Beyond the general question of whether a climate-smart conservation approach is consistent with the federal and state Endangered Species Acts, we explored the legal issues surrounding the use of some tools and approaches that are still relatively experimental in California’s freshwater ecosystems. These tools include genetics and diversity support (genetic modification, epigenetics, and hybridization), assisted migration, hatchery reform, and contingency actions, including planning for new (or “novel”) ecosystems in the event of species loss. Some of these “emerging tools” (see Table 1) may be controversial. For example, critics of assisted migration and genetic support have argued that the tools themselves can pose risks to species or to ecosystems more broadly. And our interviews revealed that some in agencies and the water and environmental community are wary of undertaking contingency actions for fear they will be perceived as essentially “giving up” on species at the brink of extinction.

We begin with the emerging tools and some of the additional legal questions they raise. We then look at contingency actions.

Emerging Tools

On balance, federal law tends to provide more guidance on emerging tools than state law, especially for assisted migration. However, both federal and state law would benefit from improved clarity and flexibility. There is a particular need for new thinking in the category of genetic support for adaptation. Most or all of these improvements could be accomplished through new internal guidance, formal policies, or new regulations specifically tailored to species protection and recovery under climate change. Even absent such changes, however, there is already a clear permitting structure for approving projects that use these emerging tools—permits that are available for scientific research, education, management, and recovery actions. We refer to these as “research and recovery permits.”

Research and recovery permits can provide significant flexibility for innovation

One general challenge with many emerging tools involves the risk of harm to listed species or their habitat. Fortunately, both the ESA and CESA have special provisions that authorize take of listed species for scientific activities or innovative efforts to support recovery under research and recovery permits. Any individual, organization, or agency that conducts an action qualifying as research or recovery that may take ESA-listed species is eligible to receive a federal research and recovery permit. If an action only takes state-listed species, CDFW can issue a permit to individuals or organizations listed as eligible. These permits differ depending on the relevant law or regulation, but they are typically limited to academics, research institutions, and similar organizations. Although CDFW can authorize third parties to undertake innovative projects using emerging tools, the department has generally shied away from doing so, especially for projects related to genetic support. Alternatively, CDFW can conduct the research and recovery work itself.

Both federal and state law authorize assisted migration, but current state policy discourages its use

Many freshwater species need to move as part of their natural life cycles. Mobility enables them to seek out the right habitat conditions, locate better food sources, find the best spawning grounds, and reproduce. But many barriers now prevent individuals from dispersing and migrating within their customary ranges, and climate change, water management, and other environmental modifications may make some habitat inhospitable. Climate-Smart Tools lays out several ways to help wildlife overcome barriers to movement, which could in turn help them maintain populations and genetic diversity under changing conditions. Law and policy often distinguish between approaches that improve access to historical habitat versus approaches that help species move to areas outside their historical range. The latter is called “assisted migration” in Climate-Smart Tools and below.

Assisting migration to areas that are outside of a species’ historical range poses distinct challenges. Property owners in the relocation area may resist, fearing that the presence of listed species will restrict their activities or create the potential for them to be charged with take of those species. To address this, on the federal side, the ESA allows USFWS and NMFS to identify relocated populations of species as “experimental” and “non-essential”—designations that can provide more flexibility in managing the relocated populations. In addition to giving conservation projects more leeway, these designations can help secure the cooperation of property owners in areas of expansion. USFWS has already designated more than 60 non-essential experimental populations, mostly for terrestrial species (e.g., the gray wolf, grizzly bear, black-footed ferret, California condor), and NMFS has provided this designation for six anadromous fish populations, including four in California. And a 2023 regulation allows USFWS to be more proactive with assisted migration by allowing the agency to determine where existing habitat may become incapable of supporting a species and to move that species to more suitable locations when appropriate (USFWS 2023).

On the state side, CDFW is also authorized to undertake or approve assisted migration to conserve and recover species, and it has broad authority to take state-listed species if it carries out the project. Although the law allows the agency to support moving species outside of their historical range, a 2017 policy discourages this option, citing the potential for unexpected outcomes (CDFW 2017a). State law is also less flexible than federal law in providing assurances regarding take liability to landowners in areas where relocations would occur. Under state law, assurances cannot be provided for take of state-listed species (unless special circumstances allow for a safe harbor agreement or the state concurs with federal assurances; see Technical Appendix A). The state can agree to support a federal experimental population, but there is no general state law for designating experimental populations.

Rules governing hatcheries may harm efforts to support the genetic diversity of native fishes

Hatcheries have been present in California since the late 19th century, and today state, federal, and private fish hatcheries produce millions of pounds of fish each year. In many respects, hatcheries are a success story. Salmon, steelhead, and trout hatcheries raise fish to mitigate for the impacts of dam construction, reservoir operations, and lost habitat. By supplementing fish populations, hatcheries support longstanding tribal, recreational, and commercial fishing activities. Hatchery fish have successfully repopulated some rivers, such as Putah Creek in Northern California, where fish from regional hatcheries have colonized the stream. And some conservation-focused hatcheries are now sustaining listed species whose wild populations have crashed—including Delta smelt, spring-run Chinook salmon, and winter-run Chinook salmon.

Hatcheries also pose challenges, however, because they tend to lower genetic diversity in wild stocks of salmonids and other native species and can select for undesirable traits (e.g., domestication). Genetic diversity is essential for adapting to changing climatic conditions and for maintaining resilience in the face of major events like heatwaves, wildfires, and flow changes. To support the genetic diversity of California’s native fishes, Climate-Smart Tools recommends considering the following hatchery management practices. This report evaluates those recommendations and concludes that—assuming adequate funding—some of these practices can be accomplished under existing law, while others would require legal changes:

• Using breeding programs to improve genetic diversity for climate resilience. As explained in Climate-Smart Tools, for species currently produced in hatcheries (e.g., salmon and steelhead), breeding programs can improve genetic diversity in hatchery stocks to help build climate resilience. At present, selective breeding is already commonly used to build desired traits. From a law and permitting perspective, the introduction of new breeding programs focused on climate resilience would raise scientific questions and would require agency approvals (e.g., take permits, recovery plans, and revision of hatchery genetic management plans). These permitting paths are readily available under the ESA and CESA and relevant regulations and policies, however, so changes in law are not needed.
• Suspending hatchery stocking or relocating hatcheries to seaward locations. Climate-Smart Tools explains that fish biologists have recommended considering these more controversial steps when there is evidence that hatchery practices have adverse effects on wild fish populations (e.g., competition, loss of diversity, and inbreeding). These recommendations suggest that an important way to protect the diversity of wild river populations would be to limit breeding between wild and hatchery stock. Permanent or long-term suspension of hatchery fish stocking would likely provoke resistance from those who depend on these stocks for fishing, although relocating hatcheries could allay some of these concerns.
  From a legal perspective, there could be some challenges to overcome. Fish stocking is mentioned in many different provisions of state law as well as state policies. Also, some hatcheries may be required as mitigation for dam operations or otherwise made a condition of environmental approvals. In addition, hatchery populations of many salmon and steelhead runs have some ESA protections, which means that one or more of the state and federal fisheries agencies, depending on the species, have authority over how the runs are managed. Separately, at least one California court has held that state law limits CDFW’s discretion to end hatchery operations—although no court has considered this question for a specific hatchery in the context of climate change. And some state and federal hatcheries may have obligations to tribes regarding the production of hatchery fish.

That said, although there are questions that would need to be answered (on a species- and hatchery-specific basis), the state and federal governments do have significant authority to manage fish and to reshape outdated hatchery practices. These authorities are discussed further in Technical Appendix A.

Both federal and state laws restrict using genetic modification to assist evolution

Even with large, diverse populations, natural selection may be insufficient to cope with future extreme conditions. Assisted evolution represents an intensive intervention to help select for individuals that can better survive warmer and drier conditions under climate change. Selective breeding in hatcheries may be appropriate for this purpose. Other, less familiar strategies include gene editing (which may include introducing new genes), or epigenetics (i.e., influencing how genes are expressed). As described in Climate-Smart Tools, both of these approaches are experimental and pose unanswered scientific questions; the legal issues are complex and somewhat different between them, particularly under state law.

Gene editing. This form of genetic modification—sometimes known as “transgenics”—has widespread commercial applications in agriculture (e.g., herbicide-resistant strains of corn), but its use in conservation applications is still limited. Indeed, many of the commercial applications (e.g., fatter farmed salmon in the US) have been controversial, reflecting public concerns over the potential harmful effects of transgenic organisms. This concern would likely be stronger in the conservation context, where transgenic species would be released into the wild and could interbreed with the unmodified species and compete for food and habitat.

The law governing federal oversight of gene editing is currently unclear. If a species is listed, ESA permissions (likely under research and recovery permits) must be obtained for any take or other impacts to the species, but there is nothing specific to gene editing in the statute or ESA regulations. Under the multi-agency Coordinated Framework for the Regulation of Biotechnology, several agencies claim some oversight over transgenic species, including the Environmental Protection Agency, the Food & Drug Administration, and the Animal Plant Health Inspection Service within the US Department of Agriculture (APHIS) (The White House 2017). Thus far, the principal focus of these agencies has been commercial applications in areas such as pesticides, agriculture, and food production (USDA et al. 2023). The EPA has approved an experimental permit for genetically engineered mosquitos, which was categorized as a pesticide project (Erwin 2023). The transgenic American Chestnut was designed for conservation purposes, to improve the tree’s resistance to disease. The project, currently on hold, faced a complex and uncertain pathway to approval before ultimately being submitted to APHIS (Erwin 2023). No federal agency has provided guidance specific to assisted evolution in fish and wildlife conservation, and permitting responsibilities remain unclear.

California law is more explicitly restrictive. The state has specific provisions addressing transgenic aquatic animals. For example, state law permits certain kinds of transgenic research but requires that the organisms be held in closed water systems. It also bans the introduction of transgenic species to the waters of the state and prohibits the spawning, incubation, or cultivation of any transgenic species of salmonids anywhere in California, including in hatcheries.

Epigenetics. Unlike genetic modification, epigenetic changes do not introduce new genetic material into an organism or remove specific DNA sequences. Rather, epigenetics works within an organism’s existing potential range of gene expression, allowing it to adapt to changing conditions. For example, laboratory acclimation and breeding have been tested to select seaweed strains that can better withstand climate stress (Pazzaglia et al. 2021). In some cases, these new traits become heritable. However, because no new genetic material is introduced or DNA sequences removed, epigenetic changes do not qualify as “transgenic” under current state definitions. At the same time, although there are no legal standards specific to use of epigenetic techniques, CDFW does have broad permitting authority generally over the possession or release of any organism that might affect native populations. And the usual CESA take provisions would also apply.

Federal law is also less than clear on epigenetics, and it is uncertain whether the tool would be covered by the Coordinated Framework for the Regulation of Biotechnology. In 2024, APHIS proposed amending its policy to cover intentional genomic alterations, which would appear to include epigenetic changes; however, these proposed standards still do not directly address conservation. Of course, any epigenetic changes that alter a species listed under the federal ESA—or that have the potential to otherwise take a listed species—would require ESA take approvals, likely under research and recovery permitting.

Federal law is somewhat flexible regarding hybridization of species; California law is unclear

Another relatively controversial tool is deliberate hybridization—the crossbreeding of individuals from different or closely related species. Plant hybridization is commonly used to generate specific desirable traits such as fast growth, appearance, and disease resistance. More recently, hybridization has been used in commercial aquaculture for fish and invertebrates, and in fish stocking. Climate-Smart Tools suggests that a similar strategy might be employed in situations where individual species are unable to adapt quickly to climate change. The report suggests that these opportunities would require careful evaluation. Sometimes hybridization—whether natural or otherwise—can result in the loss of biodiversity, such as when the genes of a common species dilute the genes of a rare species. But in other settings, hybridization supports adaptability and resilience, helping to strengthen a species and therefore protect biodiversity.

For decades, hybrids were not protected under the ESA. Even natural hybrids could not be listed as threatened or endangered for fear they would negatively affect native species or other ecosystem elements. Federal attitudes have changed, however, and today natural hybrids may be protected under the ESA on a case-by-case basis (DOI 2000). USFWS also acknowledges that human-initiated hybridization can potentially provide genetic resources that can save species from extinction. Current ESA propagation policies theoretically authorize the use of hybridization in captive breeding programs, at least where other measures have failed or are unlikely to achieve recovery.

While federal policy on hybridization has evolved, California’s policies remain unclear. On the one hand, current CDFW regulations provide a pathway for permitting hybridization in the context of commercial aquaculture and fish programs. State regulations also provide that CDFW may authorize co-mingling of hybrid and non-hybrid species, and CDFW policy allows for conservation propagation under some circumstances (CDFW 2017b.) On the other hand, at least with respect to fish, state law discourages releasing hybrids into the wild if they would impact native populations. Interviews conducted for this report also suggest that there would be resistance to the release of hybrid species because of a general reluctance to interfere with natural processes and perceptions of risk. These factors suggest that legal and policy clarity would be useful (see Technical Appendix A). Moreover, regulators, environmental stakeholders, and potentially affected property owners and resources managers will need to build organizational and cultural capacity to address these issues (see Technical Appendix B).

Contingency Actions and the Law

Even with best efforts to protect native species, some extinctions are likely in the coming decades. Climate-Smart Tools urges two types of immediate statewide contingency actions: collecting more information about and samples from vulnerable species, and planning for the management of novel ecosystems. These contingency actions offer significant conservation benefits with little risk, but they nonetheless can be controversial. Some in agencies and the water and environmental community resist acknowledging that some species may not persist within their historic range. Moreover, some in this community view activities such as seed banks as a first step toward reduced species protection—regardless of the absence of evidence for such cause and effect. To implement contingency actions, these biases must be overcome. If contingency actions are not employed in the near term, valuable opportunities to obtain knowledge about some species will be lost forever.

Fortunately, as described below, there are no meaningful legal impediments to contingency actions.

Information and sample gathering for vulnerable species can rely on research and recovery permits

As described by Climate-Smart Tools, information and sample-gathering efforts would include both historical conservation work (gathering information about species characteristics, behaviors, and habitat), along with the gathering of physical specimens and records (e.g., tissue archives, genetic libraries, and seed banks). Securing specimens, taking samples, and studying organisms raises the potential for harm to some individuals. Based on interviews for this report, researchers often view the take prohibitions under ESA and CESA as impediments to the study of listed species; they find the regulatory processes burdensome and time-consuming to navigate. This challenge could be addressed through more efficient permitting for research and recovery actions (Grenier et al. 2021). Agencies can prioritize such actions by reallocating funding and staffing to support contingency efforts related to climate response and by supporting the use of innovative approaches such as programmatic permits, which allow multiple permittees to join a pre-existing approval over time.

The state can plan for changing ecosystems and species loss

Climate change and human actions have altered, and continue to alter, land and waterscapes, creating novel ecosystems comprising a mix of native and non-native species. The changed conditions in these novel ecosystems increase the risk that some native species will become extinct. Climate-Smart Tools recommends planning for these changes to reduce ad hoc, crisis-based decision making and ultimately to improve outcomes.

There is no legal impediment to advance planning for novel ecosystems, and policymakers can plan for any eventuality—as long as stakeholders are not forced to fund analysis of scenarios that are entirely speculative. From a political and policy perspective, such planning is likely to be controversial. As noted above, some in agencies and the water and environmental community believe that planning for change implies giving up on restoring historical conditions or protecting the status quo. This is not the case. An aircraft may have life rafts and life preservers on board, but this does not mean that the pilot has given up flying the plane to its intended destination. Planning for novel ecosystems creates a framework in which people can develop a collective understanding of potential futures and explore the risks and choices presented by different scenarios. Of course, there would be debates about which conditions are foreseeable and which are speculative, but this is often true in environmental analysis.

Planning for novel ecosystems can help support investments in developing models and testing hypotheses to understand how species and ecosystems respond to change (Power et al. 2024). The process can also help build cultural, institutional, or governance capacity to confront and manage ongoing change (Technical Appendix B). Developing social capacity for discussing tradeoffs and making choices in light of available resources are critical elements of preparing for change in advance, as opposed to simply reacting to it after the fact.