United States Department of the Interior U.S. Fish and Wildlife Service IDAHO FISH AND WILDLIFE OFFICE 1387 S. Vinnell Way, Room 368 Boise, Idaho 83709 Telephone (208) 378-5243 https://www.fws.gov/idaho
Kimberly D. Bose FEB 0 1 2012 Secretary Federal Energy Regulatory Commission 888 First Street, NE Washington, D.C. 20426
Subject: Swan Falls Hydroelectric Project-Ada and Owyhee Counties, Idaho-Biological Opinion In Reply Refer To: 14420-2011-F-0318 For Internal Use: CONS-lOOb FERCNo. 503
Dear Ms. Bose:
Enclosed are the Fish and Wildlife Service's (Service) Biological Opinion (Opinion) and concurrence with the Federal Energy Regulatory Commission's (Commission) determinations of effect on species listed under the Endangered Species Act (Act) of 1973, as amended, for the proposed Swan Falls Hydroelectric Project in Ada and Owyhee Counties, Idaho. In a letter dated August 21, 2011, and received by the Service on September 1, 2011, the Commission requested formal consultation on the determination under section 7 of the Act that the proposed project is likely to adversely affect the Snake River physa (Haitia (Physa) natricina). The Service acknowledges this determination. The enclosed Opinion and concurrence are based on our review of the proposed action, as described in your August 21,2011 amended Biological Assessment (Assessment), an updated analysis of Snake River physa substrate preferences, and the anticipated effects of the action on listed species, and were prepared in accordance with section 7 of the Act. Our Opinion concludes that the proposed project will not jeopardize the survival and recovery of Snake River physa. A complete record of this consultation is on file at this office. It is important to note that our analysis of effects of the proposed action on Snake River physa are based on several assumptions (see Section 2.5.1 ofthe Opinion), necessitated by the limited information available regarding the species. Given this, it is plausible that project-related impacts may have more or less severe effects on the species than our analysis indicates in this Opinion, based on our current understanding of the species, its habitat, and potential pathways of effect. A number of the Terms and Conditions provided in this document are intended to develop information on project-related impacts of the action on the Snake River physa. We wish to emphasize that should information on these impacts indicate effects to the species or its habitat such that the probability of its persistence is reduced in the Action Area, the Commission should re-evaluate the project's effects and consider reinitiation of section 7 consultation, as appropriate. Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Clean Water Act Requirement Language: This Opinion is also intended to address section 7 consultation requirements for the issuance of any project-related permits required under section 404 of the Clean Water Act (CWA). Use of this letter to document that the Army Corps of Engineers (COE) has fulfilled its responsibilities under section 7 of the Act is contingent upon the following conditions: 1. The action considered by the COE in their 404 permitting process must be consistent with the proposed project as described in the Assessment such that no detectable difference in the effects of the action on listed species will occur. 2. Any terms applied to the 404 permit must also be consistent with conservation measures and terms and conditions as described in the Assessment and addressed in this letter and Opinion. Thank you for your continued interest in the conservation of threatened and endangered species. If you have questions concerning this Opinion, please contact Dwayne Winslow at (208) 378- 5249 or Michael Morse at (208) 378-5261.
Sincerely, ~~~ BrianT. Kelly State Supervisor
Enclosure
2 BIOLOGICAL OPINION FOR THE Swan Falls Hydroelectric Project, FERC No. 503 14420-2011-F-0318
February 1, 2012
U.S. FISH AND WILDLIFE SERVICE IDAHO FISH AND WILDLIFE OFFICE BOISE, IDAHO
Supervisor ----;.A--=---:-..- ~~.. -~-___,...___ Date ___l__ Ol__,_ /_;_1__,,,_/_ao--=-..:/~a....:;;.,__ ___ Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Table of Contents
1. BACKGROUND AND INFORMAL CONSULTATION ...... 1 1.1 Introduction ...... 1 1.2 Consultation History ...... 1 2. BIOLOGICAL OPINION ...... 3 2.1 Description of the Proposed Action ...... 3 2.1.1 Action Area ...... 3 2.1.2 Proposed Action ...... 5 2.1.2.1 Background ...... 5 2.1.2.2 Proposed Action ...... 6 2.2 Analytical Framework for the Jeopardy and Adverse Modification Determinations ...... 7 2.2.1 Jeopardy Determination ...... 7 2.3 Status of the Species ...... 8 2.3.1 Listing Status ...... 8 2.3.2 Species Description ...... 8 2.3.3 Life History ...... 9 2.3.4 Status and Distribution ...... 11 2.3.5 Conservation Needs ...... 16 2.4 Environmental Baseline of the Action Area ...... 18 2.4.1 Species ...... 18 2.4.1.1 Status of the Snake River physa in the Action Area ...... 18 2.4.1.2 Factors Affecting the Species in the Action Area ...... 24 2.5 Effects of the Proposed Action ...... 29 2.5.1 Direct and Indirect Effects of the Proposed Action ...... 30 2.5.1.1 Direct Effects ...... 30 2.5.1.2 Indirect Effects ...... 36 2.5.2 Effects of Interrelated or Interdependent Actions ...... 40 2.6 Cumulative Effects ...... 41 2.6.1 Climate Change ...... 41 2.6.2 Water Quality ...... 42 2.7 Conclusion ...... 42
i Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2.8 Incidental Take Statement ...... 44 2.8.1 Form and Amount or Extent of Take Anticipated ...... 44 2.8.1.1 Considerations in Determining Amount of Take ...... 44 2.8.1.2 Form and Extent of Take ...... 44 2.8.2 Effect of the Take ...... 46 2.8.3 Reasonable and Prudent Measures ...... 47 2.8.4 Terms and Conditions ...... 47 2.8.5 Reporting and Monitoring Requirements...... 48 2.9 Conservation Recommendations ...... 48 2.10 Reinitiation Notice ...... 48 3. LITERATURE CITED ...... 49 3.1 Published Literature ...... 49 3.2 In Litteris References ...... 53 4. APPENDIX ...... 55 APPENDIX A ...... 55 APPENDIX B ...... 70
ii Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
List of Tables
Table 1. Flow, stage height, and depth of Snake River physa collection locations on the Snake River in comparison to minimum stage height at proposed minimum flows of 3,900 cubic feet per second...... 20 Table 2. Total weighted useable area for mountain whitefish spawning habitat at discharges of 1,000 to 15,000 cubic feet per second modeled for the reaches between Swan Falls Dam and Brownlee Reservoir...... 23 Appendix A, Table 1. Frequency and proportion of substrate categories, and observed and expected substrate category use by Snake River physa in the C.J. to Weiser Reach...... 60 Appendix A, Table 2. Frequency and proportion of substrate categories, and observed and expected substrate category use by Snake River physa in the reach below Minidoka Dam...... 62 Appendix B, Table 1. Snake River data from two studies of sites from Wheaton Mountain to the Weiser Gage showing degradation of river ecological condition occurring upstream to downstream...... 74
List of Figures
Figure 1. Swan Falls Hydroelectric Project Action Area Map ...... 4 Figure 2. Snake River natural hydrograph from the U.S. Geological Survey gage at Montgomery Ferry, near Minidoka, Idaho, 1895 to 1904, prior to known dam construction on the Snake River...... 25 Figure 3. Number of days of discharge less than 5,000 cubic feet per second for water years 1990 to 2010, recorded at the Murphy gage downstream of Swan Falls Dam...... 26 Appendix A, Figure 1. Percent substrate category frequency compared to percent substrate use by Snake River physa in the C.J. to Weiser Reach...... 61 Appendix A, Figure 2. Percent substrate category frequency compared to percent substrate use by Snake River physa in the reach below Minidoka Dam ...... 63 Appendix A, Figure 3. Substrate percent occurrence for type locality reach, Upper Bliss reach and Lower Bliss reach...... 67 Appendix A, Figure 4. Percent substrate occurrence in the C.J. to Weiser Reach by dominant and co-dominant...... 68
iii Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
1. BACKGROUND AND INFORMAL CONSULTATION
1.1 Introduction The Fish and Wildlife Service (Service) has prepared this Biological Opinion (Opinion) of the effects of the Federal Energy Regulatory Commission’s (Commission) relicensing of Idaho Power Company’s (Company) existing 25-megawatt Swan Falls Hydroelectric Project (Swan Falls Project) (FERC Project No. 503-048) on the Snake River physa (Haitia (Physa) natricina). The Company proposes no capacity changes and to continue the ongoing operations of the project, with a change in the minimum flow regime to provide instantaneous minimum flows of 3,900 cubic feet per second (cfs) from April 1 to October 31 each year, and 5,600 cfs from November 1 to March 31; and continuation of the existing ramping rate restrictions of no more than 1 foot per hour and 3 feet per day. In a letter dated August 21, 2011, and received on September 1, 2011, the Commission requested formal consultation with the Service under section 7 of the Endangered species Act (Act) of 1973, as amended, for its proposal to authorize the action. This Opinion is based on the amended Biological Assessment (Assessment) submitted by the Commission (prepared by the Company) together with its request for formal consultation; joint visits to the Project Area by Service and Company personnel; joint sampling efforts for Snake River physa in the Project Area conducted by the Service and the Company, with results analyzed by a private contractor; an updated analysis of Snake River physa substrate preferences (Appendix A); meetings, conference calls, and other communication between Service biologists and Company biologists and other personnel; and other available scientific and pertinent information. The Commission determined that the proposed action is likely to adversely affect Snake River physa. As described in this Opinion, and based on the Assessment submitted by the Commission (prepared by the Company) and other information, the Service has concluded that the action, as proposed, is not likely to jeopardize the continued existence of Snake River physa. References cited in this Opinion conform to the following format in the text: page numbers or page descriptions appearing in a citation (e.g., Richards 2004, p. 22, 39-41; Richards and Arrington 2009, Appendix 11) denote that information on those pages specified in the citation reference or support information given in the sentence or paragraph in which the citation appears; page numbers appearing alone in a paragraph (e.g., p. 84) denote the same and are understood to be pages found in the last reference cited preceding the parenthetic page number; citations without associated pages numbers (e.g., Richards and Arrington 2009) are understood to refer to the general content of the cited reference.
1.2 Consultation History The Service has maintained open communication with the Company and the Commission regarding the Action since March 20, 2010. During that time, the Service provided recommendations and forwarded information needs. The Company responded to these requests
1 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project and provided needed information in correspondence to the Service, in the Assessment, and in an addendum to the Assessment submitted to the Commission. March 20, 2010 Conference call to discuss new information related to the distribution of Snake River physa in the Action Area. Participants included the Commission, the Louis Berger Group (a Commission contractor), the Company, and the Idaho Department of Fish and Game (IDFG). The Company proposed a study plan for sampling the Action Area for the presence of Snake River physa. July 27, 2010 The Service met with the Company to review a draft Snake River physa study proposal for the Swan Falls Project. July 28, 2010 The Service conducted a joint preliminary site visit with the Company to select potential Snake River physa sampling sites within the Action Area near Swan Falls Dam. August 31, 2010 The Service conducted joint Snake River physa surveys with the Company and September 1, within the Action Area. 2010 January 6, 2011 Receipt and review of draft Assessment from the Company. March 25, 2011 Filing of the Assessment with the Commission by the Company. May 24, 2011 Conference call with the Service, the Company, the Commission, the Shoshone-Bannock Tribe, and IDFG. The Commission requested that the Company include in-water work for recreation mitigation and enhancement projects (part of the Commission’s Staff Alternative in the Final Environmental Impact Statement (FEIS)) in the proposed action of the Assessment. The need for Company surveys for Snake River physa in the in-water recreation mitigation and enhancement work sites was discussed. June 3, 2011 The Service conducted joint Snake River physa surveys with the Company for the in-water recreation mitigation and enhancement work sites. June 15, 2011 Receipt of request from the Commission for the Company to conduct Snake River physa sampling of recreation mitigation and enhancement work sites for Snake River physa, with analysis of the results to be filed with the Commission in an addendum to the Company’s draft Assessment. June 29, 2011 The Service conducted joint Snake River physa surveys with the Company for the in-water recreation mitigation and enhancement work sites. August 18, 2011 Receipt of the addendum to the Assessment from the Company. The addendum included an analysis of results of the June 3 and June 29 surveys for Snake River physa in the in-water recreation mitigation and enhancement work sites. September 1, 2011 Receipt of Assessment from the Commission.
2 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2. BIOLOGICAL OPINION
2.1 Description of the Proposed Action This section describes the proposed Federal action, including any measures that may avoid, minimize, or mitigate adverse effects to listed species or critical habitat, and the extent of the geographic area affected by the action (i.e., the action area). The term “action” is defined in the implementing regulations for section 7 as “all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies in the United States or upon the high seas.” The term “action area” (Action Area) is defined in the regulations as “all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action.” 2.1.1 Action Area The Company determined the Action Area to consist of 125.4 miles of the Snake River from the beginning of Swan Falls Reservoir at river mile (RM) 469.4 downstream to the beginning of Brownlee Reservoir (RM 344) (Figure 1), based on the following reasoning. Snake River physa have been documented to occur as far downstream in the Snake River (RM 368) to just below Ontario, Oregon (Keebaugh 2009, p. 22). Company modeling of ramping rate discharge between Swan Falls Dam and Brownlee Reservoir (Bean and Stephenson 2011b, p. 6, 23-24) indicates that, if the maximum ramping rates allowed in the license are realized, changes in stage height of more than 1.5 feet could occur all the way downstream to RM 344. Further movement of stage height changes would be quickly attenuated in the Brownlee Reservoir. Since Snake River physa habitat could extend from RM 368 to the Brownlee Reservoir, it was reasonable to extend the Action Area beyond the downstream-most known occurrence of the species.
3 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
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N See accompanying metadata Legend for user limitations and liabilities; author information; and source Project Action Area _j_ citations. N Hardy, IFWO I Project Endpoints -r January 5, 2012 I Swan Falls Dam 0 10 20 40 ---====-----•Miles
Figure 1. Swan Falls Hydroelectric Project Action Area Map
4 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2.1.2 Proposed Action 2.1.2.1 Background The Swan Falls Project is located at River Mile (RM) 457.7 on the Snake River in Ada County and Owyhee County, Idaho, about 35 miles southwest of Boise (Figure 1). The original powerplant was built in 1901 to provide power to nearby mines and was the first powerplant to be constructed on the Snake River. The Company acquired the Swan Falls Project in 1916. As described in the Final Environmental Impact Statement for Hydropower Relicense of the Swan Falls Hydroelectric Project (FERC Project No. 503-048) (Federal Energy Regulatory Commission 2010, p. 15-16) the existing Swan Falls Project consists of: A 1,218 foot concrete gravity and rock-fill dam composed of an abutment embankment, a spillway section, a center island, the old powerhouse section, the intermediate dam, and the new powerhouse; A 11.5 mile long 1,525 acre reservoir with a normal maximum water surface elevation of 2,314 feet mean sea level; 12 equal width concrete spillway sections with radial gates, having a total capacity of 105,112 cubic feet per second (cfs) at reservoir surface elevation 2,318 feet, divided into two sections: the western section, contiguous with the abutment embankment, is a gated concrete ogee section with 8 radial gates; and the eastern section adjacent to the island, which contains 4 radial gates; Two concrete flow channels; Two pit-type, horizontal Kaplan turbine generators with nameplate ratings of 12.5 megawatts each; An excavated tailrace channel measuring approximately 1,400 feet long by 120 feet wide; A 33,600 kilovolt-ampere main power transformer; A 1.2 mile, 138 kilovolt transmission line; and, Appurtenant equipment. The Swan Falls Project existing licensed boundary extends from about 11.5 miles upstream of the dam to about 2,000 feet downstream of the dam. The boundary encompasses the main project access road, an equipment yard, the dam, a new powerhouse, a storage structure, an orchard, five Company-owned project houses, the transmission line, a yard where trash rack debris is dumped, and five existing project recreation sites. The Swan Falls Project is a reregulating reservoir, with limited storage capacity available to provide minimal peaking operations. However, the Swan Falls reservoir is not used to store water on a seasonal basis. The 3 feet of limited available storage between elevation 2,311 feet and 2,314 feet is used on a daily basis to re-regulate flows from the upstream C.J. Strike Project (FERC Project No. 2055). Operations are conducted to safely accommodate inflow (over which the Swan Falls Project has no control) that exceeds specified minimums: hydroelectric power can be produced as a byproduct, and the limited storage can also be used to meet short-term, unexpected peak load requirements. The current Swan Falls license, issued in 1982, requires instantaneous minimum discharge downstream of the Swan Falls dam of no less than 5,000 cfs during the irrigation season (April 1 to September 30) and no less than 4,000 cfs outside of the irrigation season (October 1 to
5 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
March 31). If the average daily inflow is less than the specified minimums, the project discharge from the powerhouse and/or spillway must be equal to the inflow to the reservoir. The existing Swan Falls Project also requires ramping rate restrictions of no more than 1 foot per hour and 3 feet per day as measured at the ramping monitoring gage located approximately 4.3 miles downstream of the dam. Under an agreement entered into on October 25, 1984, between the Company and the state of Idaho (Swan Falls Agreement), the Company’s water rights for power purposes at the Swan Falls Project, and other specified Company-owned hydroelectric projects on the middle Snake River, entitle the Company to an unsubordinated right of a 3,900-cfs average daily flow from April 1 to October 31, and 5,600-cfs average daily flow from November 1 to March 31, as measured at the Murphy U.S. Geological Survey (USGS) gage (USGS Gage No. 13172500) (Murphy gage). Pursuant to the Swan Falls Agreement, the 3,900 and 5,600 cfs minimum flows at the Murphy gage are not subject to depletion and the Company continues to be entitled to the use of the waters of the Snake River to the full extent of its water rights for the project. Should the minimum flows at the Murphy gage be less than the minimum flow amounts, the Idaho Department of Water Resources will administer upstream junior water rights as required to satisfy the 3,900 or 5,600 cfs minimum flows at the Murphy gage. If only the minimum flows are available, load-following will not be implemented; that is, ramping will not occur, and flow entering and leaving the Swan Falls Project will be equal. 2.1.2.2 Proposed Action The proposed action is to relicense the existing Swan Falls Project, which includes the decision to continue the existence of the physical structure of the Swan Falls Dam. The Company is proposing no capacity changes, and no changes to generation facilities or other major features. The Company is proposing a change in the minimum flow regime. The Company proposes to change the provisions of the current license relative to the minimum flows to be consistent with the Swan Falls Agreement and the minimum flow provisions of the license for the C.J. Strike Project (Federal Energy Regulatory Commission 2004, p. 31), resulting in the potential for minimum flows below Swan Falls Dam of 3,900 cfs from April 1 to October 31, and 5,600 cfs from November 1 to March 31 each year. The ramping rate restrictions would continue to be no more than 1 foot per hour and 3 feet per day. In addition, the Company proposes to continue to remove and dispose of aquatic macrophytes and debris that accumulate on the project trash racks in order to remove nutrients and oxygen- demanding material from the river; and to monitor water temperature and dissolved oxygen (DO) in the project outflow (water passed through the powerhouse and/or over the spillway). The Company also proposes to finalize and implement the draft Recreation Management Plan, of which the following elements may include in-water work or disturbance: Enhance the Swan Falls reservoir boat ramp by upgrading the boat ramp Improve Swan Falls Park by providing riprap or a retaining wall along the shoreline, and adding a new dock Enhance the Swan Falls downstream boat launch by constructing a two-lane boat ramp Restore flow to the channel between Swan Falls Island and the shoreline The Swan Falls reservoir boat ramp currently consists of a single-lane boat ramp on Swan Falls Reservoir located approximately 0.7 miles upstream of Swan Falls Dam. The existing ramp is
6 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project relatively flat, making it difficult to launch boats. The Company proposes to remove and widen the existing ramp and steepen the angle of the ramp. The existing dock will be replaced or repaired. Other improvements to the site will be above the high-water line. The estimated amount of wetted habitat to be disturbed for this site is 3,600 square feet (ft2). Swan Falls Park is located approximately 0.2 miles upstream of Swan Falls Dam. The Company proposes to stabilize the shoreline at the Park by placing rip rap, and will also add a dock and gangway. Construction will take place with the reservoir at its minimum headwater elevation of 2,313 feet, when the area to be disturbed will not be inundated. The unimproved, gravel boat ramp downstream of Swan Falls Dam was originally intended to accommodate canoes, kayaks, and rafts. More recently, larger motorized boat use has occurred, primarily due to the popularity of sturgeon fishing downstream of the dam. Numerous vehicles have become stuck due to the slope of the ramp and the gravel surface. The Company proposes to construct a 2-lane concrete boat ramp that will be 24 feet wide and 130 feet long. The area estimated to be disturbed below the low water line (at approximately 4,000 cfs) is 2,200 ft2. The area estimated to be disturbed when the river discharge is approximately 8,000 cfs is 3,600 ft2. The Company intends to conduct construction activities when the river discharge is low (near 4,000 cfs), if possible. Swan Falls Island is located just downstream of Swan Falls Dam on the north side of the river. The channel between the island and the shoreline is not inundated during low and moderate discharge in the Snake River because the existing culvert has silted in. The Company proposes to replace the existing culvert with a larger, deep culvert to permanently restore water flow to the channel in order to enhance riparian habitat along the channel. The Company provided two estimates of wetted area to be disturbed by construction. If discharge is 4,000 cfs, wetted disturbed area would be approximately 11,000 ft2; if discharge is 8,000 cfs, wetted disturbed area would be approximately 26,000 ft. The Company intends to conduct construction activities when the river discharge is low (near 4,000 cfs), if possible.
2.2 Analytical Framework for the Jeopardy and Adverse Modification Determinations 2.2.1 Jeopardy Determination In accordance with policy and regulation, the jeopardy analysis in this Opinion relies on four components: 1. The Status of the Species, which evaluates the Snake River physa rangewide condition, the factors responsible for that condition, and its survival and recovery needs. 2. The Environmental Baseline, which evaluates the condition of the Snake River physa in the Action Area, the factors responsible for that condition, and the relationship of the Action Area to the survival and recovery of the Snake River physa. 3. The Effects of the Action, which determines the direct and indirect impacts of the proposed Federal action and the effects of any interrelated or interdependent activities on the Snake River physa.
7 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
4. Cumulative Effects, which evaluates the effects of future, non-Federal activities that can be reasonably certain to affect Snake River physa in the Action Area.. In accordance with policy and regulation, the jeopardy determination is made by evaluating the effects of the proposed Federal action in the context of the Snake River physa’s current status, taking into account any cumulative effects, to determine if implementation of the proposed action is likely to cause an appreciable reduction in the likelihood of both the survival and recovery of the Snake River physa in the wild by reducing the reproduction, numbers, or distribution of the species Survival is the condition in which a species continues to exist into the future while retaining the potential for recovery. Recovery is the process by which species’ ecosystems are restored and/or threats to the species are removed so self-sustaining and self- regulating populations of listed species can be supported as persistent members of native biotic communities. The jeopardy analysis in this Opinion places an emphasis on consideration of the rangewide survival and recovery needs of the Snake River physa and the role of the Action Area in the survival and recovery of the Snake River physa as the context for evaluating the significance of the effects of the proposed Federal action, taken together with cumulative effects, for purposes of making the jeopardy determination.
2.3 Status of the Species This section presents information about the regulatory, biological and ecological status of the Snake River physa that provides context for evaluating the significance of probable effects caused by the proposed action. 2.3.1 Listing Status The Service listed the Snake River physa as endangered effective January 13, 1993 (U.S. Fish and Wildlife Service 1992). No critical habitat has been designated for this species. A recovery plan for the Snake River physa was published by the Service as part of the Snake River Aquatic Species Recovery Plan (U.S. Fish and Wildlife Service 1995). The target recovery area for this species is from Snake River Mile (RM) 553 to RM 675 (U.S. Fish and Wildlife Service 1995, p. 30), which includes the river reach downstream of Minidoka Dam. 2.3.2 Species Description The Snake River physa was formally described by Taylor (Taylor 1988, p. 67-74; Taylor 2003, p. 147) , from which the following characteristics are taken. The shells of adult Snake River physa may reach 7 mm in length with 3 to 3.5 whorls, and are amber to brown in color and ovoid in overall shape. The aperture whorl is inflated compared to other Physidae in the Snake River, the aperture whorl being greater than or equal to one half of the entire shell width. The growth rings are oblique to the axis of coil at about 40° and relatively course, appearing as raised threads. The soft tissues have been described from limited specimens and greater variation in these characteristics may be present upon detailed inspection of more specimens. The body is nearly colorless, but tentacles have a dense black core of melanin in the distal half. Penal complex lacks pigmentation although the penal sheath may be opaque. Tip of the penis is simple (not ornamented). The preputal gland is nearly as long as the penal sheath.
8 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
The Snake River physa is a pulmonate species, in the family Physidae, order Basommatophora (Taylor 1988, 2003). The rarity of Snake River physa collections, combined with difficulties associated with distinguishing this species from other physids, has resulted in some uncertainties over its status as a separate species. Taylor (2003) presented a systematic and taxonomic review of the family, with Snake River physa recognized as a distinct species (Physa natricina) based on morphological characters he originally used to differentiate the species in 1988. Later authors concluded that the characters described by Taylor (1988) were within the range of variability observed in Physa acuta, and placed Snake River physa as a synonym junior to P. acuta (Rogers and Wethington 2007). Genetic material from early Snake River physa collections was not available when Rogers and Wethington (2007) published, and their work did not include an analysis or discussion on the species’ genetics. More recent collections of specimens closely resembling Taylor’s (1988, 2003) descriptions of Snake River physa have been used to assess morphological, anatomical, and molecular uniqueness. Live snails resembling Snake River physa collected by the Bureau of Reclamation (Reclamation) below Minidoka Dam as part of monitoring required in a 2005 Biological Opinion (U.S. Fish and Wildlife Service 2005) began to be recovered in numbers sufficient to provide specimens for morphological review and genetic analysis. Burch (2008, 2010; in litt.) and Gates and Kerans (2010) identified snails collected by Reclamation as Snake River physa using Taylor’s (1988, 2003) shell and soft tissue characters. Their genetic analysis also found these specimens to be a species distinct from P. acuta. Gates and Kerans (2011) also performed similar analyses on 15 of 51 live-when-collected specimens recently identified as Snake River physa (Keebaugh 2009), and collected by the Company between 1998 and 2001 in the Snake River reaches from Bliss Dam (RM 560) downstream to RM 368. Gates and Kerans (2011) found that these specimens were not genetically distinct from Snake River physa collected below Minidoka Dam (but were genetically distinct from P. acuta), and provided additional support that Taylor’s (1988) shell description of Snake River physa is diagnostic (Gates and Kerans 2011, p. 6). Recent discussions at an expert panel, sponsored by the Reclamation (September 2010), yielded another hypothesis regarding the taxonomic identity of Snake River physa. This hypothesis suggests that specimens recently recovered and presented as this species may be one of two other northwestern Physids (P. concolor or P. columbiana), or some other as yet unidentified species. This hypothesis has not been tested or disproven. The Service regards results from Burch (in litt. 2008, 2010) and Gates and Kerans (2010; 2011) as the most thorough and most recent determinations of Snake River physa as a distinct taxon. 2.3.3 Life History Freshwater pulmonate snail species such as Snake River physa do not have gills, but absorb oxygen across the inner surface of the mantle, also called the pallial lung (Dillon 2006, p. 252). The walls of the mantle are heavily vascularized, and air is drawn into the mantle cavity via expansion and contraction of the mantle muscles (Vaughn et al. 2008). Freshwater pulmonates usually carry an air bubble within the mantle as a source of oxygen, replenished via occasional trips to the surface; the bubble is manipulated to adjust buoyancy and allow transportation to the surface (Dillon 2006, p. 252). However, some freshwater pulmonate species do not carry air bubbles; oxygen instead diffuses from the water directly into their tissues across the surface of the mantle (Dillon 2006, p. 252), the likely mode of respiration for Snake River physa. Since
9 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project they live in moderately swift current, individuals that release from substrates to replenish air at the surface would mean they would likely be transported some distance downstream away from their cohort and habitat of choice, and thus away from potential mates and known food sources. The pallial lung also may permit at least some physa species to survive for short periods out of water. P. virgata, a junior synonym of P. acuta (Dillon et al. 2005, p. 415), have been observed to move and remain out of the water for up to 2 hours in reaction to chemical cues given off by crayfish foraging on nearby conspecifics (Alexander and Covich 1991, p. 435). Snake River physa may have the same capability for out of water survival, but the fact that the species has rarely been collected in shallow water (less than 1 foot) and has been found in greatest abundance at depths greater than or equal to 1.5 m (Gates and Kerans 2010, p. 23) argues that shallow water or extended periods out of water are not a significant part of its life history. Diet preferences of Snake River physa are not known. Species within the family Physidae live in a wide variety of habitats and exhibit a variety of dietary preferences to match this. Physidae from numerous studies consumed materials as diverse as aquatic macrophytes, benthic diatoms (diatom films that primarily grow on rock surfaces, also called periphyton), bacterial films, and detritus (Dillon 2000, p. 66-70). P. gyrina, which co-occurs with Snake River physa in the Snake River, consumes dead and decaying vegetation, algae, water molds, and detritus (DeWitt 1955, p. 43; Dillon 2000, p. 67). Snake River physa have yet to be reared and studied in the laboratory, and the species’ reproductive biology has not been studied under natural conditions. P. acuta reaches sexual maturity at between 6 to 8 weeks at 22-24o C in laboratory conditions (Escobar et al. 2009, p. 2792). Dillon et al. (2004, p. 65) reported mean fecundity of 39.1 hatchlings per pair per week for P. acuta, but whether the Snake River physa exhibits similar reproductive output is not known. P. gyrina began mating and laying eggs when water temperatures reached 10 to 12o C, with eggs hatching in 8 to 10 days (DeWitt 1955, p. 43), and Dillon (2000, p. 119-121) presents evidence that the period of egg-laying in gastropods is somewhat dependent on snail size and water temperature. The reproductive period for Snake River physa is not known, but might be expected to generally follow that of other Snake River gastropods, with juveniles appearing in mid to late spring and numbers peaking in mid to late summer. Most members of the genus and family are not believed to live longer than one year (Dillon 2000, p. 156-162). DeWitt (1954, p. 161) stated that the lifespan of P. gyrina in southern Michigan populations was 12 to 13 months. It is reasonable to assume that Snake River physa lifespan would be similar. Water temperature requirements and tolerances of Snake River physa are unknown. Gates and Kerans (2010, p. 21) reported a mean water temperature of 22.63° C for sites occupied by the species at the time of sampling (in August and October), but it is not known if this represents an optimal range or if it happens to be the temperature range in which the species has been able to persist following anthropogenic changes to the Snake River system. Water temperatures for samples collected by the Company in the Bruneau Arm of C.J. Strike Reservoir and in the Snake River between RM 559 and RM 368 in late July to mid-August between 1998 and 2002 that contained live-when-collected Snake River physa averaged 23.4° C. The maximum temperature for cold water biota established in the CWA is 22° C. Based on available information, Snake River physa appear to be able to tolerate water temperatures slightly above the cold water standard of 22° C. Possibly of significance may be the fact that, despite intense and extensive surveys and monitoring for the Bliss Rapids snail in cold water spring habitats of high water quality, Snake
10 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
River physa have never been noted in such habitats, including those with a clear connection to the Snake River such as the Thousand Springs area. Relatively cool water of a consistent temperature might represent an outside boundary to Snake River physa’s habitat requirements. Water temperatures below 10o C are known to inhibit reproduction in P. gyrina (DeWitt 1955, P. 43), a widespread Physa species that co-occurs with Snake River physa in the Snake River. Springs deriving from the Snake River Plain Aquifer, including Thousand Springs, flow at temperatures from 14o to 16o C year around. All freshwater pulmonates studied to date are able to reproduce successfully by self-fertilization (Dillon 2000, p. 83). While self-fertilization (selfing) in pulmonates can be forced under laboratory conditions by isolating individual snails, there is considerable variation within and among pulmonate genera and species in the degree of selfing that occurs in natural populations. Of the many Physa species in North America and world-wide, studies of self-fertilization effects on population genetics seem to have been conducted only on P. acuta. Selfing and its implications for genetic variation and survival are unknown for Snake River physa. 2.3.4 Status and Distribution Existing populations of the Snake River physa are known only from the Snake River in central and south-southwest Idaho, with the exception of two (live-when-collected) specimens recovered in 2002 from the Bruneau River arm of C.J. Strike Reservoir (Keebaugh 2009, p. 123). Fossil evidence indicates this species existed in the Pleistocene-Holocene lakes and rivers of northern Utah and southeastern Idaho, and as such, is a relict species from Lake Bonneville, Lake Thatcher, the Bear River, and other lakes and watersheds connected to these water bodies (Frest et al. 1991, in litt., p. 8, Link et al. 1999, p. 251-253). The Service (1995, p. 8) reported that the Snake River physa’s “modern” range extended from Grandview (RM 487) to the Hagerman Reach (RM 573). Surveys conducted by the Company between 1995 and 2003 (Keebaugh 2009) and Reclamation from 2006 through 2008 (Gates and Kerans 2010) confirm its current distribution, based on live-when-collected specimens, from RM 368 near Ontario, Oregon (some 128 miles downstream from its previously recognized downstream range), upstream to Minidoka Dam (RM 675). Gates and Kerans (2011, p. 10) confirmed that shell morphology, diagnostic of Snake River physa, from one of the specimens collected in the Bruneau River arm of C.J. Strike Reservoir matches that of specimens with similar morphology also confirmed as Snake River physa by DNA analysis. Within this range (RM 675-368), Snake River physa have been recovered live from the reach below Lower Salmon Falls Dam (RM 573) downstream to RM 368 (and including the Bruneau Arm of C.J. Strike Reservoir) and in the Minidoka Reach (RM 675-663.5). They have not been found in the reaches between Lower Salmon Falls Dam and the Minidoka Reach (RM 573- 663.5), although surveys in this area have been sporadic. While the presence of the species in this area cannot be ruled out, the occupied range of Snake River physa consists of the Minidoka Reach and the reach between Lower Salmon Falls Dam to RM 368. The number of live-when-collected individuals and the accepted range of Snake River physa is based on the following confirmed reports.
11 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Taylor (1988), who collected: 11 live specimens of Snake River physa in 1959 from what became the type locality downstream of the Malad River/Snake River confluence at RM 569.8. As stated in his 1988 species description, these 11 specimens were not preserved The type specimen (one live individual) from the type locality in 1980 One live specimen apparently from the same location in 1981 In addition, Frest et al. (1991, in litt., p. 8) also collected but did not keep two live specimens from the type locality reach in 1988. The Company’s surveys between 1995 and 2003 collected 51 live Snake River physa specimens as previously stated (two of them in the Bruneau River arm of C.J. Strike Reservoir), and Gates and Kerans (2010, p. 21) reported collections of 274 live Snake River physa in the 11.5 mile reach below Minidoka Dam. (Kerans and Gates 2008, in litt p. 8) also reported finding 7,540 empty Snake River physa shells during their 2006 sampling, by far the largest number of Snake River physa shells reported from any surveys.) Thus, a total of approximately 340 live-when-collected Snake River physa have been confirmed from surveys conducted between 1959 and 2008, 338 of them in a stretch of the Snake River encompassing approximately 307 river miles. The species has not been recovered from the Action Area since 2001. Taylor’s most complete description of the habitat in which he collected Snake River physa is from a report prepared for the Service in July of 1982 (Taylor 1982b, in litt.): “The species is restricted to the mainstem of the Snake River, on gravel to boulder substratum in steady current. The only two living specimens found have been on boulders in the deepest accessible part of the river, at the margins of rapids. Evidently the snails live primarily in deep, swift water.” Page 2. “It lives on boulders in rapids in deep water.” Page 3. “The habitat is interpreted as in depths of 3 feet or more, throughout the white-water segment of the Snake River, with strays rarely at a lesser depth.” Page 3. In later professional documents he provided a more cursory habitat description or referenced earlier descriptions (Taylor 1988, p. 67; Taylor 2003, p. 148). In a 2004 personal communication to the Service (Taylor in litt. 2004), Taylor stated that he had made his collections of Snake River physa at low river levels, and beneath rocks and boulders “because they were the most accessible situation in which to find the snails.” He further stated that he did not believe that “undersurfaces of rocks in rapids is the only situation in which the species may live”; and that based on fossil occurrences, the species “could (and presumably, can) live in environments other than river rapids.” Gates and Kerans’ (2010) detailed study, which sampled cross sections of the river profile, characterized Snake River physa habitat below Minidoka Dam as occurring in run, glide, and pool habitats with moderate mean velocity (0.57 m/s). Mean depth of samples containing Snake River physa was 1.74 m. Live specimens were most frequently recovered from depths of 1.5 to 2.5 m, similar to that described by Taylor. Depths in which all specimens were recovered ranged from less than 0.5 m to over 3.0 m, and abundances of three or more Snake River physa per sample were found at depths greater than 1.5 m. Eighty percent of samples containing live Snake River physa were located in the middle 50 percent of the river channel (Gates and Kerans
12 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2010, p. 20). This evidence may be suggestive of habitat requirements related primarily to velocity and depth as they influence substrate deposition, and possibly other factors. The Company conducted considerable survey effort in the area of the type locality between 1995 and 2001 (Appendix A), but no Snake River physa were identified. Frest and Johannes conducted surveys in 2004 in the Hammet to Thousand Springs areas (RMs 526-584) (Frest and Johannes 2004, in litt.), which includes the type locality, but did not report the species’ presence (p. 4). A large amount of previously unsorted material from the Frest and Johannes’ (2004, in litt.) surveys was recently sorted for Physa species, with specimens identified to species (EcoAnalysts 2011, in litt.), but no Snake River physa were identified. Confirmation of the species’ continued presence in the vicinity of the type locality since 1988 remains elusive. Taylor’s (1982a, in litt.; 1988) 1959 and 1980 collections and Frest et al.’s (1991, in litt.) 1988 collection are the only known live collections from the type locality. Keebaugh (2009, p. 80) identified a single specimen collected below Bliss Dam by the Company in 2002 as Snake River physa, but because Gates and Kerans (2011, p. 11) could not extract DNA and part of the shell was missing, they could not confirm its identity. Thus Taylor’s and Frest’s collections are the only confirmed live specimens collected between C.J. Strike Reservoir and the reach below Minidoka Dam. Pentec Environmental (1991, in litt., p. 8,16) reported in 1991 the collection of two live Snake River physa above American Falls Dam at RM 740.2 and 749.1, identified as young Snake River physa by Dr. Terrence Frest. Dr. Frest qualified his identification of these specimens as Snake River physa in a letter to the U.S. Fish and Wildlife Service (Frest 1991, in litt., p. 9), stating that identification had been made based on external morphology and shell characteristics, and that the specimens could have been young Snake River physa, but also might have been young P. gyrina or P. integra. Gates and Kerans (2010, p. 22) also collected Snake River physa from a lotic pool in the wetlands a few hundred meters below the Minidoka Dam spillway. The spillway wetlands were dry ground prior to completion of the dam and spillway in 1906. The logical source of Snake River physa for the pool colony therefore would have been from somewhere upstream of Minidoka Dam. However, except for the uncertain identification of Snake River physa by Pentec Environmental (in litt. 1991, p. 16) and Frest (in litt. 1991, p. 9) at RM 740-749, no Snake River physa have been confirmed from surveys conducted upstream of Minidoka Dam. Hence, at this time the Service considers the colonies below Minidoka Dam and spillway as the upstream-most extent of the species’ current range. On a broad scale, locations where the species have been found live, including the type locality, have largely been from the free-flowing reaches below the following dams: Minidoka Dam, Bliss Dam (counting the uncertain specimen recovered below Bliss Dam), C.J. Strike Dam, and Swan Falls Dam. Free-flowing is defined here as water velocities which would generally keep gravel beds free of fine sediments in the range of depths in which Snake River physa have found. (Though only one live specimen has been found between Bliss Dam and the upper end of C.J. Strike Reservoir [RM 560.3 to 522.5], Taylor (1988, p. 69) collected 200 empty shells at the Indian Cove Bridge [RM 525.25, between Hammett and C.J. Strike Reservoir] that he identified as Snake River physa, suggesting a population somewhere upstream in this reach). Two specimens of Snake River physa have been found in the reservoir pool of the Bruneau River arm of C.J. Strike Reservoir, in an area usually characterized by very slow moving lentic
13 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project conditions. In contrast, conditions where the species has been found in impoundments of the mainstem Snake River are characterized by more swift current where the river transitions from lotic (free-flowing) to more lentic environments near the upstream-most portions of Swan Falls Reservoir and Milner Reservoir. Little is known of the species’ distribution or habitat in the Bruneau River arm of C.J. Strike Reservoir, compared to habitat conditions where it has been found in the Snake River downstream of Minidoka Dam and C.J. Strike Dam. If Snake River physa are found in more abundance in the Bruneau River system, effects analyses based on habitat descriptions in this Opinion, which are based on surveys from the Snake River mainstem, may need to be reconsidered. In an effort to clarify Snake River physa habitat use for describing the species’ distribution for this Opinion, the Service, in coordination with Company biologists, conducted an analysis (Appendix A) of Snake River physa substrate use using the Company’s substrate sampling data set and unpublished data provided by Gates from her study conducted in the 11.5 mile reach of the Snake River below Minidoka Dam for the Reclamation. The analysis examined Snake River physa substrate selection in areas where the species has been found in relatively large numbers, and also analyzed substrate composition and distribution where it has rarely been found, including the type locality. Snake River physa were found to strongly select for substrates ranging in size from pebble to gravel, and possibly from cobble to gravel. Such substrate selection contradicts Taylor’s (1982b, in litt.) accepted description of boulder to gravel substrates, with his specimens collected from boulders. Our results, however, are consistent, and statistically significant, in both the C.J. to Weiser Reach and the Minidoka reach, two sections of the Snake River separated by over 200 river miles. Pebble and gravel were the most common substrates in the Minidoka Reach (Figure 2, Appendix A). Results from Gates’ data are suggestive that relatively large, relatively contiguous areas of preferred habitat may be one factor resulting in comparatively high densities (generally less than or equal to 32 individuals per m2, but up to 40 to 64 per m2 in three samples, were found at Minidoka) and abundance of Snake River physa. These results are relative, however. While the species was found in the Minidoka Reach in the highest numbers and densities so far recorded, Gates and Kerans (2010) concluded that Snake River physa occurred throughout their study area in a diffusely distributed population, and suggested that the species rarely exhibits high density colony behavior. The question remained as to why Snake River physa have consistently been difficult to find in the reach between Lower Salmon Falls Dam and C.J. Strike Reservoir (Lower Salmon Falls/C.J. Reach), which includes the type locality reach. Discussion between Service and Company biologists led to speculation that, if the species does select for pebble to gravel or cobble to gravel, then differences in river character between the C.J. to Weiser Reach and the Lower Salmon Falls/C.J. Reach could explain its rarity in this area. Tests for differences in substrate composition and distribution were statistically significant between the C.J. to Weiser Reach and areas in the Lower Salmon Falls/C.J. Reach. Graphical display of percent dominant and co- dominant substrates by river mile in the Lower Salmon Falls/C.J. reaches clearly indicates that pebble to gravel substrates are quite rare between Lower Salmon Falls Dam and C.J. Strike Reservoir (Figure 3, Appendix A), suggesting that, under current habitat conditions, the probability of encountering Snake River physa in this reach is likely quite low. Substrate habitat could have been more favorable at the times of Taylor’s collections.
14 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Gates and Kerans’ (2010) sampling effort collected about 4.8 times more individual Snake River physa for about double the sampling effort compared to the Company’s sampling effort and collection of Snake River physa (Appendix A, p. 7-8). This raises the possibility that there are other factors in addition to the presence of a relatively large, contiguous area of preferred substrates downstream from Minidoka Dam that account for the high density and abundance in that area. American Falls Dam and Minidoka Dam both act as highly effective sediment traps (Newman 2011, in litt.). In addition, although Lake Walcott is largely operated as run of river, operations at Minidoka Dam result in water passing through the power plant and through the spillway gates being drawn from high in the water column, meaning that bottom sediments at the dam’s face are not mobilized. Water leaving the power plant and passing through the spillway gates is typically relatively free of fine sediment and quite clear, and hence macrophytes are nearly absent in the 11.5 mile reach below the dam (Newman 2011, in litt.). Proliferation of aquatic macrophytes may result from an excess of phosphorus, since phosphorus is typically limiting to aquatic plant growth (Steinman and Mulholland 1996, p. 161). Phosphorus may exist in aquatic systems as insoluble fine particles, or in soluble form adsorbed to certain classes of fine sediments (Howell 2010, p. 114). In either form, if present phosphorus is transported in streams as part of the fine sediment load. With much of the fine sediments trapped behind American Falls Dam and Minidoka Dam, phosphorus levels passing over Snake River physa habitat downstream of Minidoka Dam are lowered. Mean annual total phosphorus from the outflow of Minidoka Dam (Reclamation unpublished data) was significantly lower (P = 0.020) by 31 percent for the years 2007 to 2011 compared to phosphorus levels sampled from the outflow of Swan Falls Dam (Naymik and Hoovestol 2008, p. 25-26) for the years 2003 to 2006. Further, the highest flows are passed at Minidoka dam in summer to meet downstream irrigation demands. Data from 1950 to 2010 show that mean monthly flows below Minidoka Dam are usually highest from May through July or August (data from USGS gage 13081500 at Howell’s Ferry). This somewhat mimics a hypothetical natural hydrograph of the lowland portion of a western river fed largely by snowmelt, in which flow begins to increase with warming air temperatures in April, peaks in mid-June to early July, then tapers off quickly in late July and remains low until the following April. The system at Minidoka Dam differs from a natural hydrograph in that flows are usually artificially maintained above natural conditions well into September. The effect of high and prolonged summer flows is to keep the pebble and gravel beds free of fine sediment (and the accompanying phosphorus load) during the period of highest insolation and highest summer temperatures when primary production is highest and rooted macrophytes would be most likely to grow and reproduce. Isolated, small patches (less than 1 m2) of macrophytes first begin to appear about 3 miles above the I-84 bridge where the river begins to transition from lotic to more lentic conditions as flow enters the upper end of Milner Reservoir (Newman 2011, in litt.). Data from 1950 to 2010 show that mean monthly flows downstream of Swan Falls Dam are the inverse of the Minidoka system. Flows are highest in winter and lowest in summer, usually in July and August (data from USGS gage 13172500 near Murphy, 4.3 miles downstream of Swan Falls Dam) during the period when macrophyte production and growth would be the highest. Groves and Chandler (2005, p. 479-480) attributed proliferation of macrophytes on the cobble/gravel beds in their study areas below Swan Falls dam to nutrient loading combined with high sediment loads (and subsequent sediment deposition) passing Swan Falls Dam. One of
15 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project their study sites from 2000, at approximate RM 445.3, was located within a few tenths of a mile of where three Snake River physa were recovered: one at RM 445.8 in 1998, and two at RM 445.2 in 2001. Compared to the number of Snake River physa found by Gates and Kerans (2010) downstream of Minidoka Dam, the Company collected far fewer Snake River physa below Swan Falls Dam per sampling effort, which may be in part attributable to low summer flows and higher sediment load combined with high nutrient loads below Swan Falls Dam. In summary, the confirmed known range of the Snake River physa is from RM 675 at Minidoka Dam downstream to RM 368 above Weiser. Within this 307 mile range the species remains rare, with only 340 confirmed live-when-collected specimens taken over a 49 year period between 1959 and 2008. Its highest abundance and densities were collected from the 11.5 mile reach below Minidoka Dam, which accounts for 274 of known live-when-collected specimens. Where Snake River physa has been found in abundance high enough to assess local distribution, it appears to exist in diffusely distributed populations, and does not seem to exhibit high density colony behavior. The species seems to select for pebble to gravel—and possibly cobble to gravel—sized substrates in free-flowing reaches of the Snake River where these substrate types are maintained relatively free of fines. The species can be expected to be rare in reaches with widely scattered, low proportions of cobble to gravel substrates, as in the reach between C.J. Strike Reservoir and Lower Salmon Falls Dam. Snake River physa is patchily distributed in the free-flowing reaches from C. J. Strike Dam downstream to the Weiser area, which may be a function of an altered hydrograph, nutrient and sediment loads, and accompanying proliferation of macrophytes. The species has not been sampled sufficiently to determine abundance and density other than in the Minidoka Reach. Due to conditions prevailing in the Minidoka Reach (low sediment deposition, current velocities that keep Snake River physa preferred habitat relatively free of fines, very low occurrence of macrophytes, and relatively large and contiguous areas of preferred substrates), the Service considers the Snake River physa population in this reach to be relatively stable. 2.3.5 Conservation Needs Survival and recovery of the Snake River physa is considered contingent on “conserving and restoring essential mainstem Snake River and cold-water spring tributary habitats (Service 1995, p. 27).” The primary conservation actions outlined for this species are to “Ensure State water quality standards for cold-water biota…” (Service 1995, p. 31). Priority 1 tasks consist of:
Securing, restoring, and maintaining free-flowing mainstem habitats between the C.J. Strike Reservoir and American Falls Dam; and securing, restoring, and maintaining existing cold-water spring habitats. Rehabilitating, restoring, and maintaining watershed conditions. Monitoring populations and habitat to further define life history, population dynamics, and habitat requirements (Service 1995, p. 27-28). Priority 2 tasks consist of:
Monitoring populations and habitat to further define life history, population dynamics, and habitat requirements.
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Updating and revising recovery plan criteria and objectives as more information becomes available, recovery tasks are completed, or as environmental conditions change (Service 1995, p. 28). The conservation needs of listed species are based on the species’ habitat requirements. Habitat requirements of the Snake River physa are based on habitat where the species has been found. Recorded habitat may not necessarily represent optimum habitat, but until Snake River physa can be found and/or raised in laboratory conditions in sufficient numbers and locations that provides evidence of other habitat preferences, we must accept habitat where the species has been found as representing what we know of its habitat requirements. Information and conclusions below are based on information from the Snake River. Little is known of the conditions in the Bruneau River or the Bruneau River Arm of C.J. Strike Reservoir that could be responsible for the species’ presence in that system. As described in Section 2.3.4, the Service has concluded that Snake River physa select for substrates in the pebble to gravel range, and possibly in the cobble to gravel range, and that these substrates represent the species’ preferred habitat under existing conditions. Based on the available evidence, Snake River physa preferred habitat needs to be largely free of fine sediments during the period of highest insolation and highest summer temperatures. The range of water temperatures that occur annually in the Snake River do not seem to be limiting to Snake River physa; that is, the species appears to physically tolerate the range of temperatures experienced. Water temperatures exceeding the CWA standard alone or combined with other factors could, however, contribute to other conditions limiting to the species (e.g. excessive macrophyte growth). While there have been no studies addressing water quality requirements for this species, it is probably safe to state that excessive nutrients and other pollutants would not be of benefit to the species. The family Physidae as a whole is generally considered adapted to harsh environments, including polluted environments (Wethington 2004, p. 2). DeWitt (1955, p. 43) recorded P. gyrina as surviving low dissolved oxygen levels at low temperatures in the presence of hydrogen sulfide. The pulmonate, Lymnaea stagnalis, normally absorbs oxygen directly into its tissues in the water column. However, under low oxygen conditions, it will rise to the water surface to respire directly from the air (Rosenegger et al. 2004, p. 2621-2622). Assuming Snake River physa occurred in the Snake River below Shoshone Falls prior to the construction of Swan Falls Dam and C.J. Strike Dam, the species would have experienced pulses of nutrient loading (largely nitrogen, but also phosphorus) following salmon die-off after fall spawning (salmon were not able to pass Shoshone Falls to spawn further upstream). How these historic nutrient levels might compare to contemporary nutrient loading from agricultural and municipal sources is not known, but the combined biomass of people and livestock and the land uses needed to support them in southern Idaho suggests current nutrient inputs (and other pollution) to the Snake River are significantly higher than the levels Snake River physa and other Snake River aquatic species evolved with prior to settlement. Based on the most recent findings of the Snake River physa’s distribution and habitat preferences, the conservation needs of the species will entail the maintenance of conditions that produce or sustain beds of pebble to gravel, and possibly cobble to gravel, in good condition, defined as largely free of substrates finer than gravel, and largely free of macrophytes. This also argues for improving ecological condition, particularly by controlling temperature and reducing
17 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project nutrient load, which minimize macrophyte growth in free-flowing reaches of the river containing beds of preferred substrate. Dense and extensive macrophyte beds reduce water velocity, causing fines such as sand, silt, and clay to fall out of the water column, potentially embedding or covering Snake River physa habitat. To achieve these conditions, the following actions should be pursued: Maximize minimum flows in the Snake River, especially during irrigation season, to help safeguard water quality. Achieve total maximum daily load (TMDL) criteria for all identified water quality parameter perturbations (e.g., total phosphorus, total suspended solids).
2.4 Environmental Baseline of the Action Area This section assesses the effects of past and ongoing human and natural factors that have led to the current status of the species, its habitat and ecosystem in the action area. Also included in the environmental baseline are the anticipated impacts of all proposed Federal projects in the action area that have already undergone section 7 consultations, and the impacts of state and private actions which are contemporaneous with this consultation. The Commission has determined that renewing a license for an existing hydropower project represents a new commitment of resources (U.S. Fish and Wildlife Service and National Marine Fisheries Service 1998, p. 4-28, 4-29). On that basis and pursuant to Service policy, a section 7 analysis of the effects of a proposed relicensing action on listed species and critical habitat is done in the same way as for a new project (U.S. Fish and Wildlife Service and National Marine Fisheries Service 1998, p. 4-28). For purposes of this consultation, all past and current effects of the Swan Falls Dam and its operations on the Snake River physa, together with the effects on the Snake River physa of all past and current non-Federal activities and Federal projects (with completed section 7 consultations) in the action area, form the environmental baseline. To this baseline, the future effects of the Swan Falls Dam and its operations on the Snake River physa over the new license period will be added, along with the effects of any future interrelated and interdependent activities and any cumulative effects, to determine the total effect on the Snake River physa for purposes of the section 7(a)(2) determination for the proposed action. 2.4.1 Species 2.4.1.1 Status of the Snake River physa in the Action Area The Service presumes the presence of Snake River physa in the Action Area, although the species has not been recovered in that section of the Snake River since 2001. The Action Area extends from RM 469.4 at the upper end of Swan Falls Reservoir downstream to the upper end of Brownlee Reservoir at RM 344. The Swan Falls Reservoir is approximately 11.5 miles long, with Swan Falls Dam located at RM 457.7 The Company characterizes the river below Swan Falls Dam into two types. From the dam downstream to Celebration Park (RM 447.8), a distance of 9.9 river miles, the river flows through a constricted canyon made up mostly of bedrock and large boulder substrate (Bean and
18 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Stephenson 2011b, p. 3). The river widens at Celebration Park to form the lower reach, approximately 104 miles in length from Celebration Park to the headwaters of Brownlee Reservoir. The lower reach is shallower, more braided, with substrates dominated by gravel and sand (Bean and Stephenson 2011b, p. 3). See also Section 2.3.4 (Status and Distribution) for discussion of substrate characteristics in this reach. Swan Falls Reservoir is shallow (Bean and Stephenson 2011b, p. 3), and Google Earth images indicate that the river and canyon of all but about the upper 2 miles of Swan Falls reservoir are narrow and restricted, reflecting the limited surface area and capacity of the reservoir (1,525 acres and 7,425 acre feet, respectively) (Bean and Stephenson 2011b, p. 1). Unlike the narrow reaches between King Hill Bridge and Lower Salmon Falls Dam; however, Swan Falls Reservoir generally lacks the boulder/cobble components, with percent substrate occurrence most closely resembling the Lower Bliss Reach, depicted in Figure 3 of Appendix A. The Company’s substrate data set (1995 to 2003) includes 20 unique samples from Swan Falls Reservoir. Snake River physa habitat in the form of pebble and gravel constitute 25 percent of dominant substrates and 46.7 percent of co-dominant substrates; and cobble, pebble, and gravel make up 35 and 73.4 percent of dominant and co-dominant substrates, respectively. The distribution of substrates does not appear to vary in any discernible way with river mile in the reservoir. Pebble/gravel was found at RM 467, where the one specimen of Snake River physa from the reservoir was collected about 2 miles downstream of the upper end of the reservoir. Pebble/gravel was also recorded at RM 461, about 4 miles upstream of the dam. In addition to the single Snake River physa found in Swan Falls Reservoir, 36 live specimens have been collected by the Company at 22 locations between Swan Falls Dam (RM 457.7) and Brownlee Reservoir (RM 344) between 1998 and 2001 (Bean and Stephenson 2011b, p. 16). River miles and depth of collection (where known) within the Action Area are shown in Table 1. Maximum depths at which Snake River physa were collected in the Action Area ranged from 3 to 6 feet, and minimum depths ranged from approximately 0.5 to 3 feet.1
1 The minimum/maximum collection depths are an artifact from the Company’s sampling protocol, where subsamples at a sampling point were taken at different depths. The depths were usually recorded, but the subsamples were combined post-sampling. When Snake River physa were subsequently identified in the samples, the actual depth of the subsample in which they might have been collected could not be determined, so the Company reported the minimum and maximum subsampling depths.
19 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Table 1. Flow, stage height, and depth of Snake River physa collection locations on the Snake River in comparison to minimum stage height (2.43 ft) at proposed minimum flows of 3,900 cubic feet per second (cfs). Flow and stage height data from USGS gage at Murphy; remainder from IPC data. Stage height measurements are in feet. Minimum/Maximum stage height and flows are those recorded during working hours on the days of collection. Purpose and calculation of data for Adjusted Minimum/Maximum Collection Depth at Proposed Minimum Summer Flow are discussed in Section 2.5.1.1 (Direct Effects). Date River Minimum/ Minimum/ Minimum/ Substrate # Snake Minimum Adjusted Mile Maximum Maximum Maximum River Collected Minimum/ Collection Stage Flow (cfs) physa Stage Maximum Depth Height collected Height Collection where minus Depth at known Minimum Proposed Stage Minimum Height Summer (2.43) Flow 7/28/98 445.8 2/5 3.45-3.525 7000-7300 sand 1 1.02 0.98/3.98 7/22/98 442 2/3 3.35-3.41 6720-6940 pebble/ 1 0.92 1.08/2.08 gravel 7/20/98 433.1 1/4 3.475-3.39 6880-7110 gravel/ 1 1.045 -0.045/2.95 pebble 7/20/98 433.1 1/4 3.475-3.39 6880-7110 gravel/ 1 1.045 -0.045/2.95 pebble 7/15/98 424.3 1/4 3.51-3.43 7000-7220 gravel/ 1 1.08 -0.08/2.92 pebble 7/15/98 424.3 1/4 3.51-3.43 7000-7220 gravel/ 2 1.08 -0.08/2.92 pebble 7/15/98 424.3 1/4 3.51-3.43 7000-7220 gravel/ 3 1.08 -0.08/2.92 pebble 7/14/98 417 1/3 3.76-3.85 7920-8180 gravel/ 1 1.33 -0.33/1.67 sand 7/14/98 417 1/3 3.76-3.85 7920-8180 gravel/ 1 1.33 -0.33/1.67 sand 7/13/98 407.5 5 3.58-3.81 7420-8060 Not graded 2 1.15 3.85 7/13/98 401.9 3/4 3.58-3.81 7420-8060 pebble/ 1 1.15 1.85/2.85 gravel 7/13/98 400.1 3/4 3.58-3.81 7420-8060 sand 1 1.15 1.85/2.85 5/17/01 467.7 6 3.43-4.15 7000-9030 gravel/ 1 1.0 5.0 pebble 7/24/01 445.2 0.5/1 2.92-3.12 5570-6130 silt/ 2 0.49 0.0/0.51 boulder 7/24/01 443.6 unknown 2.92-3.12 5570-6130 cobble 2 0.49 -- 8/1/01 428.3 unknown 2.72-2.92 5020-5570 pebble/ 1 0.29 -- gravel 8/1/01 426.3 0.5/1 2.72-2.92 5020-5570 sand/silt 1 0.29 0.21/0.71 8/1/01 425.8 0.5/1 2.72-2.92 5020-5570 boulder/silt 1 0.29 0.21/0.71 8/2/01 421 unknown 2.76-2.89 5030-5800 pebble/ 1 0.33 -- gravel 8/2/01 420.5 unknown 2.76-2.89 5030-5800 pebble/ 7 0.33 -- gravel 8/2/01 403.6 unknown 2.76-2.89 5030-5800 pebble/ 2 0.33 -- sand 8/7/01 400.3 2 2.61-2.89 4720-5490 pebble/silt 1 8/29/01 367.9 unknown 2.92-3.15 5570-6210 gravel/ 2 0.49 -- cobble
20 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
There appeared to be a somewhat higher concentration in an area near Marsing, Idaho (within the Walter’s Ferry Reach, RM 441.9–395.3), with over 44 percent (16 of 36) of Snake River physa found in the Action Area below Swan Falls Dam collected in a 5.8 mile reach (RM 426.3-420.5). Fourteen of these specimens were collected on pebble/gravel substrates, and one each on boulder/sand and boulder/silt. Seven of these individuals were found in one sample at RM 420.5 in 2001; this density equates to 28 Snake River physa per square meter, comparable to densities found below Minidoka Dam. This abundance in this 5.8 mile reach from 1998 to 2001 could have suggested the potential for colonies similar in abundance and density to those at Minidoka, had the species’ presence in the area been known at the time at the time of sampling. The upstream-most location of Snake River physa collected downstream of Swan Falls Dam was at RM 445.8, about 2 miles downstream of Celebration Park. A total of 69 percent (25 of 36) of Snake River physa found in the Action Area were collected in the 25 mile reach between the specimen at RM 445.8 and the area near Marsing (RM 420.5). The remaining 11 specimens were collected in the 49 mile reach between RM 417–367.9. The 36 specimens collected in the Action Area represent 10.6 percent of all live Snake River physa collected, and 11.1 percent of live Snake River physa collected since 1998. However, the Action Area includes 32.8 percent of the species known range (101 river miles of 307 total river miles), from RM 469.4 (upper end of Swan Falls Reservoir) to RM 368 (area of downstream- most collection of Snake River physa). With the exception of the single, higher density sample collected in the Marsing area in 2001, Snake River physa have not been found in abundance within the action area. Snake River physa were only recorded in 5.6 percent of 407 samples collected in the action area between 1995 and 2003. Recent surveys conducted by the Company for the purposes of this relicensing effort (August and September 2010), which targeted preferred habitat (though not in the area of the higher concentrations found near Marsing), failed to locate any Snake River physa in 60 samples. Surveys conducted in the footprint of in-water work for the proposed recreation mitigation and enhancement sites also did not recover Snake River physa. While the area has not been thoroughly surveyed, based on the available data, Snake River physa are not abundant within the action area. The concentration of specimens found specifically in the Marsing area and in the Walter’s Ferry Reach in general may represent a second, albeit less abundant, population of Snake River physa, with the first being the population in the Minidoka Reach. If correct, Snake River physa from the Walter’s Ferry Reach may contribute to the presence and persistence of the species in reaches further downstream. The degree of impacts to Snake River physa from daily load-following operations and proposed minimum flows will stem from the amount of suitable habitat available at a given discharge, and how much of suitable habitat might be occupied during fluctuations in stage height. The amount of benthic habitat de-watered in the Action Area by Swan Falls Project operations has not been quantified. Bean and Stephenson (2011b, p. 9) reported results from a three-dimensional hydrodynamic model that estimated less than 5 percent of the benthic habitat was de-watered due to hydropower operations in the Lower Salmon Falls Reach and Bliss Reach. Extrapolating these model estimates to the Swan Falls Project, they speculated that due to differences in channel morphology between these reaches and in the Action Area, different ramping rates at the Swan Falls Project, and the smaller operating capacity of Swan Falls Dam, the amount of benthic habitat exposed in the Action Area during daily operations was likely less than 5 percent (p. 9).
21 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Bean and Stephenson (2011b) did not provide precise or specific estimates of the amount of potential Snake River physa habitat in the area that might be exposed. As discussed in Section 2.3.4 (Status and Distribution), the available evidence suggests that Snake River physa habitat can be described as: Cobble to gravel substrates relatively free of fines and aquatic macrophytes (a function of current velocity—also see discussion in Section 2.5.1.2, Indirect Effects); Mean current velocity of 0.57 meters/second (m/s); and Depths of 0.5 to 3 m, with most individuals collected from depths between 1.25 to 2.5 m. In-stream flow studies for reaches of the Snake River that include the Action Area provide a means by which to derive an estimate of potential Snake River physa habitat under different discharges. In-stream flow studies were conducted by the Service (Anglin et al. 1992) to assess the impacts of changes in the Company’s water rights under the 1984 Swan Falls Agreement between the Company and the state of Idaho on habitat for six resident fish species (including white sturgeon (Acipenser transmontanus) and mountain whitefish (Prosopium williamsoni)) in the reach between C.J. Strike Dam and the Brownlee Reservoir. Anglin et al. (1992, p. 6) separated the area between the Walter’s Ferry Bridge and Brownlee Reservoir into three reaches: Walter’s Ferry Reach (RM 441.9-395.5), Payette/Boise River Reach (RM 395.5-366), and Weiser/Farewell Bend Reach (RM 366-341). The Company (Brink 2008) conducted a similar study for white sturgeon and mountain whitefish for the 15.8 mile reach between Swan Falls Dam and the Walter’s Ferry Bridge (Swan Falls/Walter’s Ferry Reach, RM 457.7 to 441.9). In addition to incorporating field data collection and hydraulic simulations completed by Anglin et al. (1992) and utilizing updated habitat suitability criteria for white sturgeon, Brink (2008) modeled the effects of different magnitudes of water years on life stages of these two species. Both studies estimated habitat area for each species by inputting data from transects sampling current velocity and macrohabitat types (main channel, simple island, and complex island) in the study reaches and from species’ habitat suitability criteria into a habitat model to estimate hectares (ha) of total weighted useable area (WUA) in the study reaches for each species. Habitat suitability criteria included species’ requirements for velocity, substrate type, and depth. WUA was then entered into a hydraulic model to estimate WUA available at different discharge rates as measured at the Murphy gage (Anglin et al. 1992, Brink 2008) and at the USGS gages 13213100 and 13269000 near Nyssa (Nyssa gage) and Weiser (Weiser gage), respectively (Anglin et al. 1992). The habitat suitability criteria index ranges between 0.0 and 1.0, with 1.0 being most suitable. Snake River physa habitat described above is quite similar to mountain whitefish spawning habitat suitability criteria (Brink 2008, p. 29) utilized by both studies. The index ratings (bold) for velocity, depth, and substrate types for mountain whitefish spawning habitat suitability criteria are: Mean column velocity: 1.0 at approximately 0.55 m/s (index is 0.0 at both 0.0 m/s and 1.0 m/s, with the shape of the curve symmetrical) Depth: 0.0 from 0.0 to 0.1 m, 1.0 at 0.25 m up to 3.0 m Substrate size: 0.9 for cobble, 1.0 for gravel.
22 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Brink (2008) modeled WUA against flow ranging from 1,000 to 15,000 cfs. The relationship between WUA and flow for mountain whitefish spawning habitat was positive and nearly linear (p. 33) in the Swan Falls/Walter’s Ferry Reach. Anglin et al. (1992) modeled WUA against flow ranging from 3,000 to 15,000 cfs for the remaining three reaches. WUA is shown for the range of flows in each reach in Table 2.
Table 2. Total weighted useable area (ha) for mountain whitefish (MWF) spawning habitat at discharges of 1,000 to 15,000 cubic feet per second modeled for the reaches between Swan Falls Dam and Brownlee Reservoir. Swan Falls Reach Walter's Ferry Reach Payette/Boise River Weiser/Farewell RM 457.7-441.9 RM 441.9-395.5 Reach Bend Reach RM 395.5-366 RM 366-344
Flow Stage MWF Stage MWF Stage MWF Stage MWF Total (cfs) Height, spawning Height spawning Height spawning Height spawning Habitat in Murphy habitat (ft), habitat (ft) habitat (ft) habitat the Action Gage (ha)1 Murphy (ha)2 Nyssa (ha)2 Weiser (ha)2 Area at Gage Gage Gage Given Flow Rates 1000 --4 0.595 ------0.595 2000 -- 1.213 ------1.213 3000 -- 1.985 -- 708.130 ------710.115 39003 2.43 2.674 2.43 724.200 4.26 -- 1.18 -- 726.874 4000 2.45 2.715 2.45 727.270 4.29 778.462 -- -- 1508.447 5000 2.80-2.92 3.092 2.80-2.92 735.900 4.55 819.991 1.57 410.089 1969.072 56003 3.03 3.404 3.03 739.256 4.86 813.209 -- -- 1555.869 6000 3.31-3.34 3.715 3.31-3.34 790.447 -- -- 1.87 430.807 1224.969 7000 3.55 4.403 3.55 932.222 5.01 801.131 2.15 456.170 2193.927 8000 3.85-4.03 5.051 3.85-4.03 976.260 5.28 787.288 2.27-2.43 473.358 2241.957 9000 4.14 5.67 4.14 933.802 5.45 729.036 2.6 480.697 2149.205 10000 4.49-4.5 6.316 4.49-4.5 864.865 5.7 636.594 3.16 478.653 1986.429 11000 4.83-4.85 7.07 4.83-4.85 787.288 5.86 542.852 3.14 463.417 1800.627 12000 5.18-5.2 7.866 5.18-5.2 722.533 6.06 475.680 3.22 454.126 1660.205 13000 5.52-5.55 8.69 5.52-5.55 646.535 6.39-6.45 418.264 3.35-3.63 440.097 1513.587 14000 5.88 9.575 5.88 580.014 6.55 370.696 3.57-4.1 408.230 1368.516 15000 6.21-6.24 10.461 6.21-6.24 520.368 6.65 335.485 4.37 381.195 1247.509 1 From Brink (2008, p. 21) 2 From Anglin et al. (1992, p. B-21, B-28, B-35) 3 Flows from the 1984 Swan Falls Agreement 4 No data available Due to the similarity between Snake River physa habitat characteristics and the habitat suitability criteria for mountain whitefish spawning, the Service is using the estimates of mountain whitefish spawning habitat as a surrogate for Snake River physa habitat. While recognizing that the relationship between habitat needs for the two species is likely not one-to-one, given the similarities, these estimates of mountain whitefish spawning habitat represent the best estimates available for the amount of Snake River physa habitat in the Action Area. Table 2 indicates that for all but the Swan Falls Reach, there is a range of flows, specific to each reach, at which mountain whitefish spawning habitat (and therefore Snake River physa habitat) is
23 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project maximized, with the area of habitat decreasing at flows both lower and higher. Habitat in the Swan Falls Reach increases linearly with flow. Company biologists suggest that this is a function of the higher gradient and character of the river in this reach. The proportion of Snake River physa habitat in the Swan Falls Reach is quite small compared to the remainder of the Action Area. The majority of the habitat occurs in the Walter’s Ferry Reach and Payette/Boise River Reach (RM 441.9-366 inclusive). It is the Service’s position that density and abundance estimates for Snake River physa from the Company’s data and from Gates and Kerans (2010) cannot be meaningfully applied to the estimates of habitat in Table 2 at this time. Neither the Company’s nor Gates and Kerans (2010) studies were designed to estimate abundance or population. Gates and Kerans (2010) derived mean density estimates per m2 for the species in the Minidoka reach, but applying these estimates to degraded habitat in the Action Area would not be appropriate. 2.4.1.2 Factors Affecting the Species in the Action Area 2.4.1.2.1 Water Quality Water quality in the Snake River has been impacted by the cumulative effects of decades of agricultural, municipal, and industrial activities within the watershed, and by the regulation of flows. The Final Environmental Impact Statement for relicensing of the Swan Falls Project (Federal Energy Regulatory Commission 2010, p. 31-36) discusses impacts to water quality and some of the effects to aquatic resources in the Action Area. With the Swan Falls Project operated largely as run of river, impacts to water quality from the project itself may be small relative to factors that impact water quality in the Snake River watershed upstream and downstream of the Swan Falls Project (but see Section 2.5.1.2 Indirect Effects). Agriculture on the Snake River Plain is made possible by irrigation water drawn from the Snake River and its tributaries, and from groundwater withdrawals. Water quality in the Action Area is degraded due to excessive nitrogen and phosphorus, pesticides, sediment, and increased temperature, which result from non-point source returns from irrigated agricultural fields; ground water discharge; effluent from fish farms; and outflow from municipal wastewater treatment facilities (Federal Energy Regulatory Commission 2010, p. 31-33), from sources both upstream and downstream of the Swan Falls Project. Some TMDL water quality improvement projects affecting the Action Area, such as the Snake River – Hells Canyon TMDL (Idaho Department of Environmental Quality (IDEQ) 2004) and the Mid-Snake River/Succor Creek Subbasin Assessment and TMDL (Idaho Department of Environmental Quality (IDEQ) 2003), are being implemented at this time. Water quality improvements will be incremental and long term. By one estimate, achievement of TMDLs for the Snake River – Hells Canyon TMDL targets may span 50-70 years (Idaho Department of Environmental Quality (IDEQ) 2004, p. 448). However, water quality will consistently improve as treatments are applied to point and nonpoint discharges (Idaho Department of Environmental Quality (IDEQ) 2004, p. 448). Water quality issues in the Snake River are typically exacerbated under low water conditions (Federal Energy Regulatory Commission 2010, p. 33). The best depiction of natural flows in the Snake River prior to dam construction come from data recorded on a U.S. Geological Survey gage at Montgomery Ferry (7 miles downstream from the Minidoka Dam location) between 1895 and 1904, before any major dams were constructed (Figure 2) (U.S. Department of the Interior 1956, p. 146). Mean monthly flows at the Montgomery Ferry gage decreased in July,
24 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project usually reached the lowest discharge in August (2,120 to 5,710 cfs except in 1899) and remained stable between about 4,600 to 6,500 cfs through the winter into March. Minimum discharge in the Action Area would have followed a similar pattern but with likely higher flows, with the addition of perhaps between 3,000 to 4,000 cfs from the Thousand Springs area, and significant inflows from the Malad River, Salmon Falls Creek, and the Bruneau River. The discharge at Swan Falls Dam is now typically reduced during summer when water for irrigation is in high demand. Summer flows are further reduced during low water years. Mean monthly discharge data from the Murphy gage from 1950 to the present indicates a general downward trend in low summer flows.
45000
40000 1895
35000 1896 1897 30000 1898 25000 1899 20000 1900 15000 1901 10000 1902
5000 1903 1904 0 Jan Feb Mar Apr May June July Aug Sept Oct Nov Dec
Figure 2. Snake River natural hydrograph from the U.S. Geological Survey gage at Montgomery Ferry, near Minidoka, Idaho, 1895 to 1904 (U.S. Department of the Interior 1956, p. 146), prior to known dam construction on the Snake River. The source indicates there were diversion for irrigation of about 174,000 acres upstream of the gage, but did not name the diversion(s) or the location. Flow is mean monthly flow in cubic feet per second.
Figure 3 shows that flows recorded at the Murphy gage dropped below 5,000 cfs during 10 of the last 21 years. The period of discharge less than 5,000 cfs in 1992 appears as an outlier. However, flows less than 5,000 cfs occurred in consecutive years between 2001 to 2008. Number of days in which flows were less than 5,000 cfs for 10 or more days occurred in 19 percent (4 of 21) of the last 21 years (excluding 1992), and in three consecutive years there were a significant number of consecutive days in which flows were 5,000 cfs or lower. An examination of mean monthly flow data (1950 to 2010) and 15-minute flow data (1989 to 2011) from the Murphy gage shows that discharge approached the proposed summer minimum of 3,900 cfs just once on July 13, 2003, when discharge ranged between 3,990 and 3,950 cfs over 1.5 hours. (All data for the Murphy gage is available via the USGS website at http://waterdata.usgs.gov/nwis/dv?referred_module=sw&site_no=13172500 (last accessed January 13, 2012)).
25 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Number of days discharge < 5,000 cfs 80
70
60
50
40 Number of days 30 discharge < 5,000 cfs
20
10
0
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Water Year
Figure 3. Number of days of discharge less than 5,000 cubic feet per second (cfs) for water years 1990 to 2010, recorded at the Murphy gage downstream of Swan Falls Dam. Absence of bars indicates no days of discharge below 5,000 cfs for that year.
Low water conditions increase residence time in reservoirs, and allow for temperature increases due to increased insolation in both reservoirs and in free-flowing reaches. These factors lead to increases in primary productivity, phytoplankton levels, nutrient concentrations (Federal Energy Regulatory Commission 2010, p. 35), and proliferation of rooted and algal macrophytes. The net affect from these factors that degrade water quality is to impact ecological function, or ecological condition, of the Snake River. Ecological condition can be defined as “the state of the physical, chemical, and biological characteristics of the environment, and the processes and interactions that connect them” (U.S. Environmental Protection Agency 2008, Ecological Condition). The Idaho Department of Environmental Quality (IDEQ) has collected data in support of indices for use in assessing ecological impairment of Idaho rivers, including the upper- and mid-Snake River and the lower reach of the Bruneau River. The results, presented in the Idaho River Ecological Assessment Framework (Grafe 2002) and the Idaho Assessment of Ecological Condition [Rivers] (Kosterman et al. 2008), document changes in ecological condition of the Snake River over a total of 13 non-overlapping sites ranging from near Wheaton Mountain on the south fork of the Snake River (RM 874) downstream to the USGS gage at Weiser (RM 351.5). Since data from the two studies were collected in two different periods (between 1993 and 1995, and between 2002 and 2004), the results for the Snake River and the Bruneau River
26 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project could also be recording changes in water quality over time in some areas of the river. Results from both studies are summarized in Appendix B. Based on a total of eight water quality parameters for seven sites (near Blackfoot, below Minidoka Dam (RM 676), near Kimberly and Buhl, below Swan Falls Dam (RM 452.75), and at the USGS gages at Nyssa (≈ RM 385) and Weiser (≈ RM 351.5)), Grafe (2002) rated the aquatic life use support of the Snake River as good to fair from Blackfoot to Kimberly, and poor for the remaining downstream sites (Table 1 in Appendix B). Kosterman et al. (2008) and Remington and Kosterman (2008) developed a classification of ecological condition for Idaho rivers. It is important to emphasize that they were specifically classifying river ecological condition, not water quality. They used two methods for selecting a subset of least impacted stream sites: Stream data in the form of water chemistry GIS land-use metrics Based on analyses of the above data, the least impacted sites were designated as reference sites, the standard against which a set of survey tools or indices (to be developed) would be evaluated for their sensitivity to detect ecological impairment. (Remaining stream sites not least impacted were rated as moderately or highly impacted). Sample sites from the Snake River were a subset of stream sites from across Idaho, chosen from which to derive the survey indices which would be used to evaluate ecological condition of all Idaho rivers. As part of this process, a rating was made (least, moderately, highly impacted) for six Snake River sites using the water chemistry and physical habitat data and the GIS land-use metrics. The water chemistry metrics chosen explained 87 percent of the observed variability in water chemistry data across all study sites. Remington and Kosterman (2008, p. 46) found that they could use these metrics to derive a set of classification rules (Appendix B) that successfully reproduced the ecological impact status rating (least, moderately, highly impacted) of the survey sites. Of note is that the GIS land use metrics they also developed (Appendix B) classified the impact status of survey sites in close agreement with the water chemistry classification rules. (The association between these land use metrics and designation as least, moderately, or highly impacted as assessed by water chemistry perhaps should be considered somewhat closer to correlation than as strict cause and effect, but the implication is apparent: nutrient and other input from agricultural land use practices and the presence of dams impact river ecological condition. In addition to direct impacts to ecological condition, dams contribute an indirect effect: the degree of agriculture practiced on the arid Snake River Plain, and therefore a large fraction of impacts to Snake River ecological condition that result from agricultural impacts, would likely not be possible without multiple dams that provide for storage of irrigation water and production of hydroelectric power.) Once the least impacted reference sites had been chosen, Remington and Kosterman (2008) developed a set of indices with which to estimate overall river ecological condition (good, fair, poor), and individually the condition (good, fair, poor) of physical habitat, water chemistry, and the aquatic macroinvertebrate community of a river, based on comparison to the least impacted reference sites. Again, during this process, ecological condition ratings using the water chemistry/physical habitat index and the macroinvertebrate index were also made for the six sites on the Snake River. The designation of least, moderately, and highly impacted based on the water chemistry and GIS metrics, and the ecological rating of good, fair, and poor based on the
27 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project water chemistry/physical habitat index and the macroinvertebrate index, are presented for the six Snake River sites in Table 1 of Appendix B. The results from Grafe (2002), Kosterman et al. (2008), and Remington and Kosterman (2008, p. 37-62 and Appendices D-G) are in general agreement, and when considered together in Table 1 (Appendix B), document a downstream decline in water quality and ecological condition for the Snake River from southeastern Idaho upstream of Heise to southwestern Idaho near Weiser. Naymik and Hoovestol (2008, p. 25-26, 49) described water quality parameters for Swan Falls Reservoir (inflow) and downstream of Swan Falls Dam (outflow) for the water years 2003 to 2006. Mean inflow total phosphorus ranged between 0.072-0.082 mg/L, with minimum and maximum levels at 0.049-0.321 mg/L, respectively; mean outflow total phosphorus ranged between 0.077-0.093 mg/L, with minimum and maximum levels at 0.047-0.207 mg/L respectively. Minimum and maximum inflow total nitrogen ranged between 0.71-2.13 mg/L, and minimum and maximum outflow total nitrogen ranged between 0.52-2.12 mg/L. Applying the classification rules (Appendix 3) developed by Remington and Kosterman (2008, p. 46) to Naymik and Hoovestol’s (2008, p. 23, 25, 49) results for total phosphorus, total nitrogen and pH, the ecological condition of Swan Falls Reservoir and the area immediately downstream of Swan Falls Dam would be rated as highly impacted by the first classification rule, based on inflow and outflow total nitrogen. Interpretation using the second classification rule is less apparent, although it is clear that ecological condition has been impacted: maximum, but not mean, total phosphorus levels (inflow and outflow) exceeded levels for highly impacted; minimum total nitrogen exceeded levels for highly impacted for inflow and outflow for all years; and pH reached or exceeded 9.0 for parts of all years for inflow or outflow. The statistical comparison of phosphorus levels at Minidoka Dam and below Swan Falls Dam (Section 2.3.4, Status and Distribution), with phosphorus 31 percent higher below Swan Falls Dam, corroborate this conclusion. The Snake River from Swan Falls Dam to the Boise River confluence has been listed as water quality limited for bacteria, temperature, dissolved oxygen, flow alteration, nutrients, pH, and sediment (Federal Energy Regulatory Commission 2010, p. 32). To address the dissolved oxygen listing, IDEQ set a nutrient TMDL for phosphorus of 0.07 mg/L for the Swan Falls Project (Idaho Department of Environmental Quality (IDEQ) 2003, p. 175). Without empirical evidence of effects, we cannot definitively state that the determination of ecological condition in the Snake River as moderately to highly impacted throughout the known range of Snake River physa translates to impacts to the species. The work of Grafe (2002) and Kosterman et al. (2008) allows an association, however, between Snake River physa presence and abundance and the effects of agricultural and municipal land use and dams that accumulate in a downstream direction within the species’ known range, through possible impacts to habitat availability and suitability, including but not limited to: Altered hydrographs that exacerbate water quality issues; Possible effects on the species’ physiology (e.g., pollutants that may have toxic or sub- toxic effects); Increased nutrient levels that promote growth of macrophyte beds, slowing water velocity and resulting in sediment deposition over preferred substrates.
28 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Indeed, Groves and Chandler (2005, p. 479-480) reported the proliferation of rooted macrophytes and epiphytic filamentous algae that commonly covered the shallow cobble and gravel bars on their study sites between RM 448.43-437.76, and attributed this to high nutrient levels and fine sediment loads below Swan Falls Dam. In contrast, macrophytes are nearly absent from the reach downstream of Minidoka Dam where the highest numbers and density of Snake River physa have been found (Newman, in litt. 2011). Groves and Chandler (2005, p. 474, 476-477, 480-481) also noted the presence of hydrogen sulfide (H2S), indicative of anoxic conditions, among the cobble and gravel substrates in their study sites, with the highest levels in late spring. They speculated that decay of the extensive macrophyte and algal beds (the presence of which they attributed to high nutrient and fine sediment loads) during fall and winter increases biological oxygen demand, leading to anoxic conditions and production of H2S via anaerobic decomposition. H2S is toxic to most organisms that respire with oxygen, and is considered a broad spectrum toxin. It may affect several different body systems, though the nervous system is most affected. H2S forms a complex bond with iron in the mitochondrial cytochrome enzymes, thus preventing cellular respiration. Groves and Chandler (2005, p. 476-477) recorded H2S levels in some of their study sites that exceeded the lethal level for fall Chinook salmon eggs. The propensity of Physidae in general to live in harsh and polluted environments may include Snake River physa, but the Service is assuming some impact to the species from the presence of anoxic conditions and H2S in Snake River physa preferred substrates. Additional and more intensive survey efforts and laboratory studies will be needed to clarify the effects of changes in ecological condition on Snake River physa. 2.4.1.2.2 Invasive species The New Zealand mudsnail (Potamopyrgus antipodarum), a nonnative, invasive species, was collected in the Minidoka Reach in roughly the same numbers as Snake River physa (Bean and Stephenson 2011b, p. 17), but the mudsnail is by far the most abundant mollusk collected in the Action Area (Bean and Stephenson 2011b, p. 17). Competition from the New Zealand mudsnail was shown to negatively impact growth rates of the Bliss Rapids snail (Taylorconcha serpenticola), a species endemic to the Snake River drainage, under experimental conditions (Richards 2004, p. 117-118). In enclosure experiments, increasing New Zealand mudsnail densities also resulted in lower Bliss Rapids snail densities (Richards 2004, p. 117-118). The degree of competitiveness between Snake River physa and New Zealand mudsnail has not been assessed. Considering that the two species were found in about the same numbers where Snake River physa was most abundant may suggest that under what are assumed to be optimum habitat conditions for Snake River physa (in the Minidoka Reach), competition from New Zealand mudsnail is minimal. In areas supporting high numbers of New Zealand mudsnail and overlapping with Snake River physa habitat that is degraded (e.g., in the Action Area), it is possible that New Zealand mudsnail could have a competitive edge over Snake River physa.
2.5 Effects of the Proposed Action Effects of the action considers the direct and indirect effects of an action on the listed species or critical habitat, together with the effects of other activities that are interrelated or interdependent with that action. These effects are considered along with the environmental baseline and the predicted cumulative effects to determine the overall effects to the species. Direct effects are
29 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project defined as those that result from the proposed action and directly or immediately impact the species or its habitat. Indirect effects are those that are caused by, or will result from, the proposed action and are later in time, but still reasonably certain to occur. An interrelated activity is an activity that is part of the proposed action and depends on the proposed action for its justification. An interdependent activity is an activity that has no independent utility apart from the action under consultation. 2.5.1 Direct and Indirect Effects of the Proposed Action Effects of the proposed action to Snake River physa in the Action Area may result from four basic factors. Direct or indirect effects may result from interactions among these factors (listed below), and interactions with existing ecological impairment of the Snake River and with projected effects of climate change (Cumulative Effects). Fluctuating water levels, either due to load following, or by passing upstream discharges. Changes in water velocities accompanying fluctuating water levels. Decrease in minimum summer flows. The continued existence and design of the Swan Falls Dam. Fluctuating water levels may strand Snake River physa or eggs and expose Snake River physa habitat, exposing snails, eggs, and forage to desiccation and or extreme temperatures. Increasing water velocities may mobilize substrates, snails, and/or eggs, and may reduce available habitat. Decreasing water velocities may lead to proliferation of aquatic macrophytes in preferred substrates, degrading habitat and/or rendering it unsuitable. The continued presence of the Swan Falls Dam will continue any existing impacts of reduced genetic diversity, with potential effects to population viability and/or to the species’ ability to survive or adapt to changing environmental conditions. It will also continue to limit immigration of individuals from upstream populations. The design of the dam will likely continue to pass sediment into the reaches below the dam, which, combined with the nutrient load in the Snake River, will contribute to proliferation of aquatic macrophytes in preferred substrates. Direct and indirect effects stemming from these factors are discussed below. 2.5.1.1 Direct Effects Direct effects to Snake River physa could result from daily load-following operations and proposed changes in seasonal flow that result in fluctuations of water levels downstream of Swan Falls Dam, due to both de-watering of suitable, preferred habitat, and creation of conditions that could render suitable, preferred watered habitat unsuitable. The significance of impacts from de- watering will depend on the frequency with which Snake River physa or potential habitat may be exposed as a result of fluctuating water levels. If the depths at which Gates and Kerans (2010, p. 23) collected the highest abundance of Snake River physa (approximately 1.25-2.5 m) do represent a preferred depth range, then this allows a qualitative estimation of the likelihood of Snake River physa or eggs being stranded as a result of operations at the Swan Falls Project. Table 2 lists the stage heights at the appropriate USGS gage for flows up to 15,000 cfs for the three Snake River reaches (Walter’s Ferry, Payette/Boise River, and Weiser/Farewell Bend) with the largest proportions of Snake River physa habitat in the Action Area. If Snake River physa
30 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project rarely occur in abundance above a depth of 1.25 m, then this depth in feet (4.1 feet) can be subtracted from the stage heights at 15,000 cfs to yield the following results: Walter’s Ferry (Murphy gage) 6.24 - 4.1 = 2.14 Payette/Boise River (Nyssa gage) 6.65 - 4.1 = 2.55 Weiser/Farewell Bend (Weiser gage) 4.37 - 4.1 = 0.27 All three calculations give a resulting stage height less than that to be expected at the proposed minimum summer flow of 3,900 cfs, meaning that a reduction in flow from 15,000 to 3,900 cfs would not reach the depth at which Snake River physa would most likely be found. Hence, we could expect that few Snake River physa individuals or eggs would be stranded under the following conditions at flows between 15,000 to 3,900 cfs: For ordinary daily fluctuations between 15,000 and 3,900 cfs For a direct reduction in flow from 15,000 to 3,900 cfs, following the license ramping rates of one foot per day and three feet per hour It should be noted that stage height at the Nyssa and Weiser gages reflect inflow from Owyhee River and Boise River (Nyssa) and the Payette River and Weiser River (Weiser), and therefore a given cfs recorded at the Murphy gage below Swan Falls Dam, such as the proposed minimum summer flow, may register differently at the downstream gages due to input from the tributaries. This could change the stage height readings at the Nyssa and Weiser gages for flow of 3,900 cfs, but would not be sufficient to change the potential for stranding Snake River physa in the Payette/Boise River and Weiser/Farewell Bend reaches if the 3,900 cfs were implemented at Swan Falls Dam. The Service considers the probability of fluctuations between 15,000 and 3,900 cfs to occur in a 24 hour period to be very low. We have examined 15 minute stage height data provided by the Company from pressure transducers located near Marsing for the years 2004 to 2006, and from the USGS Murphy gage located about 4 river miles downstream of Swan Falls Dam for 2011. Rate of stage height changes from 2004 to 2006 varied from 0.01 to 1.32 inches per hour, with 49 percent (29 of 59 stage height change samples) of changes ranging from 0.3 to 0.53 inches per hour. The highest rate of change, 1.32 inches per hour, equates to 2.64 feet per 24 hours. The largest change in stage height observed in the 2004 to 2006 data was 18.6 inches, which occurred at a rate of 0.37 inches per hour between May 17 and May 19 of 2005 (0.74 feet per 24 hours). A nearly four foot change in stage height was recorded beginning on June 28, 2011 at the Murphy gage, when much of the Snake River volume upstream at Milner Dam (RM 639) was shunted into irrigation canals. Flow at the Murphy gage decreased by 9,630 cfs (down from 16,600 cfs), with a decrease in stage height of 3.71 feet which the Company extended over four days. The maximum rate of decrease, occurring over one 45 minute period, was 3.04 inches per hour, the equivalent of 0.25 inches every 5 minutes, about 0.05 inches per minute, or a little over 6 feet per 24 hour period. Thus, while rates of change, if continued over a 24 hour period, could lead to fluctuations in stage height exceeding that between 15,000 and 3,900 cfs, an extraordinary event (such as an emergency event) or series of events would likely be needed to prompt the Company to operate the Swan Falls Project at these ramping rates. The Company’s recent operating history indicates that ramping rates or daily fluctuations that might approach Snake River physa preferred depth conditions, if this occurs, would be implemented to safely accommodate regulation of the river that occurs far upstream of the Swan Falls Project, and that normal load following operations more rarely approach such conditions. Hence, if Snake River
31 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project physa apparent depth preference is greater than or equal to 1.25 m, the probability of individuals or eggs being stranded is quite low. The critical assumptions in this analysis are that most Snake River physa are likely to be found at depths greater than or equal to 1.25 m, and that they prefer this depth range throughout the year. The Company’s sampling method used between 1995 and 2003 did not provide for retaining the depths of the subsamples in which Snake River physa were found in the Action Area, as indicated in Table 1. While Gates and Kerans (2010) recorded depths for each sample, we cannot rule out that depths at which Snake River physa were found at Minidoka are a function of conditions specific to that reach during the times of year in which sampling was conducted. Gates and Kerans (2010) data for abundance and depth of Snake River physa occurrence is the best available. If future monitoring or studies of Snake River physa reveal a different or broader range of preferred depths, then this analysis may need to be reconsidered. It may be possible that some Snake River physa and eggs may occupy habitat at depths shallower than 1.25 m. Irregularities in the river bed and in available substrates may create conditions where preferred velocities and other habitat requirements occur at depths shallower (or deeper) than 1.25 to 2.5 m. Data in the far right column (Adjusted Minimum/Maximum Collection Depth) of Table 1 indicates the potential for exposure of Snake River physa at minimum and maximum collection depths had the proposed minimum summer flow of 3,900 cfs been implemented on the days Snake River physa were collected. After subtracting the stage height at minimum flow (2.43 feet) from the minimum stage height reached on the days of collection, the result was then subtracted from the minimum and maximum collection depths (where known) to derive an estimate of what the collection depth might have been had the minimum flow been in effect on the day of collection. Negative numbers for minimum collection depths in the Adjusted Minimum/Maximum Collection Depth column indicate samples where Snake River physa would have been stranded if they were to be found at the minimum recorded depths. No Snake River physa would have been stranded if they were to be found at the maximum depths recorded, but up to 10 Snake River physa (sum of specimens in samples with negative minimum collection depths) could have been stranded if they were located at the minimum recorded depths. If Snake River physa or eggs are stranded due to de-watering, direct effects are expected to include lethal impacts from desiccation or freezing. The effects of prolonged exposure to air under varying temperatures have not been studied for Snake River physa or its eggs. Although we know of no studies that have assessed the effects of dewatering on Snake River physa eggs, it is reasonable to assume that when the eggs of a strictly aquatic snail are dewatered and subjected to subfreezing or elevated air temperatures that they are likely to freeze or become desiccated, respectively, and die. If the reproductive phenology of Snake River physa follows that of other Snake River gastropods, with juveniles appearing in mid to late spring and numbers peaking in mid to late summer, there is likely to be less oviposition during the winter months, which will reduce the extent of such impacts on snail eggs when temperatures reach their most extreme lows. Mortality of de-watered eggs or individuals may in some areas be buffered by hyporheic and bank discharge that partially ameliorate temperature extremes. Both field and laboratory studies carried out by Richards and Arrington (2006; 2008) and Richards and Kerans (2008) and summarized by Stephenson (Stephenson 2009, p. 41-52) described desiccation studies carried out for the Bliss Rapids snail, which is also endemic to the Snake River. Bliss Rapids snails can incur significant mortality when dewatered under extreme air temperatures, and/or over prolonged durations under dry conditions. The LT50 (lethal time or
32 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project temperature at which 50 percent of individuals tested died) varied depending on snail size and whether or not the substrate surface was dry or wetted, and ranged from 2.3 hours to 6.5 days over temperatures ranging from 0.0 to 17 °C. With an adult body mass larger than the Bliss Rapids snail, the rate of desiccation or freezing upon exposure to extreme air temperatures may be somewhat slower for the Snake River physa, which could extend its LT50 time or temperature. Whether or not Snake River physa might occupy habitat that is made available by short term elevated river stages has not been studied, although the work of Gates and Kerans (2010) provides some basis from which to draw a conclusion. Gates and Kerans (2010, pg. 25, Table 1.4) found that Snake River physa were 70 percent less likely to be encountered in benthic habitats that had been exposed during seasonal dewatering. While a substantial portion of this dewatering in the river reach where they conducted their study is due to water management (flood control and storage), these effects can be assumed to be the same under a natural hydrograph. Therefore, it is also logical to assume that Snake River physa do not occupy (in abundance) benthic habitat that is created during seasonal, or short-term elevated river stages. Based on Gates and Kerans (2010, p. 25) findings, it is likely that Snake River physa will not frequently occupy ephemeral benthic habitats that are dewatered over extended durations with regularity. Aside from what is reported by Gates and Kerans 2010, pg. 10-12), no precision can be assigned to either “extended duration” nor “regularity” with regard to the Swan Falls action area. Nonetheless, it is reasonable to assume that Snake River physa that may be affected by declines in flows, due to declines in the seasonal hydrograph or major events that occur upstream of the project area, should not be regarded as attributable to hydroelectric operations at Swan Falls. Loss of Snake River physa from such declines are anticipated to have insignificant impacts to the species’ population in the Action Area. To summarize, the probability of direct effects to Snake River physa or eggs due to stranding that results from water level fluctuations stemming from implementing the license ramping rates is anticipated to be quite low, based on the available evidence. If stranding occurs, the Service assumes lethal impacts to all Snake River physa or eggs exposed to the air. The extent of direct effects due to de-watering and implementation of license ramping rates would be expected to vary with proximity to Swan Falls Dam, with greater impacts occurring nearer to the dam, for three reasons: The effect of ramping rates attenuates with distance from Swan Falls Dam, as modeled by the Company (Bean and Stephenson 2011b, p. 6, 23-24); The Walter’s Ferry and Payette/Boise River reaches (RM 441.9-366) contain most of the estimated habitat (Table 2); and, 69 percent of Snake River physa collected in the Action Area were recovered in the Walter’s Ferry Reach, suggestive of a reach with a larger amount of suitable habitat. Given the low probability of stranding or of Snake River physa occupying ephemeral habitat, losses of individual Snake River physa or eggs are anticipated to result in insignificant impacts to the population in the Action Area. Direct effects to Snake River physa due to de-watering could also include loss of habitat. Habitat that was exposed to the air would not be available for use by Snake River physa for forage or as refuge from predators. However, following the same reasoning as applied to the potential for impacts due to stranding Snake River physa or eggs, the probability of direct effects due to loss of habitat are also low, and such impacts would be anticipated to be insignificant.
33 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Daily fluctuations in flow that do not de-water suitable, preferred habitat may still have direct effects to Snake River physa or eggs by altering depth, velocity, or substrate availability. Direct effects from reduced velocity and depth may include sediment deposition over occupied habitat, resulting in suffocation or crushing of individuals or eggs. Direct effects from increased velocities that result from daily fluctuations may occur if preferred substrates are mobilized or individuals are dislodged due to increased shear stress. Table 2 indicates that available habitat decreases with higher flows, in part a function of increasing velocities. Mobilization of preferred substrates could damage or crush Snake River physa eggs. The behavior of adult Snake River physa at higher flows and current velocities is not known. Holomuzki and Biggs (1999, p. 41-44) and Holomuzki and Biggs (2003, p. 546-549), working with New Zealand mudsnails, found that: Shear stress (the drag exerted on an object from moving water) from high velocity or turbulence alone can dislodge snails from substrates, though species vary in their ability to resist shear stress Mobilization of bed sediments (ranging from gravel to cobble) will dislodge snails and that snails entrained with mobilized sediments can be crushed Mortality rates varied between 1.0 and 5.7 percent, and were slightly higher in cobble than in gravel If flows were gradually rather than abruptly increased, snails moved down into the gravel interstices Snails that moved down into gravel interstices were not dislodged as long as the gravel remained stable Dislodgement increased slightly but significantly when flood duration was increased from 1 minute to 30 minutes Holomuzki and Biggs’ experiments suggest that at least some snail species may sense and respond to changes in velocity relatively quickly, thereby avoiding mortality and dislodgement under some circumstances. Individuals that are dislodged due to increased velocity or mobilization of substrates may be transported downstream out of preferred habitat and away from reproductive cohorts, removing access to forage or reducing reproductive capacity and fitness of the originating population or of the species. As indicated on p. 33, effects of increased velocities on Snake River physa would be expected to attenuate in a downstream direction. The rates of change of discharge under a natural hydrograph may provide a basis from which to assess rates of current velocity increases that Snake River physa might have adapted prior to dam construction on the Snake River. The relationship between discharge and current velocity is not linear, but lacking data on velocity, changes in discharge provide a qualitative comparison. The year of highest mean monthly flow and the steepest decline of flow between 1895 and 1904 in Figure 2 occurred in 1896. Mean monthly flows in June, July, and August were 38,600, 17,100, and 5,710 cfs, respectively (U.S. Department of the Interior 1956, p. 146) at the Montgomery Ferry gage. Data in Table 2 allows an estimate of the rate of change between 15,000 and 5,000 cfs over 30 days, similar to the change between July and August at Montgomery Ferry. The change in flow from 15,000 to 5,000 cfs over 30 days would average 333.3 cfs per day, or about 14 cfs per hour at the Murphy gage.
34 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
This is obviously not a one-to-one comparison, due largely to the fact that actual flows for some periods in a given month in 1896 were likely higher than the means. However, the rate of change under a natural hydrograph is about three times lower than the most frequent rates of stage height (and therefore discharge) change determined from Company data between 2004 and 2006. As pointed out by Reice et al. (1990, p. 647, abstract), predictable discharge events, such as spring runoff and low summer flows, are not necessarily disturbances but a stable state to which species may adapt, meaning behavior and life history stages evolve that minimize losses to the species under stable conditions. Operations at the Swan Falls Project, such as daily load following or accommodation of large upstream discharges, are unpredictable events when measured against natural flow regimes. These may be conditions to which Snake River physa may be less adaptable, although due to variation likely to occur under natural flow regimes, some ability to adapt to a range of velocity increases can be presumed. Therefore, while some Snake River physa may be killed or harmed as velocities increase with increase in flows, the resulting losses are not anticipated to reach the level of significant impacts to the species’ population in the Action Area. Swan Falls Reservoir There was one Snake River physa collected in 2001 at RM 467.7 near the upstream end of Swan Falls Reservoir at a depth of 6 feet. Given that only the upper 3 feet of storage in Swan Falls Reservoir is commonly accessed, it is unlikely that individuals at this sampling depth would be de-watered. Increases in current velocity, however, could have direct effects on Snake River physa in the reservoir due to sediment deposition. Naymik and Hoovestol (2008, p. 32) indicate that transit time of water in Swan Falls Reservoir can vary quite dramatically. Due to this level of fluctuation, combined with the impaired ecological condition of the reservoir (Section 2.4.1.2.1, Water Quality), the Service anticipates low numbers of Snake River physa to occur in the reservoir. Changes in water velocity or de- watering are therefore anticipated to have insignificant effects to the species’ population in the Action Area. Draft Recreation Plan Elements Service biologists assisted the Company with surveys for Snake River physa in June of 2011 at the proposed sites for the four elements of the draft Recreation Plan requiring in-water work. No Snake River physa were collected at any of the sites. As a result of absence of preferred substrate types encountered during sampling, low current velocity, and known areas of macrophyte growth, the Service does not expect any measureable effects to Snake River physa at three of the sites (Swan Falls Reservoir boat ramp, Swan Falls Park, and Swan Falls Island) due to absence of suitable habitat. Gravel and cobble were recorded as co-dominant substrates at the Swan Falls downstream boat ramp site. Company biologists indicate that current velocity at this site may be enough to suppress macrophyte growth due to the presence of a back-eddy flowing over the area of proposed in-water work. The substrates and current velocity could create conditions for suitable Snake River physa habitat. While no Snake River physa were found during sampling of the construction footprint, their presence during construction cannot be ruled out. It is possible that Snake River physa individuals or eggs, if present, could be crushed as a result of construction activities, resulting in mortality. Because no Snake River physa were found during sampling, the abundance of Snake River physa, if present in the construction footprint, would be assumed to be
35 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project quite low. Therefore, any losses due to construction activities are anticipated to result in insignificant impacts to the species’ population in the Action Area, although the loss of a limited number of individuals cannot be ruled out. 2.5.1.2 Indirect Effects Indirect effects to Snake River physa could result from daily load-following operations through reduction in dissolved oxygen if water temperature increases with decreasing depth and river volume, resulting in mortality or sublethal effects to individuals or eggs. Sublethal effects to adults could involve individuals moving in an attempt to reach water with a higher dissolved oxygen content, which could include releasing from the substrate to travel to the surface to take in air, with the potential to be carried downstream and out of suitable habitat. Reduced dissolved oxygen could result in lethal and sublethal effects to adults, eggs, and developing embryos. The available evidence indicates that Snake River physa can tolerate the range of temperatures experienced in the Snake River under present conditions. Indirect effects could also result from de-watering of forage if preferred habitat is exposed to the air—when re-watering occurs, forage may not be immediately available due to effects of desiccation, assuming Snake River physa would attempt to re-occupy re-watered habitat as soon as it became available. Table 2 indicates that while more Snake River physa habitat can be rendered unsuitable by high flows, the impact of low flows, while affecting less habitat, could also be limiting to the species in the Action Area. The work of Boulton et al. (1992, p. 2204- 2205) and Blinn et al. (1995, p. 243) support the hypothesis that atmospheric exposure of the benthos due to decreasing flow that results from discharge fluctuations is a more severe “disturbance” than spring runoff or flow increases that result from hydroelectric operations, since it eliminates the benthic communities which support macroinvertebrates such as gastropods, and recovery of algae and macroinvertebrates is usually a long process. While Snake River physa might be impacted by daily load-following operations and license ramping rate throughout the Action Area, we anticipate that the potential for and magnitude of impacts to decrease in a downstream direction for reasons stated in Section 2.5.1.1 (p. 33, Direct Effects). This is also our belief due to reasons of Snake River physa depth preferences discussed under Direct Effects (p. 31-32). We anticipate that the probability of de-watering of Snake River physa habitat due to daily load-following operations or from implementing the license ramping rates will be low. Hence, indirect impacts to the species from long term effects resulting from atmospheric exposure of the benthos would be considered insignificant in the Action Area. Indirect effects may result from the continued existence of the Swan Falls Dam due to its impact on connectivity between Snake River physa populations. Completed in 1901, Swan Falls Dam was the first dam to be constructed on the Snake River in Idaho. Assuming that Snake River physa existed throughout its known range at the time, Swan Falls Dam was the first man-made barrier to divide Snake River physa populations into upstream and downstream segments. The importance of movement between Snake River physa colonies for the species reproduction and population viability is not known, but a reasonable assumption is that at least active movement (crawling upstream and downstream) and passive transport (carried downstream by current) would play important roles. The original Swan Falls Dam can reasonably be assumed to have stopped nearly all upstream movement, and limited downstream movement, although individuals might have passed over the spillway or through turbines unharmed. The current configuration of turbines and spillway gates, completed in the 1990s, would have further limited Snake River
36 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project physa upstream and downstream connectivity. The net result would be to restrict gene flow between upstream and downstream populations, and to restrict immigration to downstream populations. Working with Bliss Rapids snails, (Liu and Hershler 2009, p. 1295-1296) found no evidence that fragmentation of the Snake River by large dams in the river section inhabited by Bliss Rapids snails has resulted in reduced genetic diversity in riverine populations separated by the dams. The authors noted that passive transport of Bliss Rapids snails downstream in the Snake River mainstem, with individuals occasionally passing through the dams, would account for similar levels of genetic diversity and elevated gene flow among the mainstem populations separated by dams. The known range of Snake River physa in the Snake River, however, covers more than five times the range of the Bliss Rapids snail, and is divided by eight dams compared to three dams in the range of the Bliss Rapids snail. Given the apparent rarity of Snake River physa, it is reasonable to state that there is potential for dams to be restricting recruitment and the genetic diversity of the species in the Snake River, with possible impacts to population viability. The role of Swan Falls Dam in restricting genetic diversity and recruitment is now incremental, but is still an indirect effect to the species for the length of the renewed license. In the absence of data, the significance of this effect to the species cannot be determined at this time. As described in Section 2.4.1.2 (Factors Affecting the Species in the Action Area), the presence of Swan Falls Dam has contributed to degradation of Snake River physa habitat in Swan Falls Reservoir, despite the run of river nature of operations, due to impeded flow which creates conditions that lead to proliferation of macrophytes in the reservoir. Excessive macrophytes occurring in Snake River physa preferred habitat will degrade the habitat (see comparison between the Minidoka Reach and the reach below Swan Falls Dam, Section 2.3.4, Status and Distribution). Therefore, Swan Falls Dam will continue to maintain potential Snake River physa habitat in Swan Falls Reservoir in a degraded or unsuitable condition for much of the year over the length of the license, which is an indirect effects to the species. Indirect effects are also expected to occur from the continued existence of the Swan Falls Dam due to its design. With a reservoir length of approximately 11.5 miles, transit time of water entering Swan Falls Reservoir and exiting at Swan Falls Dam varies from about 3 hours to 30 hours at 30,000 cfs to 3,000 cfs, respectively (Naymik and Hoovestol 2008, p. 32). This translates to velocities of approximately 0.17 m/s at 30 hours to 1.7 m/s at 3 hours with the caveat that velocities will vary depending on where in the river they are measured, with higher velocities at the water’s surface in the center of the current and lower velocities near the banks and the bottom. Velocity, as measured by decreases in residence time, increases quite quickly in Swan Falls Reservoir between 3,000 cfs and about 7,000 cfs, and increases more gradually up to 30,000 cfs (Naymik and Hoovestol 2008, p. 32). As indicated in Section 2.4.1.1, about 9 of the 11.5 miles of the river and canyon in the reservoir are narrow and restricted which would serve to keep velocity relatively consistent through much of its length at a given flow and would be conducive to the transport of fine sediment. C.J. Strike Dam likely functions as an effective sediment trap for water entering Swan Falls Reservoir, but there are several sources of fine sediment input to the Snake River downstream of C.J. Strike Dam. Naymik and Hoovestol (2008, p. 3) identify several 303(d) listed streams entering the river below C.J. Strike Dam, two of which flow directly into Swan Falls Reservoir. Several small irrigation returns, which typically carry sediment, including phosphorus, from agricultural fields and run throughout the summer, also enter the reservoir. In addition, Naymik
37 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project and Hoovestol (2008, p. 14) also report that heavy local rainstorms can quickly transport large amounts of sediment into the reservoir. Daily load fluctuations may also mobilize fine sediment on the river banks in Swan Falls Reservoir. The narrow character of the Snake River in the Swan Falls Reservoir canyon combined with relatively rapid transit times would result in fine sediment frequently being carried to the area behind Swan Falls Dam. Some of this sediment likely stays suspended and passes through the powerplant or the spill gates (Stephenson 2011, in litt.) The dam itself will trap some sediment, particularly in low water years (Naymik and Hoovestol 2008, p. 15), but the design of the powerplant and the dam may also result in mobilization of fine sediments deposited near the turbine intakes and the spillway gates during operations. Company personnel report that the turbines draw water from at or near the bottom of the dam (Stephenson 2011, in litt.). Current entering the turbines may thus mobilize fine sediment deposited near the intake channels, which would pass through the turbines. Company personnel also state that the river bottom rises quickly and becomes shallow in the area of the spill gates (Stephenson 2011, in litt.). Hence, when the gates are open and in operation, they would draw water from near the bottom of the water column, mobilizing and transporting fine sediment downstream of Swan Falls Dam. In the absence of a nutrient load in the river, such a dam design would be desirable, since it allows for sediment transport and renewal that would otherwise not be possible downstream of the dam. It is the existing nutrient load in the Snake River that makes passing of sediment by the Swan Falls Dam problematic to Snake River physa. The significance of fine sediment and the accompanying phosphorus load transported downstream below Swan Falls Dam was discussed in Section 2.3.4 (Status and Distribution) and becomes apparent in comparison to the condition of Snake River physa habitat downstream of Minidoka Dam. As previously discussed (Section 2.3.4, Status and Distribution), Groves and Chandler (2005, p. 479-480) attributed the degradation of the cobble/gravel beds below Swan Falls dam to macrophyte growth resulting from nutrient loading combined with high sediment loads passing Swan Falls Dam. The combination of an altered hydrograph (overall lower flows and no high flushing flows during runoff periods), poor water quality in the form of high nutrient content (particularly phosphorus), and the transport of fine sediment that settles out under low flow below Swan Falls Dam provide the conditions that lead to degradation of Snake River physa preferred habitat below the Swan Falls Dam. The Swan Falls Project contributes little to the poor quality of water entering the Swan Falls Reservoir or to the fluctuation in flow resulting from regulation of the Snake River upstream, but the presence and design of the dam results in sediment transport (with the accompanying nutrient load) downstream that leads to indirect effects to Snake River physa. The proposed decrease in minimum flow from 5,000 to 3,900 cfs from April 1 to October 31 will also have indirect effects on Snake River physa by further contributing to macrophyte growth due to decreased current velocity in the Action Area during the part of the year when macrophytes would typically exhibit the highest rate of primary production under warm water temperatures and high insolation. The Service assumes that if the difference in flow between 5,000 and 3,900 cfs becomes available to water users upstream of the Swan Falls Project, it will be claimed and used, resulting in minimum flows of 3,900 occurring more frequently as measured at the Murphy gage. The Service also assumes that nutrient input to the Snake River from agricultural and municipal sources will remain relatively constant for at least the near future. If the two preceding statements are correct, the nutrient load in the Snake River below
38 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Swan Falls Dam will then be concentrated more frequently into a smaller volume of water. As described in the following two paragraphs, combined with decreased velocity associated with a decrease in flow, more frequent concentration of nutrients may result in increased macrophyte density and abundance in Snake River physa habitat downstream of Swan Falls Dam. Bunn and Arthington (2002) conducted a literature review of the consequences of altered flow regimes on aquatic biodiversity. They cited research on regulated Norwegian and Australian rivers to the effect that increased winter flows and reduced summer floods result in the proliferation of macrophytes in regulated reaches (p. 494-495), though they acknowledged the difficulty in separating the effects of a modified flow regime from effects of land uses that result in diffuse inputs of contaminants and nutrients (p. 502). Chambers et al. (1991, p. 254) found that macrophyte biomass was significantly and inversely correlated with current velocity within the macrophyte bed over the range of 0.01-1.0 m/s. They also found that macrophyte biomass was weakly correlated with discharge rate (or flow), and suggested that for large rivers, macrophytes are responding to localized changes in velocity and not necessarily changes in river-wide flow (p. 255-256), and therefore it can be difficult to set flow criteria that would prevent macrophyte accumulation. In in situ experiments of macrophytes growing in varying sediment textures (sand, and sand/silt mixtures), they demonstrated that increase of velocity over a range of 0.2–0.7 m/s resulted in a decrease in plant biomass irrespective of sediment texture (p. 256). They also noted that nutrient uptake by macrophytes was negatively affected by increased velocity (see also Biggs 1996, p. 137-138 for description of relationship between velocity and nutrient uptake). Their results indicated that low current velocities result in macrophyte establishment and growth, and once established the nutrient concentrations in the sediments determine macrophyte abundance and density. In addition, once established, macrophytes further reduce velocity within the macrophyte bed (p. 254), which may lead to additional sediment deposition over the macrophyte bed with the potential to maintain or increase nutrient concentrations. At velocities greater than 1 m/s macrophytes were either absent or present in negligible quantities (p. 253). At velocities less than 1 m/s, even small velocity increases resulted in a decrease in biomass (p. 256). It will be difficult to calculate the decrease in velocity that will result from decreasing outflows from Swan Falls Dam from 5,000 to 3,900 cfs from April 1 to October 31. Extrapolation from Naymik and Hoovestol (2008, p. 32) for transit times in Swan Falls Reservoir suggests a decrease from 5,000 to 4,000 cfs could decrease velocity from 0.29 m/s to 0.23 m/s, but natural variations in the river bed affecting flow below Swan Falls Dam could insert considerable variation into this estimate. The research of Chambers et al. (1991) and others cited above indicate that even small changes in current velocity will affect macrophyte growth. The existing nutrient load plays a part in macrophyte presence below Swan Falls Dam, but under decreased flow macrophyte uptake of nutrients will be greater, leading to increased degradation and a reduction in suitable Snake River physa habitat below the dam, which will be an indirect effect to the species. As modeled by the Company (Bean and Stephenson 2011b, p. 6, 23-24), changes in flow—and therefore in current velocity—resulting from daily load-following fluctuations and license ramping rates attenuate in a downstream direction. Hence, decreasing current velocity, with an expected concomitant increase of macrophyte growth and resulting degradation of Snake River physa habitat, may provide a partial explanation for the lower numbers of Snake River physa recovered downstream of the Marsing area (only 31 percent of Snake River physa found in
39 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project the Action Area were recovered downstream of the Marsing area) as described in the Environmental Baseline (Section 2.4.1.1, Status of the Snake River physa in the Action Area). Our understanding of the effect of reduced current velocity on macrophyte growth is well- supported by research. There are factors which introduce uncertainty regarding how quickly increased degradation and reduction in Snake River physa habitat might occur in the Action Area. Big water years or rain-on-snow events may interrupt the process due to the scouring effects from high flows—high flows would likely remove macrophytes and reduce or ameliorate anoxic conditions in preferred substrates. However, if the effect of climate change projections (Section 2.6, Cumulative Effects) to decrease precipitation and increase air and water temperatures in the Pacific Northwest is reasonably accurate, the frequency of low water years compared to high water years may increase by the mid-twenty first century. Recent historical data shown in Figure 3 indicates that consecutive years with low flows of less than 5,000 cfs occurring for many consecutive days in summer is a real possibility for future water years. Over the length of the license, this may amplify the effects of low flows in degrading or reducing Snake River physa habitat in the Action Area, with subsequent significant impacts to the species’ population in the Action Area. The Service considers the impacts of low summer flows, nutrient load, and sediment deposition in the Action Area, particularly in the Walter’s Ferry Reach (RM 441.9-395.5), to be the most significant threat to the persistence of Snake River physa in the Action Area. Lack of data and the interactive nature of these factors make quantifying the contribution of the proposed summer 3,900 cfs discharge and the passing of sediment by Swan Falls Dam to this threat difficult. Nevertheless, the Service considers that the potential for these factors to contribute to declines in Snake River physa numbers and habitat in the Action Area over the length of the license is high, and that this would result in significant impacts to the species in the Action Area. Draft Recreation Plan Elements Construction of the proposed Swan Falls downstream boat ramp could result in a permanent loss of Snake River physa habitat. Draft design plans provided by the Company (Newton 2011, p. 11) indicate that at low flows of about 4,000 cfs, approximately one third of the length of the proposed boat ramp would be permanently underwater. This would represent a permanent removal of up to approximately 1,032 ft2 (about 0.96 percent of one ha) of potential Snake River physa habitat. The area of possible disturbance of potential Snake River physa habitat due to construction occurring at 4,000 and 8,000 cfs represents approximately 2.5 and 2.2 percent, respectively, of estimated Snake River physa habitat in the Swan Falls Reach, and 0.04 and 0.01 percent respectively, of total estimated Snake River physa habitat in the Action Area at those discharge levels (see Table 2). Disturbance of all but 1,032 ft2 of this area (the estimated underwater area of the completed boat ramp) would be temporary. The amount of habitat temporarily disturbed and permanently lost due to construction would represent an insignificant impact, compared to the estimated amount of habitat in the Action Area. 2.5.2 Effects of Interrelated or Interdependent Actions There were no interrelated or interdependent actions identified for this Project.
40 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2.6 Cumulative Effects The implementing regulations for section 7 define cumulative effects to include the effects of future State, tribal, local or private actions that are reasonably certain to occur in the action area considered in this Opinion. Future Federal actions that are unrelated to the proposed action are not considered in this section because they require separate consultation pursuant to section 7 of the Act. 2.6.1 Climate Change Rieman and Isaak (2010) synthesized much of the existing literature on effects of climate change on aquatic ecosystems in the Rocky Mountains, including the Pacific Northwest. Isaak et al. (2011) analyzed the effects of climate change on stream and river temperatures in the northwestern U.S. and discussed the implications to salmonid fish species. Mean annual air temperatures have been warming more rapidly over the Rocky Mountain West compared to other areas of the coterminous U.S., by about 0.4° C during the twentieth century (Rieman and Isaak 2010, p. 3). Precipitation appears to be increasing in extreme western and southeastern Idaho. Precipitation data is lacking for southern and central Idaho. However, data from stream flow gages in the Snake River watershed in western Wyoming, and southeast and southwest Idaho indicate that spring runoff is occurring between 1 to 3 weeks earlier compared to the early twentieth century (Rieman and Isaak 2010, p. 7). These altered hydrographs have been attributed to interactions between increasing temperatures (earlier spring snowmelt) and decreasing precipitation (declining snowpacks). Global Climate Models (GCM) project air temperatures in the western U.S. to further increase by 1 to 3° C by mid-twenty first century (Rieman and Isaak 2010, p. 5). GCMs are in closest agreement in their prediction of significant decreases in precipitation for the interior west. Areas in central and southern Idaho within the Snake River watershed are projected to experience moderate to extreme drought (Rieman and Isaak 2010, p. 5). The nature and timing of climate change impacts to Snake River physa habitat in the Snake River are difficult to predict. Isaak et al. (2011, p. 1) demonstrated statistically significant net warming trends at seven sites on unregulated rivers in Montana, Idaho, Washington, and Oregon, including one site on the Snake River at Anatone, Washington. (While acknowledging that the Snake River is generally highly regulated, the authors noted (p. 7) that the distance between the site at Anatone and the next reservoir upstream was well in excess of the spatial lag over which stream temperatures are correlated, i.e., it was assumed that river temperatures would have equilibrated to local climatic conditions before reaching the study site.) While suggestive that temperatures in the Snake River can be expected to rise with concurrent projected air temperature increases, Isaak et al. (2011, p. 1, 11) did not find statistically significant trends at regulated study sites, though temperature trends were qualitatively similar to those at unregulated sites. They attributed this to variation among sites resulting from differences in local management policies and effects of reservoirs. Deep reservoirs can have dampening effects on fluctuations in river water temperatures, but if air and water temperatures consistently increase in the watershed, over time water temperatures in regulated portions of the Snake River must rise, as well.
41 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
As discussed in Section 2.3.1.3, Snake River physa appear to tolerate the range of water temperatures experienced in the Snake River, including temperatures that exceed the CWA upper standard for cold water biota (22° C) by as much as 1.4° C. The lethal maximum temperature for Snake River physa is not known. Lysne and Koetsier (2006, p. 234) reported the only known thermal maximum temperature tolerances for Snake River snail species; the Utah valvata (Valvata utahensis) and the Idaho springsnail (Pyrgulopsis idahoensis) ceased activity above 31.70 C and 33.70 C, respectively. A similar maximum lethal temperature for Snake River physa could reasonably be expected in that range. However, if Snake River water temperatures continue to rise as a result of climate change, indirect impacts to the species might be expected at temperatures well below a lethal maximum through effects of warmer temperatures on metabolic processes, forage, primary production, dissolved oxygen levels, predator species, through possible synergy of higher temperatures with contaminants and pH, and on habitat suitability through increasing the frequency and duration of low summer flows and by prolonging the growing season for macrophytes. 2.6.2 Water Quality Factors impacting water quality in the Action Area, described in Section 2.4.1.2 (Factors Affecting the Species in the Action Area), are expected to continue for some time. Some TMDL water quality improvement projects are being implemented at this time. In addition, the State of Idaho and other federal, state, and private entities are discussing the potential for conducting coordinated efforts to address water quality issues in the mid- and lower-Snake River. Upon implementation, such are efforts are expected to improve water quality conditions over time. However the timing and successful implementation of ameliorative actions are unclear due to lack of specific proposed enhancement projects and lack of data indicating efficacy of those actions through the license period. Hence, we assume degradation of Snake River physa habitat in the Action Area will occur throughout the license period due to the interaction of continued high nutrient load with low flows and sediment deposition, and will incrementally contribute to an existing threat to the species in the Action Area. Recreation Other, relatively minor cumulative effects include impacts from recreation. Pollutants from boats (e.g., oil and fuel, battery acid) and sediment mobilization and crushing of individuals and eggs by swimmers and fishermen in the Action Area may degrade Snake River physa habitat and/or kill, harm, or harass individuals and eggs. Such impacts are anticipated to be localized. They contribute to negative conditions for the species and could exacerbate impacts resulting from the proposed action, but in general are considered to have relatively minor and insignificant impacts to the Snake River physa population in the Action Area.
2.7 Conclusion The Service has reviewed the current status of the Snake River physa, the environmental baseline in the Action Area, effects of the proposed action, and cumulative effects, and it is our conclusion that the proposed action is not likely to jeopardize the species’ continued existence. No critical habitat has been designated for the species, therefore none will be affected. Our conclusion is based on the following rationales. The highest known abundance and density of
42 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Snake River physa occurs in the Minidoka Reach. Based on prevailing conditions in the Minidoka Reach, the Service considers this population to be relatively stable. Based on the best available evidence for Snake River physa depth preferences (1.25–2.5 m), none of the potential direct and indirect effects to Snake River physa involving exposure of habitat, individuals, or eggs as a result of the proposed action are expected, separately or cumulatively, to rise to the level of impacting the species in the Action Area in a manner that would result in population level effects. Direct and indirect effects from construction of the Swan Falls downstream boat ramp are expected to be insignificant at the population level, due to the very small percentage of habitat involved, and because Snake River physa, if present in the construction footprint, are expected to occur in very low abundance. As indicated in Section 2.5.1.2 (Indirect Effects), the Service considers the impacts of low summer flows, nutrient load, and sediment deposition in the Action Area, particularly in the Walter’s Ferry Reach (RM 441.9-395.5), to be the most significant threat to the existence of Snake River physa in the Action Area. If precipitation, air, and water temperature climate change projections for the Pacific Northwest are reasonably accurate, decreased precipitation in the Snake River Basin could result in low summer flows becoming more common and normal for much of the length of the license. If this occurs for a number of consecutive years, combined with increased water temperatures and the above ongoing impacts, the Service considers it possible for the resulting degradation of Snake River physa habitat to result in significant impacts to the species in much of the Action Area, particularly in the Walter’s Ferry reach. The largest contribution of the proposed action to this scenario consists of the reduction in minimum summer flows to 3,900 cfs and the passing of sediment (including suspended nutrients) past Swan Falls Dam, and the resulting indirect effects. The paucity of information regarding Snake River physa numbers and distribution in the Action Area makes determination of the consequences of these indirect effects to the species’ persistence in the Action Area difficult. However, flows below 3,900 cfs have not been observed in recent history in the Action Area, and without long-term population monitoring data, our assumption is that Snake River physa have been present in the action area since the construction of Swan Falls Dam, albeit in low numbers potentially due to suboptimal habitat conditions. The conclusion of significant impacts to the species in the Action Area is based on these indirect effects to Snake River physa habitat, rather than solely on numbers of individuals affected. The process of jeopardy determination involves the assessment of the effects of the proposed action in combination with any cumulative effects to determine if the proposed action will appreciably reduce the likelihood of both the survival and recovery of the species. Survival is the condition in which a species continues to exist into the future while retaining the potential for recovery (U.S. Fish and Wildlife Service and National Marine Fisheries Service 1998, p. 4-35). Assuming that the Minidoka population remains stable, the species will persist into the foreseeable future (e.g., for the length of the new license) and retain the potential for recovery if the populations in the Action Area are measurably reduced. Therefore, although under some circumstances the proposed action might significantly contribute to effects leading to adverse effects to Snake River physa in much of the Action Area over the length of the new license, this is not expected to jeopardize the species’ continued existence and recovery.
43 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2.8 Incidental Take Statement Section 9 of the Act and Federal regulations pursuant to section 4(d) of the Act prohibit the take of endangered and threatened species, respectively, without specific exemption. Take is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to engage in any such conduct. Harm in the definition of take in the Act means an act which actually kills or injures wildlife. Such act may include significant habitat modification or degradation that results in death or injury to listed species by significantly impairing essential behavioral patterns, including breeding, feeding, or sheltering. Harass is defined by the Service as an intentional or negligent act or omission which creates the likelihood of injury to listed species by annoying it to such an extent as to significantly disrupt normal behavior patterns which include, but are not limited to, breeding, feeding, or sheltering. Incidental take is defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity. Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to and not intended as part of the agency action is not considered to be prohibited taking under the Act provided that such taking is in compliance with the terms and conditions of this Incidental Take Statement. The Commission has a continuing duty to regulate the activity covered by this incidental take statement. If the Commission fails to assume and implement the terms and conditions the protective coverage of section 7(o)(2) may lapse. In order to monitor the impact of incidental take, the Commission must report the progress of the action and its impact on the species to the Service as specified in the incidental take statement [50 CFR §402.14(i)(3)]. 2.8.1 Form and Amount or Extent of Take Anticipated 2.8.1.1 Considerations in Determining Amount of Take Quantification of anticipated take of Snake River physa resulting from the relicensing of the Swan Falls Project is difficult. The species appears to be quite rare in the Action Area in terms of numbers per habitat unit, although the maximum amount of Snake River physa habitat available in the Action Area, based on data from Table 2, is two-thirds larger than the entire surface area (based on area calculations using Google Earth tools) of the Minidoka Reach. However, as noted in previous sections, it is the Service’s position that there can be no meaningful density or abundance estimates made for the species in the Action Area from which to quantify take in terms of numbers of Snake River physa individuals or eggs. Neither the Company’s nor Gates and Kerans (2010) studies were designed to estimate abundance or population size. Gates and Kerans (2010) derived mean density estimates per m2 for the species in the Minidoka reach, but applying these estimates to degraded habitat in the Action Area would not be appropriate. Given the current state of knowledge regarding Snake River physa distribution and abundance, the Service does not have the ability to exempt take on the basis of numbers of individuals affected by the proposed action. Therefore the form and extent of take described below is based on Snake River physa habitat attributable to changes in flow. 2.8.1.2 Form and Extent of Take Take will result from the proposed action by three main effects pathways:
44 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Operations associated with load following and license ramping rates leading to habitat experiencing shear stress from rapidly increasing velocities due to the Swan Falls Project accommodating changes (ramping rates) in flow from upstream of the Project, and exposure of habitat when it is dewatered due to load following; Reduction of the summer minimum flow from 5,000 cfs to 3,900 cfs, with reduced current velocity leading to proliferation of macrophyte growth and concomitant impacts to Snake River physa habitat; and Construction related impacts associated with the development of the Swan Falls boat ramp. Take may occur from effects to Snake River physa or eggs in habitat dewatered or otherwise impacted by load following and implementation of the license ramping rates, as outlined in Sections 2.5.1.1 (Direct Effects) and 2.5.1.2 (Indirect Effects). Take is anticipated to occur in the form of mortality, harm and harassment annually through the term of the license. Mortality of Snake River physa or eggs may result from exposure to extreme air temperatures and desiccation during periods of dewatering. Mortality and harm to Snake River physa or eggs due to crushing may result from mobilization of substrates during rapid increases in flow and current velocity. Harm and harassment to Snake River physa juveniles or adults may occur if they are injured when mobilized due to high shearing stress experienced during rapid increases in flow and current velocity, or if mobilized individuals are subsequently transported out of suitable habitat. While take of Snake River physa and habitat in these forms might occur throughout the Action Area, we anticipate the potential for take in these forms to decrease in a downstream direction as stated in Sections 2.5.1.1 and 2.5.1.2 (Direct Effects and Indirect Effects) as impacts from daily load-following and license ramping rates attenuate with distance from the discharge point at Swan Falls Dam. Given Snake River physa depth preferences, the frequency and amount of take that could result from these effects is anticipated to be low. Therefore, take that results from the effects of operations (flow velocities and habitat exposure associated with flows from 3,900 to 5,000 cfs) is exempted within the action area from Swan Falls Dam to the tail of Brownlee Reservoir. The largest amount of take is expected to occur due to the indirect effects of proposed minimum summer flows concentrating the existing nutrient load in the Snake River within the Action Area, as described in Section 2.5.1.2 (Indirect Effects). Combined with the effects of projected climate change and transport of sediment past Swan Falls Dam, this will contribute to proliferation of macrophyte growth over preferred substrates resulting in further velocity reduction, associated sediment deposition, anoxic conditions and H2S production, and leading to degradation of habitat from Swan Falls Dam to the tail of Brownlee Reservoir over the length of the license. Take of Snake River physa that results from proposed minimum summer flow and from sediment deposition over preferred substrates is anticipated to occur in the form of mortality, harm and harassment. Mortality of Snake River physa eggs and harm of Snake River physa juveniles and adults may result from sediment deposition (suffocation, crushing) and H2S toxicity. Harassment of Snake River physa may result from sediment deposition and proliferation of macrophytes that render preferred substrates unsuitable as habitat for foraging, reproduction, or shelter from predators or extreme environmental conditions. As indicated in Section 2.5.1.2 (p. 39-40, Indirect Effects), baseline conditions due to attenuation of current velocity at low flows may have resulted in considerable degradation of habitat and
45 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project lower abundance of Snake River physa downstream of the Walter’s Ferry Reach. Consequently, there is lower potential for take resulting from proposed minimum summer flow in this area. Therefore, take is exempted that results from the proposed minimum summer flows (reduction from 5,000 cfs to 3,900 cfs) upstream and downstream of the Walter’s Ferry Reach. However, attenuation will be less and velocities will be higher closer to the point of discharge. As suggested by the higher abundance of Snake River physa found in the Walter’s Ferry Reach, velocities have generally been sufficient in this area to sustain habitat in more suitable condition, particularly in the Marsing area. Sixty-nine percent of Snake River physa found in the Action Area were recovered from the 41 percent of the Action Area contained in the Walter’s Ferry Reach. While impacts to Snake River physa habitat resulting from implementation of proposed minimum summer flow may be less in the Walter’s Ferry Reach compared to areas further downstream, as indicated in Sections 2.3.4 (Status and Distribution) and 2.4.1.2.1 (Water Quality), habitat degradation has been documented in this reach upstream of Marsing. The reduction in flow from 5,000 cfs to 3,900 cfs will degrade habitat over baseline conditions resulting in take of Snake River physa using habitat as a surrogate. Flow volumes below 3900 cfs may further degrade habitat conditions and cause take that has not been evaluated through this Opinion. Therefore, incidental take in the action area resulting from the proposed action shall not be authorized or allowed under this Incidental Take Statement under either of the following conditions: Inflow to the Swan Falls Project is less than 3,900 cfs, discharge is less than 3,900 cfs as measured at the Murphy gage, and these measurements occur as a single event over two consecutive years, or as two separate events in the same year. o Discharge will be measured over a 3 day period to ensure that the daily minimum discharge is at least 3,900 cfs from April 1 to October 31. Inflow to the Swan Falls Project is greater than or equal to 3,900 cfs and the discharge is less than 3,900 cfs as measured at the Murphy gage.
Incidental take in the action area resulting from the proposed action is otherwise exempted when discharge from the project is greater than or equal to 3,900 cfs as measured at the Murphy gage. Given the small amount of Snake River physa habitat associated with the proposed Swan Falls downstream boat ramp relative to the amount of habitat estimated in the Action Area, and recognizing that Snake River physa, if present in the construction area, are expected to be very low in numbers, take of all Snake River physa associated with construction activities, in the form of harassment, harm, and mortality, is exempted during a single construction season within the construction footprint of the boat ramp. 2.8.2 Effect of the Take In the accompanying Opinion, the Service determined that this level of anticipated take is not likely to jeopardize the continued existence of the Snake River physa across its range. The Service anticipates that project activities, when combined with Snake River impaired ecological condition and climate change projections, may have severe adverse effects to the species. It is our opinion, however, that while the project will not promote recovery of the Snake River physa, and will negatively affect the species’ population in the Action Area, the effect is not at a level
46 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project that would reduce the likelihood of its survival and recovery. The Project will not reduce the reproduction, status, or distribution of the Snake River physa to a point where the likelihood of its survival and recovery will be appreciably reduced across its range, given the species’ current status. Specific rationales for our conclusions are provided in the previous sections (2.5 through 2.7). 2.8.3 Reasonable and Prudent Measures The Service concludes that the following reasonable and prudent measures are necessary and appropriate to minimize the take of Snake River physa caused by the proposed action: 1. Minimize the potential for take of Snake River physa snails from proposed action elements involving ramping rates and minimum flows by conducting surveys in the Action Area designed to locate Snake River physa individuals or colonies. 2. If Snake River physa individuals or colonies can be consistently located in the Action Area, collect such information as will be useful in determining effects of proposed operations to the species, and that can be gathered with minimal effort and cost. 3. Minimize the potential for take of Snake River physa from construction activities. 4. Within its legal authorities, maintain Snake River minimum flows of 3,900 cfs as per Swans Falls Agreement. 2.8.4 Terms and Conditions In order to be exempt from the prohibitions of Section 9 of the Act, the Commission must comply with the following terms and conditions which implement the reasonable and prudent measures described above and outline required reporting and monitoring requirements. The following terms and conditions are non-discretionary: 1a. Commit to a series of aquatic surveys targeted primarily to areas of previously known Snake River physa concentrations in the Action Area in order to maximize the potential for consistently locating Snake River physa individuals or colonies, over a specified number of years to be agreed upon in cooperation with the Service. Survey areas and protocols will be determined and developed in cooperation with the Service. The Commission must obtain all required Federal and State collection permits.
1b. Due to the difficulty in identifying Snake River physa in the field, potential Snake River physa specimens will initially need to be sacrificed and transported elsewhere for identification. Therefore, establish a voucher system to account for Snake River physa collections. If the species is found in sufficient numbers such that laboratory and field experience improve identification skills to the point where specimens can be positively identified in the field, the voucher system may be discontinued.
2a. If Snake River physa are found and can be consistently relocated in the Action Area, establish a regular monitoring system to track population trends. Monitoring should include some measure of cobble/pebble/gravel habitat condition, with population trend and habitat monitoring protocols to be developed in cooperation with the Service.
47 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2b. Develop protocols, in cooperation with the Service, to monitor for increases in sediment (fines) deposition and increases in macrophyte beds.
3. Schedule construction activities for the downstream boat ramp site to coincide with the least minimum flows possible given power demands, construction logistics, and water year consideration. 4. If flows are less than 3,900 cfs as measured at the Murphy Gage, the Commission (Company) must exercise its rights under the Swans Falls Agreement and Idaho law to ensure that the minimum flows are maintained. 2.8.5 Reporting and Monitoring Requirements In order to monitor the impacts of incidental take, the Commission must report the progress of the action and its impact on the species or its habitat to the Service as specified in this incidental take statement [(50 CFR 402.14 (i)(3)].
2.9 Conservation Recommendations Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the purposes of the Act by carrying out conservation programs for the benefit of endangered and threatened species. Conservation recommendations are discretionary agency activities to minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to help implement recovery programs, or to develop new information on listed species. If monitoring shows a declining population trend in the Action Area, engage in discussion with the Service to determine if project activities are contributing to the decline; and, to discuss the potential for modifying project activities in order to minimize factors contributing to the decline.
2.10 Reinitiation Notice This concludes formal consultation on the Swan Falls Hydroelectric Project. As provided in 50 CFR §402.16, reinitiation of formal consultation is required where discretionary Federal agency involvement or control over the action has been maintained (or is authorized by law) and if: 1. The amount or extent of incidental take, as identified in Section 2.8.1.2, is exceeded. 2. New information reveals effects of the agency action that may affect listed species or critical habitat. 3. New information reveals effects of the agency action that may affect listed species in a manner or to an extent not considered in this Opinion. 4. The agency action is subsequently modified in a manner that causes an effect to the listed species or critical habitat that was not considered in this Opinion. 5. A new species is listed or critical habitat designated that may be affected by the action. In instances where the amount or extent of incidental take is exceeded, any operations causing such take must cease pending reinitiation.
48 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
3. LITERATURE CITED
3.1 Published Literature Alexander, J.E., Jr., and A.P. Covich. 1991. Predator avoidance by the freshwater snail Physella virgata in response to the crayfish Procambarus simlans. Oecologia 87:435-442. Anglin, D.R., T.R. Cummings, and A.E. Ecklund. 1992. Swan Falls Instream Flow Study. Lower Columbia River Fishery Resource Office, Vancouver, Washington. AFF1-FRO-92-14. Bean, B., and M. Stephenson. 2011a. Biological Assessment for the Snake River Physa: Lower Salmon Falls FERC Project No. 2061-004, and Bliss FERC Project No. 1975-014. Idaho Power Company, Boise, Idaho. Bean, B., and M. Stephenson. 2011b. Swan Falls Biological Assessment for the Snake River physa. Idaho Power Company, Boise, Idaho. Biggs, B.J.F. 1996. Hydraulic habitat of plants in streams. Regulated Rivers: Research & Management 12:131-144. Blinn, D.W., J.P. Shannon, L.E. Stevens, and J.P. Carder. 1995. Consequences of fluctuating discharge for lotic communities. Journal of North American Benthological Society 14(2):233-248. Boulton, A.J., C.G. Peterson, N.B. Grimm, and S.G. Fisher. 1992. Stability of an aquatic macroinvertebrate community in a multiyear hydrologic disturbance regime. Ecology 73(6):2192-2207. Brink, S.R. 2008. Fish habitat vs. flow descriptions in the Swan Falls Reach of the Snake River. Technical Report Appendix E.2.3.-A. Swan Falls Project, FERC No. 503. Idaho Power Company. Bunn, S.E., and A.H. Arthington. 2002. Basic principles and ecological consequences of altered flow regimes for aquatic biodiversity. Environmental Management 30(4):492-507. Chambers, P.A., E.E. Prepas, H.R. Hamilton, and M.L. Bothwell. 1991. Current velocity and its effect on aquatic macrophytes in flowing waters. Ecological Applications 1(3):249-257. DeWitt, R.M. 1954. Reproductive capacity in a pulmonate snail (Physa gyrina Say). The American Naturalist 88:159-164. DeWitt, R.M. 1955. The ecology and life history of the pond snail Physa gyrina. Ecology 36(1): 40-44. Dillon, R.T.J. 2000. The Ecology of Freshwater Molluscs. Cambridge University Press, Cambridge, United Kingdom. Dillon, R.T.J. 2006. Freshwater Gastropods. Pages 251-259 In C.F. Sturm, T.A. Pearce, and A. Valdes, eds. The Mollusks: A Guide to their Study, Collection, and Preservation. Universal Publishers, Boca Raton, Florida.
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Dillon, R.T.J., T. Earnhardt, and T. Smith. 2004. Reproductive isolation between Physa acuta and Physa gyrina in joint culture. American Malacological Bulletin 19: 63-68. Dillon, R.T.J., J.D. Robinson, T.P. Smith, and A.R. Wethington. 2005. No reproductive isolation between freshwater pulmonate snails Physa virgata and P. acuta. The Southwestern Naturalist 50(4):415-422. Escobar, J.S., B. Facon, P. Jarne, J. Goudet, and P. David. 2009. Correlated evolution of mating strategy and inbreeding depression within and among populations of the hermaphroditic snail Physa acuta. Evolution 63(11): 2790-2804. Federal Energy Regulatory Commission. 2004. Order Issuing New License: C.J. Strike Hydroelectric Project; FERC Project No. 2055-010. Idaho. pp. 51. Federal Energy Regulatory Commission. 2010. FEIS for Hydropower License: Swan Falls Hydroelectric Project; FERC Project No. 503-048. Idaho. pp. 126. Gates, K.K., and B.L. Kerans. 2010. Snake River physa, Physa (Haitia) natricina, survey and study: Final Report. Department of Ecology, Montana State University, Reclamation Agreement 1425-06FC1S202, Bozeman, Montana. Gates, K.K., and B.L. Kerans. 2011. Snake River Physa, Physa (Haitia) natricina, identification and genetics. Department of Ecology, Montana State University, Bozeman, Montana 59717, USA. Grafe, C.S. editor. 2002. Idaho River Ecological Assessment Framework: An Integrated Approach. Idaho Department of Environmental Quality, Boise, Idaho. Groves, P.A., and J.A. Chandler. 2005. Habitat quality of historic Snake River fall chinook salmon spawning locations and implications for incubation survival. Part 2: Intra-gravel water quality. River Res. Applic. 21:469-483. Holomuzki, J.R., and B.J.F. Biggs. 1999. Distributional responses to flow disturbance by a stream-dwelling snail. Oikos 87:36-47. Holomuzki, J.R., and B.J.F. Biggs. 2003. Sediment texture mediates high-flow effects on lotic macroinvertebrates. J. Mammorth American Benthological Society 22(4):542-553. Howell, J. 2010. The distribution of phosphorus in sediment and water downstream from a sewage treatment works. Bioscience Horizons 3(2):113-123. Idaho Department of Environmental Quality (IDEQ). 2003. Mid Snake River/Succor Creek subbasin assessment and total maximum daily load. Revised Final, Boise, Idaho. Idaho Department of Environmental Quality (IDEQ). 2004. Snake River Hells Canyon Total Maximum Daily Load. Section 4.0.2.7, Implementation of phosphate, p. 448. Appendix 1. Idaho Department of Environmental Quality (IDEQ), Boise, Idaho. Isaak, D.J., S. Wollrab, and G. Chandler. 2011. Climate change effects on stream and river temperatures across the northwest U.S. from 1980-2009 and implications for salmonid fishes. Climatic Change Online First. Keebaugh, J. 2009. Idaho Power Company Physidae 1995-2003. Review Notes. Orma J. Smith Museum of Natural History, The College of Idaho. May. pp 126.
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Kosterman, M.A., D. Sharp, and R. Remington. 2008. Idaho Assessment of Ecological Condition: A Part of the EMAP Western Pilot Project. Idaho Department of Environmental Quality, Boise, Idaho. Link, P.K., D.S. Kaufman, and G.D. Thackray. 1999. Field guide to Pleistocene Lakes Thatcher and Bonneville and the Bonneville Flood, southeastern Idaho. Pages 251-266 In S.S. Hughes, and G.D. Thackray, eds. Guidebook to the Geology of Eastern Idaho, Idaho Museum of Natural History, Pocatello, Idaho. Liu, H.P., and R. Hershler. 2009. Genetic diversity and population structure of the threatened Bliss Rapids snail (Taylorconcha serpenticola). Freshwater Biology 54:1285-1299. Lysne, S., and P. Koetsier. 2006. Growth rate and thermal tolerance of two endangered Snake River snails. Western North American Naturalist 66:230-238. Naymik, J., and C. Hoovestol. 2008. Descriptive water quality of the Swan Falls Project. Idaho Power Company. Technical Report Appendix E.2.2-A, Swan Falls Project, FERC No. 503, Boise, Idaho. Newton, P. 2011. Responses to FERC additional information request: Biological Assessment, section 7 ESA. Swan Falls (FERC Project No. 503). Idaho Power Company. Peck, D., D. Averil, A. Herlihy, R. Hughes, P. Kaufmann, D. Klemm, J. Lazorchak, F. McCormick, S. Peterson, M. Cappaert, T. Magee, and P. Monaco. 2005. Environmental monitoring and assessment program - surface waters western pilot study: Field operations manual for non-wadeable rivers and streams. U.S. Environmental Protection Agency, Report EPA 600/R-05/xxx, Washington, D.C. Reice, S.R., R.C. Wissmar, and R.J. Naiman. 1990. Disturbance Regimes, Resilience, and Recovery of Animal Communities and Habitats in Lotic Ecosystems. Environmental Management 14(5):647-659. Remington, R., and M.A. Kosterman. 2008. Idaho Rivers EMAP. Pages 37-75 In M.A. Kosterman, D. Sharp, and R. Remington, eds. Idaho Assessment of Ecological Condition: A Part of the EMAP Western Pilot Project, Idaho Department of Environmental Quality, Boise, Idaho. Richards, D.C. 2004. Competition between the threatened Bliss Rapids snail, Taylorconcha serpenticola (Hershler et al.) and the invasive, aquatic snail Potamopyrgus antipodarum (Gray). Ph.D. dissertation, Montana State University, Bozeman, Montana. November. Richards, D.C., and T. Arrington. 2006. Effects of Atmospheric Exposure on Taylorconcha serpenticola Survivability: Field Studies. In: W. Clark (ed.) Effects of Hydropower Load- Following Operations on the Bliss Rapids Snail in the Mid-Snake River, Idaho: Appendix H. Idaho Power Company, Boise, Idaho. Richards, D.C., and T. Arrington. 2008. Threatened Bliss Rapids snail’s susceptibility to desiccation: Potential impact from hydroelectric facilities. American Malacological Bulletin 24:91-96.
51 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Richards, R.R., and B.L. Kerans. 2008. Laboratory Experiments Simulating the Effects of Rapid River-stage Fluctuations on Taylorconcha serpenticola, the Threatened Bliss Rapids Snail. In: W. Clark (ed.). Effects of Hydropower Load-Following Operations on the Bliss Rapids Snail in the Mid-Snake River, Idaho: Appendix F. Idaho Power Company, Boise, Idaho. Rieman, B.E., and D.J. Isaak. 2010. Climate change, aquatic ecosystems, and fishes in the Rocky Mountain West: Implications and alternatives for management. Gen. Tech. Rep. RMRS- GTR-250. U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins, Colorado. Rogers, D.C., and A.R. Wethington. 2007. Physa natricina Taylor 1988, junior synonym of Physa acuta Draparnaud 1805 (Pulmonata: Physidae). Zootaxa 1662:45-51. Rosenegger, D., S. Roth, and K. Lukowiak. 2004. Learning and memory in Lymnaea are negatively altered by acute low-level concentrations of hydrogen sulfide. The Journal of Experimental Biology 207:2621-2630. Rugg, D.J. 2003. TableSim--A program for analysis of small-sample categorical data. U.S. Department of Agriculture, Forest Service, North Central Research Station, Gen. Tech Rep. NC-232, St. Paul, Minnesota. Steinman, A.D., and P.J. Mulholland. 1996. Phosphorus limitation, uptake, and turnover in stream algae. In (F.R. Hauer and G.A. Lamberti, eds.), Methods in Stream Ecology. Pages p. 161-162 In Academic Press, Inc., San Diego. Stephenson, M. 2009. Laboratory and Field Desiccation Studies on the Bliss Rapids Snail. Chapter 2. Information Need II. In: W. Clark (ed.). Effects of Hydropower Load- Following Load Operations on the Bliss Rapids Snail in the Mid-Snake River. Idaho Power Company, Boise, Idaho. Taylor, D.W. 1988. New species of Physa (Gastropoda: Hygrophila) from the western United States. Malacological Review 21: 43-79. Taylor, D.W. 2003. Introduction to Physidae (Gastropoda: Hygrophila): Biogeography, classification, morphology. International Journal of Tropical Biology and Conservation Supplement 1:1-287. U.S. Department of the Interior. 1956. Compilation of records of surface waters of the United States through September 1950. Part 13. Snake River Basin. U.S. Environmental Protection Agency. 2008. EPA's 2008 Report on the Environment. National Center for Environmental Assessment, Washington, D.C. Available from the National Technical Information Service, Springfield, Virginia, and online at http://www.epa.gov/roe (last accessed January 19, 2012), EPA/600/R-07/045F. U.S. Fish and Wildlife Service. 1992. Determination of endangered and threatened status for five aquatic snails in South Central Idaho. Federal Register 57(240):59244-59257. U.S. Fish and Wildlife Service. 1995. Snake River Aquatic Species Recovery Plan. U.S. Fish and Wildlife Service, pp. 92.
52 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
U.S. Fish and Wildlife Service. 2005. Biological Opinion for Bureau of Reclamation operations and maintenance in the Snake River basin above Brownlee Reservoir. U.S. Fish and Wildlife Service, Snake River Fish and Wildlife Office, Boise, Idaho. pp. 342. U.S. Fish and Wildlife Service, and National Marine Fisheries Service. 1998. Endangered Species Act consultation handbook: Procedures for conducting section 7 consultations and conferences. U.S. Fish and Wildlife Service and National Marine Fisheries Service. Vaughn, B., P. Dionne, C. Hui, L. Nguyen, D. Search, and Y. Zhang. 2008. Land snails (& other air-breathers in Pulmonata subclass & Sorbeconcha clade), Available: http://shells.tricity.wsu.edu/ArcherdShellCollection/Gastropoda/Pulmonates.html (last accessed January 19, 2012) Welcker, C., J. Conner, M. Butler, and S. Parkinson. 2009. Channel unit classification, Mid- Snake River, Idaho. Appendix L, In: Effects of hydropower load-following operations on the Bliss Rapids snail in the Mid-Snake River, Idaho. W.H. Clark, editor. Idaho Power Company, Boise, Idaho. Wethington, A.R. 2004. Family Physdae: A supplement to the workbook accompanying the FMCS Freshwater Identification Workshop, University of Alabama, Tuscaloosa, University of Alabama.
3.2 In Litteris References Burch, J.B. 2008. Physa natricina and the snail family Physidae in North America. Museum of Zoology, University of Michigan. Powerpoint presentation to the Bureau of Reclamation, Boise, Idaho. May 1, 2008. pp. 71. Burch, J.B. 2010. Comparative morphology of Physa (Haitia) natricina Taylor 1988, an endangered freshwater snail. Museum of Zoology, University of Michigan, Ann Arbor. Powerpoint presentation, June 28, 2010. pp. 66. EcoAnalysts, Inc. 2011. IDP mid-Snake Frest Physa samples 2011 (IDP 2003 curated Physa). Spreadsheet listing results of taxonomic identification for Physa spp. from unsorted samples collected by T.J. Frest and E. Johannes from river mile 589-526.5. Frest, T.J. 1991. Letter to Jay Gore, U.S. Fish and Wildlife Service, Boise Field Office. A review of two studies which reported the presence of Snake River physa upstream of prior reports. June 2, 1991. pp. 16. Frest, T.J., P.A. Bowler, and R. Hershler. 1991. The ecology, distribution and status of relict Lake Idaho mollusks and other endemics in the middle Snake River. pp. 18. Frest, T.J., and E. Johannes. 2004. Survey of selected Snake River sites for Haitia natricina (Taylor, 1998). pp. 13. Kerans, B., and K. Gates. 2008. Snake River Physa natricina sampling below Minidoka Dam: 2006 interim report. Montana State University, Department of Ecology, Bozeman, Montana. pp. 19.
53 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Newman, R. 2011. Email exchange and notes from a conversation with Ryan Newman, biologist with the Bureau of Reclamation, Minidoka Dam, regarding sediment and macrophyte growth downstream of Minidoka Dam where Snake River physa were found. December 7, 2011. Pentec Environmental, Inc. 1991. Distribution survey of five species of mollusks proposed for endangered status in the Snake River, Idaho during March 1991. Final Report Pentec Project Number 00070-001. Prepared for Idaho Farm Bureau. Boise, Idaho. pp. 22. Stephenson, M. 2011. Notes from a conversation with Mike Stephenson, senior aquatic biologist with Idaho Power Company, regarding sediment transport in Swan Falls Reservoir and design of Swan Falls power plant and spill gates. December 7, 2011. Taylor, D.W. 1982a. Distribution of characteristic stream-dwelling species of freshwater mollusks in the Snake River of southwestern Idaho. Prepared for the U.S. Fish and Wildlife Service. October 29, 1982. Taylor, D.W. 1982b. Status report on Snake River Physa snail. Prepared for the U.S. Fish and Wildlife Service. July 1, 1982. Taylor, D.W. 2004. Letter to Jeffery L. Foss, Field Supervisor, Snake River Fish and Wildlife Office, U.S. Fish and Wildlife Service, reporting general areas of Physa natricina collections made in the Bliss rapids area and suggesting other possible locations of the species in Idaho. January 26, 2004.
54 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
4. APPENDIX APPENDIX A Analysis of Snake River physa (Haitia (Physa) natricina) substrate preference and distribution in the Snake River. Introduction The highest density and abundance of Snake River physa have been found by (Gates and Kerans 2010, p. 20, 23) on pebble to gravel substrates (gravel to small gravel in their study) below Minidoka Dam. Their study resulted in the most detailed information to date on the species’ density and distribution in occupied habitat. Gates and Kerans (2010, p. 7-40) collected 115 and 128 0.25 square meter (m2) dredge samples on 15 and 16 transects in 2006 and 2007, respectively, and identified 95 (2006) and 122 (2007) live specimens of Snake River physa in the 6-mile reach (RM 669 to 675) below Minidoka Dam. In 2008 they moved the study area downstream (RM 663 to 668) to reduce take of Snake River physa. This reach, located in the upper end of the Milner Reservoir, was more lentic in character, and Gates and Kerans (2010) collected only 18 Snake River physa in 113 dredge samples from this reach. Gates and Kerans (2010) study was designed in part to examine effects of annual seasonal de- watering of the river on the mollusk community below Minidoka Dam, so some samples were collected in areas that are de-watered for approximately 6 months each year. Live Snake River physa were collected in nearly 20 percent of all samples, but occurred in over 28 percent of samples taken from permanently watered areas (Snake River physa were found in only 5.8 percent of samples from the seasonally dewatered areas) (Gates and Kerans 2010, p. 20). Three samples collected in 2006 contained the highest recorded densities of Snake River physa, ranging from 40 to 64 individuals per m2 (Kerans and Gates 2008, in litt. p. 8). Density of live Snake River physa in the remainder of samples from 2006 was less than or equal to 32 per m2. Gates and Kerans (2010, p. 7-40) surveyed some of the same transects in both 2006 and 2007, and found that Snake River physa persisted in the same areas across sample years, were absent from the same areas across sample years, but also were found on previously unoccupied transects in 2007, suggesting that dispersal also occurred. Gates and Kerans (2010, p. 7-40) concluded that their results suggest that Snake River physa occurred throughout the study reach in a diffusely distributed population, and that they rarely exhibit high density colony behavior. Gates and Kerans (2010, p. 39) pointed out that the presence and high density of Snake River physa in the gravel substrate below Minidoka Dam may not necessarily correlate with the species’ optimal habitat. Gravel was the predominant substrate in the reach below Minidoka Dam. Gates and Kerans (2010, p. 37, 39) cautioned that high density below Minidoka Dam could just reflect an area where Snake River physa have been able to persist in the most numbers so far found. For a species of which so few specimens have been documented and lacking evidence of similar substrate use elsewhere in the river, this caution is valid. Between 1995 and 2003, Idaho Power Company (Company) collected substrate and benthic invertebrate samples from every Snake River mile between Brownlee Dam (RM 344) and the Snake River/Box Canyon confluence (RM 588), plus six river miles in the Bruneau River Arm of
55 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
C.J. Strike Reservoir. In addition, the Company conducted extensive surveys beginning in 2005 in the reaches between C.J. Strike Reservoir and Lower Salmon Falls Dam for use in consultation for the relicensing of dams on the mid-Snake River. The early sampling effort did not target Snake River physa specifically, but was an attempt to characterize river habitats, sample for all snail species listed during this time period, as well as support various Company in- water projects, including hydropower facility relicensing. Sampling beginning in 2005 targeted Bliss Rapids snail (Taylorconcha serpenticola) for use in consultation for relicensing of hydropower facilities on the mid-Snake River. However, data recorded for both sampling periods included dominant and co-dominant substrates (defined by the Company as the two most common substrate types in the vicinity of a sample) and water depth at the time and point of sampling. Number of samples varied among reaches depending on safety considerations, water depth, and the Company’s needs. Areas of the river bed accessible for sampling within these constraints varied between high and low water years, and with seasonal variations in water depth. Hence, sampling was not random and varied in intensity, and substrates recorded can be regarded as characterizing only a small portion of the river bed. However, substrates recorded in at least some reaches may characterize the river bed between 0 and 7 feet in depth at a given river stage height. The area in this depth range is also the area most likely to be affected by management actions that control water levels. In coordination with Company biologists, the Service has analyzed data from Gates (unpublished data) and the Company’s two sampling periods to assess Snake River physa substrate preference and to begin characterizing substrate availability in river reaches at the depths at which sampling was conducted. The analysis is presented in two sections. Section A consists of two analyses. We first analyze Snake River physa substrate selection using Company data from the area of the Snake River downstream of C.J. Strike Reservoir. The analysis of Snake River physa substrate selection downstream of Minidoka Dam that follows is based on unpublished data from Gates, followed by a discussion comparing results from both areas. Section B uses Company data and analyzes substrate occurrence and distribution in the reach between Lower Salmon Falls Dam and the C.J. Strike Reservoir, which includes the Snake River physa type locality. The analysis in Section B addresses the question of why the species might so seldom be found in the section of the Snake River from which it was first identified. Section A Methods—Company Data The entire data set encompassing both sampling periods was comprised of over 17,000 samples. Using Microsoft Excel tools, Company biologists sorted the data from Lower Salmon Falls Dam to Weiser, Idaho, to eliminate duplicate sampling and remove samples for which substrates had not been recorded. The resulting final substrate data set (or final data set) consisted of 943 unique records taken from both sampling periods, and included those samples in which Snake River physa were found. The 51 Snake River physa collected live by the Company were found in the 1995 to 2003 sampling period. Of this number, 46 specimens were collected between C.J. Strike Dam and Weiser, Idaho. Of the remainder, one was a specimen from below Bliss Dam for which identification as Snake River physa is somewhat uncertain, two came from the Bruneau River Arm of C.J. Strike Reservoir, and substrates were not recorded for two specimens (since
56 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project substrates were not recorded for these latter two specimens, these samples were likely eliminated from the final substrate data set, hence we eliminated them from the Snake River physa data set as well). Our analysis of Snake River physa substrate preference has been conducted using data from the reach between C.J. Strike Dam and Weiser, less the area in Swan Falls Reservoir (hereafter labeled the C.J. to Weiser Reach, [RM 494-469, and RM 458.4-351]). This is the reach where 46 of the 51 live specimens collected by the Company were found. In this analysis we did not include data from the Bruneau River or from the reach between Lower Salmon Falls Dam and C.J. Strike Reservoir for the following reasons: we have very limited information on substrates from the Bruneau River, and no substrate or benthic invertebrate surveys on the Bruneau have been conducted or analyzed for the presence of Snake River physa other than the Company’s life history site where the two specimens were found; and, the identity of the specimen from below Bliss Dam is uncertain, precluding definite association between Snake River physa presence and substrates in that reach. A contingency table approach (testing for differences between observed and expected values of categorical variables) was used to test for Snake River physa substrate preference in the C.J. to Weiser Reach, for which the Company’s decision to record dominant and co-dominant substrates for each sample became problematic. Relative area of dominant and co-dominant substrates (e.g., cobble/pebble) for a given sample was not quantified, and so little more information could be extracted from this description other than that cobble and pebble were the two most common substrates in the vicinity of the sample, with the dominant substrate (cobble) the most common. However, using only dominant substrates (cobble) would eliminate from the analysis the potential influence on Snake River physa presence of an important descriptor (pebble) of the river bottom in the sample area. Substrates recorded in the C.J. to Weiser reach consisted of seven basic types, in order of decreasing particle size: Boulder Cobble Pebble Gravel Sand Silt Clay The dominant/co-dominant substrate pairs present in the C.J. to Weiser reach were determined. Since there were also samples in which only a single substrate type (always labeled as dominant) was recorded, pairing of dominant/co-dominant substrates had the effect of increasing the total substrate categories for analysis of this reach from 7 to 21: Boulder/Pebble Boulder/Gravel Boulder/Sand Boulder/Silt Cobble Cobble/Pebble
57 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Cobble/Gravel Cobble/Sand Cobble/Silt Cobble/Clay Pebble Pebble/Gravel Pebble/Sand Pebble/Silt Gravel Gravel/Sand Gravel/Silt Gravel/Clay Sand Sand/Silt Silt Silt/Clay Clay When determining frequencies of each substrate category, dominant/co-dominant substrates were treated equally. That is, frequency (a count) of a substrate pair (or category, e.g., cobble/pebble) was tallied as the sum of samples in which cobble or pebble occurred as either dominant or co- dominant (e.g., as cobble/pebble or pebble/cobble), based on the previously stated rationale: that dominant and co-dominant substrates were not quantified, but eliminating co-dominants would remove important information from the analysis. Over half (14) of the substrate categories had frequencies of less than five. In a contingency table approach, substrate types are treated as categorical variables. The premise for testing for habitat selection by a species is that a species not demonstrating habitat selection will utilize (prefer or select for) all researcher-determined habitats, and can be counted in those habitats, in the same proportions in which the habitats occur. A chi-squared (also denoted as X2) goodness of fit test is commonly used to test for differences between the observed abundance of a species per habitat and its expected (theoretical) abundance if no habitat selection is occurring. The chi-squared test works well for categorical data sets with large sample sizes. However, a large number of categorical variables with a high proportion occurring in frequencies of five or less often cannot effectively be analyzed using chi-square analysis. Such a data set has a poor approximation to the chi-square distribution. (In some situations a large number of variables may also reduce the power of the test, increasing the probability of a Type I error, where a significant difference between observed and expected values is found when no difference in fact exists). There are several alternative tests including the following: G-tests (G2) or log-likelihood tests (although small sample sizes may also be problematic); Exact Fisher’s tests and exact multinomial tests, both of which involve factorial calculations which many computers will have difficulty running if the number of variables is large; and Randomization tests, which usually involve Monte Carlo type simulations.
58 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
The Service made the a priori decision to lump some of the substrate categories, based largely on the work of Gates and Kerans (2010), in order to reduce the number of variables. Gates and Kerans (2010) found few Snake River physa on large substrates (e.g., bedrock), and few on fines such as silt. Hence, in the C.J. to Weiser Reach all boulder categories (boulder/pebble, boulder/gravel, boulder/sand, boulder/silt) were collapsed into a category called boulder. All silt and clay categories (silt, silt/clay, clay) were collapsed into a category called silt. Cobble/silt and cobble/clay were collapsed into cobble/silt, and gravel/silt and gravel/clay were collapsed into gravel/silt. This resulted in 16 substrate categories for analysis: Boulder Cobble Cobble/Pebble Cobble/Gravel Cobble/Sand Cobble/Silt Pebble Pebble/Gravel Pebble/Sand Pebble/Silt Gravel Gravel/Sand Gravel/Silt Sand Sand/Silt Silt The process of tallying dominant and co-dominant substrates had the effect of removing the dominant/co-dominant characterization from a given sample, but preserved the frequency with which a given pair of substrates (without regard to dominant and co-dominant) occurred together. Therefore, pairings in this final list do not imply that the first substrate in a pairing was dominant. Results The frequency of each substrate type and the observed and expected occurrence of Snake River physa on substrate types in the C.J. to Weiser reach are presented in Appendix Table 1.
59 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Appendix A, Table 1. Frequency and proportion of substrate categories, and observed and expected substrate category use by Snake River physa in the C.J. to Weiser Reach (RM 494–469 and RM 458.4–351). Substrate Frequency Substrate Observed Snake River Expected Snake River Proportions physa Substrate Use physa Substrate Use if no Selection Occurring Boulder 8 0.057 3 3 Cobble 1 0.007 2 0.33 Cobble/Pebble 11 0.079 2 4 Cobble/Gravel 18 0.129 11 6 Cobble/Sand 7 0.050 0 2 Cobble/Silt 3 0.021 0 1 Pebble 3 0.021 0 1 Pebble/Gravel 21 0.150 20 7 Pebble/Sand 12 0.086 2 4 Pebble/Silt 3 0.021 1 1 Gravel 5 0.036 0 2 Gravel/Sand 20 0.143 2 7 Gravel/Silt 4 0.029 0 1 Sand 11 0.079 2 4 Sand/Silt 6 0.043 1 2 Silt 7 0.050 0 2 TOTALS 140 1.0 46 46 Substrate selection by Snake River physa in the C.J. to Weiser reach was tested using the Comparison of an r x c [row and column] Table to a Theoretical Distribution (a randomization test) in TableSim, a program produced by the USDA Forest Service’s North Central Research Station for analysis of small-sample categorical data (Rugg 2003). TableSim is available online at http://www.ncrs.fs.fed.us/pubs/viewpub.asp?key=1838 (last accessed January 9, 2012). A FORTRAN command line program, TableSim does not utilize a Windows platform interface, which frees considerable RAM for conducting the required calculations. The test for Snake River physa habitat selection was conducted with 50,000 simulations. TableSim output presents the results as both a chi-squared statistic and a G-test statistic. Results were P = 0.00032 for X2 ≥ 55.504 and P = 0.00002 for G2 ≥ 50.765, indicating that Snake River physa observed substrate preference differed significantly from its expected substrate use. That is, Snake River physa do not appear to utilize all recorded substrates in the C.J. to Weiser reach in the same proportions in which those substrates occur. The significance of the test results becomes apparent in Appendix A, Figure 1.
60 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
50 45 40 35 30 25 Percent substrate type frequency 20
15 Percent Snake River physa 10 substrate use 5
0
Silt
Sand
Gravel
Pebble
Cobble
Boulder
SandSilt
GravelSilt
PebbleSilt
CobbleSilt
GravelSand
PebbleSand
CobbleSand
PebbleGravel CobbleGravel CobblePebble Appendix A, Figure 1. Percent substrate category frequency compared to percent substrate use by Snake River physa in the C.J. to Weiser Reach (RM 494–469 and RM 458.4–351). Graph created using data from columns three and five in Appendix A, Table 1.
In the C.J. to Weiser reach Snake River physa were found with substrate types such as boulder and pebble/silt in about the same proportions as these substrate types occur. They seem to associate less with or avoid altogether all but three of the remaining substrate types. They appear to strongly select for cobble/gravel, and particularly for pebble/gravel, and may select for cobble, as well: Over 67 percent (31 of 46) of Snake River physa were collected in cobble/gravel and pebble/gravel substrates, whereas these substrates comprised about 27.8 percent (39 of 140) of substrates sampled. Snake River physa use of cobble alone as indicating the species selects for cobble alone; however, is open to interpretation, since cobble alone appeared in the samples just once (Appendix A, Table 1). Discussion The limitations of the C.J. to Weiser Reach data set need to be clearly stated in order to place these results and the remainder of this paper into context. A total of 1,223 samples were taken in the C.J. to Weiser Reach between 1995 and 2002 (Company unpublished data). Less the river miles in Swan Falls Reservoir, this reach has a composite distance of about 131 river miles. Total sampling effort was therefore about 9.3 samples per river mile, or roughly one sample per tenth mile. The substrate data involving this reach used in this analysis came from 140 unique samples, a subset of the final data set. The remainder of the 1,223 samples were eliminated during the sorting that produced the final data set. However, all but two of the 49 Snake River physa collected by the Company in the Snake River were identified from samples in which substrate types had been recorded, and came from the 1998 and 2001 sampling years. By comparison, Gates and Kerans’ (2010) sampling effort below Minidoka Dam, which resulted in collection of 235 live Snake River physa (does not
61 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project include specimens collected via timed samples), ranged between 19 and 22.6 samples per river mile, or about 4.8 times more individuals collected for about double the sampling effort. Snake River physa were found in 2.4 percent (30 of 1,223) of samples in the C.J. to Weiser reach, indicative of the species’ relative rarity in this portion of the river. Note, however, that the test for substrate selection is based on 140 substrate samples, or slightly more than one sample per river mile. River character and bed can change dramatically in 1 mile, and this small substrate sample size should be considered a substantial limitation. By itself, given the limitations of the data used in this analysis (small Snake River physa sample size, small substrate sample size), the results could be considered only suggestive that Snake River physa exhibit substrate preferences of cobble to gravel. Methods—Gates Unpublished Data Gates provided the Service with unpublished data from permanently watered areas in her Minidoka study area, most comparable to data collected by the Company, for use in our analysis (Appendix A, Table 2). Though Gates and Kerans (2010) did not record boulder or cobble as occurring in their samples, we included these substrates in the table (and in Appendix A, Figure 2) for comparison only with the C.J. to Weiser reach—boulder and cobble were not used in the analysis. Appendix A, Table 2 includes data from timed samples. Gates and Kerans (2010) recorded only the dominant, or most common, substrates in the vicinity of each sample. Again, we tested for Snake River physa substrate preference using a contingency table approach. Sample sizes and number of variables indicated the data would satisfactorily approximate the chi-squared distribution.
Appendix A, Table 2. Frequency and proportion of substrate categories, and observed and expected substrate category use by Snake River physa in the reach below Minidoka Dam (RM 675-663). (Gates, unpublished data). Substrate Frequency Substrate Observed Snake River Expected Snake River Proportions physa substrate use physa substrate use if no selection occurring Bedrock 32 0.131687243 18 34 Boulder 0 0 0 0 Cobble 0 0 0 0 Pebble (gravel) 102 0.419753086 154 110 Gravel (small 55 0.226337449 44 59 gravel) Sand 45 0.185185185 44 48 Silt 9 0.037037037 1 10 TOTAL 243 1.0 261 261 Results A chi-squared test (conducted in SigmaPlot 12) showed a statistically significant difference (P < 0.001, X2 = 21.978, 4 degrees of freedom) between Snake River physa observed substrate use compared to expected substrate use if the species was not showing substrate preferences. Appendix A, Figure 2 displays the percent substrate frequency and percent Snake River physa substrate use (permanently watered sample sites) found by Gates (unpublished data).
62 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
70
60
50
40 Percent substrate frequency 30 Percent Snake River physa 20 substrate use
10
0 bedrock boulder cobble pebble gravel sand silt (gravel) (small gravel)
Appendix A, Figure 2. Percent substrate category frequency compared to percent substrate use by Snake River physa in the reach below Minidoka Dam (RM 675–663). Graph created using data from columns three and five in Appendix A, Table 2.
Fifty-nine percent of Snake River physa were collected on pebble, which comprised approximately 42 percent of substrate samples. The species largely avoided silt, was found on gravel and sand more or less in the proportion in which each occurred, and was found on roughly half of the samples taken from bedrock. Pebble and gravel combined made up nearly 65 percent of the substrates sampled below Minidoka Dam, compared to cobble/gravel and pebble/gravel (Snake River physa substrate preferences) comprising only 27.8 percent of substrates from the C.J. to Weiser reach. Discussion—Company Data and Gates’ Unpublished Data Considered alone, results of habitat selection tests from either Minidoka or the C.J. to Weiser reach might not necessarily provide strong evidence for Snake River physa substrate selection. While Gates and Kerans (2010) conducted a well-designed study, their results were compared to the weight of precedence in the habitat description (boulder to gravel substratum) by (Taylor 1982b, in litt.), who first described the species (Taylor 1988), and to his statement of where he found Snake River physa (beneath boulders). Although depth and flows at Minidoka where Snake River physa were found were comparable to those described by Taylor (1982b, in litt.), large substrates were rare or absent at Minidoka. Gates and Kerans could not rule out that Snake River physa were most common on pebble to gravel because these happened to be the most common substrates in their study area (Gates and Kerans 2010, p. 37). In the C.J. to Weiser Reach, the small substrate sample size available for testing relative to the area comprising the reach (basically one sample per river mile) and the small number of Snake River physa found in the reach’s 131 river miles, considered alone, limit the value of the results, raising the possibility that results from more intense sampling efforts could indicate a different substrate preference, or no substrate selection.
63 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Considered together, results from the two studies corroborate each other. Snake River physa selection of pebble to gravel at Minidoka, 200 river miles or more upstream of Snake River physa collection sites in the C.J. to Weiser Reach, is strongly suggestive that the species’ apparent preference for cobble to gravel in C.J. to Weiser is indeed real. Conversely, corroboration of the species’ substrate selection at Minidoka by the results from C.J. to Weiser may allow a partial explanation for the high densities and abundance of Snake River physa found by Gates and Kerans (2010): the Minidoka reach may provide a relatively large, relatively contiguous area of preferred habitat, largely consisting of pebble. The significance of Snake River physa presence associated with cobble (cobble/gravel) in the C.J. to Weiser Reach and the absence of cobble in Gates and Kerans’ (2010) samples may not be known without further study. The difference between substrate types recorded by the Company (dominant/co-dominant for each sample) and Gates and Kerans (2010) (one substrate type for each sample) make it difficult to compare selection for cobble between the two study areas. Snake River physa may also select for cobble (if present), but we cannot rule out that Snake River physa found in cobble/gravel in the C.J. to Weiser Reach were responding to the presence of gravel only. Within the range of cobble to gravel, it may be that Snake River physa substrate selections depend on environmental conditions at a site-specific scale. If Snake River physa does select for substrate sizes ranging from cobble to gravel, then we might expect the species to be more rare in free-flowing river reaches where available bed material and/or flow characteristics result in low frequencies of cobble to gravel substrates. Discussions with Company biologists of the results from tests for Snake River physa substrate preference in the C.J. to Weiser Reach and at Minidoka led to speculation that the apparent rarity of the species in reaches that include Taylor’s (1988) type locality (between Lower Salmon Falls Dam and the upper end of C.J. Strike Reservoir) might be explained by differences in substrate frequency in this reach compared to available substrates at Minidoka and C.J. to Weiser. We explore this in the following section. Section B Introduction Despite repeated and intensive sampling, the species has not been recorded in the 50.5 mile reach (which includes the type locality) between Lower Salmon Falls Dam and C.J. Strike Reservoir (Lower Salmon Falls/C.J. Reach) since 1988, with the exception of the one uncertain specimen collected below Bliss Dam in 2002. It should be noted, however, that in at least some years in which sampling targeted the Bliss Rapids snail, substrate samples were not specifically examined for potential Snake River physa specimens. Dominant/co-dominant substrate types were, however, recorded, and sample size is large enough to test for differences between this reach and the C.J. to Weiser Reach. Sampling depth was targeted to the Bliss Rapids snail, which resulted in substrate composition usually recorded from depths between 0.5 to 1.5 feet, with occasional samples recorded at about 5 feet, measured from whatever stage height the Snake River was experiencing during the sample period. The Company characterizes this reach into four smaller reaches (Bean and Stephenson 2011a, p. 2-3). One reach is Bliss Reservoir, and the remaining three—Lower Salmon Falls Reach (hereafter the Type Locality Reach—the Snake River physa type locality is in RM 569 in this reach), Upper Bliss Reach, Lower Bliss Reach—are free flowing and are distinguished by differences in stream morphology.
64 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
The Type Locality Reach extends from Lower Salmon Falls Dam to the upper end of Bliss Reservoir, a distance of about 7 river miles (RM 573-566). Google Earth images show that the Snake River canyon in this reach is generally constricted, and the river narrow with the exception of three short areas with islands. Available bed material from the canyon walls is known to be largely slow-weathering basalt lava rock. The reach is dominated by glides (58 percent), followed by riffles (20 percent), pools (15 percent), and rapids (7 percent) (Welcker et al. 2009, p. 11). The Upper Bliss Reach is most similar to the Type Locality Reach. The Company delineates it as extending from Bliss Dam downstream to the King Hill Bridge, a distance of about 14 river miles (RM 560.3-546.35). Google Earth shows that the river in this area is more narrow and restricted than the Type Locality Reach. Available bed material is still largely basalt. The reach is dominated by glides (68.4 percent), pools (16 percent), and riffles (6 percent), with the remainder as rapids, bench, and chute (Welcker et al. 2009, p. 11). River character changes in the Lower Bliss Reach, which extends from the King Hill Bridge to the upper end of C.J. Strike Reservoir, a distance of about 24 river miles (RM 546.35-522.5). The canyon opens up and the river is braided among islands for long stretches. In this section we tested for and compared differences in substrate presence between the C.J. to Weiser Reach and the reaches between Lower Salmon Falls Dam and C.J. Strike Reservoir, less the river miles in Bliss Reservoir. Methods Dominant/co-dominant substrate pairs were determined for the entire Lower Salmon Falls/C.J. Reach and for the three individual reaches similar to Appendix A, Table 1. Number of substrate categories ranged between 18 and 21 in the four tests. Differences in substrate frequency between the C.J. to Weiser Reach and the entire Lower Salmon Falls/C.J. Reach, and between C.J. to Weiser Reach and each of the individual reaches were conducted using the Comparison of an r x c Table to a Theoretical Distribution in TableSim (Rugg 2003). Substrate categories were lumped to reduce the number of variables similar to the process used in testing for Snake River physa substrate preference. Data were set up to test for differences between the observed substrate frequency in C.J. to Weiser and the expected substrates in C.J. to Weiser if they did not differ from substrate proportions sampled in the Lower Salmon Falls/C.J. reaches. Substrates with a real frequency of zero in the expected values were entered as 0.5 to allow the program to run. Results Results were highly significant for all four tests. P-values equaled 0.00002 for both the X2 and the G-test, indicating that substrate frequency between C.J. to Weiser and the Lower Salmon Falls/C.J. reaches were quite different. The small P-values were cause for concern that the high number of variables might be skewing the tests toward the potential for Type I errors. As a test of this possibility, we also tested for differences between the Type Locality Reach and the Upper Bliss Reach, the two most similar reaches. Results were also highly significant (P is less than or equal to 0.0005) for differences between these two reaches.
65 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
This latter result does not necessarily negate results of the test for differences between C.J. to Weiser and the Lower Salmon Falls/C.J. reaches, but could somewhat diminish the explanatory power of the results in terms of how substrates in each reach might influence the presence or absence of Snake River physa. We considered that the natural variation among river reaches in the data collected could lead to statistically significant differences between reaches that might be obscuring results significant to the species. Sample sizes for the Type Locality and Upper Bliss reaches were large enough to allow us to calculate percent of each substrate category (bedrock, boulder, cobble, pebble, gravel, sand, silt), with percent dominant and co-dominant determined separately, for each river mile in these two reaches. Sample size for the Lower Bliss Reach was too small to display by river mile, so percent substrate types were calculated for the whole reach. This approach involves the least amount of data manipulation, and if displayed by river mile, might reveal patterns in the data relevant to the question and consistent with test results. Discussion Percent occurrence of each substrate type as dominant and co-dominant for each river mile in the Lower Salmon/C.J. reaches are presented in Appendix A, Figure 3. The results are suggestive of several things. First, consistent with the narratives of river character above, percent substrates in the Lower Bliss Reach do differ from that in the Upper Bliss and Type Locality reaches. Second, enough variation in substrate frequency exists to suggest that the latter two reaches may differ from each other, consistent with test results. Third, the predominance of large-sized substrates and the relatively low frequency of substrates selected by Snake River physa stand out in sharp contrast for most river miles in the Type Locality and Upper Bliss reaches, especially when compared to the high percent frequency of pebble to gravel in the C.J. to Weiser Reach shown in Appendix A, Figure 4. If the small substrate sample size is accepted as a reasonably accurate description of substrates in the C.J. to Weiser Reach, then we can conclude that the significant difference between C.J. to Weiser and these two reaches provides considerable explanatory power for the rarity of Snake River physa in the Lower Salmon/C.J. Reach. That is, the species’ preferred habitat in this reach is also rare.
66 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Figure3A Bid= Boulder, Bdrck =Bedrock, Cble = Cobble, Pble = Pebble, Grvl =Gravel, Snd =Sand, Sit= Silt Substrate Percent Occurrence Dom = Dominant, CoDom = Codominant Type Locality Reach RM 572-566 RM = River Mile 0 00 ~------~~-L------0 70 +------,r-----"o,rr-
:: ~ t'-.-.~T-::-~ ~,T·-~ T~-·~li'!l•~"'''l .~~•~.,..~""l ••~~or..-:~"~~--:~~--·~'l~--·~--r-~L~,.·~L,.•~--,.~ ~ ~ T ~ fj-TI ~ ~ ~ i ~ ~ ~ ~ ~ ~ ~ ~ r~1 ~ iri ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ff ~ ~T~ ~ ~ ~~ ~ ~i i i~ ~ ~~ ~ ~ ~ ~ ~~~~ ~~~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ T ~~ ~ T ~ i i i ~ ~ ~~ ~ ~~ ~ ~ ~ Tirili0 ~ ~ ~ ~ ~ ~ t 8 8 8 8 8 8 8 8 I 8 I u I 8 8 8 8 8 8 I 8 8 8 8 8 I 8 I 8 8 8 8 8 8 8 8 8 8 8 ' I 8 8 I 8 I 8 8 8 8 8 I I 8I I 8 8 8 b e y Bid Cble Fble Grvl Snd Sit Bid Cb le Pble Grvl Snd Sit Bid Cble Pble Grvl Snd Sit Bid Cble Pble Grvl Snd Sit Bdrck Bid Cble Eble Grvt_ Snd Sit Bdrck Bid Cble Pb le Grvl Snd Sit ad Cble Pble_ Grvl Snd Sit
RM 572 RM 571 RM 570 RM 569 RM 568 RM 567 RM 566 % Types of Substrate
Figure Substrate Percent Occurrence 38 Upper Bliss Reach RM 560-554
100 ,------~·~------90 +------~76,------.r-----~------~~ t======i~=====:~======1~=====~75~======~~======~~~======6050 5<~------~~------,-M----,-,------,~~·---,r------~~----~------~~------~-5·~7------~..------~--l------~--5=6~----~--~----.g,------4~41~------~3~6------j~~------40 ~~~.=-~. ------~.·~2~·.----24------l-----24--l------j----~-~-----2------~27,--,•.--_,. ,2'7------~. ----~I------~L~"------30 +•--•. • 16 • 16 • • "' "' 2 • • 2 • • • • • 4----- 1 ~~ ;~~=~;=;~~=~:.; ;;~~:;.;;;~;~~~~~~~=~~~~=~~·"~ ;:;~~=~~:~;:; ;;~;:; ~;;~;~~~~;i~==~~~~~=::;:; ~~~=:~=;;~o---tl~=~--;~,_-;~-"'-5~--;~--;~,_-{~~.::-~-;~;-.~·~_!l~;;-.,.~~-~-~~..- l'" -;..-r---::,_1__:_5~ ;;;~·.:;-_.-".5~;;;~.::-'=~:~=~~.:;-;;::-=~~:;:;;::;;~·7~r-'·~5'--T--::,_1__!1=~ r-!:l•T-i~:.:;-l'~:l-.,c~:•.,--,~·7~;;;·~;~~r-=·7~;=~·7=-l-_!1•~r~=I-T~~~-~·7~!~~=~,.~~"""'fr::"'_.=~=~~·7~ ~~ ~ ~ ~ ~ ~ ~ ~ ~~ r rn ffil ~ l ~ ~ ~ ~ ~ ~~ ~ ~ ~ ~ 1 (11 ~ ~1 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~~ ~ ~~ ~ ~~ r H ~~~~~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~n rrr~ ~~~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ r ~ ~T ~ ~ ~ ~ ~ ~~ 8 8 8 ~ ~ 8 "18 8 8 8 8 8 8 8 8 8 8 8 1 8 1 8 8 8 8 8 1 8 1 8 8 8 8 8 8 ' 18 8 8 8 8 8 "181wl8 13 8 8 8 "18 8 8 8 Bdrck Bid Cble Pble Grvj Snd Sit Bdrck Bid Cble Pble Grvl Snd Sit Bid Cble Pble Gr vl Snd Sit Bid Q:.le Pble Grvj Snd Sit Bdrck B d Q:. le Pble Grvl Snd Sit Bid Cbl e Pble Grvl Snd Sit Bid Cble Pble Grvl Snd Sit
RM 560 RM 559 RM558 RM 557 RM 556 RM 555 RM5S4
Types of Substrilllte
Figure 3B Substrate Percent Occurrence (cont) Upper Bliss Reach (continued) RM 553-547 go .------oo------00 +------~"" ------~~------~~------70 +------~~------~··------"~------~M------~------..------~------~------60 +------.r------·------..------.4~8------~.-----~47~------..------·------~------..------50 +------~._------j·-----~._------ll-----~=------·------~------.------·------~------·.------~----~l~------~~ 40 27 27 : : : 20~ .... ~ . • L U 18 18 • • • • • +----.•.--•. -~.---·--J 7 • 7 7 7 7 .• .,;."-rv ..• • " " .• 1 " .. " " " - i T.il i T ~ i ~ i~ ~ i~~ ~~.~~ ~-~~~u -~~i~i-~~i~irl~i~8~E ~ :~E ~.•~ -~ ~-~-~~~v-~~~-~· ~irl~~~:rE-~:~E ~..•~ ~~~ -...··~-~··~-~-~~ ~ ~i~~i~i~ir ~ :~E -:~E ~~ .---~ ~ il ~8 ~ ~ ~ 8 ~ ~-~8 ~~~8 il 7 8 il 7 8 ~ 1 7 8 7 1 8~ · ~~~8 il~8 l i l ~8 i i 8i~~ ~~8 ~ 8~ ili8 lirtI ~ il~--;8 , ~8 ~ ~ ~8 ~ ~ 8~ I 8 I 8 8 8 8 8 I 8 I ~ 8 8 8 8 'I 31° 18 8 8 8 8 8 8 8 8 Bid Cble Pble Grvl Snd Sit Bid Cble Pb le Grvl Snd Sit Bid Cble Pble Grvl Snd Sit Bid Cble Pb le Grvl Snd Sit Bid Cble Pble Grvj Snd Sit Bid Cble Pble Grvj Snd Sit Bid Cble Pble Grvl Snd Sit RM553 RM 552 RM 551 RM 550 RM 549 RM548 RM 547
Types of Substrata
Figure I 3C Substrate Percent Occurrence Lower Bliss Reach RM 546-522 70 ,------60 +------50 +------
30 +------
20 +---ty------ty------13 13 8
100 =- ..!.. Dom ----,l__..co•Ocrn.___-,-----1 Dom CoDom Dom I CoDom I Dcm CoDom 1 •Dom I CoDom Dom CoD ern Bid Cble Pb le ___J_ Grvl Snd Olt Types of Substrilllte
Appendix A, Figure 3. Substrate percent occurrence for type locality reach, Upper Bliss reach and Lower Bliss reach.
67 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Substrate Percent Occurrence C.J. to Weiser Reach (RM 493.2-469; RM 457.2-350.6) 35
30
25
20
15
10
5
0 Dom CoDom Dom CoDom Dom CoDom Dom CoDom Dom CoDom Dom CoDom Bld Cble Pble Grvl Snd Slt
Appendix A, Figure 4. Percent substrate occurrence in the C.J. to Weiser Reach by dominant (Dom) and co-dominant (CoDom). Key: Bld = Boulder, Cble = Cobble, Pble = Pebble, Grvl = Gravel, Snd = Sand, Slt = Silt. When this information is considered together with Gates and Kerans’ (2010, p. 37) conclusion that the species seems to exist in diffusely distributed populations even in what is apparently preferred habitat, we can conclude that while Snake River physa may exist in the Lower Salmon/C.J. Reach, the probability of encountering them is likely quite low. The fact that the first live specimens were found in this reach is remarkable in retrospect, and could have been a function of different conditions present in the type locality (e.g., higher water quality, higher availability of cobble to gravel substrate) when Taylor made his collections in 1959 (Taylor 1982a, in litt., p. 6) and again in 1980 (Taylor 1988, p. 67), or may simply have been happenstance. Several inferences can be drawn from this analysis regarding the status and distribution of Snake River physa. 1. Maintenance of conditions that produce or sustain beds of pebble to gravel, and possibly cobble to gravel, in good condition (defined in part as relatively free of substrates finer than gravel) is important to the presence, and probably existence, of Snake River physa. This also argues for establishing and maintaining water quality conditions, particularly temperature and nutrient load, which minimize macrophyte growth in free-flowing reaches of the river containing beds of pebble, gravel, and perhaps cobble. Macrophyte beds reduce water velocity, causing fines such sand, silt, and clay to fall out of the water column, potentially embedding or covering Snake River physa habitat.
68 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
2. The actual extent of cobble to gravel substrates in the C.J. to Weiser Reach, even at depths likely to be sampled, is not known. The Company recorded Snake River physa densities in the C.J. to Weiser Reach approaching those recorded by Gates and Kerans (2010) in the Minidoka Reach: 28 and 16 Snake River physa per m2 were found at RM 420.5 and RM 471.6, respectively, in 2001. These densities could have indicated the presence of patches or colonies of Snake River physa which might have been found if more intense sampling had been conducted in the area at the time, and might infer the presence of relatively more extensive cobble to gravel beds in those sample areas. In 2010, Company and Service biologists re- sampled some of the locations where Snake River physa had previously been found in the Swan Falls Dam relicensing Action Area (though not at locations with previous Snake River physa high densities), but no Snake River physa were identified (Bean and Stephenson 2011b, p. 18). 3. The presence and integrity of pebble, gravel, or cobble beds, and therefore of Snake River physa, could be impacted by actions that result in sediment deposition. Such as, movement and re-deposit of preferred substrates (e.g., passing of high flows out of season for flood control) and replenishment or lack thereof of preferred substrates. Blocking of upstream sources of preferred substrates by C.J. Strike Dam and Swan Falls Dam acting as sediment traps could potentially be problematic to the long-term presence of Snake River physa preferred habitat in the reaches between C.J. Strike Dam and Swan Falls Reservoir and below Swan Falls Dam. Studies of large particle movement (larger than silt or sand) in the Snake River could help clarify this. Of interest would be research to determine if Minidoka Dam has been similarly functioning as a sediment trap, and if this is impacting Snake River physa populations below the dam. 4. This analysis begins to match river substrate composition and distribution in the Snake River with the character of the river (i.e., all wetted portions of the river bed, prevalence of islands, the benches, and the canyon). Substrates change from boulder and cobble to gravel and sand when transitioning from the Upper Bliss to Lower Bliss reaches. The online Acme Mapper topographical display shows some historical islands that are now submerged, and islands that are semi or permanently submerged are also visible on Google Earth images in C.J. Strike Reservoir, indicating that the braided character of the Lower Bliss Reach continued for some distance into C.J. Strike Reservoir. Given the prevalence of gravel and sand in the Lower Bliss Reach, and of pebble, gravel, and sand in the C.J. to Weiser Reach (also braided), it is reasonable to conclude that construction of C.J. Strike Dam likely inundated similar habitat (i.e. Snake River physa preferred habitat) in at least some portions of C.J. Strike Reservoir. The extent to which this might have occurred could be difficult to determine.
69 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
APPENDIX B Aquatic Life Use Support and Ecological Condition for the Snake River, Idaho: A Summarization of Two Studies by the Idaho Department of Environmental Quality While there have been no studies addressing water quality requirements for Snake River physa, existing information is suggestive that water quality may influence the distribution and abundance of Snake River physa. The Idaho Department of Environmental Quality (IDEQ) has collected data in support of indices for use in assessing ecological impairment of Idaho rivers, including the upper- and mid-Snake River and the lower reach of the Bruneau River. The results, presented in the Idaho River Ecological Assessment Framework (Grafe 2002) and the Idaho Assessment of Ecological Condition [Rivers] (Kosterman et al. 2008), document changes in water quality over a total of 13 non-overlapping sites ranging from near Wheaton Mountain on the south fork of the Snake River (RM 874) downstream to the USGS gage at Weiser (RM 351.5) (see Appendix A, Table 1). The U.S. Environmental Protection Agency (U.S. Environmental Protection Agency 2008, p. 6- 3) defined ecological condition as “the state of the physical, chemical, and biological characteristics of the environment, and the processes and interactions that connect them.” The manner or degree to which these environmental characteristics, processes, and interactions perform in an ecosystem to produce a desired outcome when compared against a known or desired reference condition would be a measure of ecological impairment. Grafe (2002) developed indicators and water quality criteria for use in assessing aquatic life use support for rivers in Idaho. Among the indicators were a River Physicochemical Index (RPI), based on the Oregon Water Quality Index. Grafe tested her RPI using data from USGS trend monitoring data collected on Idaho rivers from 1993 to 1995, including the Snake River and Bruneau River. The RPI is stated as a composite score from measurements of eight water quality metrics: temperature dissolved oxygen biochemical oxygen demand pH total solids ammonia + nitrogen total phosphorus fecal coliform Her results (Grafe 2002, p. 6-1 to 6-9 and Appendices F & G) for seven sites on the Snake River are presented as scores and ratings in Appendix A, Table 1. The RPI indicates that ecological condition ranges from fair to good in the upper- to mid-Snake (Blackfoot to Kimberly), and is poor from Buhl down to the USGS gage at Weiser, with the change in condition apparently occurring between Kimberly and Buhl. Ecological condition in the Bruneau River was rated as excellent. The Idaho Assessment of Ecological Condition [Rivers] (Kosterman et al. 2008) is part of Idaho’s effort in a collaboration between western states and the EPA, called the Environmental Monitoring and Assessment Program (EMAP), to describe the conditions in western rivers.
70 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Section C of this report (Remington and Kosterman 2008) develops tools by which to assess, in a consistent and statistically defensible manner, the ecological condition of Idaho non-wadeable rivers across bioregions in the state. Results describing the degree of ecological impairment of sites from the Snake River were produced in this process. To understand implication of the results, some explanation of the process and the standards is in order. Forty-four sites were surveyed on 24 Idaho rivers between 2002 and 2004 for a number of parameters, including water chemistry, river physical habitat measures, and macroinvertebrates, using protocols from the EPA manual for non-wadeable rivers (Peck et al. 2005). The sites were classified according to ecological impact status based on water chemistry and physical habitat metrics, and on GIS metrics developed from watershed characteristics. The least impacted sites were designated as reference sites, the standard against which a set of survey tools or indices would be developed and evaluated for their sensitivity to detect ecological impairment. (The remaining sites not least impacted were rated as moderately or highly impacted.) Six sample sites from the Snake River were a subset of the forty-four survey sites. Classification was conducted using cluster analysis of principal components of the various metrics, modified by best professional judgment. The least-impacted sites were designated as reference sites. Reference sites were subsequently used as standards against which survey metrics could be evaluated for their sensitivity to detect impairment, in the process of developing of multi-metric indices that would be used to assess overall river ecological condition. Clusters from analysis of 35 water chemistry metrics (Remington and Kosterman 2008, p. 40) were highly interpretable, meaning that, when combined with best professional judgment, the results were largely successful in breaking out impact status into highly-impacted, moderately- impacted, and least-impacted survey sites (Remington and Kosterman 2008, p. 46). A four- cluster solution cumulatively explained 87 percent of the variability in the water chemistry data across survey sites. Water chemistry metrics most influencing each cluster are as follows: First principle component: conductivity and metrics associated with conductivity Second principle component: total phosphorus and pH Third principle component: pH, total suspended solids, and turbidity Fourth principle component: total nitrogen As part of the above process, a rating was made (least, moderately, highly impacted) for the six Snake River sites (Remington and Kosterman 2008, p. 48). With a high proportion of variance explained by a small number of principal components, Remington and Kosterman (2008, p. 46) were able to develop two classification rules that reproduced final ecological impact status of survey sites. First classification rule: Highly-impacted sites: Total nitrogen greater than 320 parts per billion, or micrograms per liter (µg/L) Moderately-impacted sites: Total nitrogen greater than 160 µg/L, OR, conductivity greater than 200 micro Siemens (µS) per cm2 (µS/cm2)
71 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Least-impacted sites: All other sites Second classification rule: Highly-impacted sites: Total nitrogen greater than 320 µg/L Total phosphorus greater than 160 µg/L Conductivity greater than 400 µS/cm2, OR, pH greater than 9.0 Moderately-impacted sites: Total nitrogen between 160 and 320 µg/L Total phosphorus between 80 and 160 µg/L Conductivity between 200 and 400 µS/cm2 Least-impacted sites: All other sites Cluster analysis of physical habitat metrics alone were not as successful in determining impact status of survey sites, and this method was not used in classifying reference sites. A set of five GIS metrics created from the National Land Cover Database (NLCD) coverages that measured watershed characteristics were successful in classifying survey site impact status in close agreement with impact status classified using water chemistry metrics and best professional judgment. The GIS metrics are: Percent open space Percent area in pasture or hay Percent area of cultivated crops Acre-feet per square mile of dam storage capacity Percent dam storage area The classification of impact status for the six survey sites on the Snake River using GIS metrics and modified by best professional judgment were also developed in this process (Remington and Kosterman 2008, p. 50). The impact status for the six sites based on water chemistry and GIS metrics are presented in Appendix B, Table 1. It is worth noting that GIS Land Cover metrics (developed open space, pasture/hay area, cultivated crops, dam storage capacity, and dam storage area) and Water Chemistry metrics were in agreement on the ecological impact classification for four out of six sites in the Snake River (Appendix B, Table 1). (Of the remaining sites, all on the Snake River, GIS metrics rated ecological condition less impaired on two sites, and more impaired on the third site, compared to Water Chemistry). While GIS Land Cover metrics might provide a less precise classification of ecological condition on the Snake River compared to the more direct classification based on Water Chemistry, that the two indices are in reasonable agreement may provide a strong and measurable indicator of the close association between land use (crop irrigation, land development, and water storage for irrigation and energy production) and the aggregate impact of that land use on the ecological condition of the Snake River (and other Idaho rivers).
72 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Once the least impacted reference sites had been chosen, Remington and Kosterman (2008) developed a set of indices with which to estimate overall river ecological condition (good, fair, poor), and individually the condition (good, fair, poor) of physical habitat, water chemistry, and the aquatic macroinvertebrate community of a river, based on comparison to the least impacted reference sites. (Again, during this process, ecological condition ratings using the water chemistry/physical habitat index and the macroinvertebrate index were also made for the six sites on the Snake River). Water chemistry, physical habitat, and river macroinvertebrate metrics were evaluated for their ability to discriminate between reference (least-impacted) and non-reference (moderately- and highly-impacted) sites using box plots, as well as consistency of results across Idaho rivers and bioregions. Multi-metric indices were then developed from sets of metrics with moderate pairwise correlations for use in assessing overall river ecological condition, and individually, the condition of the river physical habitat, water chemistry, and the macroinvertebrate community (Remington and Kosterman 2008, p. 42, 51-61 and Appendices D-G). Thirty-three water chemistry metrics were evaluated for sensitivity to detect impairment. The final water chemistry index consisted of four metrics: conductivity, pH, total nitrogen, and total phosphorus. Fifty-three physical habitat metrics were evaluated for sensitivity, with the final physical habitat index consisting of four metrics: pools, as a percent of a reach; areal proportion of littoral filamentous algae cover; riparian disturbance (proximity weighted pressure); and littoral fish cover (areal proportion of boulders). A combination of the water chemistry and physical habitat indices (WCPHI) improved discrimination between reference and non-reference sites over either index alone. The eight combined metrics fell into three general types: conductivity and pH detect general impairment; areal proportion of filamentous algae, total phosphorus, and total nitrogen detect excess nutrients; and riparian disturbance, areal proportion of boulder, and percent pool detect riparian area and/or stream channel disturbance. Remington and Kosterman (2008, p 57-62) evaluated a river macroinvertebrate index (RMI) developed by Grafe (2002, p. 3-1 to 3-19 and Appendix C) for sensitivity to impairment, and found that it discriminated poorly between moderately- and highly-impacted (non-reference) sites due to statistical reasons. Remington and Kosterman developed two other indices using EMAP macroinvertebrate metrics which performed better than the RMI but which still did not discriminate impact status adequately for similar reasons. They included the results from one of these indices (developed using three metrics provided by the EPA) in their report (p. 62), but concluded that at the time of publication, no macroinvertebrate index could be recommended that reliably predicted impairment at river sites outside the EMAP survey site sample (Remington and Kosterman 2008, p. 61). The set of metrics with the best performance were species richness of Ephemeroptera, Plecoptera, and Trichoptera; percent of individuals that are non-insects; and percent of individuals that are Plecoptera. The ecological rating of good, fair, and poor based on the water chemistry/physical habitat index and the macroinvertebrate index, are presented for the six Snake River sites in Table 1.
73 Kimberly D. Bose, Secretary 14420-2011-F-0318 Federal Energy Regulatory Commission Swan Falls Hydroelectric Project
Appendix B, Table 1. Snake River data from two studies of sites from Wheaton Mountain to the Weiser Gage showing degradation of river ecological condition occurring upstream to downstream. River miles are approximate. Wheaton Heise Firth Blackfoot Howell's Kimberly Buhl Thousand No C.J. Murhpy Walter's Opalene No Nyssa Weiser Mountain RM RM RM 764 Ferry RM 620 RM Springs water Strike Gage Butte Gulch water Gage Gage RM 874 851 776 Gage RM (East of 596 RM 584 quality Dam RM 453 RM 443 RM 429 quality RM RM 674 Twin (West data RM (4.75 data 385 351.5 (1 mile Falls) of between 494 miles between below Twin 1000 below RM 429 Minidoka Falls) springs Swan & RM Dam) and Falls 395 Murphy Dam) Gage Grafe (2002) Index Scores are 0-59 = Very Poor; 60-79 = Poor; 80-84 = Fair; 85-89 = Good; 90-100 = Excellent RPI -- Fair to Good Fair (83.3) Poor Poor Poor Poor reported Good (86.0) 2 yrs data (72.1) (78.8) (74.3) (75.4) as (84.8) 5 yrs 2 month Ranking data data (Score) Kosterman et al. (2008) Indices L = Least Impacted, M = Moderately Impacted, H = Highly Impacted G = Good, F = Fair, P = Poor Water M M M H H H Chemistry GIS M M H H M M WCPHI F F P P P P MIVM F G F P P P From Grafe (2002) RPI: River Physicochemical Index, a single composite score, based on the Oregon Water Quality Index, from 8 water quality parameters: temperature, dissolved oxygen, biochemical oxygen demand, pH, total solids, ammonia + nitrate nitrogen, total phosphorus, and fecal coliform. Results are based on data from a single year unless otherwise indicated. From Kosterman et al. (2008) Water Chemistry: River site-impact classification based on 4 metrics: Conductivity, pH, total nitrogen, total phosphorus. GIS: River site-impact classification based on 5 GIS Land Cover metrics: Developed open space (%), pasture/hay area (%), cultivated crops (%), dam storage capacity density (acre-feet per square mile), dam storage area (%). WCPHI: River site-impact classification based on a combination of Water Chemistry and Physical Habitat Index (WCPHI) metrics: General impairment detected by conductivity & pH; Excess nutrients detected by areal proportion of filamentous algae, total phosphorus, & total nitrogen; Disturbance to riparian area/stream channel detected by riparian disturbance, areal proportion boulder, & percent pool. MIVM: Macroinvertebrate Index. River site-impact classification based on 3 metrics: Number of Ephemeroptera, Plecoptera, & Trichoptera taxa; individuals that are non-insects (%); & individuals that are Plecoptera (%).
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