male announcer: this program was made possible with generous support from the open rivers fund, a program supported by the william and flora hewlett foundation, patagonia media grants, the maybelle clark mcdonald foundation, the freas foundation, the dalton family trust, and the north umpqua foundation. ♪♪♪

♪♪♪ shane anderson: the world has not lost an entire race of salmon since the prehistoric saber tooth went extinct over 5 million years ago. ♪♪♪ shane: but now time is running out for the last wild runs of spring chinook, arguably, the most revered pacific salmon. ♪♪♪ ♪♪♪

deborah giles: salmon are the most amazing species on the planet, and really, if you're talking about one group of those salmon, the spring chinook salmon are at the top of that list. silas whitman: spiritual importance, that fish is very pronounced. russ thurow: friend of mine calls them mariners and mountaineers, and that's really an apt description of these fish. they're basically the best of the best, and these fish are at really high risk of extinction. mike miller: spring run's just a good example of a species that is so critical from an ecological, a cultural, and an economic perspective, yet it's just disappearing, and they've been disappearing for decades, and nobody's really done anything about it. they're the lost salmon. ♪♪♪

shane: i've spent the better part of the past decade documenting wild salmon, the places they live, and the issues they face. ♪♪♪ ♪♪♪ shane: the magic of wild salmon is their connection to place. with every species, life history, and migration genetically designed and intimately connected to their home waters and ecological communities, there are still some places left on earth where you can see landscapes come alive during the annual migrations. ♪♪♪ shane: but closer to home, the fabric that wild salmon weave throughout the northwest continues to unravel at alarming rates, with many species from many places at risk.

♪♪♪ shane: as the first salmon to arrive home, the spring run of chinook have one of the most fascinating migrations in the animal kingdom. they're a species of desire for an entire ecosystem, but victims of the modern world. they've been the sacrament and cornerstone for some of the oldest civilizations in north america and one of the most sought-after fish on earth that triggers a cult-like following of fishermen. ♪♪♪ shane: chinook have the largest range out of any pacific salmon, but springers only exist in the southern end, where over half the genetically unique populations have already been extirpated. ♪♪♪ shane: so, why has one of the most revered animals on earth been allowed to virtually disappear from the

vast number of rivers they once called home? and what does their future hold? these questions led me on a two year journey throughout salmon country in search for the last wild springers, while exploring their connection to people and place and a new genetic discovery that could help save the king of salmon before it's too late. mike miller: my name's mike miller. i'm a genetics professor in the department of animal science at the university of california davis, and this is my genetics lab. my goal as a geneticist is to use genetics to improve conservation outcomes for threatened and endangered species. we've probably worked on more species than just about anyone else on the planet.

we've been pretty interested in the genetic basis of migration characteristics, and we've worked on that in a number of species from, you know, monarch butterflies to pacific salmon. in many ways, the application of genetics to issues in conservation have been pioneered in salmon for the last 50 years. salmon are always at the forefront of how to use genetics in the most efficient way to help conserve species. and one of the reasons is that many salmon populations are threatened or endangered or are already extinct. and over the last 20 years, as methods within genetics have changed, and some of these methods are methods that i was involved in developing, it became possible to really do high resolution genetic analysis of virtually any species. and when that became possible, i knew what i wanted to work on. obviously, i wanted to work on salmon.

one of the most striking variations within a biological species of salmon is differences in adult migration timing. so, spring chinook verses fall chinook, for example. so, i wanted to understand the gene or the genes that were involved in that process, but then also how that genetic variation evolved. david montgomery: if you look at what happened in the period when the pacific salmon diversified during about 20 million years ago and 10 million years ago, the whole physiography, the topography of the western edge of north america changed radically. the olympic mountains came up. the northern california coast ranges were up. the cascade range got taller. the mountains on the edge of western north america changed right in that period when the pacific salmon evolved into the species we know today from the ancestral salmon. the evolution of the topography shaped

the evolution of the pacific salmon. in other words, the salmon evolved right along with the landscape that we know today. shane: chinook are the largest and most diverse out of the five species of pacific salmon, and evolved to have different seasonal migrations. in alaska, in the northern hemisphere, they migrate in the summer when rivers are free from ice. and in the southern end of the range, they predominantly return in the spring, summer, and fall. ♪♪♪ shane: they're born in fresh water nests called a redd, where their home waters are imprinted into their dna before migrating to the ocean where their body chemistry changes as they adapt to salt. ♪♪♪ shane: their ocean migrations are based off their rivers of

origin as they travel thousands of miles over several years, foraging for food and utilizing internal compass navigation until a primal instinct calls them home, where they're able to smell their way back to the very waters they were born in. mike: salmon populations become adapted to these very specific environments. when i say adaptation, i'm talking about genetic differences that cause individuals to have distinct characteristics that allow them to be successful in the habitat, in this very specific habitat that they've evolved to utilize for thousands of years. shane: a spring migration allowed chinook to reach habitats that no other salmon could by getting a head start on long migrations and timing spring runoff perfectly to ascend waterfalls. mike: so they migrate up in the spring over summer through really harsh conditions. but the benefit they get is they get to spawn a couple months

earlier than what fall chinook would be able to spawn, and it gives them a competitive advantage. ♪♪♪ shane: after returning home from one of the most arduous journeys in the animal kingdom, they will select a partner and pass down 15 million years of genetic information to the next generation, before making the ultimate sacrifice. one of the few animals on earth that will never know their offspring. ♪♪♪ shane: just as salmon coevolved with the landscape, people coevolved with them.

shannon wheeler: the nez perce have been documented 16,500 years, the oldest archeological site in north america. to this day, it is a nez perce site. and so it pretty much crushed the ice bridge theory. that relationship to salmon is part of our creation story. silas: naco'x kuus, naco'x kuus, naco'x kuus is the generic name for the salmon, but usually it applied to spring chinook, which were the first ones coming in. they're probably the filet mignon of the fish world when they cook them. the oil has got a magical propensity to do healing. salmon were the ones that said, "we will help to save these people. and to make sure that their time on earth is spent wisely, we will give of ourselves.

naka williamson-cloud: because of that ancient covenant we had with the salmon as the first one that stepped forward on our behalf, and all those that lined up behind him, that it's the way that we also show the salmon that we still need him, we still appreciate him, and that's part of what's bringing him back is to fulfill his promise to our people. their spiritual well-being and our physical well-being is attached to these traditional foods, as well. from that standpoint, you know, i think genetically salmon is imprinted on our dna because if you think about the generations, thousands, going back thousands of years that our people have subsisted on these, and those are the foods that our bodies know. mike: willamette falls in this area was a hub for people

long before people of european ancestry started colonizing the west, and it was a hub because it was such an important salmon fishery. i wish i could've seen them in person before they looked like this. the west was colonized through oregon city, which was the end of the oregon trail. i was born at willamette falls hospital. my great grandma worked at the diner for almost 40 years. her great grandfather came to oregon on the oregon trail. you know, just growing up, salmon was such an important part of the culture. it's just what people talked about, you know. it was just an area of blue collar, salmon fishermen.

mike: i never planned to become a geneticist, that's for sure. the only thing i'd actually ever thought about becoming was a fishing guide. there's still a spring chinook fishery. it's primarily supported by hatchery fish. the fishing's just not as good as it used to be. it's inconsistent. there's some years where the returns are really low. and willamette produced a large number of spring chinook, certainly hundreds of thousands, if not millions each year. now all the major tributaries have unpassable dams on them. you know, we've degraded the habitat so substantially that the willamette barely supports any natural production of spring run.

shane: willamette falls was the end of the oregon trail but the beginning of western expansion, where new ideology of manifesting destiny changed the ancient relationship with salmon. wilbur stockish: we had a commerce system in place, and salmon was our economy. and as soon as the settlers arrived, and they disrupted it. they wanted to catch them all, because they thought it would never end, not realizing that our people never took more than we could use. that's why there was millions of fish. shane: as unregulated harvest was in full swing, the west was being built on the backs of salmon. rivers were turned inside-out in search for gold. ancient forests were liquidated and entire watersheds dammed. ♪♪♪

wilbur: each one of these dams right now that are built here are built on village sites and are built on fishing places. shane: to mitigate for the loss of salmon, fish hatcheries were seen as the silver bullet. by creating a factory production system, it was assumed that salmon would no longer need rivers to provide fisheries. wilbur: that was the promise: we will supplement and rebuild. you'll have more fish than you have previously had. ♪♪♪ tasha thompson: genetic advances have happened really, really rapidly over the last few years. this is being called the golden age of genetics right now. genetics basically says how you inherit different characteristics from your parents.

we have one copy of our dna from our mom, right, and one copy of our dna from our dad. and salmon are exactly the same. that dna contains this instruction manual to build everything in the organism. if you're a fish it says how or where to put scales. it tells you what you're supposed to eat, if you're supposed to be afraid of the killer whale or not. it contains everything. i joined mike's lab right as they were working on the initial discovery, and that was life-changing for me in so many different ways. mike: so, geneticists are interested in variations. so, when you're looking out in nature, and you see a variation within a species, genetics is about understanding that variation. tasha: a species can be incredibly diverse within that species, and that's the case for chinook salmon.

mike: if spring run chinook were to disappear, it was thought that they could re-evolve rapidly from fall run chinook. tasha: we took spring chinook, and we took fall run chinook, and we compared their dna across large sections of their genome, and we found that there was this one single region that had this gene called greb1l that was different between spring run and fall run chinook. and the difference we see between spring chinook and fall chinook is just screaming. like, it's a huge difference. mike: i thought it was really cool, you know. we figured out the spring run gene. i know that at least five endangered species act petitions that have been submitted directly based upon our research. four were in chinook salmon, and one was in steelhead. steelhead also have early and late migrating form, and it turns out it's the exact same gene and evolutionary mechanism

that produces summer run versus winter run steelhead. that genetic variant at the single gene is so important to protect, because if that disappears, we might have to wait a million years to get it back. tasha: that risk is what's going to end up being factored into the endangered species act. ♪♪♪ richard nixon: these problems will not stand still for politics or for partisanship. shane: the endangered species act is one of america's bedrock environmental laws that was enacted by the nixon administration in 1973 with unanimous support from the senate. and today, 28 distinct population segments of salmon have been listed as threatened or endangered. mike: the endangered species act doesn't just protect distinct biological species, but there's a clause in

it that also legally protects what are called distinct population segments within a biological species. that distinct population segment clauses is the reason why most species are protected--for example, grizzly bears or bald eagles. if the endangered species act only protected distinct biological species, chinook salmon could go extinct in california, in oregon, and washington, but the overall biological species wouldn't be threatened or endangered, because there'd be some healthy individuals in alaska. it's important to conserve this diversity, this subspecies level diversities, adaptations to distinct geographic areas. the question is, well, what constitutes a distinct population segment of salmon? our results show that spring run do warrant some kind of protection under the endangered species act. but right now spring run populations and fall run populations are grouped into the same conservation unit.

shane: current management can be problematic in rivers like the klamath, where tens of thousands of fall chinook still return and provide a harvest opportunity for local communities, compared to the spring run that's on the brink of extinction. shane: right now, the driving force behind the conservation policy has been that if spring run disappear, they can easily come back. we found that that's not the case, right? if spring run disappear, they're gone forever. i thought, well then obviously the conservation policy would change, but i was really naïve. i didn't realize the power that politics can have on science. ♪♪♪ shane: the columbia basin was once home to the largest chinook population on earth, before 60 dams

wiped out two-thirds of their genetic diversity. but one of the greatest races of salmon still exists and travels over 800 river miles past eight dams and climbs over 6,000 vertical feet into idaho's middle fork of the salmon river. ♪♪♪ shane: since fall chinook are unable to make this epic migration, this is one of the few populations of spring chinook that are listed under the endangered species act. russ: it's the largest wilderness area in the lower 48. a lot of the drainage is still intact. so, the middle fork is particularly unique, because it supports one of the few remaining wild populations of spring, summer chinook in the entire columbia basin. we assessed populations across the whole drainage, and only 4% of the existing spring, summer chinook habitat still supports

wild chinook like we have here in the middle fork. in all those other drainages, they've either been extirpated, or they've been altered by hatchery fish introductions. these fish are still the native wild genetic population. and we have diversity both within tributaries and across tributaries. ♪♪♪ russ: there's an account in the lewis and clark journal where they write, "salmon numbers are almost inconceivable." they were talking about chinook. how many salmon? the historical account suggests somewhere between 10 and 16 million adult chinook entered the columbia each year. two to six million of those came into the snake basin that were part of here in the salmon. ♪♪♪ shane: finding wild spring chinook today in the snake basin is no easy task, and at an average of one adult salmon per

river mile, the middle fork is the last bastion, where russ has been monitoring these unique populations for over four decades. russ: just keep a low profile. you might want to get your tripod set up in case she turns and starts digging. russ: a lot of the fish will spawn in the same riffle where they came out of the gravel as fry. our fish produce a lot of eggs. the average female produces about 5,000 eggs.

some people call these the ultra marathoners, the mariners and mountaineers of the salmon world. these fish are migrating over 800 miles to here, and they're climbing close to 6,600 feet in elevation at this spot, and there's no others in the world that do that, so they're the best of the best, the rarest of the rare. basins like the middle fork that are very high elevation are going to maintain cold air refugia, even in the face of a changing climate. and so the fish here have a better chance of surviving as lower elevation areas are warming. shane: don't they have different characteristics where they select the strongest mate? russ: yeah, and i mean what we're witnessing here right now is natural selection here on the spawning beds today. the dominant males are driving off the lesser males, and they're jockeying for position next to the female to get their sex products in the mix, so that

they're part of the next generation. that's what all the fighting and driving each other away and stuff is. all those things are an adaption that has been developed over millions of years to make these fish the strongest they can be. and if they weren't, we would not have them anymore. they'd have been gone decades ago. it's hard to predict how long they have, but some scientists have said probably about four generations. mike: those fish are so unique. if those fish are lost, they're not gonna come back in any kind of timeframes that humans think on, which i think it is tragic, when you consider how unique and how amazing they are. and, you know, that's not even considering what that would mean to the tribes that have relied on them for thousands of years. nakia: so, we're here today practicing our

tradition of coming to catch the salmon. this area we call yawwinma or rapid river, which means the cold water. and right with the junction with the mu'lpe or the middle salmon river, which was a traditional campsite of the nez perce people going back thousands of years. many of our families originated from this area along the salmon river. this has become a more important fishery for nez perce people is because the salmon river doesn't have any dams on it. one of the largest chinook fisheries for the nez perce people are sitting behind dworshak dam currently. ♪♪♪ nakia: we have only a few places that have remained good enough to still continue our fishing practices. ♪♪♪ nakia: so, the supplementation efforts that

happened right here, the ability to try to mitigate for those dams that have been built on many of these rivers, but still we find us at the point where maintaining those genetics or maintaining the stock that originated from these places, which is important, it don't look like it's sustainable without us taking another step. ♪♪♪ russ: honestly, every time i see these wild fish in this high-quality habitat spawning, it gives me hope, because they have overcome a whole lot of obstacles to still be here. we're about 2% of what was here in the '50s and '60s. we, as humans, tend to judge a resource's condition based on our current experience of that. and so a lot of people really don't comprehend what the historical chinook runs were and what the true potential is.

so, there's a long history of studying chinook in idaho. really starts back in the 1940s. in about 1957, idaho fish and game standardized surveys in six different middle fork tributaries, including marsh creek. the middle fork supported close to 50,000 adults. that was through the 1950s, '60s, before the precipitous declines. shane: the collapse of the middle fork spring chinook directly correlated with the construction of four controversial dams on the lower snake river that would have unintended consequences for migration. russ: the migration corridor in the snake and columbia has been dramatically altered. there are now 325 miles of reservoir in what was once a free-flowing river. and those reservoirs and the dams that create them have dramatically increased the mortality in migrating smolts, in particular, but also adults.

within the columbia basin, you know, there have been efforts to recover salmon steelhead for close to 40 years now. i think the estimate now is over 18 billion dollars have been spent on those efforts, and yet our fish are still at very high risk of extinction based on the most recent national marine fisheries service recovery plan. shannon: turn those bigger dials. breach the dams. that's the one we can control now, let's do it. i'm pretty sure it's going to work. science says yes. russ: the comparative survival study reaffirms it again, and essentially says that if the snake is restored, we'll see at least a threefold increase in run sizes, and if the snake restoration is coupled with maximum spill at the remaining columbia dams, that would result in a fourfold increase. you get another 1,000 adults back in here, and that's just going to keep building each generation, and