Summer steelhead workshop report offers a new path to protection

Summer steelhead by Shaun Thompson
summer steelhead | Shaun Thompson

By Scott Greacen, FOER Conservation Director

Over the last few years, Friends of the Eel River has been calling particular attention to summer steelhead in the Eel River. These extraordinary fish certainly deserve the spotlight. What makes their fascinating story of summer steelhead urgent today is the peril they face. If current trends continue, these marvels of evolution will disappear from the Eel watershed in our lifetimes.

A quick recap: steelhead, Oncorhynchus mykiss, are generally described as the anadromous form of rainbow trout. On the North Coast of California, most steelhead are winter-run. They come up their natal river in December through April, spawn immediately, then die or return to the Pacific. Some steelhead, however, enter freshwater in the late spring, swim far up their watersheds to remote canyons where they spend the hot summer months sheltering in deep cold pools. When the fall rains come, these fish climb higher up their watersheds than any other salmonid, often surmounting obstacles that have been thought barriers to fish passage in the process. These summer steelhead have long been recognized as different from their winter-run cousins in both their bodies and their behavior.

Similarly, spring-run Chinook salmon in the Klamath watershed’s Salmon River are strikingly different from their fall-run cousins. Both summer steelhead and spring chinook have suffered disproportionately from the impacts of our industrial society on their freshwater habitats. The dozens of spring Chinook which still return to the Salmon River are the last remnant of runs that were probably larger than the fall chinook runs before the US colonized the region.

We think recent science confirms that summer steelhead are different from their winter-run cousins in ways that are truly significant for the biology and evolution of these fish. That is to say, summer steelhead are different in precisely the ways that the federal Endangered Species Act (ESA) was intended to recognize and protect. But when FOER asked the National Marine Fisheries Service (NMFS), the federal agency responsible for the conservation of anadromous fish under the ESA, to list North Coast summer steelhead as a distinct unit, NMFS denied our petition. However, a June NMFS report from a workshop of the leading salmonid researchers, hosted by NMFS’ own specialists, offers hope that an emerging consensus around the genetic basis of run timing in salmonids could provide a foundation for greater recognition and protection of summer steelhead.

In general, biologists understand most important aspects of physical development in higher organisms to be governed by the complex interplay of many genes. For example, as the report notes, recent DNA studies have confirmed that height in humans is associated with many thousand genetic markers spread throughout the human genome. Similarly, for decades, biologists have believed that run timing in salmonids results from the interplay of a large number of genes, each with relatively small effect. 

Working from that assumption, the increasing scarcity, or even disappearance, of summer steelhead themselves would not necessarily mean the genes that produce summer steelhead would be lost. If early run timing is just one potential outcome of a complex genetic mix, the summer steelhead genes would, in all likelihood, still be floating around in the winter steelhead population. Even if breeding populations of summer steelhead populations were lost, summer steelhead could still re-emerge from a recovering winter steelhead population as it increased in numbers. 

What Mike Miller and his colleagues at UC Davis have found is the opposite of what theory predicted. Instead of many genes working to influence run timing, they found a single small site at the same spot in both the steelhead and chinook genomes that appears to control run timing and the physiological and behavioral differences between early- and late-migrating fish. If a fish gets two copies of the early-return gene, they are summer steelhead. If they get two copies of the late return gene, they are winter-run steelhead. And if they get one copy of each, they probably try to enter freshwater in late summer, when North Coast river temperatures are generally lethal for salmonids. 

As well, the UC Davis lab found evidence the early return gene in both steelhead and chinook are each the result of unique mutation events, each of which then spread across populations which had previously only been late-returning fish. The finding that the same very small genetic region controls the trait in both species bolsters the conclusion that there are not many other mutations which could create the same trait variations. 

The conservation implications of these insights are profound. The selection pressure on fish that have only one copy of the early return gene means that once summer steelhead, or spring chinook, are gone, the genes that make them possible are gone as well. Summer steelhead will not re-emerge from the winter chinook population if they are extirpated. They will be extinct in that tributary, unless and until a new influx of early-run strays comes into the watershed from a nearby source population that still maintains early-run fish and is strong enough to have strays. 

The Eel River is fortunate to still have populations of summer steelhead breeding in the Middle Fork Eel River and the Van Duzen. Recent reports suggest there may even be a few fish in the North Fork. (There don’t appear to have been summer steelhead in the South Fork, based on the historic samples available.) But the mean of Middle Fork Eel population counts is only about 770 individuals, while that of the Van Duzen is about 148 per year. Taken together, all the spawning populations of summer steelhead left on the North Coast likely total fewer than a thousand fish. And every population is in long-term decline.

Perhaps most tragic of all, the southernmost run of summer steelhead been extinguished by Scott Dam for the last century. In its 2016 Multispecies Recovery Plan, NMFS noted that “(t) he Upper Mainstem Eel River steelhead population was once the longest-migrating population in the entire [Distinct Population Segment]. Restoring access to historical habitat above Scott Dam is essential to recovering this population.” In the same document, NMFS estimated that “Scott Dam currently blocks access to 99 percent of the potential habitat available to this steelhead population,” and noted that “steelhead have not had access to this habitat since 1922.”

In summary, summer steelhead are barely hanging on across the North Coast. Like spring chinook, they are clearly Endangered by the federal ESA’s standard. (“If current trends continue, they will be extinct in 100 years.”) But NMFS still lumps winter and summer steelhead together in a single unit that stretches from Redwood Creek to the Mattole, including the Mad and the Eel. This “North Coast steelhead” population is listed under the ESA as Threatened. (“Will become Endangered within a century if current trends continue.”)

Seen through the UC Davis insights, this looks like a recipe for extinction of summer steelhead on the North Coast. Their studies strongly suggest that if we fail to conserve summer steelhead as a unique life form, we will lose the adaptive potential they embody. The early-migrating genes will be gone. 

Thus, it was very interesting to read the report issued this June on a workshop on salmonid genetics hosted this February in Seattle by NMFS. The bottom line: even NMFS now accepts that the UC Davis researchers have it right. Run timing in steelhead and chinook is driven by a tiny but powerful gene. That’s great! The federal ESA actually requires agencies to use the best available science, and that science just got updated to agree with the argument we made for listing summer steelhead. 

But no, that doesn’t mean we can list North Coast summer steelhead now. The report underscores the fact NMFS cited to reject our petition to list summer steelhead across the region as a single unit: “(D)ifferent life-history types within the same stream are genetically more similar than either life-history type is to the same type in a different stream.” Indeed, summer steelhead in the Middle Fork Eel share more of their genome with winter steelhead from the Middle Fork than they do with summer steelhead from the Van Duzen or Redwood Creek. This makes sense, if we think of the early migration gene spreading across steelhead populations, each of which was already adapted to its own watershed.

The report provides a helpful graphic summary of how winter and summer-run steelhead are related across tributaries within a region, and how they could be listed under the ESA in ways consistent with the scientific evidence. Scenario I illustrates the relatively close overall genetic relationships between winter (A) and summer (B) steelhead in any given stream. 


Remember, NMFS currently lists winter and summer steelhead as a single unit across the North Coast. This corresponds to scenario IV in the report’s figure. So, when we asked NMFS to split that unit to list summer steelhead separately across the North Coast, while we were following NMFS’s own logic, what we were asking for was Scenario V. (Harsh buzzer sound.) What NMFS appears to be telling us that while they don’t think the best available science supports listing summer steelhead across the region as a single unit, the science would support listing them as entirely separate units in every tributary, as in Scenario II. 

Of course, federal agencies generally don’t list every single unit of every species separately because it’s a pain for regulators and affected industries. But that’s a policy question. The economic factors which create resistance to multiple listings may be politically powerful. But the ESA explicitly bars NMFS from considering economic factors in a listing decision, just as it requires the agency to follow the best available science. NMFS has an obligation to prevent the extinction of North Coast summer steelhead.


1 Since steelhead/ rainbow are classified as members of the genus Oncorhynchus along with all of the Pacific salmonids, it would arguably make more sense to call rainbow ‘freshwater salmon’ than it does to call steelhead ‘anadromous trout.’ Anyway. 

2 Or unless a source of the early-return gene can be found in landlocked rainbows in the same watershed – as we have above Scott Dam on the upper mainstem Eel.

3 (For salmon, these units are ESUs, or Evolutionarily Significant Units; for steelhead, DPSs, or Distinct Population Segment. It’s a regulatory mess that leads back to the fact that rainbows are governed by the US Fish and Wildlife Service because they live in freshwater, but their relatives that run to saltwater are regulated by NMFS.)