Delta Stewardship Council: Independent science review panels and the biological opinions

Panel at the Delta Stewardship Council discusses the effectiveness and impact of the yearly independent science panel review of the biological opinion RPAs for operations of the state and federal water project

The National Marine Fisheries Service and the U.S. Fish and Wildlife Service have each issued a biological opinion on the long-term operations of the Central Valley Project and State Water Project that include Reasonable and Prudent Alternatives (RPAs) designed to alleviate jeopardy to listed species as well as avoid adverse modification of critical habitat.

The RPA for the biological opinion pertaining to salmon, steelhead, and sturgeon requires Reclamation and NMFS to host a workshop no later than November 30 of each year to determine whether any measures prescribed in the RPA should be altered in light of information learned from the prior year’s operations or research.  Although not a requirement in the Delta smelt’s biological opinion, the review was later expanded to consider implementation of the biological opinion for Delta Smelt.

The Delta Science Program has been organizing these reviews since 2010.  The scientists on the panels through the year have remained consistent, with four of the six scientists having participated in the reviews every year.

The intent of the review is to inform the fish agencies about the effectiveness of the prior year’s water operations and regulatory actions prescribed by their respective biological opinion’s Reasonable and Prudent Alternatives (RPAs), the portion of the biological opinion that specifies the regulatory requirements for the project.  The goal is to incorporate new science and make appropriate and scientifically justified adjustments to their future implementation.

At the April 28th meeting of the Delta Stewardship Council, representatives from the federal fish agencies and the Bureau of Reclamation discussed how the reviews have resulted in changes to management, and gave their perspectives on the results of the reviews.  Seated on the panel was Garwin Yip, Water Operations and Delta Consultations Supervisor with the Central Valley Office of the National Marine Fisheries Service; Kaylee Allen, Field Supervisor with U.S. Fish & Wildlife Service’s Bay Delta Office, and Ron Milligan, Operations Manager for the Central Valley Operations group with Bureau of Reclamation.

Here’s what they had to say.

GARWIN YIP, Water Operations and Delta Consultations Supervisor with the Central Valley Office of the National Marine Fisheries Service

Garwin Yip began with the background for the Long term Operations Biological Opinion (LOBO) reviews.  “The National Marine Fisheries Service issued a biological opinion that determined jeopardy for some of the listed species in our jurisdiction as well as adverse modification of critical habitat, so we issued a Reasonable and Prudent Alternative (RPA),” he said.  “That’s part of the Endangered Species Act.  One of the requirements is for NMFS and Reclamation to co-host along with an independent organization, in this case it’s the Delta Science Program, an independent review of the last year’s operations.”

DSC GarwinEach word in that charge was scrutinized by everyone up our chains to make sure that we knew what we were asking for and the panelists especially knew what they were expected to do,” he said.  “There are some limitations, like to the extent that we wanted the panel to review how we operated pursuant to the RPA; we didn’t want the panel to review the science leading to the conclusions that we determined – the jeopardy and the adverse modification.  We didn’t want the panel to come up and brainstorm ideas for better ways of doing business because the RPA is the RPA, and we expected and assumed that we used best available science, so the narrowness for the panel was to review the previous year’s operations and recommend minor changes to implementation of specific RPA actions.”

In 2010 when NMFS was developing the annual review, Mr. Yip acknowledged they wondered ‘what they had gotten themselves into’ and were unsure of how to do an annual review of the SWP and CVP in just two days.  “So we asked the Delta Science Program to help us be independent and draw from experts in the country, specific experts based on knowledge of operations and listed species, salmonids and Delta smelt,” he said.

For the first two years, they had technical teams submit annual reports and give presentations – from Clear Creek, fish passage, American River, Stanislaus River, Sacramento River, and the Delta – there were a lot of presentations which were pretty much a gloss-over of all the operations, he said.  “The panel appreciated the enormity of this project, but also requested we start being more specific, what are the main issues from each year’s operations that we really need help in understanding the needs of the species and how operations affected those needs,” he said.  “So starting in 2012, the reviews became more focused on the specific issues they needed help with scientifically to better manage the system and adaptively manage.

In 2011, we had a big water year, and the response from the panelists was, ‘you better not have any problems in this type of water year; the question is how are you going to operate when there’s less than full reservoirs,’” Mr. Yip said.  “So then came four years of drought conditions.  The last four years, especially 2014 and 2015 were really tough all the way around – for fish, water exports, the environment, and operations; there were a lot of meetings, negotiations, discussions, and just hard discussions we had on decisions and operations, so I think in 2014 & 2015, the independent panel weighed in and really helped us out.”

Mr. Yip said that while they did build in drought operations as part of the RPA, they did not contemplate the extent of multiple years of drought, having low reservoirs to begin with, and all the different needs throughout the water year.  The status of studies started being included in the reviews.  “It wasn’t to ask the panel for input and recommendations on these studies; it was just to let them know the state of the art stuff that we’re working on,” he said.  “More recently with the RAFT, the temperature modeling for the Sacramento River with enhanced particle tracking modeling, we did ask the panel to weigh in on how is this study was designed and if there was anything missing in the assumptions built into the model, as far as the model runs and results that could inform management.”

As far as the successes, the panelists in 2010 in the report questioned why in the Shasta operations would they “waste water” by providing habitat so far downstream when the fish aren’t there to use it, Mr. Yip said.  “The RPA requires the downstream-most location that could provide the coldest water throughout the year, and that’s what it is, and so that’s how we operated.  There were hiccups in the monitoring, there was a lack of aerial redd surveys that year, so we really didn’t know where the winter-run redds were.  Since then, we’ve adjusted operations, especially because of drought conditions, we didn’t have the cold water necessary to provide to the downstream most, so we started taking a hard look at where the redds were. In coordination with California Department of Fish and Wildlife and with drought funding, they set out crews on a regular basis, weekly if not daily, to monitor the caracasses and do aerial redd surveys to try to fine tune management of the species and stabilize flows throughout the season to protect as much as we can.  That was one of the main recommendations we were able to adopt.”

He said there were many other recommendations that have been helpful.  “Some of the recommendations from the panel are academic as far as science, and my first thought is that we have limitations through the Endangered Species Act about what we can change as far as the requirements in the RPA, and unfortunately it’s the minimum to avoid jeopardy as opposed to the great ideas out there to recover the species.  We have limitations in how much we can implement as far as the recommendations.”

Each year, the panel asks the tough questions we either have responses to or they are things that we didn’t think about,” Mr. Yip said.  “That helps keep us honest as far as operations and effects on water supply and the environment in general and also the listed species that we’re charged to protect and restore.”

KAYLEE ALLEN, Field Supervisor with Fish & Wildlife Service’s Bay Delta Office

Kaylee Allen began by noting that the U.S. Fish and Wildlife Service did not include the requirement for a science review in their biological opinion that was written in 2008 for Delta smelt, and it is only in recent years that they began utilizing the review.  “I’m going to describe the experience that we’ve had specifically with our incidental take methodology that we’ve presented to the panel for the last two years and it’s helped influence our thinking as we move from what we had in the biological opinion towards a new method of determining incidental take.”

DSC KayleeThe Endangered Species Act prohibits the ‘take’ of endangered fish and wildlife where take is defined as ‘harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, collect, or attempt to engage in any such conduct.  The Act also defines two types of take: incidental take, which is take that is incidental to an otherwise lawful project, as and direct take, which would be to collect species to conduct research on them for instance, she said.  “At the time we do a biological opinion, if we determine that there will be adverse effects to species, we estimate how much take will occur if the project is implemented as described, and that’s what is included in the incidental take statement; that take is exempted from the prohibition against take under the ESA.”

In the 2008 biological opinion for Delta smelt, salvage at the projects is used as a surrogate for incidental take.  “It’s the place that we can see, we can count what’s coming through the system, but we know there is take associated with the project that we don’t see at salvage,” Ms. Allen said.  “In the biological opinion, we calculated incidental take by coming up with a cumulative salvage index, or a CSI, and that’s multiplied by the Fall Midwater Trawl, which is one of the surveys that we use each year to try to determine the relative abundance of Delta smelt.  In our biological opinion, that CSI was calculated on a three-year dataset, and that dataset was chosen because that was the most consistent with what an RPA year would look like, a year that was consistent with our Reasonable and Prudent Alternative.”

In 2014, Reclamation and Metropolitan Water District proposed a new method of calculating that CSI, which was termed the Proposed Alternative Method, or the PAM; that PAM was brought to the science panel in 2014.  “The primary difference with the CSI is that it would be based on a larger dataset than what was in the biological opinion.  The panel supported the basic concept of using modeling to expand that dataset, and the panel found that if we were going to use that method, that they would recommend applying what is called the Monte Carlo procedure to the dataset, but overall, the panel found that the PAM was no better than what we’re doing in the biological opinion, so they wouldn’t recommend that we make that switch.”

Based on the feedback that we got from the panel, Reclamation reinitiated consultation shortly after the panel had reviewed the PAM and proposed using the PAM instead of what we had in our biological opinion,” she said.  “Because the panel found that it was no better but also found it was no worse, we wound up accepting the use of the PAM for the 2015 water year, although we did modify it by applying the Monte Carlo procedure, as the panel had recommended, which is a statistical method that’s a little more random than normal regression analysis, so it’s trying to get a more random dataset.”

They did apply that for incidental take of adult Delta smelt in 2015; in the meantime in 2015, staff has been working very diligently on calculating incidental take based on absolute abundance instead of relative abundance.  “This is an attempt to move towards a proportional entrainment analysis, which is what the panel has supported both in 2014 and in 2015.  This is a method that uses a ratio of adult salvage to December spring Kodiak trawl from which we calculate an absolute abundance.”

The panel reviewed this method in 2015 and they highlighted two areas they felt needed further consideration,” she said.  “We took those comments and did some additional work on that method; however, we decided ultimately to just pilot that method this year and continue to work with the modified PAM method that we had from 2015 so that we could see what we did see for incidental take this year and how our method matched up to that.  We also at the panel presented some earlier work on this newer method that I was talking about, and the panel did provide us some comments that we have been able to incorporate and we’re continuing to work on that, so hopefully this year or the next year after, we’ll see a new method of calculating incidental take that will be more tied to the population.”

One of the take homes from this year’s panel was that we need to do a better job of explaining how we’re using these different pieces of the biological opinion, she said.  “I think those of us Section 7 wonks tend to forget that the rest of the world has no idea what we’re talking about half the time when we’re talking about this stuff, so I think for us, we need to do a better job of explaining the context of what we’re looking at, and I think that will help us in future years to get more from the panel that is helpful to us in responding to these issues.”

That is what I have to say.  If you have any questions …

RON MILLIGAN, Bureau of Reclamation

Ron Milligan began by saying that back in 2008 when Reclamation put their biological assessment together and initiated consultation with both services, they got two biological opinions covering the operations for the CVP and the SWP and the various species involved.  “The geographical magnitude of what we’re dealing with, and the idea that we’re going to have RPAs and different individual actions on these multiple species, you put that altogether, and then how do you implement that across water year types that maybe weren’t contemplated or weren’t necessarily fresh in people’s minds or combinations of storages and hydrology,” he said.

DSC MilliganThe first couple years was a matter of sorting out the criteria and making them work between the two opinions also within the criteria of the State Board’s requirements from our permits from our water rights, so how do you make this all work and still work within your contractual framework,” he said.  “It was very useful to have something like the science review for us to put together what we had been contemplating of how do we operate to those things, and could we make improvements, and how could we do that in a way that didn’t compromise the science or the species protections that we have.”

Sometimes it was good, too, to get out of that Section 7 box and be able to talk through with a set of smart people that could ultimately understand if you explain it to them what we were trying to do,” he said.  “Sometimes what they said made a lot of sense, and some of those made us think about some changes and I think in the first years, those really made a lot of sense and were helpful for us.  In the years after that and certainly by having consistency with people on the panel, there was a little bit of a redundancy in the sense that it seems like it’s the same thing, so how do we freshen this up so we get down a little bit deeper into some of the issues, particularly when certain things would come up year after year.

I think as we progress a little deeper into things like prolonged drought and as some new science has developed over the course of time since the opinions were put together, where is a good place to have these discussions,” he said.  “It’s nice to have something like the annual review and an independent science panel to bounce ideas off and the incidental take question was a real good example of that.  We could get some fresh eyes on this and be able to take a look at how we are going to be able to deal with this or what would be a good way to approach this, and does it make sense.”

In the terms of adaptive management, it’s nice to have something there, whether you need it or not once a year, a group that you get all this information together and try to be able to tell your story, and I think that’s really been the value of this process,” Mr. Milligan said.  “Looking ahead, I think we continue to think about how to make the process value added.  There’s always this unusual balance of finding people that have some familiarity with California water and the Delta, but that are independent that they haven’t touched any of this so they’ve been kind of sequestered off to the side, and they can take a completely fresh look.  … You have to make sure that you find folks who are able to step back and really take a fresh look at some of these issues.”

Reclamation has been utilizing the process as best they can, he said.   “We appreciate the Council’s engaging with us on this and finding ways to integrate and the adaptive management, both on the actual operations side of this as well as reviewing what we’ve done and finding better ways to do business, I think adds a lot to this process. … Maybe we got some comments but that just didn’t quite fit and probably wasn’t that useful, but there were some other things that when you take to heart and you work with it for a year or two, so we’ve been able to evolve our operations and our implementation of the RPAs in ways that have made things better.  It’s a growing process and it’s not necessarily linear, but I do think it has a lot of value to us.”


Councilmember Mary Piepho noted that at the previous panel, DSC Piepho 9one of the participants had said that the current operations are divorced from the hydrology of the state or the weather patterns.  Do you have any thoughts on that?, she asks.  Council Chair Randy Fiorini clarifies that the point was the pumps have been running at 1500 cfs, the Sacramento River has been at 60,000 cfs and down from there, so there was the assertion that the exports don’t match up with the hydrology.

Ron Milligan said that there is certainly a mix.  “The structure of some of the RPAs does lead to your fate in the wintertime and to some degree into the spring, rising and falling with San Joaquin River flows.  So if you have a circumstance where Sacramento River hydrology looks a whole lot different than San Joaquin River hydrology, you’re going to get some very unusual answers.  Through this drought period specifically, the cumulative effect of drought and the way the hydrology has played out has hit the San Joaquin River much more harder.  The previous three years have been critically dry classifications for San Joaquin River with a dry year thrown in this year.  Given the way some of the RPA sections are written, whether they are Old and Middle River flows or ratios of San Joaquin River flow to pumping rates in the springtime for San Joaquin fisheries, those are going to be very linked to San Joaquin River hydrology, regardless of what’s been happening in the Sacramento, so in the winter you’re going to see these types of things at their most pronounced.”

Summer hydrology or summer operations are going to be much different as a comparison of last year to this coming year,” Mr. Milligan continued.  “Last year, there were very low cumulative storages up in the upstream north reservoirs, very dry basin conditions, very low Delta outflows, barrier in the Delta to manage salinity so we don’t get a huge intrusion event, that’s one extreme; versus the other extreme where you are probably close to full plant capacity running in the south Delta at the SWP and the CVP  being driven by the fact that you have some better conditions in the upper reservoirs and you are making releases as you are trying to head down to your projected flood pool levels you need to be at come fall, so there’s a volume of water that needs to move through the system and can be used to make deliveries.  So when you get to that point in time, you’re going to say that it seems to have matched the hydrology of the previous winter and the storage levels now seem to be matching up with that operations, but in the winter period, particularly the opinions do tend to be more biased to what’s going on with the San Joaquin River, and even though you may have 100,000 cfs of excess flow, total Delta outflow, you may be very constrained as San Joaquin River is only at 3-4000 cfs, and that’s going to play into this, particular when you’re concern is that negative flow across the Delta from north to south.”

We’ve seen a downward trend with Delta smelt over the last several years, but I think after this last dry period, we’ve seen historic lows in every abundance index that we use,” said Kaylee Allen.  “So while I understand water users wanting to take advantage of this water year, we also want to be able to take advantage of this water year to help the population of smelt and see if we can do something for them to help those numbers rebound just a little bit.  One of the things we consider when we’re implementing the RPA is what the abundance of the species is and based on this historical low numbers, we’ve had to take a slightly more protective view when we feel there are smelt in areas of entrainment because we’re trying to do our best to keep this population holding on, so I wouldn’t say it’s divorced from the hydrology, I would say it’s a result of the hydrology that we’ve seen over the past several years.”

The hydrology lends itself to the effects on our species,” said Garwin Yip.  “During the drought, we had relaxations of Delta outflow and various metrics that our salmonids rely on to get into the Delta to rear, and ultimately to get out the Golden Gate bridge.  During a higher water year, like 2011 and experienced now, it’s kind of a conflict as far as this is the prime opportunity to increase water supply, increase exports, but it’s also an opportunity for salmonids to “rebound” – to have an opportunity for them to actually survive into and out of the Delta.  This year in particular, it’s more important for winter run, for example, because they took a really hard hit in 2014 and 2015, so this water year is more important because it’s the third of three winter run cohorts.”

Another comment from the earlier panel was that there wasn’t any real positive evidence of the biological opinion’s value since they’ve been implemented nine years ago, asked Councilmember Mary Piepho.  “We’ve been through five years of drought, and through that almost ten year period, we’ve been in dry years.  Do we consider the lack of smelt population a hydrological impact, an environmental impact, is it a biological opinion impact – obviously it’s maybe all of the above, but we can’t look to the biological opinions as protecting these species because they are still in decline over a period of nine years …

As far as our limitations and Section 7, the request from Reclamation is on operations, and that’s why we’re focused on operations and have these impositions and requirements on operations,” said Garwin Yip.  “It’s not so much picking on water supply, but that’s the federal action.  In its entirely, there are so many different stressors out there from the existence of the dams, we have gravel or lack of gravel, we have warm water, noxious weeds, contaminants – you name it, it’s out there, so we’re focused on operations, only because that’s what the biological opinion, that’s what’s the federal action is.  We are taking a look at all these other stressors and to the extent that we can manage those through a federal nexus and different avenues, we’re working on those also.”

Councilmember Piepho: “So could you list that the biological opinions are not the only stressor in the Delta.”

Mr. Yip: “Correct.”

I would say in the defense of my endangered species implementing colleagues that the biological opinions are not a recovery plan,” said Mr. Milligan.  “The recovery plan is a much broader thing.  The opinions are related to the operations of the two projects.  It’s hard to say what would occur if you didn’t implement the RPAs; obviously folks will have their different theories, but I think it’s important to keep an eye out that there is a broader sense of recovery and actions that are beyond just the projects and there can be debates whether there is too much focus on the projects and not on these other stressors, but that’s where you have to look.  It’s probably not fair to say, implementing this biological opinion and saying it’s not doing it, well maybe it’s a holistic approach that needs to come into play …  The biological opinions are not meant to be the long and short of everything that needs to happen here.”

For more information …

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