The Evolutionary History of Batrachochytrium dendrobatidis

EPA Grant Number: FP917107
Title: The Evolutionary History of Batrachochytrium dendrobatidis
Investigators: Richards-Hrdlicka, Kathryn
Institution: Yale University
EPA Project Officer: Lee, Sonja
Project Period: September 1, 2010 through August 31, 2013
Project Amount: $111,000
RFA: STAR Graduate Fellowships (2010) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Fellowship - Ecosystem Services: Aquatic Systems Ecology


Chytridiomycosis, an epidermal infection caused by the emerging infectious fungal pathogen Batrachochytrium dendrobatidis (Bd), is a major driver implicated in the worldwide decline of amphibian populations. I use next generation sequencing technology to identify new genetic markers in Bd and apply them in a series of population genetic analyses, some of which intend to uncover Bd’s global origin(s). I also apply similar techniques to describe how Bd has evolved through time in a focused region of the world, New England, by comparing genetic variation from contemporary and museum-preserved Bd DNA from within host (amphibian) tissues.


A new fungal pathogen, Batrachochytrium dendrobatidis (Bd), is partly responsible for the global decline of amphibian populations. I analyze the genetic variation of Bd on a global scale to address its geographic origins. I also apply similar techniques to describe how Bd has evolved in New England (NE), by comparing the genetic variation of contemporary to museum-preserved Bd DNA from within amphibian tissues. Results from my research will identify where Bd came from and how it evolves.


My dissertation research will be addressed in three Aims. For Aim #1 I will develop new molecular markers by sequencing 21 new Bd isolates on the next generation sequencing platform, Illumina. The genomes will be aligned and mined for new molecular markers (single nucleotide polymorphisms [SNPs] and microsatellites). The end result of Aim #1 will be a table listing all markers and which hierarchical level of variation they address: worldwide, among regions, or within populations. In Aim #2 I will assess the genetic variation among isolates of Bd and identify its geographic origin. In addition, I intend to estimate the following population parameters: levels of variation in each population, demographic inferences (i.e., whether the genetic diversity indicates a stable, shrinking, or growing population), patterns and levels of genetic differentiation between samples, and the level of genetic intermixing between samples from different locations. The sampling and analytical procedures described in Aim #2 will allow me to understand patterns and levels of gene flow at different time scales, from events that occurred many generations ago to genetic exchange that occurred only one or a few generations ago. For Aim #3 I will describe Bd’s genotypic differences between contemporary and decades-old infections. Across New England, I will compare the genetic variation between contemporary sites and animals from similar locations yet preserved in museum collections. We know little about Bd prevalence in New England; reportedly, it is endemic. But most importantly, New England has been suggested as the origin of its worldwide spread. These analyses in Aim #3 may determine if the variation in genes implicated with virulence or evolution of virulence deviate from neutral expectation for the same population samples. Addressing genotypic differences between epidemic and endemic sites will help Bd researchers and conservation managers understand the genetic basis for observed phenotypes, namely virulence.

Expected Results:

There are two major scientific contributions within this research proposal. The most obvious is to finally understand from where Bd originated and how it subsequently spread throughout the world. If conservation measures are to protect amphibians from future declines, it is important to understand how Bd moves between and within amphibian communities. The second major achievement this research aims to accomplish is applying cutting-edge next generation sequencing techniques to a large set of individuals, or pathogenic isolates in this case. While next generation sequencing is becoming more popular and the sought after technology, rare is it that multiple, entire genomes of a non-model organism are being sequenced. Plus, the results are directly applicable to two of today’s most pressing environmental issues, as determined by the National Research Council: biodiversity conservation and infectious diseases within the environment.

Potential to Further Environmental/Human Health Protection:

Amphibian populations are declining worldwide, taking ecosystems they help to regulate with them. In light of their decline, we are beginning to understand the crucial role amphibians play in regulating primary productivity, organic matter processes, insect and riparian predator abundances and diversity, and energy transport between aquatic, riparian, and terrestrial ecosystems. We understand that to preserve aquatic, riparian, and terrestrial ecosystems, amphibian populations must be protected. One measure that can help equip our conservation efforts is to understand the population genetics of Bd, a major driver in the amphibian decline crisis. Implementing population genetics in conservation programs is a well-founded practice. Population genetics can uncover how the invading pathogen adapts and evolves in newly introduced regions and the resulting geographic patterns of how the pathogen colonizes and spreads between regions. Uncovering any evolutionary response by the pathogen holds great promise in preventing the decay of aquatic ecosystems by stabilizing amphibian populations.

Supplemental Keywords:

Batrachochytrium dendrobatidis, amphibian, emerging infectious disease, pathogen, fungus, chytrid, extinction, next generation sequencing, population genetics, invasive species, quantitative PCR, ancient DNA, SNPs, microsatellites,, RFA, Scientific Discipline, Ecosystem Protection/Environmental Exposure & Risk, Genetics, amphibians, Environmental Microbiology, Biochemistry, Ecology and Ecosystems, molecular genetics, biodiversity, biopollution, New England, parasitic infestations, population decline, amphibian decline, multiple pathogens, fungal pathogens, mortality, amphibian bioindicator

Progress and Final Reports:

  • 2011
  • 2012
  • Final