Quest; 410; Restoration of the San Joaquin River

Following the Q radio production was produced in high definition tonight on Quest for more than 60 years. Parts of the San Joaquin River have been drained to provide water for thirsty farms. Quest looks at an ambitious effort to bring California's second longest river and its historic salmon run back to life. And have you ever wondered what your most ancient ancestor looked like. Take a ride in these scientists were diverse. Evolution a machine to find out. Major funding request is provided by the National Finance foundation. Additional support provided by the Amgen foundation BSD backed Bill Junior foundation the William K. Bose Jr. Foundation the Durkin Charlene Capps NL

Foundation and the Valdes family foundation support is also provided by. Long ago in the shadow of the snow covered mountain tops a mighty river was born. It tumbled down mountainsides and ran through forests and wetlands. It nourished the earth as it flowed through the bally giving life to a multitude of birds trees people and an abundance of fish. There are historical accounts that the residents near the town of Fryatt would have a hard time sleeping at night because of the sound of the salmon moving upstream. But in less than a generation long stretches of this great river ran dry. The river beds became part and barren and the fish and birds disappeared as the water was siphoned off to quench the thirst of California's booming

agribusiness. This is the story of California's San Joaquin River. But the ending has yet to be written. The San Joaquin is 330 miles long the second longest river in California. At one time. It was famous for salmon. Historically the San Joaquin River used to have the second largest salmon run in the state. Hundreds of thousands of spring run in fall run should of used to return every year. By the early 1900s the population of the San Joaquin Valley was growing fast. And River water was already being diverted for agriculture and hydro power causing a dramatic decline in the number of salmon. Still the river flowed continuously from the Sierras to the Sacramento San Joaquin Delta the watershed bustled with commerce. There were riverboat races and family resorts for fishing swimming and boating. But it was not to last the

rivers era of abundance came to an abrupt end with the construction of Frya dam north of Fresno in 1942. The decision to build the dam was a calculated choice by politicians and powerful landowners to trade fish for farms miles of river were all but drained as water was rerouted to irrigate a million acres of arid land from are said to Bakersfield. Within a few years the Chinook salmon ceased to exist in the upper reaches of the sea unlucky river. The thing that's most remarkable to me about them is that in spite of all the changes that have occurred and alteration to their habitat and historical conditions that they still somehow persist you know are the largest of the salmon species. They travel thousands of miles spending three to five years in the open ocean before returning to their river origins to spawn.

Salmon returning to spawn can get up to 50 60 pounds. The interesting thing is when they come back out they may lose 60 percent of their body weight. They essentially stop eating when they reach the freshwater system and spawn and die. Salmon have an explosive burst of speed and the ability to leap as high as six feet. Physical traits essential for the difficult journey upstream. But the dams on the San Joaquin were built too high for the powerful fish to traverse and tunics salmon have been barred from 90 percent of their ancestral spawning grounds for more than 50 years. Today the dwindling population found in San Francisco Bay's Delta hangs on the edge of extinction. But that could soon be changing. In 2004 after environmental organizations including the Natural Resources Defense Council and the bay Institute sued the Federal Bureau of Reclamation a federal judge ordered that water be

returned to the river. Two years later the government and the environmental groups along with the fry and water users authority representing thousands of farmers agreed to a historic court settlement to restore the San Joaquin River and reintroduced spring and fall run chinook salmon. We knew going into this that making all those parties happy would be very challenging to near impossible. Jason Phillips job with the Bureau of Reclamation is to manage this delicate balancing act and make sure the commitments of the settlement are implemented. What they should look like is a river system that can handle the flows that are called for in the settlement. Well it also can support adjacent agriculture can support a recreation that can support habitat and wildlife corridor or through all the reaches. This is the most ambitious and unique river restoration project that has been undertaken. Other rivers have been. Restored and

enhanced. In this case we have a river that quit flowing as a year round a river for about 30 miles. The river began its return in October 2009 as water flows from Frye and dam were gradually increased flows up to forty five hundred cubic feet per second up from 500 are planned under the settlement scientists believe that will provide enough water to sustain salmon and leave adequate supplies for farms in urban centers. Already the river is wet from the dam to the delta. Restoring water and restoring the habitat will help bring back our historic salmon runs. But there are a lot of other native fishes that will benefit from restoring the San Joaquin. There also be a lot of habitat that's created along the banks and that's going to benefit a lot of migratory birds that fly up and down the central valley every year.

Since Frank dam was built in more than 80 percent of its water diverted the east side of the sea in Joaquin Valley has been some of the most productive farmland in the United States. Under the settlement water will flow down the river year round all the way from Frye and dam to the delta. The deal requires farmers to restore 15 to 17 percent of the water they've been taking up until. Now. Many of the area's farmers are nervous. All of this can be cut back severely. We just don't know how much yet. I don't know how many guys will be able to go out and actually plant for generations of Jim Eriksson's family have worked this land in Madeira County growing peaches omens and other crops since his grandfather bought the property in one thousand twenty but less water and higher costs mean hard times for many family farmers. Jim tried talking his sons out of staying on the farm. You try to convince them to get out of because it is an easier way of life somewhere else. But the

pride I have of home. As you can hear. It's. This great. Water is the lifeblood of the farm so the Eriksson's are looking for ways to do more with less. Originally were all flood irrigation. We are now putting in lycra sprinklers drip irrigation. We'll spend the 20 20000 25000 dollars per year for just the water. While growers make changes to compensate for reduced allocations. Increased water to the river is already transforming the landscape. One hundred and fifty three miles of river from Fryatt dam to the confluence with them are said River in your tour Loch are being restored river habitat will be created. Barriers will be removed and new passageways built threatened spring run Chinook salmon are to be reintroduced by the end of 2012 and nurtured until their self-sustaining while.

Now this. This is a river right. Gerald Hatter is a senior scientist with the California Department of fishing game as the closing increase. His team of researchers and engineers measures the water levels and tracks the speed of the current. They carefully monitor the temperature which is key to salmon survival. Making sure the San Joaquin water is cold enough will be a considerable challenge particularly for spring run salmon. They'll hold over and cooler holding pools until befall when they spawn. That means if they have to be in the system during the summer and river temperatures in the San Joaquin system typically are not suitable for that. Spawning females lay and hide their eggs in the gravelly river bottom where the shallow water moves rapidly over the rocks infusing the river in the row with oxygen. The stretch of river being

restored for the salmon is divided into five breaches that pose a range of predicaments. Reach one begins directly below fry and Gammon has always had water year round. But downstream a gravelly forward where reach to begins the river starts to dry up. For decades much of the twenty four miles of reach 2 has been waterless most of the time. Reach to. Terminates right here at the Mendota pool. Most of the area upstream of this pool is a sandy dry riverbed. Most of the water in the Mendota pool is pumped from the Delta via the Delta Mendota canal to be delivered to agriculture in the Central Valley. The Mendota Dam is one of the major barriers to salmon but rather than adapting the structure scientists decided to avoid the dam and pool altogether.

If we were to let the river flow as it currently flows we would have to make sure that the fish didn't get sucked into the irrigation water. Rodney Eade was chosen to be the independent restoration administrator. He and his team of experts advise the government agencies leading the river rescue. The construction of a river bypass will take water in from the river upstream of the pool and cut across and below the pool to rejoin the river farther downstream by a hundred fifty yards or so. As many as a dozen Urias will require large scale restoration work. For example the flood gates on reach for at sea and slew are big dead ends for fish. This part of the San Joaquin River hasn't had flow in it for quite a number of years and under the restoration program these gates will get rebuilt in a way that will make them both serve as a flood control purpose that they currently have but also so they're

fish friendly so that juvenile and adult salmon can move through these gates safely. It could be decades before we see if the restoration project achieves its goals. But one thing is certain the CM what he will become a living river again and the success of this restoration could decide the fate of the Chinook salmon species whose fabled forbearers were born in the cool ripples of the sea and Joakim a century ago. We're going to be restoring a living river to being back historic salmon runs and to do it in a way that reflects the modern world we live in where water supply now has a lot of different demands for agriculture and for urban uses as well as for the environment. The San Joaquin River restoration program is really a model for a water resource issues in California. Looking for Bay Area hikes discover local science and nature online with Quest

explorations. Use our interactive maps to find photos trail information and insights from local naturalists at KQED dot org slash Quest. When I was a little boy my parents only saw my rear end because I was bent over turning over logs and stuff and rocks and bringing stuff home and collecting anything strange. I in fact discovered that I could make a living doing what I love to do since I was a little boy and that was basically studying weird stuff. I'm an evolutionary biologist I study who's related to whom which is the baseline of all biological endeavor. Typical trouble free drugs issue. You heard it here first. I'm fascinated with behavior. That's a classic way would you see. It. Better water loss through the day. Then even though you. Know.

It's great. You know a lot about the mammal dunno lots about the birds but it's how little we know about the little stuff. It would surprise you. Oh he's wonderful. If you watch on television. Some of these specials on the Serengeti where we know the number of hairs on the south end of a northbound I ina but the frog sitting on the rock next door may be a brand new species and we have no clue. I'm fascinated with the way that organisms deal with hostile environments and frogs which are are my specialty. African frogs are ideal for this because they're so incredibly sensitive that in fact they make a marvelous indicator of Environmental Health for the past thirty eight years of 39 years I've been bringing back stuff from Africa. I'm a very lucky guy. I was born in San Francisco and I found a place in the city I was born but that's 150 years old and the oldest scientific institution in the United States west of the Mississippi and I got a job and I've been here ever since and probably have had more fun per unit time than anybody else.

Be a part of quest every day on our community science blog comment on stories see exclusive behind the scenes producer's notes and get breaking news from the Bay Area science writers KQED dot org slash Quest. Somewhere far from civilization in the deepest densest jungle alone paleontologist Bush whacks through the undergrowth he's searching for the bones of long dead animals. But this isn't the jungle and David Haussler isn't a paleontologist. Paleontologist study evolution by digging up fossils and working out how the animals changed their morphology their shapes through the ages.

We take the DNA of living animals and work backwards to what the DNA must have looked like. 10. 40 100 million years ago. Hostler is a professor of biomolecular engineering at the University of California Santa Cruz. He specializes in understanding the DNA of extinct creatures. But you won't catch him with a shovel in his hands. We actually look at the DNA of living species. And we use the computer to take that DNA. And trace it back. To find out how it looked in the past. And how it changed over the millions of years to create the different species that we see today. It may be a letter. Down for Jurassic Park and the easiest but real dinosaur DNA is simply too fragile to survive the 200 million years since the Jurassic period. If you want to find the DNA of extinct beasts How is Louise revolutionary new process called computational genome IX may be

your only bet. Why it would be great if we could recreate the DNA as it was from the ancient species by digging up old fossils and extracting the DNA. Unfortunately it's very difficult to get DNA that's older than about 100000 years. If the ks to the point where you can't determine the letters of the DNA of 100000 years as an eyeblink. We're talking about a hundred million years for the evolution of mammals. Although his process is quite complex David hostlers is simple. So we don't actually find the animals themselves or their remnants the bones but we can reconstruct with the computer analysis what their genomes looked like. And it genome. Is what determines the animal's shape. And size and behavior. The genome is the total amount of DNA in one cell. You can think about it as all of the information it takes to make a complete

animal from starting from a single fertilized egg cell. It's actually an enormous amount of information about three billion letters APC's T's and G's. Are needed to describe all of the information in the genome each one stands for a chemical base and they're all arranged in this long famous double helix that you see. Thanks to the Human Genome Project an exact detailed map of the human double helix was completed in 2003. The genomes for other mammals like mice dogs and chimps followed comparing the genomes of various mammals to the human genome has yielded some surprising results. We discovered that there were much longer stretches of 100 percent matches than anybody believed could exist. We call these the ultra conservative elements of the human genome. Intonations happen all the time all over the genome. But in the important regions most of the changes are detrimental they

reduce fitness their changes to important and critical functional elements and it's hard to randomly find a change that will improve the element. So whenever we see an element that's unchanged for hundreds of millions of years we know that nature is trying to change that and failed. That means that element is really important. It turns out that all mammals share 40 percent of our genome. That means we can be sure we all inherited the unchanged portion from the original mammal. From a single shrew like nocturnal creature lived about a hundred million years ago. You have a species descendant that are as different as a blue whale is to a mouse is to a human. The evolution of placental mammals is an extraordinary opportunity to understand evolution in action. What in the genome allows this enormous diversity of body plan that we see. In different mammals. Think about dogs. The different breeds

of dogs exhibit an enormous diversity of size behavior and all of these are caused by changes that happen in the genome relatively quickly. What makes mammal genome so malleable. One way for Hausler to study the flexibility of the mammalian genomes is to run evolution in reverse looking for what genes changed in when using a complex set of computational simulations. He's even managed to back figured the genome of our common ancestor to an accuracy of 98 percent. But he's also learned some interesting things about modern humans. So the algorithm we called reverse evolution is a computer method for turning the clock back as it were. The computer actually compares all three billion bases of the human DNA to all three billion bases of the mouse DNA to all three billion bases of the dog DNA etc.. It's an enormous amount of

computational effort we have a very large cluster with more than a thousand central processing units all churning away doing these comparisons. We scanned the. Genomes of animals. Looking for regions that hadn't changed for hundreds of millions of years and then suddenly changed a lot in the human genome. Suddenly we found one of the most dramatically changed elements may be involved in the evolution of the human brain. We call the element. Human accelerated Region 1. This human accelerated region one gene nicknamed har one now lies at the core of the team's ongoing research. Now our common ancestor with the chimpanzee had a brain about the size of the chimpanzee. So the difference came in the human lineage sometime in the last 3 million years. Something changed in the DNA that caused the human brain to be much larger than its ancestral form. In the hunt for our common mammalian ancestor. How Islam may have touched

on the essential thing that makes us human. One of the genes responsible for our huge brains we take those elements of DNA and we take them into the wet lab and we try to figure out what they do. Right now. We also have the capability to synthesize DNA and try it out in cells. You can actually change the whole gene. And then look at how the mouse develops differently. We can even reconstruct the ancestral version of this gene as it existed 50 or 100 million years ago. And then see how the mouse behaves with the old version of the gene versus the new mouse or human version of the gene. It's pretty obvious that David Haussler isn't from the old school of paleontology but in the search for the true nature of the ancient animals DNA is rapidly becoming the new dig site and computers are the shovels bringing back the dinosaurs is still well out of

reach. Neither the genomes nor the genetic science are ready for it. But in the end how is lers work may not only give us a clearer picture of our common the Malian ancestor. It might just offer us a better understanding of ourselves. My passion what drives me to look at this is to understand. How humans became human. How a whale became a whale. How a leopard became a leopard. These. Are the stories of evolution the changes and the DNA will ultimately be the story that we understand. Of how the different animals that roam this planet so successfully today came to be the way they are. Did you find this week's stories interesting. You can log on the web 24/7 or download Podcasts from Apple's iTunes. You can

also hear Quest Radio Live Monday mornings at 6:30. Thirty eight point five on the radio dial. And remember to check out our online explorations and our educator guides Quest. Major funding request is provided by the National Science Foundation.

Additional support provided by the Amgen foundation BSP back Bill Jr. Foundation the William K. Bose Jr. Foundation the Durkin Charlene Capps NL Foundation and the vedettes family foundation support is also provided by KQED HD Productions.