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EECG Embarkation: Testing genomic mechanisms and consequences of species persistence in rediscovered amphibians

Kyle Jaynes holding a Jambato Harlequin frog (Atelopus ignescens) in the field in 2019 (credit: Sarah Fitzpatrick).


About the author

Kyle Jaynes (he/him) is a PhD Candidate in Dr. Sarah Fitzpatrick’s lab at Michigan State University. Heis broadly interested in the evolutionary ecology of amphibians and reptiles, and currently thinks mostly about conservation genetic applications to endangered amphibians. Visit Kyle’s website or follow him on twitter for updates on his work.

As a conservation biologist, I think (and worry) about what the near future looks like for biodiversity on our planet, which species I’ve met that my kid will never see, and the startling speed of  this loss. As an evolutionary biologist, I wonder what species will persist, what traits or mechanisms underlie those outcomes, and to what extent we can predict and harness that information. In an era of unprecedented human-driven biodiversity loss, we also hold unprecedented tools and information to halt it. As a human, I remain inspired by the diversity on our planet, and hopeful in our capacity to protect it. 

My hope is distilled in part from the organisms I study: Harlequin frogs (genus Atelopus), a species rich genus of toads in Central and South America that are highly susceptible to a global amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd for short or ‘Chytrid fungus’). Many species drastically declined and disappeared in conjunction with the emergence of the pathogen in the 

Sangey plot of Harlequin frog extinction and rediscovery trajectories. From Jaynes et al. (2022).

1980s and 1990s, and they are often cited as an iconic example in the global amphibian decline crisis (La Marca et al. 2005). I study the rediscovered species thought to be extinct but instead persisted in small populations (sometimes for decades), and reappeared despite the odds. In my first dissertation chapter, we characterized Atelopus rediscoveries and estimated that up to 32 species, representing one third of these species previously missing, had been rediscovered in the last two decades (Jaynes et al. 2022; Fig. 1). Their story offers sage advice that I use in many aspects of my personal and professional life: when life gets hard, persist

While their persistence is compelling, many rediscovered species likely remain on the brink of extinction. For example, we reported an intriguing trend that the longer a species was thought to be missing, the lower their heterozygosity (Jaynes et al. 2022). Using limited historical samples sourced from natural history collections, we also showed loss of heterozygosity post-decline in the Jambato Harlequin frog, Atelopus ignescens (Fig. 2), a species missing for nearly 30 years and officially declared Extinct by the IUCN before rediscovery in 2016. It is clear that rediscovery does not equal recovery. 

A female Jambato Harlequin frog (Atelopus ignescens) in the wild in 2019 (credit: Kyle Jaynes).

We still have much to learn about Atelopus rediscoveries. What are the consequences of population declines? Are there genomic mechanisms underlying their persistence? Taken together, how have demographic declines impacted populations at the genomic level, potentially constraining their adaptive potential and continued ability to persist in changing environments? 

I aim to answer some of these questions with my next projects, thanks in part to AGA EECG funds. Our research team has designed a whole-exome capture panel resource for Atelopus ignescens, which contains detailed genomic information relevant to Bd response. We are applying this panel on multiple relict species that have varying decline histories with the goal of uncovering a more detailed picture of the potential genomic contributions underlying persistence. 

 We hope the outcomes of this work will provide powerful insights into conservation applications for the many organizations working to assist current and future Atelopus rediscoveries, such as the Atelopus Survival Initiative, Alianza Jambato, Centro Jambatu de Investigación y Conservación de Anfibios, and Amaru Bioparque Cuenca, among others. Stay tuned! 



Jaynes, K.E., M.I. Páez-Vacas, D. Salazar-Valenzuela, J.M. Guayasamin, A. Terán-Valdez, F.R. Siavichay, S.W. Fitzpatrick, & L.A. Coloma. (2022). Harlequin frog rediscoveries provide insights into species persistence in the face of drastic amphibian declines. Biological Conservation, 276, 109784. 

La Marca, E., K.R. Lips, S. Lötters, R. Puschendorf, R. Ibañez, J.V. Rueda-Almonacid, R. Schulte, C. Marty, F. Castro, J. Manzanilla-Puppo, J.E. García-Pérez, F. Bolaños, G. Chaves, A.J. Pounds, E. Toral, & B.E. Young. (2005). Catastrophic population declines and extinctions in neotropical Harlequin frogs (Bufonidae: Atelopus). Biotropica, 37(2), 190-201. 

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