen. Our manuscript describing the global distribution of major Bd lineages was recently published in PNAS. By forming an opportunistic, collaborative network with amphibian biologists around the world we were able to genotype 222 new Bd samples collected from 24 different countries. Our study presents the discovery of a new divergent lineage of Bd and advances our understanding of the global distribution of this pathogen.
Find paper published in PNAS here.
Media stories about this research published in Berkeley News, Mongabay, Daily Nexus.
global Bd phylogeny
Genomics of near extinction and persistence
In Panamá, two closely related harlequin frog species (Atelopus varius, Atelopus zeteki) are threatened with extinction due to Batrachochytrium dendrobatidis (Bd). We sequenced 186 Atelopus tissues collected before and after the Bd outbreak in Panamá using a custom exome capture assay and found an overall decrease in genetic diversity. We uncovered a set of disease-related candidate genes that warrant further study and found preliminary evidence of admixture in the largest contemporary A. varius population, suggesting the potential for genetic rescue. We propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the population level.
Find paper published in Global Change Biology here.
Atelopus varius juvenile
New methods for genotyping Chytrid
The most common non-invasive method of 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. We developed a custom Bd genotyping assay that uses microfluidic PCR technology to amplify many carefully-selected regions of the Bd genome. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole genome data. We are currently working on implementing this new method across scales and expanding the number of target loci.
Paper describing the method published in Molecular Ecology Resources HERE.
Paper describing one unusual implementation of the method published in PLOS ONE HERE.
swabbing a glass frog