RESPONSE TO FEBRUARY 16, 2018 REQUEST FOR ADDITIONAL INFORMATION, RESOURCE AGENCY LATE FILING, AND OTHER RELATED INFORMATION ATTACHMENT T

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1 RESPONSE TO FEBRUARY 16, 2018 REQUEST FOR ADDITIONAL INFORMATION, RESOURCE AGENCY LATE FILING, AND OTHER RELATED INFORMATION ATTACHMENT T DISTRICTS ANALYSIS AND COMMENT ON USFWS ATTACHMENT 5: USE OF COMULATIVE ACRE-DAYS AS A FLOODPLAIN MITIGATION MEASURE: FISHBIO COMMENTS

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3 FISHBIO Comments on USFWS Attachment 5 The USFWS used data from the Stanislaus River, ignoring juvenile salmon survival indices for the Tuolumne River that are readily available. On page 41 of the January 29 filing, the USFWS states that The rotary screw traps in the Tuolumne River are not set up to measure juvenile to smolt survival, so the Stanislaus River must act as a surrogate in this regard (Attachment 1 USFWS 2014). This is entirely false. FISHBIO staff established the operations at both sites on the Stanislaus in 1996, and established the same monitoring strategy on the Tuolumne River in The placement and operation (following CAMP guidelines) of the Tuolumne River and Stanislaus River RSTs provide for equivalent data sets for their respective river. There is no reason why the Stanislaus RSTs would need to be used as a surrogate for the Tuolumne RSTs related to juvenile salmon survival. The USFWS conclusion that February through June flows drive juvenile salmon survival by inundating floodplain habitats in the lower Tuolumne River must be rejected. Fish that have left the Tuolumne River do not have access to floodplains in the lower Tuolumne River and the correlation between flow and survival weakens through time. Annual indices of juvenile salmon survival have been calculated in the Tuolumne and Stanislaus rivers by dividing abundance estimates from trapping sites near the mouth of each river by abundance estimates from trapping sites near the downstream boundaries. These survival indices are almost entirely driven by fry survival during migration, a point which the USFWS analysis fails to recognize. In wetter years with freshets, fry survive to the lower RST. In dry years, and absent natural freshet or pulse flows in February, almost no fry survive to the lower trapping sites. As these fry are quickly migrating through the lower river corridors and leaving the tributaries in January through March, they do not benefit from later floodplain inundation in the river that they are exiting. For example, 54% of total passage at Waterford and 5 of total passage at Grayson in 2011 occurred prior to February 1 (Figure 1). Since at least half of the juvenile migrants had already left the Tuolumne River before the floodplain inundation period identified by USFWS, they were not present to potentially utilize inundated floodplain habitats of the lower Tuolumne River during February-June. On average, about 6 of juvenile salmon migrate as fry by the end of February and 85% by the end of March (Figure 2). Therefore, most of the survival that the USFWS is counting as related to floodplain usage is from early outmigration of fry which do not reside on or benefit from floodplain access for any length of time, and not at all after mid- to late- March. The impact of fry migration, and the positive correlation between fry migration and flow, is clearly illustrated through regression analysis of monthly flow volumes relative to annual survival indices from the rotary screw traps on the Tuolumne River. February flows are the strongest predictor of annual juvenile survival indices on the Tuolumne River, explaining 98% of the variability (Figure 3). 1 During subsequent months, flow explains less and less of the variability in survival. This makes sense as fewer and fewer individuals remain in the river to be influenced by flow or other 1 When combined with the results of the Otolith Study (W&AR-11), wherein it was found that fish that leave the Tuolumne River as fry represent a very small percent of the subsequent adult escapement (<5%), flows intended to maintain high habitat suitability for fry in the upper portions of the Tuolumne River are part of the Districts Preferred Plan. FishBio Comments Page 1 Don Pedro and La Grange Hydroelectric Projects

4 conditions such as floodplain inundation, as outmigration progresses. The same holds true for the Stanislaus River (Figure 4). The USFWS conclusion that February through June flows drive juvenile salmon survival by inundating floodplain habitats in the lower Tuolumne River must be rejected because fish that have left do not have access to floodplains in the lower Tuolumne River and the correlation between flow and survival weakens through time. The USFWS analysis falsely assumes than an acre inundated in June has the same value as an acre inundated in February. Migration occurs through time, and consequently, the proportion of the population remaining to rear in the Tuolumne River decreases through the migration period. Thus any potential benefit of floodplain inundation decreases through time, yet the USFWS analysis treats an acre day in early June when <1% of the juvenile population remains in the river with the same value as an acre day during fry rearing in February. The cumulative acre-day analysis fails to take into account the potential benefits of timing and/or duration of inundation associated with individual floodplain activation flow events. Two hypothetical flow scenarios as examples of this are early vs. late inundation and short vs. long inundation periods (Figure 5). While both of these flow scenarios result in the same number of acre-days and the same volume of water, they would provide for very different biological responses. The USFWS acre-day analysis period extends to June 15, but there is limited support for floodplain benefits for salmonids beyond April. Moyle et al. ( ) reported prevalence of non-native species on floodplains and very limited habitat use by Chinook salmon after April. 3 The trend of decreasing catch and increasing fish size observed in April to June 2017 is a pattern repeatedly observed based on long-term monitoring data (TID/MID 2016). Flood releases in 2017 provided an opportunity to conduct additional sampling of floodplain habitat. However, the increased number of sample events in space and time did not result in an increased number of lower reach sites being occupied during April through June, despite 2017 being one of the wettest years on record. The 2017 seine surveys showed relatively consistent catch of juvenile Chinook salmon at all sampled floodplain sites. However, the proportion of occupied sites was lower than most other wet years. Despite flows consistently greater than 5,000 cfs during 2017, seining provided no evidence of increased floodplain usage during April through June. Similar results have been observed on the Stanislaus River, with no salmon documented in any off-channel habitats sampled downstream of Oakdale over 3 years (2013, 2014, & 2017) during the mid-april to mid-may period. 2 Moyle PB, Crain PK, Whitener K Patterns in the use of a restored California floodplain by native and alien fishes. San Francisco Estuary and Watershed Science 5: The USFWS acknowledged this itself in comments it provided on the State Water Board s draft Phase 1 changes to the Bay Delta Plan, wherein USFWS states on page 17: The benefits of floodplain inundation in later spring months (May and June), must be offset by the potential use by warm water predators. By May and June many of the salmon may be gone from the tributaries, especially in drier, warmer years. iff.pdf FishBio Comments Page 2 Don Pedro and La Grange Hydroelectric Projects

5 USFWS references the Stanislaus River as proof that floodplain inundation has lead to a functional fall-run Chinook salmon fishery. The USFWS January 29, 2018 filing (page 37) claims that comparison of weir counts and flows on the Stanislaus and Tuolumne rivers provide evidence that environmental flows have resulted in a functional fishery on the Stanislaus. First, this claim is entirely dispelled by the numbers of adipose fin clipped fish observed. Of the more than 12,000 salmon counted in the Stanislaus during 2015, 26% were ad- clipped indicating hatchery origin. Since hatcheries ad-clip approximately of the salmon released, this indicates that all of the adult salmon migrating past the Stanislaus River weir in 2015 were from hatcheries. With no detectable proportion of naturally-spawned salmon in the Stanislaus River this can hardly be described as a functional fishery. There is no hatchery on the Stanislaus or Tuolumne rivers. These fish did not rear in or migrate through either of these streams as juveniles and thus could not have benefitted from any inundation of floodplain in the Tuolumne or Stanislaus rivers. Once again the USFWS completely disregards the fact that a fish must be present in an environment to benefit from it. It is easy to understand why record numbers were observed in the Stanislaus River during Production from the Merced River Hatchery increased substantially during brood years 2012 and 2013 from less than 400,000 to approximately 1.5 million. The increase in production from Merced River Hatchery corresponds to adult salmon returning at two and three years of age during 2015, and is probably the most significant factor contributing to the high salmon abundance observed in the Stanislaus River during The other significant factor contributing to increased abundance of adult salmon in the Stanislaus River during 2015 was a shift in hatchery release locations. Until recently, it was common for the Merced River and Coleman National Fish hatcheries to release most of their production at or near the hatcheries. This changed recently as releases from Coleman Hatchery shifted from -12% off-site to 62% in brood year 2013 and 10 in 2014 and Merced River Hatchery shifted to releasing their fish far downstream at Jersey Point. The shift to releasing juvenile salmon in Bay and Delta both increased their survival and tendency to stray to other streams. At the same time, production from Merced River Hatchery more than tripled. Finally, the USFWS claim also ignored the impact of water hyacinth on the 2015 Tuolumne River adult upstream migration timing and abundance. Migration timing was later in 2015 than in any other year since weir monitoring began in 2009, and suggested delayed fall-run Chinook salmon migration in the Tuolumne River. Low early-season passage counts during 2013 and 2014 were also suggestive of delayed migration in the Tuolumne River. Unique to these years was the extensive growth of water hyacinth that occurred in the lower Tuolumne and San Joaquin Rivers. In the annual report to FERC it was estimated that water hyacinth covered 12.5% of riverine habitat between the San Joaquin River at Vernalis and the Tuolumne River weir during fall 2015, and this was an increase over 2013 and Note that the blockages were upstream of the confluence of the Stanislaus River and the San Joaquin River, and thus migration to the Stanislaus was not impaired by water hyacinth (Figure 6). The USFWS analysis assumes a linear relationship between survival and acre-days. The analysis is entirely driven by the 2006 and 2011 data points. There is only one data point across the range of 877 acre days to 98,621 acre days which is a substantial void. The one data point within this range (16,817 acre days in 2010) is similar to observations at 877 acre-days or FishBio Comments Page 3 Don Pedro and La Grange Hydroelectric Projects

6 less, and there are indications that factors other than flow or floodplain inundation are at play. For instance, there were no acre-days accumulated in 2009, yet this was the third highest survival index recorded at 7.5% (using USFWS numbers, not updated from 2017 RST report). In 2007 there were also no acre-days accumulated, yet survival was the second lowest recorded at 1.8%. Interestingly, cumulative discharge during February 1 through June 15 in 2007 (97,796 acre-ft) was higher than discharge during 2009 (88,973 acre-ft). The 2009 survival estimate also reflects the third consecutive dry year, yet survival indices increased over this period from 1.8% to 7.5%. This trend is not explained by floodplain inundation, cumulative discharge, or flows to control non-native predators. The unique factor in 2009 was run-off events that resulted in several turbidity spikes that were the highest ever recorded. The USFWS analysis assumes that correlation equals causation without exploring other mechanisms which may influence survival. There is no evidence of a direct relationship between inundated floodplain and salmonid success on the Stanislaus or Tuolumne Rivers. USFWS (2014) found a significant relationship between juvenile survival and floodplain acredays, with floodplain acre-days explaining 77% of the year to year variation in juvenile survival. This reference implicitly leads the reader to believe that it is floodplain inundation that is associated with the increased survival of juvenile Chinook salmon, and not another possible mechanism. It is true that it is positively correlated, but other lines of evidence provide reason to reject this hypothesis and provide support for an alternate explanation. Unless the reader scrutinizes USFWS 2014 (which is a non peer-reviewed annual progress report) and is familiar with the river system, it would not be apparent that the flow:survival relationship is driven strongly by February flows and fry outmigration as discussed previously. USFWS conclusion has seriously flawed logic with no foundation of solid data analysis. 1. The USFWS states that it must rely upon the Stanislaus River because comparable data do not exist for the Tuolumne. This is false. 2. The USFWS identifies February 1-June 15 flows as driving juvenile salmon survival without exploring other temporal intervals. February flows explain most variation in survival, and the influence of flow decreases in subsequent months. Fish must be present in an environment to benefit from it. 3. The USFWS takes the same flawed approach by substituting floodplain acre-days for flow. 4. The USFWS claims that environmental flows have resulted in a functional fishery on the Stanislaus. There was no detectable proportion of naturally-spawned salmon in the Stanislaus or Tuolumne rivers during There is no hatchery on the Stanislaus or Tuolumne rivers. These fish did not rear in or migrate through either of these streams as juveniles and thus could not have benefitted from any inundation of floodplain in the Tuolumne or Stanislaus rivers. Once again the USFWS completely disregards the fact that a fish must be present in an environment to benefit from it. 5. The cherry-picked comparison between the Stanislaus River and the Tuolumne River escapements during 2015 completely ignores the influence of water hyacinth, which combined with changes in hatchery stocking practices, provides a clear rationale for the differences in observed escapement between the streams. FishBio Comments Page 4 Don Pedro and La Grange Hydroelectric Projects

7 Estimated Passage Flow Figures Jan 1-Feb 1-Mar 1-Apr 1-May 1-Jun 0 Waterford Grayson Flow Figure 1. Daily estimated passage at Waterford and Grayson during Figure 2. Mean date (and 95% confidence intervals) when percentage passage metrics (in 5% increments) were met for juvenile Chinook salmon at Waterford RST ( ). FishBio Comments Page 5 Don Pedro and La Grange Hydroelectric Projects

8 10 5 R² = Feb. Flow Volume (TAF) 10 5 R² = Mar Flow Volume (TAF) 10 5 R² = Apr Flow Volume (TAF) 10 5 R² = May Flow Volume (TAF) Figure 3. Total monthly flow at La Grange and annual juvenile survival indices on the Tuolumne River, FishBio Comments Page 6 Don Pedro and La Grange Hydroelectric Projects

9 10 5 R² = Feb Flow Volume (TAF) 10 5 R² = Mar Flow Volume (TAF) 10 5 R² = Apr Flow Volume (TAF) 10 5 R² = May Flow Volume (TAF) Figure 4. Total monthly flow at Ripon and annual juvenile survival indices on the Stanislaus River, Notes: 1996 index low - upper site began sampling began several days before lower site. Assumed 10 in 1998 since calculated value of 169% exceeds maximum possible value. No index for 2006 sampling incomplete. FishBio Comments Page 7 Don Pedro and La Grange Hydroelectric Projects

10 Flow (cfs) Feb 1-Mar 1-Apr 1-May 1-Jun Early Late Flow (cfs) Long Short 0 1-Feb 1-Mar 1-Apr 1-May 1-Jun Figure 5. Hypothetical hydrographs showing the same volumes of flow released early or late or as long or short duration pulses. FishBio Comments Page 8 Don Pedro and La Grange Hydroelectric Projects

11 Figure 6. Water hyacinth blockages identified between Vernalis and Fox Grove based on analysis of aerial imagery (Imagery dates: 10/21/15, 10/31/15 and 11/28/15. FishBio Comments Page 9 Don Pedro and La Grange Hydroelectric Projects