Career: using recombination in a hybrid zone to interrogate pathogen evolutionary genetics

The National Science Foundation Division of Environmental Biology awarded California State University, East Bay Foundation, Inc. $1,037,584 on August 1, 2026, under the Biological Sciences program to investigate the evolutionary genetics of amphibian chytrid disease in a hybrid zone.

The research collects disease samples from amphibians infected by hybrid strains of the chytrid fungus in the Atlantic Forest region of southern Brazil to identify key genes underlying disease traits such as virulence and transmission potential. The study examines the evolutionary outcomes of hybridization between a globally pandemic strain and a locally endemic strain of the pathogen, testing whether recombined hybrid genotypes exhibit altered fitness, virulence, or transmission characteristics. The project includes student and educator training in fungal biology and genomics.

Performance occurs in Hayward, California, with a period of performance through July 31, 2031. The funding is classified as a Project Grant under the Biological Sciences assistance listing (CFDA 47.074).

Abstract

New diseases are a major threat to global biodiversity, crop security, and human health. Understanding the genetics of emerging pandemics can shed light on how diseases adapt as they spread to new habitats and new hosts. Naturally occurring hybrids between genetically distinct parents can present a valuable opportunity to understand the evolutionary histories of the parent lineages including in disease systems. When hybrid individuals are successfully produced in nature, inheritance patterns in their genomes can provide insight into the parental genes that have diverged the most. These observations are critical to the understanding of the evolutionary origins of the parent lineages. This research focuses on an active hybrid population of amphibian chytrid disease in the atlantic forest region of southern brazil. This project will collect disease samples from amphibians infected by hybrid strains to ultimately identify the key genes underlying disease traits such as virulence and transmission potential. A detailed understanding at the genetic level of how new diseases evolve will be critical to controlling future outbreaks and for biotechnological advancements, especially as diseases are increasingly introduced to new habitats. In addition, this research will support education by training students and educators in fungal biology and genomics. Sometime in the last century, a global pandemic strain of the amphibian chytrid fungus was introduced to southern brazil where a less virulent, locally endemic strain of the disease had already been present. Preliminary evidence shows that this secondary contact has resulted in the production of recombined hybrid genotypes between the original pathogen lineages. This project will investigate the evolutionary outcomes of anthropogenic hybridization between these divergent disease strains. Specifically, this study will test whether hybridization between pathogen lineages can result in rapid virulence evolution and altered disease outcomes. This study will utilize a combination of field sampling for pathogen isolates, whole genome sequencing, and experimental infection approaches to address these questions. The results of this study will provide insight into the outcomes of fungal pathogen divergence and strain recombination which remains poorly resolved. This project will also provide opportunities for US k-12 science educators to participate in authentic research and field experiences, and to develop and sustain thoughtful k-12 scientific pedagogy through facilitated peer communities. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.