Genomic signatures of demographic declines in an imperiled amphibian inform conservation action

Abstract

Catastrophic population declines due to disease often lead to fragmented remnant populations and loss of gene flow. Managers are left to determine appropriate conservation actions to recover and maintain population persistence. The recent utilization of genomic data to assist in species recovery now allows us to combine genome-wide surveys of differentiation and diversity with the identification of potentially adaptive regions to develop conservation plans that incorporate ecological and evolutionary processes. The unprecedented global decline of amphibian populations due to the pathogen Batrachochytrium dendrobatidis has increased the need to apply genomic tools to amphibian conservation practices. We show here how understanding genetic characteristics of remnant frog populations affected by disease can be applied directly to restoration efforts. Cascades frogs (Rana cascadae) occur in the mountainous regions of the Pacific northwestern United States and have declined dramatically at the southern edge of their range in California. We conducted genome-wide surveys within this region to inform conservation and reintroduction efforts. We found strong north-south genetic differentiation between Oregon and California and novel spatial structure within California. Genetic diversity was lower in California than Oregon and genetic drift was the most important driver of genetic diversity and population structure in California, making conservation efforts aimed at boosting overall genetic diversity most urgent. Spatial genetic structure of populations within California suggests that reintroductions to Lassen Volcanic National Park, where they were recently extirpated, should use remaining source populations south of the park. Our findings support the treatment of California's R. cascadae populations separately from the rest of their range and highlight the importance of conservation genomics in applied species conservation.

Genomic evidence for adaptive differentiation amongMicrohyla fissipespopulations: Implications for conservation

“…Levels of genetic diversity and patterns of population differentiation in many amphibians have now been successfully assessed using genetic markers, typically microsatellites (Andersen et al., 2004; Beebee, 2005; Burns et al., 2004; Jehle et al., 2005; Nair et al., 2012; Nair et al., 2012; Yang et al., 2016; Zheng et al., 2021). As such, these studies have typically been limited to a few genetic loci, although studies based on a larger number of markers have started to emerge (e.g., Funk et al., 2018; Guo, Lu, et al., 2016; Hardy et al., 2021; Thörn et al., 2021). Yet, the genetic underpinnings of adaptations in natural populations of amphibians are largely unknown, although quantitative genetic methods have revealed adaptive differentiation in important life history traits (e.g., Berven, 1982; Laugen et al., 2003; Laurila et al., 2002; Palo et al., 2003).…”

In situ treatment of juvenile frogs for disease can reverse population declines

“…Eggs are laid shortly after snowmelt and larvae almost always metamorphose in the same year, adulthood (i.e., reproductive age) is reached in roughly 3 to 4 years, and the total life span can exceed 10 years; post‐metamorphic life stages overwinter in aquatic habitats that do not freeze solid (Pope et al 2014). Cascades frogs are thought to have been historically abundant at the southern end of the Cascades Range in northern California, but precipitous declines became apparent in the 1990s and only a handful of populations remain in the region; most of these remnant populations are declining and at risk of extirpation (Pope et al 2014; Hardy et al 2021).…”