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ABSTRACT Studying declining and rare species is inherently challenging, particularly when the cause of rarity is emerging infectious diseases (EIDs). Tracking changes in the distribution of pathogens that cause EIDs, and the species made scarce by them, is necessary for conservation efforts, but it is often a time and resource intensive task. Here, we demonstrate how using environmental DNA (eDNA) to detect rare species—and the pathogens that threaten them—can be a powerful tool to understand disease dynamics and develop effective conservation strategies. Amphibian populations around the world have undergone rapid declines and extinctions due to the emerging fungal pathogen,Batrachochytrium dendrobatidis(Bd). We developed and validated a qPCR assay using eDNA sampling methods for some of the most imperiled amphibian species, harlequin frogs (Atelopus varius,Atelopus zeteki,andAtelopus chiriquiensis), and applied this assay in concert with a standard qPCR assay forBdin rainforest streams of Panamá. We confirmed the presence ofAtelopusat sampling locations across three regions. In addition, we used genomic analysis of eDNA samples to show thatBdin Panamá falls within the Global Panzootic Lineage, a lineage associated with disease‐induced declines. We detectedBdDNA in most of our historic sites, and its concentration in water samples correlated with stream characteristics and the pathogen load of the local amphibian community. These results suggest that some populations ofAtelopuspersist in their historic localities. They also show how eDNA analysis can be effectively used for monitoring species presence, pathogen concentrations, and the distribution and spread of pathogen lineages. EIDs are a growing threat to endangered species around the world. Simultaneous detection of rare and declining host species and their pathogens with eDNA will help to provide key insights for effective conservation management.
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This content will become publicly available on June 18, 2027
Amphibians After Disease‐Induced Declines: Genetic Insights Into Population Recoveries
ABSTRACT Infectious diseases can cause severe population declines, reducing genetic diversity, ecological function, and prospects for long‐term survival. Such declines often result in genetic bottlenecks, with small, isolated populations that are especially vulnerable to extinction due to genetic drift and inbreeding. Chytridiomycosis, caused byBatrachochytrium dendrobatidis(Bd), has led to global amphibian declines. Yet, some populations now show signs of recovery, even thoughBdis present and pathogenic. In this study, we use a genomic approach to investigate the genetic patterns underlying recoveries in three amphibian species from Panama that experiencedBd‐related declines followed by apparent recoveries:Colostethus panamansis,Lithobates warszewitschiiandSachatamia albomaculata. These species differ in life history traits and dispersal capacities, allowing us to examine how such differences influence genetic signatures of recovery. Here, we employed a frog‐specific genomic capture assay to analyse the effective population sizes, population structures, and both genome‐wide and immune‐specific genetic diversity. Our results reveal recent genetic bottlenecks and low effective population sizes across all three species, consistent with evidence of past disease‐driven declines. However, we found distinct patterns of gene flow and immune genetic diversity among species. These findings suggest that gene flow may serve as a key demographic and adaptive contributor of recovery in some species by introducing novel genetic variation. Understanding how populations recover from infectious disease impacts is critical for informing conservation efforts. Our study provides insights into the genetic signatures associated with recovery and highlights the importance of species‐specific traits in shaping evolutionary responses to emerging diseases.
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- PAR ID:
- 10709720
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 35
- Issue:
- 12
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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