Full opinion text
ORDER RE CROSS MOTIONS FOR SUMMARY JUDGMENT (GRANGE DOCS. 29, 39, 43; MID II Docs. 79, 90, 94) OLIVER W. WANGER, District Judge. TABLE OF CONTENTS I. INTRODUCTION........................................................1119 II. BACKGROUND..........................................................1120 A. Relevant Endangered Species Act Provisions ............................1120 B. Biological Background on West Coast 0. mykiss .........................1122 C. Administrative Histovy...............................................1123 1. The ESU Policy..................................................1123 2. The DPS Policy ..................................................1124 3. The Interim Hatchery Listing Policy................................1125 4. Initial Listings for the Populations at Issue..........................1126 5. The Alsea Decision and the 2001 Status Review.......................1126 6. The Modesto Irrigation District v. Evans Decision....................1129 7. Revised Hatchery Listing Policy....................................1130 D. The Challenged Listing Process........................................1131 E. Challenged Prohibitions and Protective Regulations......................1139 III. SUMMARY OF PLAINTIFFS’ MOTIONS..................................1140 A. Grange Motions......................................................1140 B. MID II Motions......................................................1141 IV. STANDARD OF REVIEW................................................1142 V. ANALYSIS..............................................................1143 A. Standing............................................................1143 1. Standing of the Grange Plaintiffs...................................1144 2. Standing of the MID II Plaintiffs...................................1146 B. Hatchery-Bom v. Naturally-Spawned: Challenges to the Manner by Which NMFS Treated Hatchery 0. mykiss During the Listing Process ...........................................................1147 1. Grange’s Claim That NMFS Acted Unlawfully by Defining Some of the DPSs to Include Hatchery Fish but Then Distinguished Between Hatchery and Naturally-Spawned Fish During the Listing Process.................................................1147 a. Two of the Five Challenged DPSs Do Not Include Hatchery Fish.......................................................1147 b. Alsea does not Control the Outcome of this Claim.................1147 c. Parsing Grange’s Naturally-Spawned v. Hatchery-Bom Challenge to Detemiine the Appropriate Standard of Review____1149 d. Chevron Deference............................................1151 e. Does the ESA Unambiguously Preclude Draunng Distinctions Between Naturally-Spawned and Hatchery-Bom Fish During Any Stage of the Listing Process?......................1151 f. Was the Approach Used by NMFS During the Listing Process — Emphasizing the Health of Natural Populations and Considering Hatchery-bom Fish Only Insofar as They Contribute to the Health of Natural Populations — a “Permissible Construction” of the ESA?...............................1153 (1) Statutory Language Regarding Protection of Ecosystems and Implying That Natural Populations Should Be Protected...............................................1154 (2) The Best Available Science Demands That Distinctions Be Drawn Between Naturally-Spawned and Hatchery-Bom Fish, Even If Both Are Part of the Same DPS...............1157 C. Anadromous v. Resident: Challenges to NMFS’ Treatment of Resident 0. mykiss During the Listing Process.................................1161 1. Did NMFS Sufficiently Justify Departing from its Past Practice of Applying its Own ESU Policy to Instead Apply the Joint DPS Policy?.................................................... 1161 2. Is the Designation of a Steelhead Only (ie., Anadromous Only) DPS Contrary to Statutory Intent?....................................1172 a. Alsea Does Not Control the Outcome of This Claim...............1172 b. Grange’s “Sparingly” Argument................................1172 c. Does Designation of an Anadromous Only DPS Conflict with the Statutory Language ‘Which Interbreeds When Mature”?.... 1174 (1) Legal analysis under Chevron..............................1174 (2) Does the ESA Unambiguously Preclude Excluding Some Interbreeding Members of a Population from a DPS?----1174 (3) Is the Agency’s Interpretation of the Statutory Language Reasonable?............................................1176 (4) Factual Analysis..........................................1177 3. Grange’s Abandoned Third Claim For Relief Re: “Illegal Construction of Distinct Population Segments”.....................1177 4. MID’s Argument That NMFS’s Decision to Separate Anadromous and Resident Forms of 0. mykiss is Inexplicably Inconsistent With Prior Treatment of Other Fish Species With Resident and Anadromous Life Histories......................................1178 a. Cutthroat Trout .......................................'.......1180 b. Bull Trout...................................................1181 5. Is NMFS’s Decision to List Steelhead-Only DPSs Supported by the Best Available Science?..........................................1181 a. Discreteness..................................................1182 (1) MID’s Argument That the Data Has Not Changed ............1183 (2) Lack of Consistently Distinguishable Characteristics Between Life History Forms..............................1183 (3) The Cause of Distinctions Between Life History Forms........1184 (4) The Three Independent Scientific Reports....................1186 (5) The Role of Genetics and Reproductive Isolation in the DPS Policy .................................................1189 b. Significance..................................................1193 D. MID’s Argument Concerning Distinctions Drawn Between HatcheryBom and Naturally-Spawned 0. mykiss..............................1194 1. MID’s Argument That NMFS Unlawfully Used Genetic Discreteness as the Sole Reason to Exclude Nimbus and Mokelumne Hatchery-Bom Steelhead, but Then Ignored the Close Genetic Relationship of Co-Occurring Resident and Anadromous 0. Mykiss in Deciding to Exclude One but Not the Other from the Listing........................................................1195 2. MID’s Argument That NMFS Acted Unlawfully by Excluding the Nimbus and Mokelumne River Hatchery-Spawned Steelhead Based on Genetics, While Including in the DPS Their Naturally-Spawned Progeny...............................................1196 3. NMFS’s Exclusion of Nimbus and Mokelumne River Hatchery-spawned Steelhead While Including Genetically Similar Naturally-Spawned Populations on the Lower American River, the Mokelumne River, Putah Creek, and the Calaveras River............1198 E. Grange’s Challenge to NMFS’s Selective Application of ESA § 1(d) Protections to Naturally Spauming 0. mykiss and Only Those Hatchery 0. mykiss Which Have an Intact Adipose Fins................1199 VI. CONCLUSION...........................................................1202 I. INTRODUCTION Before the court for decision are two sets of cross-motions for summary judgment filed in two separate, but similar lawsuits, California State Grange, et al. v. National Marine Fisheries Service, et al., 1:06-CV-00308 OWW DLB (“Grange”), and Modesto Irrigation District, et al. v. Carlos M. Gutierrez, et al, 1:06-CV-453 OWW {“MID II”), which have been consolidated for the purposes of summary adjudication. {Grange Docs. 29, 39 & 43; MID II Docs. 79, 90 & 94.) The Grange lawsuit concerns the listing of five populations of West Coast steelhead (a life form of Oncorhynchus mykiss (O. mykiss)) as threatened or endangered species under the Endangered Species Act (“ESA”). A coalition of forestry interests led by California State Grange (collectively, “Grange”) challenge all five listings, arguing that, in reaching the listing determinations, the federal defendants unlawfully distinguished populations of anadromous 0. mykiss from populations of resident 0. mykiss, and populations of naturally-spawned 0. mykiss from hatchery-born 0. mykiss. {Grange Compl. at ¶ 1.) Three non-profit organizations dedicated to the promotion of fly fishing and to the conservation of fishery resources have intervened in that lawsuit. {Grange Doc. 38.) MID II is a more factually detailed challenge to the listing of the Central Valley Distinct Population Segment of 0. mykiss, one of the five listings at issue in the Grange suit. The plaintiffs in MID II, a coalition of irrigation districts (collectively “MID”), similarly argue that federal defendants unlawfully distinguished between populations of anadromous and resident 0. mykiss, and between populations of naturally-spawned and hatchery-born 0. mykiss. Four non-profit organizations dedicated to the promotion of fly fishing and to the conservation of fishery resources have intervened in that lawsuit. {MID II Doc. 34.) Although Grange and MID II share the same administrative record, a largely common factual backdrop, and many common issues, the cases are not identical, and these differences are separately analyzed. II. BACKGROUND A. Relevant Endangered Species Act Provisions. The purposes of the Endangered Species Act (“ESA”), 16 U.S.C. §§ 1531, et seq., are “to provide a means whereby the ecosystems upon which endangered species and threatened species depend may be conserved, [and] to provide a program for the conservation of such endangered species and threatened species.” 16 U.S.C. § 1531(b). The term “conservation” is defined to mean: ... the use of all methods and procedures which are necessary to bring any endangered species or threatened species to the point at which the measures provided pursuant to [the ESA] are no longer necessary. Such methods and procedures include, but are not limited to, all activities associated with scientific resources management such as research, census, law enforcement, habitat acquisition and maintenance, propagation, live trapping, and transplantation, and, in the extraordinary case where population pressures within a given ecosystem cannot be otherwise relieved, may include regulated taking 16 U.S.C. § 1532(3). Section 4(a) of the ESA directs the Secretary of Commerce or the Secretary of the Interior to “determine whether any species is endangered or threatened.” 16 U.S.C. § 1533(a)(1). The Secretary of Commerce has delegated this authority to the National Marine Fisheries Service (“NMFS”); the Secretary of the Interior to the United States Fish and Wildlife Service (“FWS”). When determining whether a species is “endangered” or “threatened,” NMFS must consider: (A) the present or threatened destruction, modification, or curtailment of its habitat or range; (B) overutilization for commercial, recreational, scientific, or educational purposes; (C) disease or predation; (D) the inadequacy of existing regulatory mechanisms; or (E) other natural or manmade factors affecting its continued existence. 16 U.S.C. § 1533(a)(1). More generally, The Secretary shall make [listing] determinations ... solely on the basis of the best scientific and commercial data available to him after conducting a review of the status of the species and after taking into account those efforts, if any, being made by any State or foreign nation, or any political subdivision of a State or foreign nation, to protect such species, whether by predator control, protection of habitat and food supply, or other conservation practices, within any area under its jurisdiction, or on the high seas. 16 U.S.C. § 1533(b)(1)(A). The ESA defines “species” to include “any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature.” 16 U.S.C. § 1532(16). The ESA does not define the term “distinct population segment” (“DPS”) or provide further direct guidance as to the scope and meaning of the term. Alsea Valley Alliance v. Evans, 161 F.Supp.2d 1154, 1157 (D.Or.2001). To the maximum extent possible, “concurrently with making a determination ... that a species is an endangered species or a threatened species,” NMFS is directed to “designate any habitat of such species which is then considered to be critical habitat. ...” 16 U.S.C. § 1533(a)(3). Once a species is listed as threatened or endangered under the ESA, it is unlawful for any person to “take” members of the species without a permit. 16 U.S.C. § 1538(a)(l)(B)-(C) [ESA § 9(a)(1)(B)-(C) ]. NMFS “shall issue such regulations as [it] deems necessary and advisable to provide for the conservation of [threatened] species.” 16 U.S.C. § 1533(d) [§ 4(d) ]. In the case of threatened fish or wildlife, NMFS “may by regulation prohibit ... any act prohibited under section 1538(a)(1) [§ 9’s take provisions].... ” Id. Pursuant to § 4(f) NMFS must “develop and implement plans ... for the conservation and survival of endangered species and threatened species listed pursuant to this section, unless [the Secretary] finds that such a plan will not promote the conservation of the species.” 16 U.S.C. § 1533(f). “[T]he Secretary must not merely avoid elimination of that species, but is required to bring the species back from the brink sufficiently to obviate the need for protected status.” Fed’n of Fly Fishers v. Daley, 131 F.Supp.2d 1158, 1163 (N.D.Cal.2000). B. Biological Background on West Coast 0. mykiss. 0. mykiss exhibit a highly complex life cycle. All 0. mykiss are born and rear in fresh water. After spending anywhere from a few hours to several years in freshwater areas, some 0. mykiss, commonly known as “steelhead,” migrate downstream to the ocean. In order to do so, they undergo a physiological change, known as smolting, which enables them to live in saltwater. Juvenile and subadult steelhead spend one to five years foraging in the Pacific Ocean before returning to fresh water to spawn. For the most part, steelhead return to spawn in the fresh water stream where they were born, although some stray to “non-natal” streams. 69 Fed.Reg. 33,102, 33,108 (June 14, 2004). The present distribution of steel-head extends from Kamchatka in northeast Asia, across to Alaska, and down the length of the west coast of the United States to the border between the United States and Mexico Id. at 33,109 For reasons that are not well-understood, some O. mykiss never smolt, remaining in fresh water throughout their lives. These freshwater “resident” O. mykiss are known as “rainbow” (or “redband”) trout. Id. at 33,106. The steelhead life form is considered to be important to the health and continued viability of O. mykiss populations. According to the Northwest Fisheries Science Center (“NWFSC”), an arm of NMFS, steelhead “represents] a critical component of the species’ evolutionary ‘bet-hedging’ strategy for coping with environmental and ecological challenges.” AR 1460 at 3. For example, even if a particular resident O. mykiss population is decimated by a disturbance event in a particular river, such as a disease outbreak or low water year, the anadromous steelhead that return to the area in subsequent years can repopulate the river. The Recovery Science Review Panel (“RSRP”), a panel of scientists that meets once a quarter to, among other things, review NMFS recovery plans, concluded that “[t]he anadromous component of a salmonid ESU, by maintaining the population’s access to ocean habitat and food resources, can affect productivity over the short term and the probability that the ESU can persist in the long term____ [Estimates suggest that eliminating the anadromous component of steelhead eliminates fish from 99.97% of their potential natural habitat.” AR 1471 at 9. Under some circumstances, either life form (steelhead or rainbow trout) can yield offspring that follow the alternative life form. However, NMFS’s Pacific Salmonid Biological Review Team (“BRT”), an expert panel of scientists from several federal agencies, concluded that the frequency of such occurrences are “relatively rare, and there is even less empirical evidence that, once lost, a self-sustaining anadromous run can be regenerated from a resident salmonid population.” AR 2185 at 211. A separate panel of scientific experts, led by Dr. Jody Hey, (the “Hey Panel”) found that while “[r]esident populations of 0. mykiss have often been established from resident, steelhead, and mixed sources ... the reverse process has been documented to have occurred just once.” AR 793 at 14. Because the prospect of regeneration of steelhead from resident populations is speculative, the Hey Panel concluded that “it is important to conserve the evolutionary potential of the anadromous component of the conservation unit.” AR 793 at 14. The RSRP reached similar conclusions, finding “only one published report of anadromy developing from a resident population ... that of the Santa Cruz River [in] Patagonia,” AR 1471 at 6, as did the Independent Scientific Advisory Board (“ISAB”), which noted that there is no reliable method to predict where and when resident populations are possible of reestablishing anadromy at all, “much less within a timeframe important to recovery,” AR 581 at 25. Moreover, even if it were possible to conclude with more certainty that resident populations could reestablish anadromous runs, there would still be a scientific basis for addressing the reasons for the decline of anadromous populations. The BRT found that “if the conditions that promote and support the anadromous life history continue to deteriorate ... the expectation would be that natural selection would gradually eliminate the migratory or anadromous trait from the population, as individuals inheriting a tendency for anadromy migrate out of the population but do not survive to return as adults and pass on their genes to subsequent generations.” AR 2185 at 211. C. Administrative History. 1. The ESU Policy. In 1991, NMFS promulgated its “Policy on Applying the Definition of Species Under the Endangered Species Act to Pacific Salmon,” referred to as the “Evolutionarily Significant Unit” Policy or the “ESU Policy”. 56 Fed.Reg. 58,612 (Nov. 20, 1991). The ESU Policy provides that a population of Pacific salmonids is considered to be an ESU, and therefore may be considered for listing under the ESA, if it meets the following two criteria: (1) It must be substantially reproductively isolated from other nonspecific population units; and (2) it must represent an important component in the evolutionary legacy of the species. Id. The ESU Policy is an interpretation by NMFS of what constitutes a “distinct population segment.” This interpretation has been found to be a “permissible agency construction of the ESA.” Alsea, 161 F.Supp.2d at 1161. Until recently, NMFS applied this policy to all salmonid species, including 0. mykiss, for the purposes of defining ESUs. 2. The DPS Policy. Concurrent with the development of the ESU Policy, NMFS and FWS developed a joint policy to “clarify their interpretation of the phrase ‘distinct population segment of any species of vertebrate fish or wildlife’ for the purpose of listing, delisting, and reclassifying species under the [ESA] ...” (“Joint DPS Policy”). 59 Fed.Reg. 65,884 (Dec. 21, 1994). A draft Joint DPS Policy was published in 1994, id., public comment was solicited on it, and a final Joint DPS Policy was published in 1996, 61 Fed.Reg. 4,722 (Feb. 7, 1996). The Joint DPS Policy relies on three factors to determine whether a population may be considered a DPS: 1. Discreteness of the population segment in relation to the remainder of the species to which it belongs; 2. The significance of the population segment to the species to which it belongs; and 3. The population segment’s conservation status in relation to the Act’s standards for listing (i.e., is the population segment, when treated as if it were a species, endangered or threatened?). Id. at 4,725 (emphasis added). A population segment of a species is considered “discrete” if it satisfies either one of the following conditions: 1. It is markedly separated from other populations of the same taxon as a consequence of physical, physiological, ecological, or behavioral factors. Quantitative measures of genetic or morphological discontinuity may provide evidence of this separation. 2. It is delimited by international governmental boundaries within which differences in control of exploitation, management of habitat, conservation status, or regulatory mechanisms exist that are significant in light of section 4(a)(1)(D) of the Act. Id. (emphasis added). If a population segment is found to be discrete, its biological and ecological “significance” is evaluated, “in light of Congressional guidance ... that the authority to list [DPSs] is to be used ‘... sparingly’ while encouraging the conservation of genetic diversity.” Id. The significance analysis may include, but is not limited to, an evaluation of: (1) persistence of the DPS in an ecological setting unusual or unique for the taxon; (2) evidence that loss of the DPS would result in a significant gap in the range of the taxon; (3) evidence that the DPS represents the only surviving natural occurrence of a taxon that may be more abundant elsewhere as an introduced population outside its historic range; or (4) evidence that the DPS differs markedly from other populations of the species in its genetic characteristics. Id. The Joint DPS Policy recognizes that “[b]ecause precise circumstances are likely to vary considerably from case to case, it is not possible to describe prospectively all the classes of information that might bear on the biological and ecological importance of a discrete population segment.” Id. If a population is found to be both “discrete” and “significant,” it is evaluated against the five factors set forth in ESA § 4(a) in order to determine whether listing the population as endangered or threatened is warranted. Id. The Joint DPS Policy finds that the ESU Policy is “consistent with” and is a “detailed extension of’ the Joint DPS policy. Id. At the time the Joint DPS Policy was first promulgated, NMFS indicated that it would “continue to exercise [its alternative ESU Policy] with respect to Pacific salmonids.” Id. (NMFS recently determined that it is more appropriate to apply the DPS policy to 0. mykiss, a policy shift that is discussed in greater detail below.) 3. The Interim Hatchery Listing Policy. In 1993, NMFS published an “Interim Policy on Artificial Propagation of Pacific Salmon Under the Endangered Species Act,” 58 Fed.Reg. 17,573 (April 5, 1993) (“Interim Hatchery Listing Policy” or “Interim Policy”). In this Interim Policy, NMFS indicated that “[g]enetic resources important to the species’ evolutionary legacy may reside in hatchery fish as well as in natural fish, in which case the hatchery fish can be considered part of the biological ESU in question.” Id. at 17,574. The policy also provided that “[hjatehery fish considered to be part of the ESU could also be included as part of the listed species and protected under the ESA.” Id. Determinations about existing hatchery fish were conducted by first determining whether “available information” indicates that either: (1) the hatchery population in question is of a different genetic lineage than the listed natural populations, (2) artificial propagation has produced appreciable changes in the hatchery population in characteristics that are believed to have a genetic basis, or (3) there is substantial uncertainty about the relationship between existing hatchery fish and the natural population.... Id. at 17,574-17,575. If any of the above characteristics were present, “the existing hatchery fish will not be considered part of the biological ESU and will not be included as part of the listed species.” Id. If, however, available information “indicates that existing hatchery fish can be considered part of the biological ESU, a decision must be made whether to include them as part of the listed species.” Id. In general, “such fish will not be included as part of the listed species ... [although] [a]n exception may be made for existing hatchery fish if they are considered to be essential for recovery. ...” Id. The policy also explained that “[u]nder any scenario, progeny of fish from the listed species that are propagated artificially are considered part of the listed species and are protected under the ESA.” Id. The Interim Policy provided that “a listing determination for an ESU depended solely upon the relative health of the natural populations in an ESU, and that most hatchery stocks determined to be part of an ESU were excluded from any listing of the ESU.” 70 Fed.Reg. 37,204, 37,205 (June 28, 2005). 4. Initial Listings for the Populations at Issue. In 1996, NMFS completed a comprehensive status review of 0. mykiss populations in Washington, Oregon, Idaho, and California and published a proposed rule identifying 15 ESUs within that broad geographic area. Five of the ESUs were proposed to be listed as threatened, five as endangered. 61 Fed.Reg. 41,541 (Aug. 9, 1996). (Four of the remaining five proposed ESUs were ultimately found not warranted for listing, while one was identified as a candidate for listing. Id.) Following this proposal, FWS became concerned that NMFS would expand its proposed listing to include the resident form of 0. mykiss. As a result, staff from FWS met twice with staff from NMFS to discuss the treatment of resident 0. mykiss in the proposed listing. AR 2314-05 at 1. FWS then wrote to NMFS on July 29, 1997, and stated that FWS had sole jurisdiction over the resident form of 0. mykiss and therefore “any listing decision regarding rainbow [trout] rests with [FWS].” Id. FWS also indicated its belief that the two “behavioral forms can be regarded as separate DPSs” and therefore would not support any listing which included the resident form of 0. mykiss “absent evidence suggesting that the resident rainbow trout needed the [ESA’s] protection.” Id. Subsequently, NMFS revised the proposed listing to apply to only five ESUs of steelhead, two as endangered, including the Southern California ESU, and three as threatened, including the Central California Coast and South-Central California Coast ESUs. 62 Fed.Reg. 43,937 (Aug. 18, 1997). On March 19, 1998, NMFS listed two additional ESUs as threatened, including the California Central Valley ESU, but determined that the other three proposed ESUs, including the Northern California ESU, did not warrant listing at that time. 63 Fed.Reg. 13,347 (March 19, 1998). After further review, NMFS determined that the Northern California ESU warranted listing as threatened. 65 Fed.Reg. 36,074 (June 7, 2000). 5. The Alsea Decision and the 2001 . Status Review. Over approximately the same time period and applying the same policies and procedures used during the above-described O. mykiss listing process, NMFS completed a status review of west coast salmon, and issued a proposed rule to list six ESUs of coho salmon as threatened. One of the proposed listings was for the “Oregon Coast ESU.” NMFS subsequently revoked this proposed listing based in part on conservation measures being undertaken as part of the Oregon Coastal Salmon Restoration Initiative. See Alsea, 161 F.Supp.2d at 1159. Subsequently, in Oregon Natural Resources Council v. Daley, 6 F.Supp.2d 1139 (D.Or.1998), NMFS was found to have acted unlawfully in considering the conservation measures and was ordered to reconsider its decision. On August 10, 1998, NMFS issued a final rule listing the Oregon Coast coho ESU as threatened. See Alsea, 161 F.Supp.2d at 1159. Despite the fact that the ESU included nine hatchery populations, “NMFS only listed all ‘naturally-spawned’ coho inhabiting streams between Cape Blanco and the Columbia River.” Id. In reaching this listing decision, NMFS applied its April 5, 1993 Hatchery Policy to the coho salmon. 63 Fed.Reg. 42,589. NMFS concluded that nine Oregon hatchery populations were part of the same Oregon Coast ESU as the natural populations. However, the hatchery populations were not included in the listing decision because the hatchery populations were not “deemed ‘essential’ to recovery.” Id. Although excluded from the listing decision, NMFS stated that it might consider using these hatchery populations for future recovery but that “in this context, an ‘essential’ hatchery population is one that is vital for full incorporation into recovery efforts.” Id. Id. The Alsea plaintiffs argued that the listing was invalid, arguing the distinction NMFS drew “between hatchery spawned and naturally-spawned coho is untenable under the ESA because the ESA does not allow the Secretary to make listing distinctions below that of species, subspecies or a distinct population segment of a species.” Id. at 1161. The Alsea court began its analysis by examining NMFS’s ESU policy, pursuant to which “a species is considered an ESU, and hence a DPS, if it is ‘substantially reproductively isolated from other conspecific population units’ and ‘represents an important component in the evolutionary legacy of the species.’ ” Id. (citing 56 Fed.Reg. at 58,618). This policy, the court concluded, is a “permissible agency construction of the ESA” and the “factors used to define it, geography and genetics, are within permissible limits under the ESA.” Id. (citing PanAmSat Corp. v. FCC, 198 F.3d 890, 894 (D.C.Cir.1999)) & 1162 n. 5 (genetics and geography are permissible considerations during the listing process). Alsea found that the listing had a fundamental flaw. The central problem with the NMFS listing decision of August 10, 1998, is that it makes improper distinctions, below that of a DPS, by excluding hatchery coho populations from listing protection even though they are determined to be part of the same DPS as natural coho populations. The ESA “specifically states in the definition of ‘species’ that a ‘species’ may include any subspecies ... and any distinct population segment (DPS) of any species ... which interbreeds when mature.” 16 U.S.C. § 1532(16); Southwest Center for Biological Diversity v. Babbitt, 980 F.Supp. 1080, 1085 (D.Ariz. 1997). Listing distinctions below that of subspecies or a DPS of a species are not allowed under the ESA. Southwest Center, 980 F.Supp. at 1085. Yet,. this is precisely what the NMFS did in its final listing decision of August 10, 1998. NMFS concluded that nine hatchery stocks were part of the same Oregon Coast ESU/DPS as the “natural” populations but none of the hatchery stocks were included in the listing decision because NMFS did not consider them “essential for recovery.” 63 Fed.Reg. 42,-589. The distinction between members of the same ESU/DPS is arbitrary and capricious because NMFS may consider listing only an entire species, subspecies or distinct population segment (“DPS”) of any species. 16 U.S.C. § 1582(16). Once NMFS determined that hatchery spawned coho and naturally-spawned coho were part of the same DPS/ESU, the listing decision should have been made without further distinctions between members of the same DPS/ESU. Id. at 1162 (emphasis added). The Alsea court next noted, in dicta, that the listing of only the naturally-spawned population “could arguably be proper under the ESA if the NMFS had defined ‘hatchery spawned’ coho as a separate DPS____” Id. at 1162. However, under the facts and circumstances of that case, the Alsea court surmised that such a definition was not reasonable: Here, hatchery spawned coho are likely not “substantially reproductively isolated” from naturally-spawned coho because, once released from the hatchery, it is undisputed that ‘hatchery spawned’ coho and “naturally-spawned” coho within the Oregon Coast ESU share the same rivers, habitat and seasonal runs, among other factors. It is undisputed that “hatchery spawned” coho may account for as much as 87% of the naturally spawning coho in the Oregon coast ESU. In addition, hatchery spawned and natural coho are the same species, and interbreed when mature (Id. at ¶ 4). Finally, the NMFS considers progeny of hatchery fish that are born in the wild as “naturally-spawned” coho that deserve listing protection. Id. at 1162-63 (citations omitted). The court concluded NMFS’s listing decision was arbitrary because it “creates the unusual circumstance of two genetically identical coho salmon swimming side-by-side in the same stream, but only one receives ESA protection while the other does not.” Id. Finally, Alsea rejected NMFS’s argument “that its listing decision does not contradict the terms of the ESA because the listing decision, and relevant polices, are in accordance with ESA goals that prioritize ‘natural’ salmon populations and ‘genetic diversity’ within those populations.” Id. Although I agree with the general concept that “genetic diversity” is one factor in the long term success of a threatened species, and thus is one of many underlying goals of the ESA, genetics cannot, by itself, justify a listing distinction that runs contrary to the definition of a DPS. The term “distinct population segment” was amended in the ESA in 1978 so that it “would exclude taxonomic [biological] categories below subspecies [smaller taxa] from the definition.” H.R. Conf. Rep. No. 95-1804, at 17 (1978), reprinted in 1978 U.S.C.C.A.N. 9485, 14855. Congress adopted the DPS language stating: The committee agrees that there may be instances in which [the Fish and Wildlife Service] should provide for different levels of protection for populations of the same species. For instance, the U.S. population of an animal should not necessarily be permitted to become extinct simply because the animal is more abundant elsewhere in the world. Similarly, listing populations may be necessary when the preponderance of evidence indicates that a species faces a widespread threat, but conclusive data is available with regard to only certain populations. S. Rep. No. 96-151. Thus, Congress expressly limited the Secretary’s ability to make listing distinctions among species below that of subspecies or a DPS of a species. Here, the NMFS listing decision was based on distinctions below that of subspecies or distinct population segment of a species. Therefore, the NMFS’s listing decision is arbitrary and capricious, because the Oregon Coast ESU includes both “hatchery spawned” and “naturally-spawned” coho salmon, but the agency’s listing decision arbitrarily excludes “hatchery spawned” coho.... Id. at 1163. Following the Alsea decision, in 2002, NMFS began a review of the 27 West Coast salmonid listings. AR 12; AR 807; AR 808. One of the purposes of this review was to further consider the relationship between the resident and anadromous forms of O. mykiss. See Modesto Irrig’n Dist. v. Evans, 1:02-CV-6553 OWW DLB (“MIDI”), Doc. 79 at 55. 6. The Modesto Irrigation District v. Evans Decision. On December 11, 2002, the MID I plaintiffs filed suit against NMFS regarding its 1998 decision to list the California Central Valley O. mykiss ESU as threatened. The MID I Plaintiffs alleged that NMFS violated the ESA and the Administrative Procedura Act (“APA”) by: (1) listing naturally-spawning, but not hatchery, populations of O. mykiss; and, (2) listing anadromous, but not resident, members of O. mykiss in certain rivers within the Central Valley of California. (Id. at 3.) On May 12, 2004, this Court issued a decision on plaintiffs’ motion for summary judgment in MID I. (MID I, Doc. 79.) With respect to the first allegation, as in Alsea, NMFS’s final rule pertaining to the listing of the Central Valley steelhead, issued March 19, 1998, included hatchery populations as part of the ESU, but listed as endangered only naturally-spawning steelhead. The federal defendants conceded this claim, acknowledging, that, under Alsea, “distinctions below that of a distinct population segment when making listing determinations are improper.” (Id: at 28.) Federal defendants also admitted that the 1998 listing of the Central Valley California steelhead was “legally flawed” in light of Alsea, and did not oppose plaintiffs’ motion for summary judgment on that claim. (Id.) However, intervenors, a coalition of fisheries resource advocacy groups, did oppose plaintiffs’ motion for summary judgment, arguing that hatchery-spawned steelhead are not only not eligible for listing under the ESA, but that they should not have been included as part of any ESU in the first place. (Id. at 29.) The district court first rejected intervenors’ argument that NMFS’s decision to include hatchery populations in the ESU should be declared unlawful. Intervenors allege [federal defendants’] determination that “hatchery populations ... [were] part of the same ESU as the naturally-spawned populations” is unlawful. Intervenors’ conclusion is predicated on their contention that, given the nature of hatchery fish, “[protecting [them] cannot be reconciled with the ESA’s purpose and provisions. Intervenors admit, however, that NMFS added some of the hatchery populations to the ESU based on its conclusion that the stocks had not diverged from wild steelhead to such a degree that they could never be used for recovery.” Intervenors provide selected passages from the AR and Federal Register to support their claims that hatchery fish threaten wild populations. The AR cited, however, does not contain sufficient evidence to invalidate NMFS’ classification of the hatchery population. Assuming that the hatchery fish do pose a threat of harm to the naturally-spawned population, there is insufficient evidence to decide whether this threat rises to such a level as to preclude classification of hatchery spawned population in the same ESU or DPS with naturally-spawned steelhead. Even assuming that hatchery fish “can pose serious threats” as Intervenors claim, no studies indicate that they do so in this case. Where a significant scientific dispute exists over an issue within the agency’s expertise, deference is ordinarily required. [Federal defendants’] classification does not require that fish hatcheries replace natural ecosystems. Intervenors do not explain why the use of hatchery fish as a conservation tool precludes their ESA listing. Although excluding hatchery populations from the listing may be “[c]onsistent” with the ESA, there is no evidence indicating that the ESA requires or necessitates such exclusion. NMFS’s studies also indicate that hatchery populations could be useful in the recovery of wild steelhead and that when interbred, the two form a distinct genetic group. Intervenors do not provide their own scientific evidence to prove that Defendants’ classification was arbitrary, capricious, and unlawful. (Id. at 35-36 (internal citations omitted).) The district court next considered intervenors’ argument, based on National Association of Home Builders v. Norton, 340 F.3d 835 (9th Cir.2003), that it was unlawful for NMFS to include hatchery-born 0. mykiss in the ESU/DPS, but only list naturally-spawned fish. In Home Builders, the Ninth Circuit suggested that FWS could have subdivided a particular owl population into smaller DPSs. Intervenors argued that this indicates NMFS could have listed a unit smaller than an ESU under the ESA. The district court found Home Builders to be inapplicable, reasoning: Intervenors ... confuse two separate issues. The issue in Home Builders was whether FWS properly applied the DPS Policy when it classified the Arizona pygmy-owl population as a DPS. The issue here is whether the NMFS could list under the ESA a unit smaller than a DPS. As a result, the holding in Home Builders does not conflict with that in Alsea and is not binding on this case. (Id. at 38 (emphasis added).) The district court next addressed plaintiffs’ allegation that NMFS violated the ESA by listing only anadromous 0. mykiss, while excluding resident fish from the listing. Plaintiffs maintained that the resident fish had been made part of the ESU and therefore, under Alsea, the listing of only anadromous fish was unlawful. The issue was factual: “whether resident and anadromous populations are groups within the same DPS or are separate DPS[s], distinguished by their behavior.” (Id. at 41-42.) After reviewing the evidence, the district court recognized NFMS’s conclusion: “resident 0. mykiss should be included in the listed steelhead ESU ‘in certain cases,’ such as ‘(1) where resident 0. mykiss have the opportunity to interbreed with anadromous fish below manmade barriers or (2) where resident fish of native lineage once had the ability to interbreed with anadromous fish but no longer do so because they are currently above human-made barriers and are considered essential for recovery of the ESU.’ ” Id. at 43. Plaintiffs did not allege that this two-part test was insufficient or that NMFS failed to apply it properly. The court concluded: Given that [federal defendants] did not classify resident steelhead as part of the DPS, [federal defendants] did not err in the same way as they did in failing to account for hatchery-bred populations in the listing decisions. Whether [federal defendants] erred in failing to classify resident 0. mykiss as part of the DPS is a separate question, and Plaintiffs do not provide enough evidence from the AR or otherwise to support a finding that the agency’s ruling here was unlawful. The issue remains “unclear.” Plaintiffs motion for summary judgment that NMFS’s failure to list resident populations under the ESA [is] impermissible is DENIED. Id. at 43 — 14. 7. Revised Hatchery Listing Policy. In light of the Alsea decision, NMFS announced it would reconsider its Interim Hatchery Listing Policy. 67 Fed.Reg. 6,215, 6,217 (Feb. 11, 2002). NMFS published a proposed revised hatchery listing policy on June 3, 2004, 69 Fed.Reg. 31,354, followed by a final revised Hatchery Listing Policy (“HLP”) on June 28, 2005, 70 Fed.Reg. 37,204. In the HLP, NMFS first emphasized that “[a] key feature of the ESU concept is the recognition of genetic resources that represent the ecological and genetic diversity of the species. These genetic resources can reside in a fish spawned in a hatchery (hatchery fish) as well as in a fish spawned in the wild (natural fish).” Id. at 37,215. In delineating an ESU for listing consideration “NMFS will identify all components of the ESU, including populations of natural fish (natural populations) and hatchery stocks that are part of the ESU.” Id. Those hatchery stocks “with a level of genetic divergence relative to the local natural population(s) that is no more than what occurs within the ESU: (a) are considered part of the ESU; (b) will be considered in determining whether an ESU should be listed under the ESA; and (c) will be included in any listing of the ESU. ” Id. (emphasis added). Status determinations (i.e., determinations as to whether the ESU should be listed as threatened, endangered, or neither) for steelhead ESUs “will be based on the status of the entire ESU.” Id. However, “NMFS will apply this policy in support of the conservation of naturally-spawning salmon and the ecosystems upon which they depend, consistent with section 2(b) of the ESA (16 U.S.C. 1531(b)).” Id. (emphasis added). Accordingly, “[hfatchery fish will be included in assessing an ESU’s status in the context of their contributions to conserving natural self-sustaining populations. ” Id. (emphasis added). Specifically, the effects of hatchery fish on the status of an ESU will depend on which of four key attributes— abundance, productivity, genetic diversity, and spatial distribution — are currently limiting the ESU, and “how the hatchery fish within the ESU affect each of the attributes. ” Id. (emphasis added). The presence of hatchery fish within the ESU can positively affect the overall status of the ESU, and thereby affect a listing determination, by contributing to increasing abundance and productivity of the natural populations in the ESU, by improving spatial distribution, by serving as a source population for repopulating unoccupied habitat, and by. conserving genetic resources of depressed natural populations in the ESU. Conversely, a hatchery program managed without adequate consideration of its conservation effects can affect a listing determination by reducing adaptive genetic diversity of the ESU, and by reducing the reproductive fitness and productivity of the ESU. In evaluating the effect of hatchery fish on the status of an ESU, the presence of a long-term hatchery monitoring and evaluation program is an important consideration. Id. NMFS concluded that “[m]any hatchery programs are capable of producing more fish than are immediately useful in the conservation and recovery of an ESU and can play an important role in fulfilling trust and treaty obligations with regard to harvest of some Pacific salmon and steel-head ■ populations.” Id. Accordingly, NMFS determined that, where appropriate, it will “exercise its authority under section 4(d) of the ESA to allow the harvest of listed hatchery fish that are surplus to the conservation and recovery needs of the ESU, in accordance with approved harvest plans.” Id. at 37,215-37,216. D. The Challenged Listing Process. On June 14, 2004, NMFS issued new proposed listings for 27 ESUs of West Coast salmonids. 69 Fed.Reg. 33,102. NMFS first applied its ESU policy to define the 27 ESUs, noting that the.Alsea court had approved of the ESU Policy as an interpretation of the statutory term “distinct population segment.” 69 Fed. Reg. 33,111. Five -California O. my kiss ESUs were defined: Southern California, South-Central California Coast, Central California Coast, California Central valley, and Northern California. Neither the Southern California nor the South-Central California Coast proposed 0. mykiss ESUs included hatchery stocks, but the other three (Central California Coast, California Central Valley, and Northern California 0. mykiss ESUs) were proposed to include two hatchery programs each., 69 Fed.Reg. at 33,llT-SS,118. With respect to the inclusion of resident (versus anadromous) 0. mykiss, NMFS found that “no suite of morphological or genetic characteristics has been found that consistently distinguishes between the two life-history forms.” Id. at 33,113. Consistent with the ESU Policy, NMFS evaluated the “extent of reproductive isolation and biological divergence from other populations within the ESU.” Id. NMFS found, overall, that populations of 0. mykiss from the same life history form that were geographically separated were more genetically divergent from one another than were resident and anadromous forms found in the same geographical area. Id. In previous listings, NMFS carefully examined the relationship between nearby resident and anadromous populations to determine whether the resident population belonged in the ESU. Id. As a general rule, given that the available data suggested that “resident rainbow trout and steel-head in the same area generally share a common gene pool (at least over evolutionary time periods),” both resident and anadromous populations were included in the same ESU. Id. However, resident populations above long-standing natural barriers and those populations that resulted from the introduction of non-native rainbow trout, were excluded from ESU. Id. In the case of resident populations upstream of impassable human-caused migration barriers (e.g., large mainstem hydroelectric dams), NMFS found “insufficient information to merit their inclusion in steelhead ESUs,” but recommended these populations be “evaluated on a case-by-case basis as more information becomes available on their relationships to below-barrier populations, or on the role these above-barrier resident populations might play in conserving below-barrier populations of 0. mykiss.” m: After Alsea, the BRT adopted a similar framework for determining the ESU/DPS membership of resident 0. mykiss populations geographically associated with anadromous populations: These evaluations were guided by the same biological principles used to define ESUs of natural fish and determine ESU membership of hatchery fish: the extent of reproductive isolation and biological divergence from other populations within the ESU. Ideally, each resident population would be evaluated individually on a case-by-case basis, using all available biological information. In practice, little or no information is available for most resident 0. mykiss populations. To facilitate determinations of the ESU/DPS membership of resident 0. mykiss, the BRT identified three different cases, reflecting the range of geographic relationships between resident and anadromous forms within different watersheds: (1) No obvious physical barriers to interbreeding between resident and anadromous forms; (2) long-standing natural barriers (e.g., a waterfall) between resident and anadromous forms; and (3) relatively recent (e.g., within the last 100 years) human-imposed barriers (e.g., a dam without a fish ladder) between resident and anadromous forms. The BRT adopted the following working assumptions about ESU membership of resident fish falling in each of these three cases. -Where there was no obvious physical barrier to interbreeding between the two life-history forms, resident fish were considered part of the ESU. Empirical studies show that resident and anadromous 0. mykiss are typically very similar genetically when they co-occur with no physical barriers to migration or interbreeding. Where long-standing natural barriers separate resident and anadromous forms, resident populations were not regarded as part of the ESU. Many populations in this category have been isolated from contact with anadromous populations for thousands of years. Empirical studies show that in these cases the resident fish typically show substantial genetic and life-history divergence from the nearest downstream anadromous populations. In cases where the resident fish were separated from the anadromous form by relatively recent human actions (e.g., impassable dams and culverts), the BRT was unable to justify any particular default assumption. The two life-history forms most likely coexisted without any barriers to interbreeding prior to the establishment of the manmade barrier(s). However, as a result of rapid divergence in a novel environment, or displacement by or genetic introgression from non-native hatchery rainbow trout, these resident populations may no longer represent the evolutionary legacy of the 0. mykiss ESU. Given these uncertainties, the BRT left unresolved the ESU membership of 0. mykiss above recent (usually man-made) impassable barriers. In the absence of information indicating that they are part of a common ESU, NMFS does not find such above-barrier populations to be part of the 0. mykiss ESUs under review. Id. at 33,113-114. (These working assumptions are referenced by the parties and the administrative record as the “null hypothesis.”) Based in part on these conclusions, NMFS proposed that all five 0. Mykiss ESUs include resident rainbow trout below impassable barriers that co-occur with anadromous populations. Id. Resident rainbow trout located above one particular impassible barrier were considered part of the Central California Coast proposed ESU because genetic data indicated they were more similar to each other and to other populations within the ESU than they were to outside populations. Id. at 33,118. Once the ESUs were defined, NMFS assessed the extinction risk faced by each ESU. NMFS relied in part upon conclusions reached by the BRT, which evaluated the risk of extinction to the various ESUs based upon the “performance of the naturally spawning populations in each of the ESUs____” Id. at 33,110. To perform this evaluation, the BRT employed the “Viable Salmonid Populations” (“VSP”) criteria, developed “to provide a consistent and logical reference for making viability determinations and are based on a review and synthesis of the conservation biology and salmon literature.” Id. Specifically, “the viability of salmon and steelhead ESUs is characterized by the health, abundance, productivity, spatial structure, and genetic/behavioral diversity of the individual populations within the ESU.” Id. ESUs with fewer populations are more likely to become extinct due to catastrophic events, and have a lower likelihood that the necessary phenotypic and genotypic diversity will exist to maintain future viability. ESUs with limited geographic range are similarly at increased extinction risk due to catastrophic events. ESUs with populations that are geographically distant from each other, or are separated by severely degraded habitat, may lack the connectivity to function as metapopulations (i.e., a group of interconnected subpopulations) and are more likely to become extinct. ESUs with limited diversity are more likely to go extinct as the result of correlated environmental catastrophes or environmental change that occurs too rapidly for an evolutionary response. ESUs comprised of a small proportion of populations meeting or exceeding VSP criteria may lack the source populations to sustain the non-viable declining populations during environmental downturns. ESUs consisting of a single population are especially vulnerable in this regard. Id. at 33,110-33,111. NMFS acknowledged that the BRT’s work was hampered by limited data: As noted above, little or no population data are available for most resident 0. mykiss populations, greatly complicating assessments of ESU-level extinction risk.... As was often the case, no data on the abundance, productivity, spatial structure, or diversity were available for resident populations in an ESU. Id. at 33,113. Nevertheless, based on available data, the BRT concluded that, even with the presence of large resident populations, the complete elimination of the anadromous population might be irreversible. The BRT noted that the presence of relatively numerous resident populations can significantly reduce risks to ESU abundance. However, there is considerable scientific uncertainty as to how the resident form affects extinction risk through its influence on ESU productivity, spatial structure, and diversity. The threats to 0. mykiss ESUs extend beyond low population size and include declining productivity, reduced resilience of productivity to environmental variation, curtailed range of distribution, impediments to population connectivity and reproductive exchange, depleted diversity stemming from loss or blockage of habitat and associated erosion of local adaptation, and erosion of the diversity of expressed migratory behaviors. Thus, the BRT concluded that, despite the reduced risk to abundance for certain 0. mykiss ESUs due to numerically abundant residents, the collective contribution of the resident life-history form to the viability of an ESU in-total is unknown and may not substantially reduce extinction risks to an ESU in-total (NMFS, 2004). Based on present scientific understanding, the BRT could not exclude the possibility that complete loss of anadromous forms from within an ESU may be irreversible. Id. at 33,113-114. After analyzing each ESU under the VSP criteria, the BRT assessed the ESU’s extinction risk based on the performance of the naturally spawning populations. Id. at 33,111. The BRT’s assessment of ESU-level extinction risk uses categories that correspond to the definitions of endangered species and threatened species, respectively, in the ESA: in danger of extinction throughout all or a significant portion of its range, likely to become endangered within the foreseeable future throughout all or a significant portion of its range, or neither. As discussed above, these evaluations do not include consideration of hatchery stocks included in ESUs, and do not evaluate efforts being made to protect the species. Therefore, the BRT’s findings are not to be considered recommendations i'egarding listing. The BRT’s ESU-level extinction risk assessment reflects the BRT’s professional scientific judgment, guided by the analysis of the VSP criteria, as well as by expectations about the likely interactions among the individual VSP criteria. For example, a single VSP criterion with a “High Risk” score might be sufficient to result in an overall extinction risk assessment of “in danger of extinction,” but a combination of several VSP criteria with more moderate risk scores could also lead to the same assessment, or a finding that the ESU is “likely to become endangered.” Id. at 33,111. NMFS treated the BRT’s recommendations as “a partial assessment of the ESU’s extinction risk,” but not as a final determination as to whether listing was warranted. NMFS then incorporated an assessment of the “contributions of within-ESU hatchery programs to the viability of an ESU in-total.” Id. at 33,112. The result is NMFS’s Salmonid Hatchery Inventory and Effects Evaluation Report (“SHIEE Report”), an assessment of the contributions of ESU hatchery programs on ESU viability and extinction risk. See id.; AR 1459. NMFS proposed to list the Southern California ESU as endangered, and the other four California ESUs as threatened. Id. at 33,162-33,163. Following the publication of the proposed listing, NMFS commissioned three separate, independent scientific evaluations, in part to examine the use of the null hypothesis as a means of identifying members of a DPS using the ESU Policy. First, the Salmon Recovery Science Review Panel (“RSRP”), comprised of seven scientists from U.S. and Canadian universities, was convened to provide guidance on the scientific and technical aspects of recovery planning for West Coast populations of salmon and steelhead. AR 1471 at 1. The RSRP concurred with the BRT’s “null hypothesis” that separation of anadromous from resident forms by the existence of longstanding natural barriers justified the decision that the two forms not be considered part of the same DPS under the ESU Policy. AR 1471 at 6. In April 2005, the second panel, the ISAB, concluded that “the presence of both resident and anadromous life-history forms is critical for conserving the diversity of steelhead/rainbow trout populations and, therefore, the overall variability of ESUs.” AR 1443 at 39. Finally, on June 13, 2005, the Hey Panel issued a written report responding to four questions posed by NMFS. Pertinently, NMFS asked the Hey Panel: “Is there a reasonable biological justification for excluding from a conservation unit resident populations that are similar to anadromous populations in that unit?” AR 1442 at 13. Beginning with the three scenarios developed by the BRT in the null hypothesis, the Hey Panel found that where anadromous and resident O. mykiss co-occur and are located below impassible barriers, the null hypothesis’ conclusion that both members belonged in the same ESU was correct. Id. at 13-15. The Hey Panel stated: “In those cases where the two populations co-occur and the lifestyle variation is present as a polymorphism, then it would be biologically justified for the conservation unit to include both the resident and anadromous fish.” Id. at 15. NMFS staff concluded that these three studies “strongly confirm” and are consistent with its recommended final listing determinations that included both resident and anadrmous forms of O. mykiss in the same ESU. AR 2215R (email from Scott Rumsey to others within the National Oceanographic and Atmospheric Administration, of which NMFS is a part). Following an initial public comment period of 90 days, NMFS extended the public comment period two times. 69 Fed.Reg. 53,031 (Aug. 31, 2004); 69 Fed.Reg. 61,348 (Oct. 18, 2004). NMFS received comments disagreeing with the proposal to include rainbow trout in the ESUs and criticism on how it considered resident rainbow trout in evaluating the risk to the continued existence of the entire ESU. 70 Fed.Reg. 37,219, 37,220 (June