Drawing boundaries with DNA to improve conservation

by Ryan Peek

Foothill Yellow-legged Frogs have begun to spawn, laying small snow-globe sized egg masses in streams and rivers. They are one of the few stream-breeding frogs endemic to California and Oregon. This species is a good indicator of stream health because they link aquatic and terrestrial ecosystems and are strongly tied to natural seasonal cues associated with local hydrology. Historically, they occurred in streams and rivers throughout California and Oregon, but, as with many amphibians, they have precipitously declined in many parts of their range due to river regulation, habitat loss, and disease.

First petitioned for listing under the California Endangered Species Act (CESA) in 2016 by the Center for Biological Diversity, the California Fish and Game Commission recently listed Foothill Yellow-legged Frogs (Rana boylii) in February 2020. But unlike other species listed under CESA, Foothill Yellow-legged Frogs are one of the first species where genetic data were used to introduce more nuance into the regulatory process. Only a few other species have used a genetic basis to identify groups for listing under the CESA. For example, Coho Salmon Oncorhynchus kisutch (listed in 1995) used a single status listing for the species based on existing genetic data. Similarly, the Fisher (Pekania pennanti) was also listed/not listed using evolutionarily significant units (ESUs), but the species is extremely geographically separated, unlike the historically wide-ranging Foothill Yellow-legged Frog. For Foothill Yellow-legged Frogs, different genetically distinct groups were given different listing status (Threatened, Endangered, or listing not warranted at this time). This listing is not an endpoint, it reflects successful collaboration between researchers and regulators to provide a pathway to better prioritize long-term management and conservation of one of California’s iconic species.

Fig. 1. A Foothill Yellow-legged Frog (Rana boylii).

While protecting and conserving one of our few native frog species is important, using the same uniform listing and management strategy for every frog population in California may not be practical. The Foothill Yellow-legged Frog has a large range that historically encompassed most of California, thus a blanket approach to listing and conservation management across the state may not be very effective. Different regions of the state have different impacts on the species; therefore it makes sense and is likely more effective and cost-efficient to manage conservation at a regional scale. A more nuanced approach also avoids placing a regulatory burden on entities in areas where the species appears to be doing well. Finding options to build more flexibility into the system we use to manage and conserve our natural resources is important for long-term success. The crux of this success is best illustrated by a deceptively straightforward map (Figure 2). Despite its simplicity, this map is a result of several years of genetic research and collaboration between multiple agencies and universities. Its use in the state listing process is a relatively novel application of conservation genetics.

Ultimately the boundaries on this map provide a flexible but robust way to prioritize each clade or genetic group  independently. Because each group is genetically distinct, the map allows us to describe each group using metrics that include genetic diversity as well as landscape change and flow alteration. Measuring genetic diversity within and among each of these groups is important because genetic diversity provides a species with the ability to adapt to changing conditions (i.e., evolve). A loss of diversity often signals extreme population and range reductions, and is associated with a loss of fitness (reproductive success and survival). Genetic data enables us to quantify which groups had more or less genetic diversity, and this was combined with regional information about the impacts of flow regulation, habitat alteration, and disease, to identify which groups may be most at risk of extinction. This allowed the CDFW to identify, prioritize, and list each clade separately, and make clade-specific listing recommendations, which provided a much more practical way to evaluate and apply CESA in a historically wide-ranging species (CDFW 2020).

And importantly, there was consensus in these findings; a separate independent study conducted at UCLA found a strikingly similar pattern, lending additional support to these genetic boundaries (McCartney-Melstad et al. 2018). The boundaries on this map can be updated, and these data provide additional benchmarks that give us insight into the status and health of different populations which can be compared across time and location. Translating the information that DNA provides us provides a powerful tool to help bridge the need for “the best available science” in conservation, but ultimately the most effective tools rely on our ability to collaborate and communicate across boundaries.

The map shows the genetic boundaries for distinct interbreeding populations, called clades, for the Foothill Yellow-legged Frog. This map helped define how and where the Foothill Yellow-legged Frog would be listed under CESA, and it provides a unique and powerful way to use DNA as a way to inform conservation.

Fig. 2. Foothill Yellow-legged Frog (Rana boylii) genetic groups or “clades.” (Peek 2018).

Drawing boundaries with DNA is not new. Delineating geographic ranges for organisms based on their underlying genetic code has been one of the foundational components of population genetics, but integrating this information into legal conservation frameworks like the state and federal Endangered Species Acts has been a slow process. The Endangered Species Act requires decisions be based on the “best available science.” While this sounds like a decision that would be heavily based on quantifiable data, it requires judgement and interpretation to incorporate the full spectrum of biological data when classifying a species as Endangered, Threatened, or listing not warranted. With the advent of modern genetics, the types of data that can be used can be powerful and informative, but also complicated and very dense. So how do we use genetic tools and translate this information into defensible policy and legal conclusions?

In an era where we can generate more data than ever before, where specializations abound, and the competition to maintain funding to conduct research has greatly emphasized novelty, the ability to translate across disciplines and find ways to effectively apply science may seem rare. Ultimately, there is a continuum between research and management, and from a management perspective, the best information is actionable, discrete, and can be integrated into existing policy frameworks. For scientists interested in applied research, this means understanding the context where the research may be used, identifying what gaps exist within a given framework, and actually talking with the folks who will use the science.

When I started my dissertation, I tried to think critically about what would be useful for management. I spent time talking to resource managers at state and federal agencies, and I tried to maintain communication and collaborations throughout the process. In particular, I tried to ask what pieces of information or research would be critical for helping inform conservation of the species. Maps are crucial for identifying, prioritizing, and planning, so identifying and refining boundaries for conservation units (distinct populations, or clades) was an important component in the listing process. In the end, some key pieces of my dissertation were used in the Status Review used for the California Department of Fish & Wildlife (CDFW) listing recommendations for the Foothill Yellow-legged Frog (CDFW 2019). While it is bittersweet to work with a species that is at risk of extinction, it is encouraging to participate and contribute in a meaningful way to a conservation process as a scientist.

Ryan Peek is a post-doctoral researcher at the Center for Watershed Sciences, UC Davis.

Further Reading:

California Department of Fish and Wildlife (CDFW). (2019). A Status Review Of The Foothill Yellow-legged Frog (Rana boylii) In California. https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=174663&inline

CDFW. (2020). Notice of Findings for Foothill Yellow-legged Frog (Listing Decision). https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=177905&inline

McCartney-Melstad, E., Gidiş, M., & Shaffer, H. B. (2018). Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining Foothill Yellow-legged Frog. Heredity121(2), 112–125.

Peek, R.A. (2018). Population Genetics of a Sentinel Stream-breeding Frog (Rana boylii) [Ecology]. PhD Dissertation. University of California, Davis.

Peek, R. (2020). Rana boylii Population Genetics website. https://ryanpeek.org/flexdash_rabo.html


Laura Patterson has been instrumental as an contributor and collaborator; she coordinated and prepared the status review report for CDFW. In addition, Brad Shaffer, Sarah Kupferberg, Amy Lind, Sarah Yarnell, and Jennifer Dever have all provided data and critical research towards conservation of this species.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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