Delta smelt symposium, part 3: The path forward: Climate change, recovery planning, and restoration

Liberty Island emergent tidal marsh sliderbox
Emergent tidal marsh at Liberty Island
Presenters discuss climate change, extinction, artificial propagation and stocking, and tidal marsh restoration

Coverage of the Delta and longfin smelt symposium, Is Extinction Inevitable?, continues

The second round of presenters provided a long list of potential causes for species decline, and conference attendees weren’t feeling very optimistic.  Is there anything we can do to preserve and restore the species?  In this post, presenters look to the future at the intersection of recovery planning, restoration efforts, and the hard decisions that lie ahead.

Presentations featured in today’s post

Click on the link to jump to presentation or simply scroll to read each in sequential order:

DR. LARRY BROWN: How will climate change induced warming affect Delta smelt?

Studies foresee significant changes in the maturation window

Larry BrownBIO: Dr. Larry Brown is a Research Biologist with the U.S. Geological Survey, California Water Science Center.  Dr. Brown has over 35 years experience working in California aquatic systems. He has published over 80 scientific articles and reports on California fishes, benthic macroinvertebrates and benthic algae.  Dr. Brown is currently involved in studies of the California stream systems as well as ongoing work in the San Francisco Estuary, including the effects of climate change on selected fish species.

Dr. Larry Brown gave a presentation on climate change and the potential effects on Delta smelt.

Larry Brown Delta smelt_Page_05One thing I always like to stress when I give this talk is that we’re not talking about direct mortality of fish,” he began.  “We know Delta smelt can actually move around the estuary pretty easily now based on recent work, so this is more about habitat compression.  As climate change kicks in and these outer areas get warmer, these fish are going to move.  They are not going to sit there and wait to die, they are going to do the best they can to find some place where they can make a living.”

Larry Brown Delta smelt_Page_06Dr. Brown noted that this work has been going on for a while.  “The first two papers that were published were based on some of Bill Bennett’s early work summarizing field distributions and some early work at the hatchery trying to define what the thermal niche of the species is,” he said.  “At the last Bay Delta Science Conference, I got to talking with other people, and we realized we have a chance to combine these climate change predictions with actual very good physiological thresholds and end points, so that’s what we did.  That work has been published in this PLOS-One paper that came out a few months ago.”

Dr. Brown said he’s be talking about two things in his presentation:  “One is what we call the maturation window, which I’ll describe a little better in a minute, and that’s based on about 24C end point which is the temperature at which juvenile fish start expressing genes associated with stress, and then the beginning of the spawning window.  I used the old spawning window of about 15 to 20 degrees centrigrade; that’s now considered to be 12 to 20 degrees centrigrade, it’s just a relative difference so these results still apply.”

Larry Brown Delta smelt_Page_08He then explained the concept of ‘maturation window’.  “Our basic is idea that fish are spawned; and as spring and summer progressing, water can get really warm,” he said.  “We think if it gets above 24 degrees, these fish are going to be lucky to break even to have grown a little bit.  So if you’re in a really warm phase like this 2090 projection, probably you’re lucky to make it through this time period and survive.  You probably haven’t put on a lot of length, you’re probably in pretty poor condition.  Then as the temperature drops, assuming there’s food around, you have a chance to eat, and then as you get closer to the beginning of the spawning window, you’re developing eggs and such, so this period where things seem to be good for growth and maturation is what we call the maturation window.”

Larry Brown Delta smelt_Page_09In a life history context, this is kind of how it lays out,” he said.  “We have this juvenile period from about June through December where fish can grow, and depending upon how long warm temperatures extend through this period, that period for growth maybe long or short.  Maturation usually starts happening December-ish, and then continues to the first spawn, which is February or March.  So we’re looking at how much good conditions fish have temperature-wise for accomplishing these things.”

Larry Brown Delta smelt_Page_10Dr. Brown then briefly discussed how they modeled projected water temperatures in the Delta.  “There are these big climate change models that are downscaled to your region of interest,” he said.  “We had downscaled water temperature data over the Delta.  There are a number of stations in the Delta that have collected water temperatures, some for longer periods of time than others; for stations with two years of more of water temperature data, we could build these little regression models based on air temperature and water temperature at the station the day before, and basically the amount of sunlight the Delta is getting.  Wayne Wagner developed these very simple regression models that we then took the projected air temperatures, used to calculate projected water temperatures in the Delta; this actually worked really well.  So our final output was 100 years of projected water temperatures at selected sites.”

Larry Brown Delta smelt_Page_11From 100+ recent climate-change projections from CASCaDE 1 models, they chose four scenarios; the results he is going to show are for the least changed scenario (a little bit warmer and no change in precipitation) and the most changed scenario (quite a bit warmer and drier).  “The important thing to realize is that what at the time was an extreme scenario is now considered middle of the road, maybe a little on the high side of the middle, but definitely not an extreme scenario,” he said.

Larry Brown Delta smelt_Page_12In the most recent paper, these are all the sites we looked at,” he said, noting there were sites in the north Delta, along the Sacramento River, along the San Joaquin, and out in the bays, from the confluence outward.  “Based on historical data up until this time, the San Joaquin River is actually pretty warm already.  The Sacramento is generally cool; the north Delta is similar to the Sacramento, generally a little warmer, and the bays are generally cool because of the marine influence from San Francisco Bay.”

He noted that he would be showing data from sites in the Delta that have been pointed to as the best habitat that’s still out there, which would be the north Delta, Decker Island on the lower Sacramento River, Jersey Point which is the best there is on the San Joaquin, Mallard Island, and Martinez, which is on the west side of Suisun Bay.

Larry Brown Delta smelt_Page_14Dr. Brown then presented a slide showing how the duration of the maturation window progresses over the century, noting that the data shown are the medians within each decade, as well as the maximum and the minimum.  “You can see they decline, and for the red, the warmer scenario, they actually decline quite a bit; the less severe scenario of course not as much.   Jersey Point, the San Joaquin is the worst habitat we have now, it actually starts at a lower value but still declines, and you can see the red one declines by like 50 days generally.”

Larry Brown Delta smelt_Page_15He said it’s the same for Liberty Island, the Deep Water Ship Channel, and Decker Island as well.  “Throughout the range of the Delta smelt, as the century progresses, this maturation window is going to contract,” he said.  “What that means is you’re going to have smaller fish with less time to produce eggs which is probably going to result in the population level decrease in fecundity of the population, unless they figure out someplace else to do their thing.”

Larry Brown Delta smelt_Page_16He then presented the data for all the sites, noting that he calculated the percent loss of the spawning window based on 272 days from June to February.  “With the least changed scenario, it’s on the order of 15%.  If you look over here on the more severe scenario, we’re talking loss of about a quarter of that maturation window, which can’t be a good thing.”

Larry Brown Delta smelt_Page_18He then presented the latest climate change scenarios the IPCC 5th assessment, noting that there were ten climate change models and two greenhouse gas scenarios, for a total of twenty scenarios.  “I calculated the water temperatures, and what I did was plotted the average daily temperature for the period from July to September.  Then I plotted temperatures from 2020 to 2099; there are horizontal lines showing this 24C where stress begins and 27C where mortality begins.  I didn’t have time to plot the old scenarios on top of the new ones, but these definitely include some more severe scenarios than we’ve looked at in the past.

What you can see is not good news,” he said.  “The red arrow shows about mid-century and by that time, Liberty Island, so the north Delta, and the lower Sacramento River, almost all the time, the summer temperatures are going to be at least stressful, if not lethal.  Not good news …

Larry Brown Delta smelt_Page_19Of course Jersey Point is bad already, so it looks the worse; but even if we get out to the confluence, things are looking pretty bad, and even out into Suisun Bay, things are going to get toasty out there, too.”

Dr. Brown then gave his conclusions.  “Significant changes in the maturation window occurred at all Delta sites examined.  The new scenarios indicate there’s going to be no non-stressful habitat in the Delta at all, so presumably fish are going to move out into Suisun Bay where there isn’t anything to eat, so that leaves us with adaptation.”

I usually get a question of, are they going to go into saltier water, or are they going to learn to tolerate the temperatures, and I don’t know,” he said.  “You need to actually integrate that with where the turbidity is, where the food is, and any other factors like contaminants that you can think of.”

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DR. JIM HOBBS: Synthesis of Biology, Ecology and Status of Smelt in the San Francisco Estuary: Where do we go from here?

In order to avoid extinction, we need bold ideas, such as artificial propagation, says Dr. Hobbs

Jim HobbsBIO:  Dr. Jim Hobbs is a Professional Research Scientists and Lecturer in the Department of Wildlife, Fish and Conservation Biology, University of California, Davis.  Dr. Hobbs is also a member of the Coastal and Marine Sciences Institute and Interdisciplinary Center for Plasma Mass Spectrometry at UCD and the chair of the conservation committee for the California-Nevada Chapter of the American Fisheries Society.  His research focuses on the addressing important fisheries resource management questions in estuarine and marine environments in California, Oregon, Washington and Idaho.

Dr. Jim Hobbs began the third session with a synthesis of what we’ve learned about the biology and the ecology and the status. “Both species have collapsed and are now at the point where detection in our monitoring surveys is becoming really rare,” he said.  “We are looking at 0s in our indices in the future, which is a really important issue for management, because they use those indices for setting take issues and other sorts of things, so this is really a major issue.  There are a lot of people concerned about the extinction of these species.

With respect to existing protections for those species, he said that the way we have our biological opinions established and the original recovery plan clearly is not good enough.  “We’ve been trying to recover the species for the last 15 years and we’ve been watching it go down and down and down again, so I think it’s pretty obvious that what we’re trying to do to save the species is not working.  And I’m really concerned that they are already dead, but they don’t know it yet, as Bill said.”

We are in this position because we have failed to develop and implement a real viable recovery plan, he said.  “We haven’t had a good plan. We’ve had several different accords and agreements between stakeholders and agencies that we would try to manage the system in a way to do the best we could for the smelt, but still provide water, because water is an important issue.  Our dual goals to try to do both things in the estuary have clearly not worked.”

Dr.  Hobbs said another issue is the overemphasis on salvage.  “The numbers of fish that are killed at the pumps are clearly important, but how we manage that, how we on a day to day basis, how we try to manage exports to minimize the killing of fish is shortsighted in the sense that we don’t really get a better grasp of how flow and how that volume of water actually promotes the production of smelt, so I think one of the problems is that overemphasis and micromanagement approach to trying to manage this species.”

Another issue is we’ve had a death by a thousand cuts,” he said.  “That conceptual model makes my head hurt.  There are so many different factors that are going on simultaneously amongst different life stages, different seasons, and we’re trying to figure out exactly which one is most important so we can figure out which knobs to turn to save these species, and like I said, that is clearly not working.  It’s really impacting the science ability to actually come up with the key factors that are occurring at any given moment.  It seems like it’s a constant moving target, and science has done its best to sort of figure these things out, but still we are in the situation we are in.”

Hobbs-Smelt Symposium_Page_04That comes down to the lack of our management and political will to stay the course.  We’ve had plans in place, but yet we constantly are changing, we are constantly evolving, trying to fix the situation, trying to micro-manage exports, trying to come up with alternative solutions to save the species other than actually saving the species, so we’ve been kind of dancing around the problem rather than directly addressing it, and I’m probably as guilty of this as anyone else.  This is a science conference, and what we’ve basically seen in the last 20 or so years is a rapid increase in the number of publications on Delta smelt in particular, but it hasn’t translated into more species or more fish.  Both species are in near extinction levels.”

Dr. Hobbs said that at the Western Division meeting of the American Fisheries Society, he was talking with some of the other conservation chairs of the other chapters, and they recommended that he look at the recovery plans for some of the other species in the West that are on the endangered species list.  So he looked at three species recovery plans: the Upper Colorado River has four species that are endangered; the pecos bluntnose shiner, a species native to New Mexico, and the Oregon chub, which is a success story as the species was just recently delisted.

Hobbs-Smelt Symposium_Page_06 Upper Colorado River endangered species:  The Upper Colorado River has the same problems as much of the west:  too much water extraction that is impacting native species, major habitat alterations, the loss of streams, the loss of braided streams, and loss of wetland habitats.  They are doing some similar things, such as addressing and managing flow rates, instream flow protections, major habitat restoration such as setting aside areas that have wetland habitats and trying to reconnect them with floodplain habitats, he said.

Other things are quite different. He said.  “They have a pretty extensive plan to remove and eradicate invasive species, which they realized that it is a difficult task, but for the sake of trying to do something, they are putting a lot of effort into trying to manage and remove non-native fish.  There’s also a lot of research and monitoring.  They are also doing a lot of education and outreach which I think is one of the things that we’re really lacking; we have not created a voice for these species for the communities that we live in.  It’s really important to get community buy in to understand the kind of things that we’re trying to do to save these species, so across the board, education and outreach continually is important.

Hobbs-Smelt Symposium_Page_07Pecos Bluntnose Shiner: The pecos bluntnose shiner is similar; in New Mexico, they are extracting too much water, and in fact, there are parts of this river that actually go dry, he said.  “Here we’ve got a situation like we do in the Colorado where we’ve had major habitat alterations and loss of flows.  In this case, they are talking about trying to enforce the state and federal laws; they are consistently overriding what protections they have because the cities and the communities need freshwater more than they need fish.”

Hobbs-Smelt Symposium_Page_08The Oregon chub:This is a nice success story,” he said.  “They’ve been able to do a bunch of restorations along the Williamette River in Oregon, and also with their research, monitoring, education, and outreach, all these sorts of things that are recurrent themes,” he said.  “They also did propagation and stocking.  They’ve had a pretty active program to manage and stock fish into somewhat natural ponds.  There isn’t a golf course in Arizona that doesn’t have razorback sucker in it, and it’s wildly successful, it keeps the species alive, and they do it in such a way that the fish can grow up as natural as possible.  They are able to tag and track these fish and put them back in the wild and for the most part, they behave relatively normally, and it buys the researchers time to figure out a strategy to save the species and it allows them to restoration on a time scale that’s going to be realistic to save the species, so having this ability to do stocking and propagation has actually been really important in all these situations, particularly with the Oregon chub.”

With respect to a Delta smelt recovery plan, we can continue to manage flows and minimize salvage as we have been; then there is the process to build the Delta tunnels.  “We’ve been relying on twin tunnels as our conservation plan for two species where the connection between those two things is very tenuous at best, yet that’s our best strategy that we have right now,” he said.  “We can continue to do research and monitoring, and I think that’s important, but it has to go hand in hand with a real strategy.  We have restoration being planned, but honestly that’s 20 or 30 years down the road, and Larry just showed us right now, we may not have that much time.  We may need to take actions much sooner.

We’ve had some ideas about non-native species reductions, but it’s going to be a big challenge to try to actively remove non-native species.  We can go out and try to remove all the SAV, and create lots of jobs, but will it have a benefit? I don’t know,” he said.  “Propagation and stocking is the one direction we could go; we need to be integrating this with habitat restoration and management, conducting research, figuring out the best strategy to do this.”

Hobbs-Smelt Symposium_Page_10Dr. Hobbs said he was reading a paper from last year looking at the Endangered Species Act and its conflicts with conservation; he presented a diagram for the paper.  “We’re looking at whether we are in the risk of extinction; I think for both species now, I think we can agree that we are getting close to being high.  Can we reduce the threats in its historic range in a meaningful time? I think we’re at no right now.  What’s the likelihood of being able to ameliorate those threats in the near future?  I think we’re starting to go between very low and moderate, with restoration, but it’s going to take a long time.”

So here we are, we are at a very low level of being able to fix our situation, so that leaves us with two choices,” he continued.  “We abandon what’s happening now, we take novel steps to recover the species.  We could do propagation in ponds, we can integrate it with the restoration we’re doing right now, and we can learn a lot in the process and figure out how to do it right, or we could be complacent and do what we’ve been doing, and we already know where that’s taking us, it’s taking us to extinction.”

With respect to artificial propagation, Dr. Hobbs pointed out that both species currently are already in culture at the fish conservation and culture lab down in Byron run by UC Davis, and a lot of work’s being done to optimize those conditions to keep those species alive.  “We know that both species can complete its life cycle in freshwater so that makes things a little easier because these pond habitats could be done in freshwater parts of the Delta,” he said.  “But both of these species are very sensitive to summer temperatures, so that has to be taken into consideration.  Maybe we can do some habitat modifications to make summer temperatures a little cooler, add vegetation cover, willows – lots of ideas.”

He acknowledged there are many things to contend with, but he believes it to be quite tenable.  “There were historically ponds within the Delta, little dead end sloughs with ponded habitats where these fish probably actually utilized these habitats, and I think restoration should be moving in this sort of direction, and we could do this now.”

Hobbs-Smelt Symposium_Page_13At Twitchell Island, there is already a carbon sequestration site with enough vegetation that it’s keeping water temperatures relatively cool during the summer.  “I don’t if this would work, but I think we should be trying because otherwise what else are we going to do,” he said.

There’s also the Yolo Bypass, he said.  “The Yolo Bypass is a very productive system, we’re seeing growth rates of Delta smelt up there that are higher than they’ve been anywhere else in the estuary, and it’s really hot up there, so somehow these fish are able to make it up there somehow,” he said.  “We need to be investigating more about what’s going on in this area and there are a lot of options that we can do, the Nigiri project for salmon is growing salmon on rice fields as we speak, and it’s working pretty well.  I think it’s something that we as a community need to embrace and try, because we only have two options at this point, and I don’t want extinction, so I think we should try something.”

That’s it.

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DR. PETER MOYLE: Extinction in California fishes: Ecological, biological, legal, real

Dr. Peter Moyle discusses the process for declaring a species extinct

Peter MoyleBIO: Peter Moyle has been working on the ecology and conservation California’s freshwater and estuarine fishes since 1969, culminating in Inland Fishes of California (2002, UC Press). He has co-authored numerous papers on the ecology, status and trends of California’s native and alien fishes. Ongoing research focuses on climate change, reconciliation ecology, and fishes of the Delta and Suisun Marsh. He is Distinguished Professor Emeritus in the Department of Wildlife Fish and Conservation Biology and associate director of the Center for Watershed Sciences, UC Davis.

Moyle extinction_Page_02Dr. Peter Moyle began by saying that the Delta smelt and longfin smelt may indeed be facing extinction in the near future, so he would put these potential extinctions into a broader context, and then describe how to deal with extinction as a phenomenon.

This is a really depressing topic,” he acknowledged.  “It is widely agreed we have entered the sixth mass extinction of life on earth, only this time is not massive volcanic eruptions or a comet hitting the earth; it’s us.  We have met the enemy and he is us.  There’s growing attention being paid to this and books being written.  If you want a more positive look, there’s a book called Dodging Extinction which is quite readable.  This is a topic which is on people’s minds.  Humans clearly are having a major impact on the climate and the species that are here.”

This is especially in freshwater systems, he noted.  “Here in California, we are seeing extinctions looming in our systems, and these arguably rival tropical rainforests in the rates of extinction, or at least those that are projected.  In California alone, almost 60% of our native fishes are extinct or in danger of extinction in the coming decades.”

Moyle extinction_Page_04 Moyle extinction_Page_05

He presented a slide from a study of the status of California native fishes, and noted that all the species are on downhill slides.  “If you add climate change to the equation, it’s not just Delta smelt that are in trouble from climate change, but it is lots of other fish as well.  That number goes from 50% to over 80% of the species facing extinction by the end of the century, and this is also based on a study that was published a couple years ago.”

We all know about extinction of prehistoric animals like the dodo bird, which is definitely the symbol of extinction, he said.  “But it turns out to be only one kind of extinction.  So in this talk, I want to answer these questions in relation to fish, especially fish in California: what is extinction, how is it declared, and how should it be determined, which will be a proposal of sorts.”


So what is extinction?  Dr. Moyle said he found eight ways to talk about extinction.  “While we all think we know what extinction is – that is the global extinction of species, there are other ways to look at it, so I’m going to work my way through this list and tell you about other kinds of extinction.  This is perhaps a bigger topic than you thought.”

Moyle extinction_Page_08Conservation-reliant species:  “These are species that are basically on life support, and will become globally extinct without our assistance in maintaining their populations, or would be extinct already, for that matter.  The winter-run Chinook salmon is a good example in California of such a species.  If we weren’t actively maintaining the species, they would probably be gone or hanging on by just a few fish.”

Moyle extinction_Page_09Functionally extinct species:  “These are once abundant species that are so rare in their habitats that they no longer play a significant role in their ecosystems.  This means they are headed for real extinction; the first sign of that is of course they are so rare that they can’t play much of a role in the systems in which they live.  Longfin smelt and Delta smelt are probably good examples of this, although it’s always interesting to look at the predation studies on Delta smelt and see that even 50-100 years ago, they didn’t seem to be major prey for various species, but right now we know they are rare.  They are artifacts of past ecosystems.”

Moyle extinction_Page_10Regional extinction:This is what some people prefer to call extirpation.  This happens when a species disappears from its geographically distinct part of its range, but what you can’t recolonize naturally.  The bulltrout is a good example of this in California; it’s gone from its only own known habitat in California, the McCloud river, although its widely distributed across the western United States and in Canada.”

Moyle extinction_Page_11Extinct in the wild:These are species that exist only as captive populations.  It is basically an extreme form of conservation reliance.  These example I give here is the Mojave tui chub, which exists in only artificial ponds in Zzyzx Springs and a few other places.  It’s absent from the Mojave River; it’s present only in ponds, and we may be seeing more and more fish in this category as time goes on.”

Moyle extinction_Page_12Extinct in their native range:  “These are fish that still have viable populations outside their native range as a result of introductions, and the Sacramento perch is a good example.  There is a fishery for it in Crowley Reservoir over on the east side of the Eastern Sierras and in Pyramid Lake, Nevada.  There are about a dozen locations around the west where it’s present, but it’s gone from its natural habitats.  This is a species with a lot of potential for reintroducing.”

Moyle extinction_Page_13Visual extinction:  “These are the extinctions that most people understand – the ones where the species is really gone.  A visually extinct species is one that no one has seen for a while, so it is generally thought to be extinct, but without any firm proof.  By the IUCN definition, there has to be no reasonable doubt that a species exists to declare extinction.  Then you have the question, what’s reasonable doubt of whether or not the species is gone?  This is very hard to determine for fish that live in habitats that are hard to see into; most fish do not live in clear water, especially the species that live in broad habitats like the Delta.  It’s really hard to tell if they are really gone or not as they get down below the threshold of detection of our standard sampling techniques.”

Complete (global) extinction:  “Absolute extinction or global extinction is obviously the one everybody agrees on.  When you think of extinction, this is generally what you think about.  This is where a species is gone for good and there’s no reasonable doubt that it’s extinct.  Surprisingly these are often hard to determine.  The two California examples are the thicktail chub and the clear lake splittail, both of which disappeared; the thicktail chub was last caught in the 1950s, the splittail, the last one was in the 1970s, but it wasn’t described as a species until after it was extinct.”

Moyle extinction_Page_15Resurrection:  “Then we have the possibility of resurrection or extinction reversal.  There is serious talk about this for some species – passenger pigeon, for example.  Obviously it has limited applicability and only if you have extreme optimism would you think this is an option.”


So then the question becomes how does global extinction get declared; how do you determine when a species is really extinct or not, especially with fish?” said Dr. Moyle, acknowledging he had a law student do some research on this.  “As far as I can tell, there is no process for declaring a species extinct.  The closest process we have is to delist the species that has been listed as endangered under the federal and state ESAs.  And if it’s absent from its habitat, it can be declared extinct.”

He then gave the list for how things work.

  1. The species must be listed under state and federal endangered species act.  “If you’re not a listed species, you can’t go extinct,” he noted.
  2. All recovery actions have to fail.
  3. The innovative desperation measures also have to fail.
  4. Then the formal process is you have a five year review. “All endangered species at both the state and federal level have a five year review, and presumably at the end of that five year review, if the biologists doing that five year review determine that the species is gone, then they can start the actions towards delisting it, and that’s the only thing you can do really.  You can’t declare a species extinct but you can delist it, take away all its protections and assume it doesn’t need it any longer.  That’s really de facto extinction.”
  5. At the federal level, the Director of the US FWS has to approve the decision, or the Secretary of the Interior or Commerce, if it’s the National Marine Fisheries Service.
  6. At the state level, the Department of Fish and Wildlife presumably has to petition the Fish and Game Commission to declare extinction. “None of this has been done, but that seems to be the procedure that’s available,” he said.

Moyle extinction_Page_17Dr. Moyle then presented an arrow diagram of how this would proceed.   “The alternative is to call in the God Squad at the federal level which is the federal endangered species committee made up of the heads of the various agencies and cabinets to really make this decision that it is extinct.  But this decision tree right now … I don’t think anybody thinks of the delisting process as being an extinction declaring process.

How should extinction be determined?  “There are really no widely accepted criteria for this,” he said.  “Let’s say you are starting a five year review of a species, and no individuals have been seen for a while.  How do you reach the conclusion then that there’s no reasonable doubt that the species is extinct?  As far as I can tell, there are no widely accepted criteria.  In the past before the endangered species act, extinction was done by an informal consensus of experts; it just sort of seeps into the literature that the species was extinct.

The IUCN has a much simpler rule,” he continued. “If you don’t see it for 50 years, its extinct.  Sometimes species get rediscovered.”


Dr. Moyle then gave his proposal for how fish in California should be determined extinct, noting that as far as he can tell, there is nothing in place at this time.

  1. Recovery measures have to fail.You have to at least try for recovery, including ordinary and extraordinary measures.”
  2. Then you determine it is absent from routine surveys.If the Delta smelt disappears from all the various surveys, that’s a pretty good indication that perhaps it is extinct.”
  3. To confirm this, you should conduct intensive surveys in likely and unlikely places.Do everything you possible can to find out if the species is present or not.  Look in places like reservoirs that you haven’t looked before, even though it’s pretty remote that they would be there.”
  4. Conduct your routine surveys for a number of generations. “If the generation is one to five years, you want to go through ten generations before you declare it extinction.  Generation times greater than that, you can do five generations.  This is not concrete; the idea is if its isolated to a really small habitat like a pupfish in a spring, maybe one generation is enough.  Obviously for Delta smelt, once you’ve stopped finding it, you want to wait at least ten years, assuming it still exists.”
  5. Then determine the likelihood of the species is still extant. “Use an expert opinion, asking everybody who worked on the fish, look at existing data, and do some really heavy duty modeling to find out if there are any indications that might be missed.”
  6. Present the findings to a multiagency committee, and the committee then makes a recommendation to the director of the CDFW or Fish and Game Commission.The way I think it should be is the Governor should declare extinction if you get to that point, or the president, if it’s a federal action.”

In summary …

Extinction is likely to be common in the future,” Dr. Moyle said.  “It does come in many flavors, it’s not just a simple phenomenon.  The legal means exist to delist species because of extinction, but there seems to be no legal way to declare extinction itself, and there needs to be a formal process needed for their determination, given the number of extinctions we’re likely to have in the future, but I’m really hoping the Delta and longfin smelts won’t be our test case.”

So thank you.

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DR. LENNY GRIMALDO:  Examining Rearing Habitat of Larval and Juvenile Longfin Smelt in the Upper San Francisco Estuary: A Case to Move to Uncharted Waters

Tidal marsh restoration could benefit longfin smelt

Lenny GrimaldoBIO: Dr. Lenny Grimaldo is a senior fisheries biologist with ICF International. A former employee of CDWR and USBR, Lenny has spent nearly twenty years conducting research on native fishes in the upper SF Estuary. Lenny is currently serving as the lead investigator for Delta Smelt entrainment studies under the Collaborative Science and Adaptive Management Program. During the past couple years he has led successful efforts to develop tagging technologies for Delta Smelt and is currently leading a number of early life history studies of Longfin Smelt in shallow waters of the upper San Francisco Estuary. Lenny received his PhD in Ecology from UCD and a M.S. from SFSU’s Romberg Tiburon Center.

Lenny Grimaldo_Page_03Dr. Lenny Grimaldo began by presenting a graph showing the relationship between the Fall Midwater Trawl Index and spring outflow and noting that it’s been published in different papers.  “As much as the literature has talked about this relationship and we’ve discussed this, I sort of feel like it’s been a crutch, because we just focus on the indices and the spring outflow, but we really haven’t approached the underlying conceptual model about what’s driving this relationship and what’s going on in the spring.”

The things that have been discussed in the literature are that when you have high outflow, presumably there’s a lot more fish that are created and those fish do well, and they grow and survive into the fall,” he said.  “That’s the underlying conceptual model; it’s pretty simple.  I think that’s not unreasonable to think about it that way.”

Lenny Grimaldo_Page_04But you can’t define a species habitat by outflow alone, he pointed out.  “You have to think about the dynamic and spatial habitat, and this figure from Peterson in 2003 really illustrates this connection between stationary and dynamic habitat.  It’s really the combination of the two that drives the species abundance in an estuarine system.”

Dr. Grimaldo noted that in his presentation, the data he will be discussing comes from the Department of Fish and Wildlife’s 20mm survey and tidal marsh surveys that he has done.

Lenny Grimaldo_Page_05He presented a chart showing the relationships between flow and larval/juvenile abundance with data from the 20mm survey from 1995 to present.  “So your hypothesis should be, during the spring, there should be a lot of fish, right? So let’s take a look.”

Lenny Grimaldo_Page_06But if you look at the relationship between spring abundance and spring outflow for the same period, it actually shows the opposite relationship.  You actually have less fish under higher outflow conditions,” he said.  “There are two interpretations that I make from this graph.  One is well, maybe there’s not a lot of them but they are surviving really good and they’re making it to the fall.  The alternative hypothesis is that we’re actually not sampling their full window; we have a truncated window where the fish actually occur, so this is a problem.  It’s a problem for when we’re looking at the different indices and doing different life stage analyses between the surveys.”

Lenny Grimaldo_Page_08Looking at the data of the 20mm survey to see where the longfin smelt are at, it’s pretty interesting that the densities in San Pablo and Napa are completely overwhelming the signal in the 20 mm survey, and it’s not driven by just a few years, he said.  “In fact, if you look at the whole time series, you see that the Napa River densities really are contributing quite a bit to the densities in the 20mm survey.  San Pablo as well.  This is not to say that Suisun Bay and the Delta, that there’s none there; we see them in all the other surveys, but this is interesting to me in thinking of the mechanisms that are underlying that relationship that’s shown in the papers.  It’s interesting because I want to know what’s the proportion of the fish from these different areas that actually recruit to the Fall Midwater Trawl.  I don’t know if we have the historical data to answer that, but I think in future years, that’s something we should strive for is trying to figure out the differential contribution of these fish to the Fall Midwater Trawl.”

Lenny Grimaldo_Page_09He next presented a slide of graphs showing the relationship between longfin smelt densities and selected environmental variables.  “What was interesting here was the relationship between EC, specific conductance, and the density of larval longfin smelt from the 20mm survey.  The shaded area is the 95% confidence intervals for the smooth fits of this relationship, and what I want to highlight here is that we actually predict the 20mm, the GAM predicts quite a bit of catch, all the way up to 20,000 EC, so that’s a pretty broad salinity window, that’s about 2 to 15 ppt there.”

Lenny Grimaldo_Page_10Dr. Gimaldo then presented a contour plot showing mean longfin smelt density for the entire period by specific conductance.  “What you see is that for the whole survey period is that the center of the distribution of the survey is to the west, so this is going back to the relationship between spring outflow and spring abundance.  I think that what’s going on is there’s a lot more fish that are residing to the west than we previously thought.

Just to show that this isn’t just a one-year phenomenon, he displayed the charts for all the years, starting in 1995.   “You see this from the start of the survey, this very westward distribution of longfin smelt in the surveys,” he said.  “It isn’t until a dry year in 2004 where you see that the densities are centered more in Suisun Bay, and then 2008-09 some of the more recent years, and then of course the drought years.  During the drought years, the center of distribution is shifted more towards the east.”

The problem here is that we’re not capturing that full distribution, Dr. Grimaldo said.  “We designed the survey in a way that would capture Delta smelt abundance, but maybe that sampling regime doesn’t work so well for longfin smelt,” he said.

Lenny Grimaldo_Page_15Looking at the GAM output, this really allows you to provide a picture of what’s actually going on and when and why they might actually be in the Napa River,” he said.  “For example, if you look at the Napa River, the EC values were way too high to support longfin smelt, so in the drought, that makes sense, we didn’t have enough outflow, maybe there wasn’t enough outflow to trigger or attract fish into the area, or maybe they did spawn but they died because of the stress with the salinity, but these sort of patterns really highlight when and why we find longfin smelt when we do.”

Lenny Grimaldo_Page_16Dr. Grimaldo wanted to get an understanding of the potential mechanisms.  “During different outflow conditions – low, medium, and outflow, depending on where the salinity gradient is and based on what we just saw on where longfin smelt are distributed relative to that salinity gradient, there’s a ton of different mechanisms that could be happening all the way from past Carquinez all the way to San Pablo Bay during high outflow years versus in low outflow years,” he said.  “It looks like most of the action would be happening in the Delta, but we all know that San Pablo is functionally very different than the Delta.   The Delta is truly not a good place to be, but the mechanism.  We don’t have Egeria densa in San Pablo, so there are different things that are going on.”

Lenny Grimaldo_Page_17He next presented a slide of the E and L data from the Bay surveys from 1980 to 1989 where he plotted yolk sac data, noting that these are 0 to 7 days old from the San Pablo Bay stations.  “What we found actually a good number of larvae that were found in San Pablo.  This suggest to me that under some of these early, especially these early wet years in the 80s, that there was fish spawning in and around San Pablo Bay, so if you think of a potential mechanism, increased spawning habitat with increased flow might be one mechanism that leads to more fish during those high outflow years.

Lenny Grimaldo_Page_18He then presented a graph of zooplankton abundance by region, plotted for the series of 20 mm data.  “They don’t sample the Napa River, but if I had to make a case, I would tell you to go into the Napa River as I think it’s pretty interesting,” he said.  “In San Pablo Bay, the food densities – the adult calenoids are through the roof through most of this time series; you can see Suisun Bay depressed and Suisun Marsh a little higher as is Carquinez, so one mechanism that could be happening in San Pablo Bay that is why we see a lot of longfin smelt there could just be that there a lot of food.”

Lenny Grimaldo_Page_19Dr. Grimaldo then presented a plot from the 20mm survey.  “I just picked one time period when longfin smelt were really abundant, and what I found for the adult calanoids was that they were really thick as bugs up there in the Napa River, so maybe another mechanism for why we see so many fish up in the Napa River could be related to food density up there.”

He acknowledged that the volume of the Napa River is not all that large, so expanding the population may not represent a lot of fish.  “I think it’s something work looking at,” he said.  “We’ve done some preliminary analyses and even when we extrapolate just one channel in the Napa, keep in mind there’s this whole marsh network that’s not sampled and that the population estimates from the Napa still overwhelm the signal from the other regions in most years.

Lenny Grimaldo_Page_20He then turned to discuss the tidal marsh survey.  A few years ago when they started the study, they looked at Google Earth and picked out some different marshes that looked as if they might support fish.  They called them uncharted waters because it just said ‘marsh’; a lot of exploration was necessary to figure out what channels they could sample in.

Lenny Grimaldo_Page_23We had a paired design, so we sampled inside the tidal marshes and the open water shoals; we wanted to compare densities of fish between those two habitats, and then a third comparison is to compare the densities with the CDFW SLS survey stations,” he said  “The one thing that was interesting was if you look at the SLS stations, the mean depth sampled in this area is over 7 meters which is about 25 feet deep, where our target was about 2 meters, so we were sampling very different habitats.”

Lenny Grimaldo_Page_25Overall what we found was that we caught a lot more fish in 2013,” he said. “It really highlighted that these marshes are supporting quite a bit of longfin larvae.  The densities were actually higher in the open habitats than the marsh habitats for both years, and we didn’t find a difference between our combined marsh shallow habitats with the channel habitats.”

Lenny Grimaldo_Page_26He then looked at the yolk sac larvae data or 0 to 7 day old fish.  “I pulled out some tracks from where we caught these larvae that were a few days old, maybe they hatched that day, and we were finding them far into the interior of these channels, so to me, this is the best evidence we have showing where longfin smelt spawn in the estuary.  Shallow open areas and within the tidal marshes.

Lenny Grimaldo_Page_28In doing the GAM analysis for our data, what we found was a similar predicted smooth fit with the salinity where we predicting catches all the way up to 8 ppt, and this is actually pretty consistent with some of the nice work that Jim has done with the otolith analysis showing that some of the larvae for otolith microchemistry had a 2 to 6 ppt signature, so there’s good correspondence,” he said.  “I think this is important because the original conceptual model or paradigm was that a lot of spawning was going on in the Sacramento or San Joaquin River for longfin smelt.  Obviously that happens. We see a lot of yolk sac larvae.”

Lenny Grimaldo_Page_31However, I think there’s actually spawning going on throughout all these shallow areas and marshes based on our study, and one of the reasons we don’t see differences with the CDFW program is that these fish are actually coming out of these marshes and dumping into the channels,” he said.  “I think there is promise to restore some habitat for longfin smelt, just stay downstream of Antioch.  There’s lots of marsh habitat that can be opened up a lot more from Chipps Island; I know people have been talking about Tule Red; I think all these areas would support larval longfin smelt.”

One of the other parts of this story is that I do think there is a lot more spawning going on in the SF Bay tributaries.  I think we need to spend more time out here in San Pablo and the tributaries,” Dr. Grimaldo concluded.Lenny Grimaldo_Page_32

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DR. ROSEMARY HARTMAN: Are tidal wetlands the new miracle cure?

Tidal marsh restoration holds the potential of benefits for Delta smelt, but we won’t know for sure until more restoration sites are built

Rosemary HartmanBIO:  Dr. Rosemary Hartman is an environmental scientist who has worked for CDFW for two years. She is responsible for monitoring primary and secondary production in tidal wetland restoration sites, focusing on the relationship between invertebrate communities and fish. She received her doctorate in ecology from UC Davis in 2014.

Dr. Rosemary Hartman from the California Department of Fish and Wildlife’s Fish Restoration Program Monitoring Team then gave a presentation on the potential for tidal wetlands restoration to benefit smelt.

We’ve heard about altered habitat that the smelt are currently experiencing,” she began.  “The extensive array of wetlands and channels that used to exist are gone; they are in channels with riprap banks surrounding subsided islands, and productivity in the system has greatly decreased.  To make matters worse, the operation of the state and federal water projects is causing some direct entrainment and a lot of altered flows in the system.”

Fortunately, we do have some controls on humans’ use of the Delta,” she said.  “It’s obviously politically contentious, and the drought has made the situation more politically contentious.  There’s a lot of political cartoons of fish versus people, and ‘it’s this stupid little 3inch fish that’s taking away all of our water,’ but legitimately people do have a lot of interest in the Delta.  They would like freshwater both in the Delta and for export.  Many people live and work and farm land in the Delta and they would prefer farmland to marshy fields of tules.  All of this of course is tied to the California economy, which even the most environmentally-friendly of us still live in California, and would like the state to not go totally bankrupt.”

Delta smelt however also live in the estuary, and they would prefer water to have a natural flow regime and salinity regime, food, habitat for refuge from predators, as well as refuge from high temperatures and areas to spawn,” she said.  “Historically, smelt got the raw end of this deal.  However, due to the Endangered Species Act, there have been some compromises on the restrictions to when and where water can be exported from the Delta, which has caused some amelioration of the flow regime and turbidity regime in the Delta.”

What I’m here to talk about is the potential for purchasing some of the land in the Delta, and restoring it to a more natural habitat.  This will ideally increase the production of food for Delta smelt, and potentially provide that refuge from predators, from high temperatures, areas to spawn, more area to be smelt in.”

Hartman miricle cure_Page_04Dr. Hartman then briefly reviewed the various rules and regulations.  “The particular policy that I’m talking about is the endangered species act, in Section 7, says that the government must limit any potential harm of its actions on endangered species,” she explained.  “The operation of the state and federal water projects is harming Delta smelt, so the Department of Water Resources and the Bureau of Reclamation consulted with US FWS and said, what can we do to mitigate for the operation of these pumping plants.  One of the reasonable and prudent alternatives (meaning mitigation measures) is restoring 8000 acres of tidal wetlands and associated subtidal habitat.  This is directly responding to the biological opinion they wrote at the time for Delta smelt, the California Endangered Species Act incidental take permit for longfin smelt, and somewhat for salmonids.”

The restoration is being implemented through a partnership between the California Department of Water Resources and the California Department of Fish and Wildlife through the Fish Restoration Program with a target completion date of 2018.  “Spoiler alert:  it’s probably not going to happen by 2018 but we’re working very hard,” said Dr. Hartman.

So if Delta smelt are pelagic and live in open water, why restore tidal wetlands?  “Lenny went right before me talking about longfin smelt spawning in these tidal wetland channels, and there’s been a lot of hints dropped throughout the day about the potential benefits of tidal wetland habitat.  Tidal wetlands were historically what was in the Delta, and maybe more smelt were in these Delta habitats when they existed, but currently, there just aren’t very many tidal marshes left in the real freshwater areas of the Delta.”

Hartman Tidal Wetlands ModelDr. Hartman said they do have hypotheses of how a tidal wetland would benefit Delta smelt, even if they are not spending all of their time in the dendritic marsh networks.  “It might provide pockets of thermal refugia, and it will provide an increase in productivity, both through export of plant matter and detritus from the emergent wetlands themselves, and through shallow open water that is associated with these tidal wetlands that will provide large shallow and long residence time areas in which phytoplankton can kind of cook and then be exported to the surrounding channels.  Also people have been talking about increase in the shallow area increasing turbidity which we know we’ll help with predation issues.”

There is also some plasticity in the Delta smelt diet.  “Smelt aren’t just eating the calanoid copepods; they are also eating some of these demersal arthropods that are often associated with wetlands, and during the drought right now, some of the diet work in our office at CDFW has been finding incidence of smelt eating terrestrial insects and some of the different sources of productivity that aren’t normally thought of to go with smelt.”

These are all hypotheses,” Dr. Hartman acknowledged.  “We still haven’t built many of these sites and haven’t seen smelt responding to them yet because we just haven’t studied it enough.  While there’s been a lot of increase in research on smelt in the past 10, 15 years, the majority of it has been in more open water systems.  When these restoration sites are going to be built, we need to figure out how we’re going to tell that they are having the desired effect.”

So my group organized a project workteam through the Interagency Ecological Program, bringing together all the experts in smelt ecology and wetland ecology to develop a framework to allow restoration sites to make monitoring plans to monitor the effectiveness of the site.  “When I say effectiveness, I mean ‘is it actually benefitting smelt’, not ‘did you build a wetland’ because that is the low bar that most mitigation sites are given.  We want to say, ‘did that wetland help smelt’.”

Hartman miricle cure_Page_09They started by putting their conceptual model of how wetlands will help smelt into some diagrams and text and used those to get really specific testable hypotheses that could be backed up through specific metrics and recommended methods.  The framework also gives recommendations for how to analyze the data and integrate it with existing datasets so we can get as much out of these datasets as monitoring plans are made for specific projects.

Hartman miricle cure_Page_10One of the projects that will be monitored is Prospect Island. “Right now it’s just a big island at subtidal and intertidal elevations up in the Cache Slough area which is one of the target areas for restoration, the hotbed of Delta smelt,” she said.  “Our prescription for this site is we’re going to knock some holes in the levee, dig out some channels, build a berm, open it up to the tides, let it produce food, and let the fish come in and use it.”

Hartman miricle cure_Page_11 The workteam is working to figure out how to test whether or not Prospect Island is going to have the hypothesized productivity and habitat benefits.  “So we’re taking the objectives, such as enhancing productivity, and making specific hypotheses like high residence time will increase production; we’ll use hydrodynamic models of where areas of the site with higher residence time and lower residence time are, measure phytoplankton and zooplankton, compare that to regional datasets, and use that data to make adaptive management decisions, potentially changing things onsite or using it for future projects.”

You notice I haven’t shown any graphs or hard data today,” she said.  “That’s because it turns out restoration is a lot harder than we thought it was when the biological opinions were written in 2008.  The Department of Water Resources in partnership with Fish and Wildlife has been working really hard on this.  We’ve had a lot of hurdles to overcome, including issues acquiring land, especially given the constraints on what the state is allowed to pay.  We need to apply for environmental permits, which are well intentioned, certainly, but the same environmental permits that need to be filled out if you are building dam also have to be filled out when you are doing a restoration site, so sometimes that slows things down.  We even need permits to monitor the Delta smelt that the site is being restored for, and we’ve been having a difficulty getting those, so there are just a lot of constraints there.

There are also some basic engineering and construction constraints, Dr. Hartman said.  “A lot of these sites are wet and need to figure out how to actually move that much earth from point A to point B in a reasonable amount of cost.  There are salinity and water quality effects that are caused by wetland restoration that need to be taken into account;  the smelt is also not the only endangered species in the estuary, and Prospect Island also happens to be excellent potential Giant Garter snake habitat.  So projects may have to mitigate or take other endangered species into account when they are designing the projects.”

There still are a lot of scientific unknowns,” she said.  “We still don’t know where Delta smelt spawn.  The best theory is they spawn on sand because they do in captivity, so should we build more sandy shoals on Prospect or should we build tidal sloughs like Lenny has been finding with longfin smelt?  The only way to know is if we go out there and monitor the sites we build.  We need to give it our best try in building the best site we can, and then go through the steps of adaptive management to monitor the sites and make recommendations for changes to the site or future sites.”

This is also just an excellent unprecedented scientific opportunity,” Dr. Hartman said.  “The stakes are very high; and the operation of the water projects is tied to this.  Right now we’re hoping that tidal wetlands are the miracle cure but only if we only really do rigorous scientifically-sound effectiveness monitoring can we say for sure.

Question: What type of food do you expect to grow on Prospect?

Prospect Island is going to have quite a bit of shallow open water as well as emergent vegetation, and shallow open water especially with longer residence time could be very productive for phytoplankton and the copepods and the zooplankton that have been the staple of smelt diets, but the emergent marshland is also potentially a great source of detritus that enters the food web through the detrital loop … other parts of the Delta smelt diet are less well known, but once smelt are in areas with a lot of emergent marsh vegetation, such as Liberty Island, they are found eating these sources of food.”

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Coming up tomorrow …

The symposium concludes with Dr. Peter Moyle moderating a lively panel discussion.

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