Whole exome sequencing identifies the potential for genetic rescue in iconic and critically endangered Panamanian harlequin frogs

Abstract

Avoiding extinction in a rapidly changing environment often relies on a species' ability to quickly adapt in the face of extreme selective pressures. In Panamá, two closely related harlequin frog species (Atelopus varius and Atelopus zeteki) are threatened with extinction due to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Once thought to be nearly extirpated from Panamá, A. varius have recently been rediscovered in multiple localities across their historical range; however, A. zeteki are possibly extinct in the wild. By leveraging a unique collection of 186 Atelopus tissue samples collected before and after the Bd outbreak in Panama, we describe the genetics of persistence for these species on the brink of extinction. We sequenced the transcriptome and developed an exome-capture assay to sequence the coding regions of the Atelopus genome. Using these genetic data, we evaluate the population genetic structure of historical A. varius and A. zeteki populations, describe changes in genetic diversity over time, assess the relationship between contemporary and historical individuals, and test the hypothesis that some A. varius populations have rapidly evolved to resist or tolerate Bd infection. We found a significant decrease in genetic diversity in contemporary (compared to historical) A. varius populations. We did not find strong evidence of directional allele frequency change or selection for Bd resistance genes, but we uncovered a set of candidate genes that warrant further study. Additionally, we found preliminary evidence of recent migration and gene flow in one of the largest persisting A. varius populations in Panamá, suggesting the potential for genetic rescue in this system. Finally, we propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the local population level. Our data lay the groundwork for genetically informed conservation and advance our understanding of how imperiled species might be rescued from extinction.

The Last Two Remaining Populations of the Critically Endangered Estuarine Pipefish Are Inbred and Not Genetically Distinct

“…Population-level inbreeding coefficients found in S. watermeyeri (F IS = 0.10-0.12) were similar to those of several other threatened fish species, such as the Chinese sturgeon, Acipenser sinensis (F IS = 0.148; Liu et al, 2018) and red-tailed barb, Gonoproktopterus curmuca (F IS = 0.115; Musammilu et al, 2014), and they exceeded those of the Sichuan taimen, Hucho bleekeri (F IS = 0.003; Zhang et al, 2020). The magnitude of mean coefficients of inbreeding based on pairs of individuals (F ab ) in S. watermeyeri (F ab = 0.31-0.40) was similar to that reported for the endangered Pyrenean desman, Galemys pyrenaicus (0.33; Escoda et al, 2017), and mean relatedness (r ab = 0.02-0.05) approached that for the critically endangered harlequin frog Atelopus varius (0.049; Byrne et al, 2021).…”

A review of chemical defense in harlequin toads (Bufonidae: Atelopus)

“…These sister species are closely related ( Fig. 3 a; Lötters et al, 2011 ; Ramírez et al, 2020 ) and a recent whole-genome analysis does not support the species boundary between them ( Byrne et al, 2020 ), suggesting that A. varius and A. zeteki are the same species. A. varius and A. zeteki exhibit intraspecific variation in the presence and absence of TTX and ZTX AB.…”

“…While A. zeteki from El Valle de Antón, Panama are the most studied sources of ZTX AB ( Table S1 ), the use of metagenomic analyses on the microbiome of this species is complicated by the possible extinction of A. zeteki in the wild, and uncertainty regarding whether captive A. zeteki retain ZTX AB ( Lukowski and Narayan, 2019 ). However, populations of A. varius persist in El Copé, Coclé, Panama as of 2016 ( Byrne et al, 2020 ) and ZTX AB was detected in A. varius collected near El Copé in 1971 ( Yotsu-Yamashita et al, 2004 ). These A. varius populations could be promising subjects for metagenomic research in search of ZTX AB-producing bacteria.…”

“…Chytridiomycosis, a disease caused by the fungal pathogen Batrachochytrium dendrobatidis, is implicated in many of the declines ( La Marca et al, 2005 ; Lampo et al, 2017 ), and habitat loss and degradation are likely also important drivers ( Gómez-Hoyos et al, 2020 ; Jorge et al, 2020b ; Santa-Cruz et al, 2017 ) . Recently, several Atelopus species thought to be extinct or locally extirpated have been rediscovered ( Barrio Amorós et al, 2020 ; Enciso-Calle et al, 2017 ; Escobedo-Galván et al, 2013 ; Tapia et al, 2017 ); however, these rediscovered populations are still at risk of extinction due to habitat loss, invasive species, low genetic diversity, and chytridiomycosis ( Byrne et al, 2020 ; González-Maya et al, 2018 ; Kardos et al, 2021 ). Atelopus extinctions not only risk the loss of irreplaceable biodiversity but also threaten the persistence of toxins that are unique to the genus.…”

Linking pathogen–microbiome–host interactions to explain amphibian population dynamics

“…Consistent with these results, we detected a relatively lower nucleotide diversity in the Bd ‐infected frogs. Other amphibian populations impacted by Bd have shown dramatic decreases in genetic diversity, such as the contemporary Panamanian populations of Atelopus varius (Lichtenstein & Martens, 1856) (Byrne et al, 2021). This species has been on the brink of extinction, but population recoveries suggest the evolution of host defence mechanisms (Voyles et al, 2018).…”