An Analysis of Differential Delayed Mortality Experienced by Stream-type Chinook Salmon of the Snake River

In the Anadromous Fish Appendix of the US Army Corp of Engineers (USACE) Environmental Impact Statement on the Lower Snake River Hydrosystem Alternatives for recovery of Snake River salmon and steelhead (hereafter referred to as A-Fish ), the National Marine Fisheries Service (NMFS) suggested that transportation effectiveness of spring/summer chinook may have improved markedly in recent years. The NMFS conclusion was based on estimates of \u27D\u27-values (the differential delayed survival rate between transported fish and fish that migrated in-river) for 1994-1995 (NMFS, 1999). NMFS suggested, if \u27D\u27 is high (estimated in A-Fish at 0.8) and extra mortality of in-river and transported smolts is unrelated to the hydropower system, transportation options may meet recovery standards as well or better than natural river options. NMFS also suggested that further studies could reduce the uncertainty about true values of \u27D\u27 and provide greater confidence to make a decision on the alternative management action needed to recover listed Snake River salmon and steelhead. In this analysis, we demonstrate that the evidence is compatible with a wide range of ‘D’ values, but only a small portion of this distribution is as high as the A-Fish estimate. We also present evidence that the extra mortality of in-river fish is related to the hydrosystem. We analyzed a suite of plausible assumptions used in the calculation of \u27D\u27. Based on our analysis of the 1994-1996 PIT-tag data, there is a wide range of possible \u27D\u27-values. The NMFS\u27 estimate falls at the upper end of this distribution (90th – 95th percentiles). Alternative \u27D\u27-values, based on what we believe to be more reasonable assumptions, were closer to 0.48. Because \u27D\u27 is a modeled value (and not a measurement, as implied in the A-Fish), it is very sensitive to the suite of assumptions made and how the data are grouped. \u27D\u27 estimates were most sensitive to: (1) whether or not fish that were transported from downstream collection/transport sites (Lower Monumental (LMO) and McNary (MCN) dams) were included in the group of fish used to estimate transport smolt to adult return rates (SAR); and (2) how reach survival rate estimates were extrapolated down to Bonneville Dam (BON). In 1994 the ‘D’-value estimated using four collection projects was much lower than two collection projects. However, in 1995 and 1996 the difference in ‘D’ using two and four collection projects was not as dramatic as in 1994. Therefore, the estimated high ‘D’-values are mainly driven by this single assumption for one year. Based on past and proposed future transportation operations, it is unclear why fish transported at the lower two projects were excluded from the NMFS analysis. Transported fish are subjected to stress, injury, and crowding at the collection projects. In addition, the physiological state of fish may be poorly synchronized with the time of saltwater entry for transported fish. These factors could explain the higher delayed mortality experienced by transported fish as suggested by a consistently estimated ‘D’ value that is less than 1. We disagree with the NMFS assertion that “ongoing direct experiments that contrast the return rates of tagged fish that pass through the hydrosystem versus the return rates of transported fish can resolve this question in a clear and unambiguous manner”. While a few components of the \u27D\u27-value estimate are measurable, the sensitivity analysis highlights differences in assumptionsand uncertainties that are not likely resolvable in the near term. In addition, low numbers of returning adults and small numbers of smolts for wild spring/summer chinook salmon may hamper reducing the uncertainty in estimates for reach survival rates and SARs for a non-detected group. Therefore, data are unlikely to perfect our understanding of \u27D\u27 or eliminate the uncertainty in the most influential assumptions. The hypothesis of extra or delayed mortality due to hydrosystem passage has an empirical basis, as well as biological rationale. Based on recent PIT tag data we also found evidence that delayed mortality of both in-river and transported smolts was related to hydropower. More specifically, the evidence suggests that, at least for collected and bypassed smolts, there is a difference between the patterns of direct passage survival rates and SARs. Smolts first detected and transported from the downstream projects (LMO and MCN) had lower SARs than smolts collected and transported from higher up in the system. Similarly (as reported in the A-Fish), SARs of in-river smolts decreased as the number of times the fish were collected and bypassed increased. These pieces of information provide evidence that the Snake River spring summer chinook extra mortality is related to the juvenile migration hydrosystem experience. Based on results from life-cycle modeling (Marmorek and Peters 1998b), transport based management options lead to a high likelihood of recovery only when ‘D’ is high and the source of extra mortality is not related to the experience during hydrosystem passage. However, when extra mortality is hydrosystem related (which our analysis supports), the natural river options are still the most likely management action to recover these stocks, even if ‘D’ is high (which our analysis does not support). Simply studying ‘D’, if that were possible, without determining the source of extra mortality, yields little additional insight into effects of the different management actions on Snake River spring/summer chinook recovery. Given the dangerously low level ofthese populations, we do not believe it is prudent to make management decision on the configuration and operation of the Snake and Columbia hydrosystem for the next 5-20 years (i.e. delaying a decision preserves status quo configuration), based solely on one optimistic assumption about the effectiveness of past and current hydrosystem operations

Partnering with Beaver to Improve Fish Habitat: An Example of Cheap and Cheerful Restoration to Provide a Population Benefit to an Endangered Species

Anthropogenic activities such as timber harvest, agriculture, and grazing have greatly altered the habitat of salmon and steelhead in streams of western North America. Perhaps equally as important but rarely mentioned as a major impact to fish habitat is the great reduction of beaver. Beaver were distributed in high densities across much of North America prior to European settlement, however intense trapping more than century ago nearly exterminated beaver in several regions. Although salmonids have coexisted with beaver for millions of years, skepticism exists about the benefits dam building activities play. In fact, removal of beaver dams from streams is still a management activity employed in some states to try to improve salmonid fisheries. Thus, it is not surprising that using dam building beavers as a means of restoring streams is uncommon. Channel incision is a degraded state of fish habitat that is found ubiquitously throughout the world. We have suggested that beaver dams and beaver dam analogs can greatly accelerate the recovery of incised channels. We conducted a watershed scale experiment where we built beaver dam analogs to encouraged beavers to build dams to improve fish habitat in an incised stream. We observed several rapid changes to the stream environment following restoration. We also found survival, abundance, and production of juvenile steelhead increased following these changes. We believe management of streams that include beaver as part of the environment will benefit salmonid populations

Quantifying Stream Habitat: Relative Effort Versus Quality of Remote Sensing & Ground-Based Survey Techniques

Numerous field and analytical methods exist to assist in the quantification of the quantity and quality of in-stream habitat for salmonids. These methods range from field sketches or \u27tape and stick\u27 ground-based surveys, through to spatially explicit topographic and aerial photographic surveys from a mix of ground-based and remotely sensed airborne platforms. Although some investigators have assessed the quality of specific individual survey methods, the inter-comparison of competing techniques across a diverse range of habitat conditions (wadeable headwater channels to non-wadeable mainstem channels) has not yet been elucidated. In this study, we seek to quantify relative quality (i.e. accuracy, precision, extent) of habitat metrics and inventories derived from different ground-based, boat-based and remotely sensed surveys of varying degrees of sophistication, as well as enumerate the effort and cost in completing the surveys. Over the summer of 2010, seven sample reaches of varying habitat complexity were surveyed in the Lemhi River Basin, Idaho, USA. Complete topographic/bathymetric surveys were attempted at each site using separate rtkGPS, total station, ground-based LiDaR, traditional airborne LiDaR, and imagery-based spectral correlation methods. Separate, georectified aerial imagery surveys were acquired using a tethered blimp, a drone UAV, and a traditional fixed-wing aircraft. Preliminary results from the surveys highlight that no single technique outperforms the others across the full range of conditions where stream habitat surveys are needed. The results are helpful for understanding the strengths and weaknesses of each approach in specific conditions, and how a hybrid of data acquisition methods can be used to build a more complete quantification of salmonid habitat conditions in rivers of the Columbia River Basin

Environmental drivers of instream wood: models from the Columbia RIver Basin, USA

<p>Environmental drivers of instream wood: models from the Columbia RIver Basin, USA. Poster presented at the 2014 Joint Aquatic Sciences Meeting, Portland, OR.</p