Presentations take an in-depth look at the analyses for salmonids, sturgeon, Delta smelt, and longfin smelt; panel gives initial recommendations
Coverage of the independent science panel review of the draft biological opinion for the California Water Fix project continues with this second of two parts. For the background, introductory remarks, and presentations on the project and the Section 7 consultation process, please see part 1 here: California Water Fix Aquatic Science Peer Review, Part 1: Overview of the project and the endangered species consultation process
in this second part of coverage, Marin Greenwood and Rick Wilder with consultants ICF International gave presentations on the aquatic analyses for salmonids, Delta smelt, and longfin smelt; the panel then deliberated and returned with some initial findings. A final report is expected in the upcoming weeks.
Salmonids and sturgeon effects analyses
Marin Greenwood began noting that he will be presenting work that’s been done, and they are seeking input from the panel which is laid out in charge question #2, ‘How complete are the selected analyses in the BA for evaluating potential effects on the target listed species?’ Mr. Greenwood noted that he and the others have been working in a collaborative process that began during the development of the BDCP.
“One of our initial steps when we were transitioning to Cal Water Fix was to get together, look at what methods we actually had from the BDCP which worked, which ones might need some refinement, and what additional methods might be needed,” he said. “There was administrative draft released, and from that we received comments and additional methods, so it’s been definitely a collaborative process as we’ve gone along with the agencies. In some cases, there were smaller technical teams working on specific analyses as well.”
The physical modeling that was done is an important foundation, he said. Cal-SIM II, described in Appendix 5A, is an 82-year monthly simulation with a monthly time step that incorporates climate change assumptions for 2025 coinciding with the initial operations of dual conveyance, and incorporating all the relevant regulatory criteria. “An important point is that it’s a planning tool to compare long-term trends,” he said, emphasizing that ‘compare’ and ‘long-term trends’ were the important words. “We don’t want to focus in on results for any particular year, for example, but higher-level planning summaries, exceedance plots, averages by water types, things like that are definitely appropriate. It tries to represent real-time operational adjustments to some extent but it’s quite limited.”
Another physical model used was the DSM 2, described in appendix 5B, which gives a simulation of flows, velocity, and stage, as well as a particle tracking module and water quality or salinity. Attachment 5 to appendix 5B has the monthly-to-daily mapping of historic flows to represent daily variability, but does not include the day to day flows that might change on a daily basis because of operational changes. “It’s a representation of daily variability that one might expect, but it’s not a simulation of a change in flows that could result from a daily time step operational decision,” he said. Hec-5Q is another physical model used for water temperature and upstream tributaries, he said.
“Those basic analyses feed into many of the biological models that we have in the working draft biological assessment and the incidental take permit materials that you received,” he said. “In some cases, our summaries are actually more like the raw physical modeling information depending on whether we can actually make the link or not to the biological model.”
Mr. Greenwood then briefly stepped through a few slides showing modeling results.“This is the long-term exports illustrating the potential for greater exports in the wetter months where there would be potential for north delta diversions, for example, and possibly less exports later in the year because of that flexibility, and overall somewhat greater exports under the post action as opposed to the no action alternative. As a result, the dual conveyance that’s proposed, there will therefore be less South Delta exports,” he explained, noting that in appendix 5A, the modeling results are broken down by water year types. “There are resulting differences, then, in delta outflow because the overall operational differences between the scenarios. North delta diversions are represented as well.”
He then turned to the species-specific presentation, first presenting a slide of the relevant documents for the Chinook salmon, 
Delta smelt, and sturgeon analyses, noting that there is Chapter 5, along with a number of supporting appendices, and a description of the proposed action is in Chapter 3.
Mr. Greenwood then began with the salmon and sturgeon effects analyses, noting that he would be talking mostly about salmon. Chapter 5 is divided into construction effects, maintenance effects, operations effects for water facilities with the operational effects divided into Delta effects and upstream effects, the effects of construction and maintenance of the conversation measures themselves that are proposed, as well as the cumulative effects and final effects of monitoring activities. The effects on southern killer whale won’t be discussed today, he noted.
“The water facility construction effects is generally a qualitative discussion, discussing the potential for different effects from the construction of the different facilities that are proposed, and cross-referencing to the different avoidance and minimization measures that are proposed as well,” he said.
“There are a couple of quantitative analyses; one is pile driving which uses a spreadsheet tool from the National Marine Fisheries Service,” he said. “It’s done assuming a worst case scenario where all the pile driving is impact driving and there’s no attenuation of the pile driving. That’s the daily straight worst case; in fact, it’s hoped that a lot of the pile driving that would be done would actually be (unknown) pile driving, and that it would be possible to effectively attenuate noise.”
“The other quantitative analysis that’s included is a GIS analysis for the facility direct impacts – essentially a footprint of the facilities,” Mr. Greenwood said. “Basically the amount of compensation that’s proposed for these impacts depends on whether it’s a temporary impact or permanent impact. A permanent impact has a five to one ratio, temporary impact has a three to one ratio. There are different types of habitat, tidal wetland and channel marsh and habitat for different features. Water facility maintenance is also a qualitative discussion of the different features, referencing the different avoidance and minimization measures that are being proposed to minimize those effects.”
The operational effects are divided into near-field effects which are things that are happening very close to the facilities, such as entrainment or impingement of fish on fish screens, and far-field effects, which are the overall operational effects that operations could have on species within the Delta; those include mortality within the Delta as well as effects on habitat.
For the near-field effects, Mr. Greenwood started with the north Delta exports. For entrainment, the screen size would physically exclude fish of about 22 millimeters, so juvenile salmon would be excluded from entrainment, he said. “There are other effects, of course, that could potentially occur, so we looked at the potential to analyze impingement, screen contact, and screen passage time, using studies from UC Davis fish treadmill studies,” he said. “The equations for screen contact gave results didn’t work very well, so the focus was on screen passage time.”
“Applying the relationships, with this graph you can see that potentially for the combination of the 0.2 feet per second proposed, approach velocity and different sweeping velocities, the potentially the passage times might be very long,” he said. “There is some uncertainty because our calculations gave results that are much longer in terms of the estimates than the actual trials, which were two hours long generally. And they don’t consider whether fish may actually be more motivated in terms of going downstream or not, as opposed to being in the lab environment. so there are some uncertainties about the time passage calculations.”
Another important effect is the potential for predation at the North Delta Diversions. “This is recognized as being an issue of great importance,” Mr. Greenwood said. “We have a short qualitative discussion referencing the study at Glenn Colusa Irrigation District study by Vogel in 2008. We would like your feedback on how useful and how applicable you think it is for the biological assessment or the biological opinion, because it’s quite a different situation. It’s the best available information in terms of pretty much being the only survival study along a fish screen that’s comparable length to what’s proposed for Water Fix – over 1,000 feet long – but it’s in quite a different situation as you can see here. It’s in an oxbow of the Sacramento River instead of being main stem; it’s also very far upstream as well.”
“We also talk a little bit about the BDCP bioenergetics calculations that we did as part of the BDCP work, which again, there are uncertainties given the different assumptions we can make about the density of the predators and things like that,” he said. “The overall conclusion that we had is predation certainly is a potential issue for the North Delta Diversions, but it’s uncertain as to what the extent could be, particularly in relation to not having great information about baseline predator densities and so on. That’s something that would definitely be studied moving forward.”
Mr. Greenwood noted that there is a conservation measure for localized reduction of predatory fishes, or trying to reduce the numbers at that specific location, but there’s a lot of uncertainty to that as well, and it’s very much a part of adaptive management.
For south delta exports, the salvage density method gives a seasonal weighting of export differences by species occurrence based on historic patterns of species occurrence, he said. A new analysis based on a published paper allows calculations of salvage as a function of Sacramento River flow, and South Delta exports combined. “Maybe not surprisingly, given the large differences in South Delta exports, both of them suggest less entrainment under the proposed action and no action alternatives, especially the bigger differences in wetter years.” He noted there is considerable variability in the estimates, and included is a qualitative discussion of predation about the differences in entrainment.
Turning to the far field effects, Mr. Greenwood noted there was biological modeling as well as summaries of the physical modeling from DSM2. “For the channel velocity analysis that we did, we selected a number of important channels within the delta that were modeled, and under the basic conceptual model of less positive flow being less good, we generally characterize what those differences were,” he said. “Overall, the positive flows are generally greater in the South Delta because of less South Delta exports, and then generally less in the North Delta because of the North Delta diversion effects.”
Entry into the interior Delta was based on DSM2 modeling, which looked at what proportion of flow is entering the interior delta where survival of juvenile salmonids is generally lower than fish remaining in the main stems. Because of less river flow in the North Delta, there’s potential for interior Delta entry in the North Delta, but because of the proposed Head of Old River Gate in the South Delta, there was considerably less entry into Old River, he said.
Recognizing the potential for the greater interior Delta entry in the North Delta, a conservation measure is proposed to have a non-physical fish barrier at Georgiana Slough, so a discussion of the pilot studies that were done in 2011 and 2012 and the percent reductions that they had for the different species that were tested is included, he said.
Mr. Greenwood then explained how the Delta Passage Model works. Fish start upstream of the entrance to the Yolo bypass, which is represented in the model as an alternative migratory route. Both the no action alternative and the proposed action have the proposed modifications to Fremont Weir, so that’s not a differentiator between the two scenarios, he noted. The fish that remain in the main stem Sacramento River are subject to flow survival relationships, so this is basically where the effects of the North Delta diversions are captured. As they approach junctions, they enter junctions, in some cases straight proportional to flow, other cases with specific relationships based on data. For those fish that enter within the interior delta, there’s a flow survival relationship with exports, which is expressed as a ratio of survival within the interior delta to survival in the Sacramento River. “So to some extent, it reflects the less flow of the north delta diversions for the proposed action alternatives because it’s a ratio, and that kind of weakens this relationship even more in relation to these flow survival relationships,” he said.
The graphs show some of the modeling results of indirect mortality within the Delta across the range of water year mean differences. “In relative terms, 2-7% less under the proposed action for winter-run chinook salmon, and 1-4% less for spring-run chinook under the proposed action,” he said.
Another tool that we use to assess through delta survival was a spreadsheet model implementation of Newman 2003 work, which was actually on fall-run chinook, but the timing was sufficiently similar that it felt appropriate to include for spring run chinook and salmon. “It’s important to note here is that the difference in survival per change in Delta exports, compared to flow, is quite similar in terms of its effect,” Mr. Greenwood said. “We seem to see that during the spring period or spring run chinook, the migration period is far from focused. There wasn’t really a difference between the proposed action and the no action alternative I think largely because of this offsetting of the two different things. So during this spring period, the overall operations in terms of exports were quite similar between scenarios.”
Mr. Greenwood presented a table showing winter-run survival by water year type, divided by each North Delta Diversion bypass flow level. “This is survival weighted by the proportion of the population moving in, and it assumes the same intra-distribution as the delta passage model,” he said. “It shows that during these pulse protection flows, which are the minimal North Delta Diversions, there’s little difference between the scenarios. But as you gradually increase the bypass flow levels, the differences increase. So the sum of each of these is what you get your overall survival from.”
Mr. Greenwood then presented a slide showing the proposed North Delta Diversion flow constraints. “With the pulse protections, after the initial pulse of fish with a maximum of 300 CFS per intake, there would be very little permitted north delta diversions,” he said. “When the pulse ends, there would be more diversion permitted, and after certain criteria are met, we transition into level 2 and level 3 diversions. This is the example of December to April; there are other slightly different criteria for some of the other months.”
Moving into habitat suitability, Mr. Greenwood then presented a slide to illustrate the concept of what a bench is. “In the Sacramento River, there’s a lot of bank protection, riprap and so on,” he explained. “In recent years, the renewal of those protective areas with riprap has generally required some additional habitat, so benches are often included. The wetland bench is intended to be inundated pretty much all year round, so it matches with the summer and fall water level; there is a riparian bench that can be inundated in the higher flow months, winter and spring. The concern there is that the North Delta Diversions could remove water to the extent that it could drop below the level of the bench, particularly the riparian bench. That’s what this analysis was focused on looking at.”
So for the bench inundation analysis, they used available data for a number of different benches; there is basically a maximum and a minimum elevation and the length of the different benches, which were matched up to the nearest DSM 2 hydro modeling node to determine stage and from that, it’s determined whether or not the bench would have been inundated. Once the depth was worked out, they determined the habitat suitability for juvenile Chinook salmon. “That calculation was basically done every 15 minutes, but our summaries are fairly coarse level, because ultimately this is being derived from Cal SIM,” he said. “We’re looking at differences, averages by water year types and things like that. So it was done for the whole simulation period, 1922 to 2003. We focused on December to June – the winter, spring – an important time for juveniles.”
The output is a bench inundation index that ranges from a value of zero indicating no inundation, to a value of one, meaning optimal depth 100% of the time. “The results of the index showed that in some water year types, there could be 20-30% less inundation,” he said. “So accounting for the overall length of the benches that we looked at, it was proposed about 1.3 miles of channel habitat would be restored as compensation for that potential effect.”
There are a number of other analyses included in the habitat suitability section, he noted.
In terms of life cycle models, he said they used the same lifecycle models used previously for the BDCP, which have been refined somewhat since then. He pointed out that the that there aren’t upstream operational differences between the projects, so the results are generally driven by the in-Delta differences between the two scenarios.
“IOS is a model that for the Delta portion of it,” he said. “It includes the Delta Passage Model; it also has upstream components representing temperature survival relationships, and for basically the early development of the fry in stages, and then in the ocean there’s ocean survival based on harvest and a couple other variables, but they aren’t things that are different between the two scenarios that we’re interested in. The results showed that with moving through time, the two scenarios diverge in terms of the estimates of escapement. As they diverged, so did the confidence intervals. This was based on a number of reruns essentially of the model to generate these confidence intervals, so the confidence intervals are quite wide; the confidence intervals overlapped in all years.”
OBAN is a statistical model rather than the mechanistic model that is IOS. The relevant in Delta components are the number of days the Yolo bypass is inundated, whether the Delta cross-channel is opened or closed, and South Delta exports; it doesn’t have anything that could be used to explicitly represent north Delta diversions, he said. “So to explore what different levels of North Delta Diversion mortality could do, various scenarios were run in addition to a basic proposed action scenario that looked at these factors under proposed action,” he said. “Additional mortality was imposed for 1%, 5%, 10%, and 50%, just to illustrate to what extent North Delta Diversion mortality could have an effect. There are upstream and ocean components as well. Ocean components don’t differ, and the upstream components don’t differ much.”
As with IOS, Mr. Greenwood noted that there was a lot of overlap in the escapement estimates between the two scenarios; Appendix 5D has a fairly extensive write-up and a nice exploration of the OBAN results.
“One of the plots I find quite useful is Figure 5D-183, and I’m definitely be interested in getting the panel’s opinion on this one,” he said. “This basically looks at proposed action and how the different scenarios with the additional North Delta Diversion mortality affect the probability of escapement under the alternative being greater than or equal to under the no action alternative. The up shore of this is that it’s suggested that over 5% of North Delta Diversion mortality could cancel the benefit of less South Delta Exports. As I mentioned before, OBAN has a representation of South Delta Exports, but it doesn’t have representation of North Delta, so we added that in. Based on looking at these different scenarios, about 5% to cancel out. There’s a lot of variability in these, I think this would be something very useful for the panel to consider.”
For green sturgeon, the framework is similar to the one used for salmon. There is the salvage density which gives a general sense of the differences in south delta exports, based on the appearance of species has historically occurred in the Delta. There is an examination of the habitat effects of differences in the Delta outflow, which assumes that green sturgeon could respond in the same way to white sturgeon, and outflow is the main mechanism.
Upstream impacts
Rick Wilder then took over the presentation to discuss upstream effects. He began by noting that the effects analysis is divided by the two rivers, the Sacramento and the American River, and is further divided into individual species and life stages. “All of the potential upstream impacts are evaluated relative to changes in reservoir operations; that’s really the only mechanism for this project to affect upstream rivers,” he said. “From that, instream flow can be affected, so we evaluated the five components of flow that we thought would influence fish: the timing, frequency, magnitude, duration, and the rate of change of flows. It also would affect water temperature, as reservoir operations affect water temperature. So we focused on the relative frequency and magnitude of exceedance above certain water temperature thresholds that we got from literature. We also have a couple models that predict mortality based on certain thresholds that don’t necessarily agree with the thresholds that we use for our other analysis.”
Mr. Wilder pointed out that this was a collaborative effort, noting that they 34 multi-agency meetings between April and September last year to hammer out the methods, go through the results, and do the write-ups towards the end of the process. “We feel this is a really comprehensive analysis,” he said. “We tried to evaluate every potential mechanism possible upstream, and I feel like we did a pretty good job at it. We also use a lot of novel and creative techniques for filling data caps and uncertainties; I hope you find that that’s the case as well.”
Two rivers were evaluated; the Sacramento and American River; the other rivers that are part of this system were screened out early on for two main reasons, he said. The first reason is that there was a lack of effect found for those rivers. “In determining this, this was a large collaborative effort where we all got in a room and looked at flows and water temperatures throughout the year for these rivers. And these rivers include the Trinity River, Clear Creek, and the Stanislaus River. We found no difference between the project with and without, so we screened those out,” he said. “The reason we didn’t include the Feather River because it’s being covered under a different consultation, the relicensing of Oroville.”
The species covered are winter and spring-run Chinook salmon, both of which are found in the Sacramento River only, Central Valley steel head which are found in both rivers, and then green sturgeon which only found in Sacramento River, he said.
Mr. Wilder said he’d be discussing the individual analyses for each of the species, but he reiterated that they don’t always have the ability to link the physical modeling outputs to biological analysis. “When that happened, we really relied on the default method of comparing flows between flow outputs for CalSIM between the no action alternative and the proposed action, looking at things like exceedance plots and box and whisker plots and comparing mean monthly difference, or even percentile differences with and without the project. And this relied on the key assumption that more flow is better for fish.”
However, that’s not always the case as he will show in this first example, but for a lack of anything else, they had to rely on that assumption, he said. “So this first example, we combined the spawning egg incubation and alevins, which are pre-emergent fry – the individuals that still live in the next before they come out, similar to how a baby bird doesn’t leave its nest for a while,” he said. “This is specific to flow, so the analysis is split into flow effects and water temperature effects. This first analysis dealt with availability of suitable spawning habitat. We used field data collected by the US Fish and Wildlife Service back in the early 2000s, where they calculated the weighted useable area, or the WUA; it was calculated as the surface area of physical habitat instream and underwater, weighted by a suitability at a range of flow rates with suitability is defined as substrate particle size, water depth, and flow velocity.”
“The top figure represents the Sacramento River and tells you that there are different segments that they use, and what you end up with is a curve like the one in the upper right which shows these different segments and these weighed useable area units on the Y axis as a function of flow. You can see that this goes up to a point as flow increases, but it also goes right back down. So suitable area does not always increase as flow increases.”
“We used these curves to evaluate how the project would operate versus without the project by including it with these CalSIM outputs, which we were then able to produce these either an exceedance plot which I’ve plotted here, or we also look at the results as a mean difference by month and water type of when the fish were present,” he said. “There are of course limitations to this technique, and we include those in the methods section.”
Another analysis performed was for redd scour, which occurs when there are high flows in the river that mobilizes sediments that can either crush, destroy, or bury the redds or their nests. Redd scour tends to operate on a much shorter temporal scale than CalSIM’s monthly timestep; probably a day is the most appropriate timescale, but it can be as small as minutes to hours. “So to overcome this, we looked at the historical gauge data for a couple locations, and we plotted as scatter plots the mean monthly flow versus a maximum or the highest daily flow in that individual month,” Mr. Wilder said. “We did this between December and April which scour would most likely occur.”
He noted that they determined through a literature search that around 40,000 cfs is probably an appropriate level to look at as the scour threshold, although there is a lot of variation in the literature; this was used for both the Sacramento and the American River. The plot shows the highest daily maximum for a given month plotted versus the mean monthly flow for that given month at Keswick Dam in the Sacramento River. “We found the minimum mean monthly flow on the X axis that corresponded to that 40,000 daily max flow, that would allow us to determine a mean monthly flow that we could then use for CalSIM to estimate when we expect to find a daily max flow of 40,000 CFS, or in other words a scatter flow. We then compared the frequencies of when this would occur between the project and the no action, and then reported the results.”
Another analysis performed for the spawning, egg incubation, and alevin life stages and flow was red dewatering risk, which occurs when you start with a higher flow, fish will spawn, and then the water level will drop during that incubation and alevin period, and the redd essentially goes dry or dewaters. “To do this analysis, we followed individual cohorts of each month during the spawning period for a period of three months, which was an estimate of how long that post-spawn period was until the fry would emerge from the redd,” Mr. Wilder explained. “So for example, if we had a spawning period of January and February, we would follow a January cohort through February, March, April; then we’d follow a February cohort through March, April, and May. We used CalSIM data to record the minimum flows after this three month spawning period. So for January, we followed it for three months, recorded the minimum flow during that three month period, and then also for February.”
The spawning flows and dewatering flows were applied to tables from the US Fish and Wildlife Service, and the dewatering estimated based on that, he said.
Mr. Wilder then turned to the analysis for water temperature, noting that it applies to all life stages, and is not specific to spawning eggs and alevins. The threshold analysis was done using the daily HEC-5Q models for the Sacramento and American Rivers and comparing the frequency and the magnitude of exceedance of water temperature thresholds between the no action alternative and the proposed action. He noted that there are thresholds for the species, life stages, and locations within the river, and in some cases we actually have more than one threshold for each location.
Mr. Wilder then described the process used for the threshold analysis. “First of all, we added up the total number of days exceeding a given threshold by water type and month that the life stage was present for both the no action alternative and the proposed alternative. On days exceeding that threshold, we summed the cumulative degree days as a degree day total, and divided it by the number of days exceeding the threshold to give us an average daily exceedance. We then determined how biologically meaningful we thought the result would be, defining biologically meaningful as meeting two criteria: First of all, if the difference in the frequency of exceedance between the no action alternative and the proposed action was greater than 5%, which was based on best professional judgment of the group of biologists in the room. The second criterion we used was the difference in average daily exceedance was greater than a half a degree between the NAA and the PA. That was based on conversations with individuals in the room at the time, that thought that it was a reasonable differential that could be resolved through real-time operations.”
There are two biological models used to assess water temperatures for eggs. One is the Reclamation Egg Mortality Model which applies only to Chinook salmon, and only to the American River because the fall run in the American River is the only race that that has this model, he said. This analysis estimates the temperature-related mortality for three life stages: pre-spawned eggs, fertilized eggs, and pre-emergent fry or alevins; it was updated with some recent redd distribution data that came from aerial redd surveys conducted by the California Department of Fish and Wildlife. The second model was SALMOD, a Chinook salmon model for the Sacramento River. “It monitors not only temperatures but flow effects as mortality of early life stages through the juvenile life stage, and it follows cohorts through time through multiple life stages,” he said. “It acts kind of like a life cycle model but it’s not a true life cycle model because it doesn’t have any year over year carry-over. In other words, it starts off with the same pre-populated egg number in the following year. We also updated this model with the aerial redd survey data as we did for the egg mortality model.”
Mr. Wilder said they tried to do a juvenile stranding analysis, which occurs when there are very high flows in some of the channels, and there is a rapid flow reduction, and fish get stranded in these channels. “We really didn’t have the kind of information we needed to do this analysis,” he said. “We do provide a description of how we tried a couple things and it didn’t work, and ultimately, we talk about the ramping restrictions that are currently in place under the biological opinions that we expect to carry forward into the proposed action, so we conclude that there really shouldn’t be much difference between the with and without project.”
Mr. Wilder then summed up the results. “Basically, upstream flow and water temperatures at the proposed action were largely similar to those under the no action alternative,” he said. “There were some reduced flows and elevated water temperatures seen in fall months and depending on how you look at it, summer months as well. This can be explained by the fact that the new north delta intakes provide this operational flexibility to be able to export additional excess runoff in these winter and spring months. This reduces the need to release stored water in fall months which would ten reduce flows in the fall, but it does indicate that carry-over storing and cold water pool would be higher in following years, so that’s actually a good thing.”
“CalSIM is a long-term planning model that uses a pre-defined set of generalized assumptions that it uses across this entire 82 year period, and it can’t account for the numerous real-time decision making processes that would be occurring all the time at a sub-monthly temporal scale, and thus the model outputs do not exactly match what the operators would do in real time, and we can’t expect it to based on how the model was developed,” he said. “Rather, the results are intended to be a reasonable representation of the long-term trends of the state and federal facilities for comparative purposes only. And after showing these results and speaking to some pretty senior level operators of CVP and SWP, we feel pretty confident that the proposed action has the operational flexibility to be able to use real-time management to minimize whatever effects we’ve seen in the CalSIM outputs that we’ve presented.”
Delta smelt effects analyses
Marin Greenwood then discussed the Delta smelt analyses. He began by noting that US Fish and Wildlife Service requested a particular structure for analysis which is different from the one used by NMFS. “We have effects to individuals considered, and then we have population level effect which is basically considering those effects to individuals and what proportion of the population might be affected,” he said. “Then discussions of effects on critical habitat in relation to the PCEs (primary constituent elements) with PCE1 being physical habitat spawning substrate, PCE 2 is water quality, PCE 3 is river flow for migration transport, and PCE 4 is the salinity in terms of low salinity in north stream habitat. And then construction, maintenance, operations, effective conservation measures, effective monitoring activities, and cumulative effects.”
For the water facility construction again, the main difference between the salmonids and the Delta smelt is the acreage for compensation. “The Delta smelt being an annual species, we can consider these impacts to be permanent impact, so they have a higher mitigation ratio for all the components five to one, so this is why you see these acreages,” he said.
Water facility maintenance starts with the qualitative discussion that talks about the different potential effects of maintenance, and references the different avoidance and minimization measures in place to limit potential effects, he said.
As for facility operations, Mr. Greenwood said he would be focusing largely on North and South Delta effects and habitat effects, which is the combined effect mainly of the north and south delta exports on habitat within the delta, and upstream.
They were encouraged in review of some of the earlier drafts to try to come up with a proportion of the population of the Delta smelt that could be affected by north delta exports. Using the egg and larval survey from the early 90s, he looked at the volume of the area and the density of fish in relation to the broader area, and estimated the density of larvae in the intake area to be about .25% as the location of the North Delta intakes is outside their main range. “That’s slightly better than a back of an envelope calculation maybe, but not much more,” he said.
As part of some of the reviews, they were asked to address the issue of whether Delta smelt migrating adult life age could reach as far upstream as the North Delta Diversions by tidally surfing. “We did a particle tracking modeling analysis that included a simple behavior where Delta smelt adults basically would be in the upper portion of the water among flood tide, versus the lower 10% of the water on ebb tide to simulate the behavior that’s been recently seen for the species in terms of tidally surfing upstream,” he said. “This is a portion of the table that considers whether fish got as far as the north delta diversions. They didn’t, nor did they actually get past Isle 10 which is further downstream on the Sacramento River, so this suggests by the tidal surfing mechanism which seems to be the main mechanism for migrating upstream, we wouldn’t expect there to be smelt there.”
An analysis of whether Delta smelt could be entrained at the North Delta Diversions found that the Delta smelt being slightly smaller than the juvenile salmonids at 20 to 21 millimeters could be entrained. “We looked at that with the UC Davis fish treadmill study information the showed there is potential for some mortality of delta smelt that are passing the screens. This generally increases as the sweeping velocity past the screens increases.”
Mr. Greenwood acknowledged that they may have difficulty passing the intakes if they’re moving upstream and they’re not able to tidally surf in their region. “It would be a screen that’s designed to have good sweeping velocities that might be challenging for migrating adult delta smelt to pass, and so to look at that, we included an analysis of the potential to migrate upstream past the fish screen if the fish was on that bank moving upstream. This suggests that based on the swimming ability of the fish, it may be unlikely.”
“Recognizing that potential, it’s proposed based on the preliminary estimate of the amount of spawning habitat upstream of the intakes, that 55 acres of habitat would be included as compensation and the proposed action,” he said. “That’s a number that would be more refined based on more detailed surveys of the amount of sandy habitat, under the hypothesis that the sandy habitat is the preferred spawning habitat.”
For the effects of South Delta exports on Delta smelt, they used equations from the U.S. Fish and Wildlife Service’s biological opinion. One of those equations focuses on migrating adults and Old Middle River flows. “This analysis suggests that because of the dual conveyance operations, there’s definitely the potential for there to be less entrainment under the proposed action compared to the no action alternative,” said Mr. Greenwood. “But this doesn’t capture the real-time operational adjustments that would occur under the proposed action, as well as the no action alternative.”
They also looked at larvae and young juvenile entrainment at the South Delta facilities, again using equations from the Fish and Wildlife Service biological opinion, one from March to June averaging period, and one within April to May averaging period. The equations incorporate the hydrodynamic effect of South Delta exports and Old Middle River flows, and include an overall distribution of the larvae and juveniles represented with X2, the distribution of the salinity field, he said. “Generally, these don’t show large differences between the proposed action and the no action alternative, but again, they don’t capture the real-time operational adjustments that would occur both under the no action alternative and under the proposed action.”
Mr. Greenwood then turned to habitat effects, starting first with abiotic habitat. (Abiotic refers to the non-living components of the habitat, such as water, light, radiation, temperature, humidity, atmosphere, and soil.) The abiotic habitat index focuses on the two main variables of salinity and turbidity. He acknowledged that there were concerns and issues with this method. “Basically we applied this, and because of the fact that the project as well as the no action alternative have both included the full X2 criteria from the Fish and Wildlife Service biological opinion from 2008, there’s very little difference between the two scenarios,” he said. He noted that the DSM2 analysis for water temperature showed little difference within the Delta, primarily because air temperature is the main drive of the water temperature.
A sediment removal analysis was performed, which estimated 10-11% potential sediment removed, which could have an effect on water quality in the long term, he said. “It’s obviously a concern for Delta smelt which has clear associations with turbid water at various life stages,” he said. “The analysis references the avoidance and minimization measures of developing and implementing a sediment reintroduction plan to try and off set that potential effect.”
An analysis of potential entrainment of food web materials was done, using historical data that looked at the density of the phytoplankton carbon in the Sacramento River water multiplied by the volume exported, and then related that to the density downstream location of phytoplankton times the volume of the Delta to come up with an estimate, he explained. “There generally would be 5% or less removal,” he said. “ This doesn’t try to quantify in situ production, or the potential for less in the delta exports, which could result in the San Joaquin River would come in, and that has a higher density of phytoplankton carbon in it.”
A couple of analyses were done looking at microcystis. One analysis looked at the locations where microcystis had been shown to occur within the Delta, so they documented with CalSIM modeling the percentage of the months within the period of occurrence – July, August, September, October, November, where conditions were within that range and that microcystis has been observed. They also included an analysis of residence times based on sub-regions; particles are released within each of these sub-regions the residence time calculated from that, based on the basic idea that a longer residence time could be more beneficial for microcystis. This analysis was done over a sub-set of 25 years, which were selected to represent the range of flows across the full 82 years.
“The results vary by sub-region, so we had some regions on the Sacramento River where the residence time was low regardless of the scenario,” he said. “The Sacramento Deep Water Ship Channel residence times are very unaffected by operations; it’s essentially very tidal environment, and the residence time you can see doesn’t vary much. There are certain parts of the Delta, particularly in the South Delta, where there’s potential for residence time to increase because of less delta exports because of dual conveyance, but there is potential to mitigate that by switching some of the pumps in those months which are months of less concern generally for listed fish species to South Delta pumping instead of North Delta pumping.”
Longfin smelt analytical framework and effects analysis
The last presentation was on the longfin smelt analytical framework and effect analysis.
Marin Greenwood began by noting that they are not at the same part in the process of the Section 7 consultation for longfin smelt; they have just a couple of different analyses at this point. “In this draft analytical approach, we focus some discussion on setting the scene for a couple of the main factors that are affected by operations which we can model and in effect analysis, other effects will also be considered as we move forward to be more consistent with what we have for the other species,” he said. “We have a section talking about the analyses that would be included in the 2081 permit application; these include the larva entrainment risk and transport based on DSM2 particle traffic modeling. We also talk about outflow or X2 abundance relationships, and we have a section talking about future potential analyses that would be conducted as part of collaborative science and adaptive management, but that wouldn’t occur within the timeframe for the ITP application. Then we step through a section that talks about the further take analysis that we need to do.”
The first request is for absolute estimates of take and effects. “We’re cautious when we’re thinking about something like a particle tracking modeling in terms of giving us an absolute sense of the proportion of the population that might be entrained, but we feel that depending on, when looking at the assumptions, that could actually be one way of getting the sense of the proportion of the population if we’ve done a good job of characterizing a reasonable distribution of the population,” Mr. Greenwood said. “The outflow-abundance regressions give estimates of abundance for a given outflow, certainly with some confidence intervals and variability around them, but they do give estimates for the different scenarios, and from those, a percent of the population difference between scenarios could be derived.”
“For adult and juvenile delta entrainment, we may not be able to come up with an estimate of taking an absolute sense in terms of having a good predictive equation or something like that, but we think that we would have a good perspective on whether they could be similar or less than currently occurs, so we’d be able to at least provide some perspective in that regard,” he continued. “For the north delta diversions, we would generally focus our discussion on the portion of the population that might occur near the North Delta Diversions.”
The second request is to consolidate the take estimates from the different sources such as the entrainment effect and the outflow effect to provide a proportion of the population that would essentially be taken. “The larva estimates would already be a percent of population,” he said. “The adult estimates would be from previous estimates that have been done for the 2009 ITP application, just getting a sense of the proportion of the population, and especially given that we would expect it to be less under the project based on proposal operations. For juvenile south delta entrainment, we think this could possibly be done based on extrapolations from the survey data, so coming up with a population about accounting for the efficiency of the survey nets, and combining those different things which are basically entrainment, south delta entrainment estimates, and then find a way to combine the percent difference estimates from the flow-abundance regressions.”
The third request was basically a population analysis estimating the cumulative effect of the project over the ITP term. “This is thinking about if you have an effect each year that might that wrap over one year to another, could that have an effect over time? So what we have written there as far as the proposed approach, but looking at the relationship, it doesn’t seem like the existing population level analyses have shown entrainment or proxies of entrainment to be a driver of population dynamics. Therefore, our proposed focus is on the differences in winter spring outflow to perhaps give effect. There aren’t any tools we could really use for that to characterize the year over year, so our proposed approach is to do a qualitative discussion.”
Mr. Greenwood then turned to the draft take analysis, noting that the section on construction effects is still in process, and there isn’t anything for maintenance effects, but those can be included as they move forward. There are two main analyses: one for Delta Outflow Effect, and the other for Entrainment and South Delta entry, he said. He also noted that there aren’t protocol mitigation measure effects, conservation measure effects, and monitoring activity effects. The overall application will include an analysis of potential for jeopardy as well.
He then presented a graph from a 2009 paper that looked at outflow or X2 abundance relationships for different species, one of them being the longfin smelt. The regressions done included X2 slopes, intersect, and step changes. “We didn’t do this analysis including the step change, we just did the slope generally stays consistent across periods,” he said. “As we showed earlier in the operations, somewhat less outflow in winter can give an effect on X2 which is what translates into these differences here. Not large differences, but still differences.”
To illustrate the variability and the results in relation to the confidence intervals, he presented a graph using confidence intervals based on the X2 slope, noting that the confidence intervals are broad in in comparison to the differences between the mean estimates, the red being the proposed project and NA being the no action alternative.
For the analysis of entrainment at the North Delta intakes, the egg and larva survey data was used to compare the densities of long-finned smelt in this upstream intake area versus in the downstream area. “The difference is bigger for long-finned smelt between upstream and downstream although a good point was made recently to me that this is an area of flux in terms of the flows of generally moving downstream, so whether that could actually have an effect on the densities that you sample, that’s potential, whereas these areas are more tidal. That could be an effect there in terms of the accumulation in certain areas versus the flux. That’s a point to consider on that.”
Panel’s initial recommendations
On the second day, the panel met for the morning in closed session, and then presented their initial recommendations later that afternoon.
Panel chair Charles “Si” Simenstad began by giving the key points and perspectives of the panel. “We really believe the project is more than incremental change in the system, and it really needs to be acknowledged that assuming no or minimal change is not appropriate,” he said. “Also there’s just a tremendous amount of uncertainty, from knowledge about the species to knowledge about system performance and the likely response to the change to the new conveyance system. At the same time, we recognize that there are a lot of gaps in the best available science that could be incorporated into an approach to the biological opinion.”
“Given that lack of concern about the level of uncertainty that we perceived in the documents and the biological assessment and given the bottom line on the safeguards of the Endangered Species Act, that really suggests that there are some major safeguards that need to be put into place to implement this,” he continued. “There’s a dependence on an undefined adaptive management as sort of the routine approach expressed in the biological assessment and we believe it really requires a much more explicit quantitatively rigorous and credible process based on equally rigorous monitoring and research.”
Mr. Simenstad reminded that there are two major elements to the panel’s charge, one of them dealt with the biological opinion analytical approach, and the other with the individual species analysis. He started with the first part of the panel’s charge, How well is the analytical approach designed to adequately assess potential responses of the target listed species to the effects of the proposed action (i.e., both direct and indirect effects of the project)?
The panel was asked how well does the analysis consider a couple of the key models and templates, especially for salmonids. “We felt those were very adequately utilized and appropriate,” he said. “How effective are the conceptual models in the review for the target aquatic species incorporated, we found some inconsistencies in that, and definitely room for improvement. Particularly for instance, very accurate conceptual models for Delta smelt, but less so for longfin smelt.”
As for how well does the analytical approach for the target aquatic species explains exposure, response, and risk at the individual population diversity level, the panel felt the approach needs to better address the uncertainties which are ample. Whether the approach for assessing affects provides a scientifically defensible approach for evaluating new adverse affects to aquatic species to the north Delta, in addition to any changes in adverse effects on existing south Delta and improvements could be made, the panel said this is quite variable. “In some cases, very adequately addressed with the best available science, and sometimes not,” Mr. Simonstad said.
As to the second part of the charge regarding the supporting analyses for the target species, as to whether the appropriate analytical tools and models were used, the panel said generally yes. “Whether assumptions are plainly stated and scientifically sound and whether there are uncertainties and limitations on the methods of the BA aquatic species analyses and on longfin smelt analytical approach are clearly stated, they could definitely be better qualified and quantified,” he said. “There are a lot of hidden assumptions that really need to be expressed.”
The panel expressed concerns about the climate change analysis only going out to 2030. “We’re still a little concerned about limiting it to 2030 and going at least to 2100, even acknowledging uncertainties with doing that.”
As to whether the species analyses incorporate information from existing synthesis reports, the panel said that they need more time to examine this and will address this item more specifically in the written report.
How adequately does the biological assessment analyses and longfin smelt analytical approach support a scientifically defensible approach for evaluating new adverse effects, and how adequately will it support any changes in the existing south Delta facilities? “Again, the best available science supports the approach, but there is still so much uncertainty in that that the uncertainty really needs to be brought forward in the analyses,” he said.
As to the question of the longfin smelt evaluation, the panel acknowledges that the best available science is extremely limited, and that given the target time frame to prepare a biological opinion, it’s hard to imagine they can come up with anything new.
“One of our main points that we came up with as we thought about the project as a whole was that the overarching theme that we needed to start with is that this project is more than an incremental change to the system,” said one of the panel scientists. “This isn’t just putting in one little channel; this isn’t putting in a culvert type of change; it’s not the type of analysis you sometimes do for these kinds of assessments. This is a total replumbing of the entire Delta. You’re going to be totally changing how the system works and how the physics works. You’re going to change the distribution of San Joaquin River water to Sacramento River, you’re going to be changing the water quality throughout the system, you’re going to be changing the tides in some places, where you had unidirectional flow, you’re now going to have a tidal flow, so you have to be aware that this is a major, major change. As a result, there are going to be some very high uncertainties on the fishes’ response to this major change.”
“I think the panel is pleased with the concerted efforts that were made to characterize uncertainty in the biological assessments, the species specific assessments – you did what you could,” said another one of the panel scientists. “I think there are some cases where you could do more. My concern is that the uncertainties are understated in one important way. I think a great job was done in representing the uncertainty of the future environment by using the 82 year simulation strategy under various scenarios, and then representing the variability you expect to see in the future due to year to year changes. I think that was really well done. However, that may be a minor source of uncertainty, relative to what I believe is a much major source of uncertainty. The models that we have to try to understand how fish respond to their environments have created quantitative uncertainty. It’s pretty hard to tease this out in the case of process-based models, and there are several places in the analyses where that model uncertainty was incorporated, which is good. In some of the statistical models, I think it was often underrepresented.”
“The current problem is that when the BA results are being passed on up or used to construct the BO, that they look too good,” he continued. “What you see when you look at those boxes and plots which would represent the variability over time, they represent the future environmental variability, is you see lots of box plots where the red and blue are side by side, they are kind of narrow, and they overlap a lot, and so the conclusion you draw is that the NAA and the PA outcomes are essentially the same. And that’s a legitimate conclusion if those box plots really are that narrow. The uncertainty about what’s going to happen to survival or to entrainment, really the variability is that low, if those two boxes are really wide, then they still overlap a lot, they still can overlap all the way, but then you have less assurance that the two outcomes really are the same because both of them are so uncertain. I think that is a more realistic message to have the BA assessments show.”
“There was also concern about some things that are simply not possible to assess at the new diversion sites in the north,” said another panel scientist. “There’s an existing prey-predator relationship, a certain density of predators at these sites, and it would be a potential learning experience to see how the predation pressure changes at these sites, with potential impingement locations for fish in the river. I think the BA was pretty convincing in its analysis of the Delta smelt not being very abundant near the diversions, but there are other species that could be impacted by a change in the predator field, so that’s a opportunity that shouldn’t be lost in learning what goes on before and after.”
“There’s also a fundamental lack of evidence on certain life stages of fish, notably the smelts, not knowing where the Delta smelt spawns, not being able to identify the eggs, not having the clear understanding of larval behavior in terms of how larvae respond to changes in flow fields, which will in turn change how they are distributed in the estuary,” he said. “Also information on the vital parameters that influence survival and the contribution to future generations is the more concern. Vital rates reflect the reproductive capacity over the lifetime of the fish; birth rates, mortality rates.”
“The approach to the biological opinion relied heavily on the viable salmon population document and the viability analysis; both documents are excellent documents,” said another panel scientist. “It makes sense to rely upon those documents for impact analysis by the project. A key component of these reports and the approach is to examine how the project might affect diversity of salmonids including the life history diversity of those fish; however we have relatively little information on the life history diversity of some of the salmonids in this basin. … Looking at the analysis of how the project may affect salmonids, it’s important to determine to what extent each one of these life history strategies may be impacted differently by the project effects.”
“Another important aspect of population dynamics for all species, not only salmon and Delta smelt, is density dependence; this is brought up in the viable salmon population document,” said another panel scientist. “In the Columbia Basin, it was often assumed even by scientists that density dependence was low simply because population levels were so low, and therefore density was not an important factor, but after gathering lots of information, we found very strong density dependence. An important aspect of density dependence is whether or not density dependence is compensatory or depensatory. Depensatory, the population can be destabling and is something you want to avoid; an example is where a predator population consumes a constant number of juvenile fishes and therefore a high percentage of the fish population, prey population, when that population is low, it causes a much higher percent mortality at those low population levels and causes the population to decline.”
“For winter chinook salmon, we noticed that chinook smolt passage through the Delta is much higher during wet years compared to dry years, and according to the Delta passage model analyses, there was a more adverse effect caused by the project during dry years,” he continued. “This might turn out to be a compensatory type mortality, even though climate and environmental type factors are often density dependent, but what I mean by that is that in dry years, it could be relatively low numbers of fish migrating into the Delta, and on top of that, you have higher than normal mortality caused by the project and the removal of water from the Delta area, and this could potentially cause a compensatory type response, which would be especially important to look at in the analysis when it occurs over multiple years such as a prolonged drought.”
One of the scientists on the panel notes that the guidelines state in multiple places and multiple times to ‘try to cope with uncertainty’. “Yet, when I read the draft biological opinion, the word uncertainty barely turned up, and where it did turn up, it dealt with uncertainty about future environments, not about uncertainty about the outcome of how fish respond to the environments,” he said. “I think the panel would really like to see the draft BO try to say more about how the BO plans to treat uncertainty.” He noted that there are many decisions based on a true/false decision: “In many of these cases, you can’t get a clear true/false answer, based on the data and based on the models available because of this high uncertainty, so I think it would be useful if the draft biological opinion could include some language about what to do when that happens – when you have high uncertainty where you can’t make a clear true/false decision in your logic stream. What will be the strategy in that case? I think that this high uncertainty will be clearer to the people making the draft biological opinion and the biological assessments, if the uncertainty at least in some cases is as fully represented as possible.”
“As a result of all this uncertainty and keeping in mind the strong and clear mandate in Section 7 to err on the side of the species when there’s insufficient data, the panel really feels strongly about the need for a really explicit commitment to ongoing learning and research through adaptive management and to explicitly identify triggers that will result in the initiation of consultation if necessary,” said another panel scientist, noting that the triggers for reinitiation of consultation seem a little bit vague. “It could be really important not to leave it like that, not just let it depend on whether someone spontaneously thinks it’s time for a reinitiation, it’s important to weigh those decision points out in advance.”
There are many references to adaptive management in the document, but few details about how adaptive management would be implemented, she continued. “What we really hope to see in the draft biological opinion is there needs to be more information about how adaptive management will be organized and structured … would there be independent peer review of the adaptive management program, those kinds of details we think should be in the draft biological opinion. Also, it should be addressed how adaptive management will be funded, all the monitoring that will be necessary to learn more and deal with continued response to new information. … We think that for a project that’s so important like this, it’s such a significant change in the system, that the need to insure there is ongoing learning and testing and experimentation and hypothesizing, and that really needs to be made clear in the biological opinion how that will be done.”
“We do intend to make objective recommendations both for the analytical approaches as well as trying to reduce uncertainty in the biological assessment and how to address the uncertainties when you move to the biological opinion,” said Mr. Simonstad. “It’s a bit premature for us to make those recommendations, but you are going to see a suite of suggestions and recommendations on how to really contribute to a better biological opinion.”
For more information …
Sign up for daily email service and you’ll never miss a post!
Sign up for daily emails and get all the Notebook’s aggregated and original water news content delivered to your email box by 9AM. Breaking news alerts, too. Sign me up!
