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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 April 1, 2027
Genomic Correlates of Disease Recovery in Natural Populations of the Sierra Nevada Yellow‐Legged Frog ( Rana sierrae )
ABSTRACT In our rapidly changing world, evolution is likely to play an important role in facilitating the resilience of wildlife populations. The Sierra Nevada yellow‐legged frog (Rana sierrae) provides a rare example of recovery following severe declines caused by the amphibian chytrid fungus (Batrachochytrium dendrobatidis). However, the role of evolution in facilitating this recovery remains circumstantial. In this study, we sought to gain insights into the potential role of evolution by comparing genomes of frogs from naive and recovering populations located in close proximity. Using multiple methods to scan frog genomes for signatures of selection, our study reveals several genomic variants associated with frog recovery. Specifically, we identify outlier gene variants across genes related to skin integrity and intracellular regulation, an interferon‐related gene and a recovery‐associated variant in RIN3—a gene that may play a critical role in disease defence and wound healing. Finally, we report no differences in genetic diversity between naive and recovering populations. Our study provides a rare example from natural populations that suggests that evolution can produce individuals that harbour adaptive alleles and allow population recovery in the presence of novel stressors. These findings complement recent research on rapid amphibian evolution in response to disease and provide mechanistic hypotheses for how individuals can prove resilient to disease outbreaks.
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- Award ID(s):
- 2120084
- PAR ID:
- 10709728
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 35
- Issue:
- 8
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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