19756 Federal Register / Vol. 77, No. 63 / Monday, April 2, 2012 / Proposed Rules 

DEPARTMENT OF THE INTERIOR 

Fish and Wildlife Service 

50 CFR Part 17 

[Docket No. FWS–R8–ES–2008–0045: 

4500030113] 

Endangered and Threatened Wildlife 

and Plants; 12-Month Finding on a 

Petition to List the San Francisco BayDelta Population of the Longfin Smelt 

as Endangered or Threatened 

AGENCY: Fish and Wildlife Service, 

Interior. 

ACTION: Notice of 12-month petition 

finding. 

SUMMARY: We, the U.S. Fish and 

Wildlife Service (Service), announce a 

12-month finding on a petition to list 

the San Francisco Bay-Delta distinct 

population segment (Bay Delta DPS) of 

longfin smelt as endangered or 

threatened and to designate critical 

habitat under the Endangered Species 

Act of 1973, as amended (Act). After 

review of the best available scientific 

and commercial information, we find 

that listing the longfin smelt rangewide 

is not warranted at this time, but that 

listing the Bay-Delta DPS of longfin 

smelt is warranted. Currently, however, 

listing the Bay-Delta DPS of longfin 

smelt is precluded by higher priority 

actions to amend the Lists of 

Endangered and Threatened Wildlife 

and Plants. Upon publication of this 12- 

month finding, we will add the BayDelta DPS of longfin smelt to our 

candidate species list. We will develop 

a proposed rule to list the Bay-Delta 

DPS of longfin smelt as our priorities 

allow. We will make any determinations 

on critical habitat during the 

development of the proposed listing 

rule. During any interim period, we will 

address the status of the candidate taxon 

through our annual Candidate Notice of 

Review (CNOR). 

DATES: The finding announced in this 

document was made on April 2, 2012. 

ADDRESSES: This finding is available on 

the Internet at http:// 

www.regulations.gov at Docket Number 

[FWS–R8–ES–2008–0045]. Supporting 

documentation we used in preparing 

this finding is available for public 

inspection, by appointment, during 

normal business hours at the U.S. Fish 

and Wildlife Service, San Francisco 

Bay-Delta Fish and Wildlife Office, 650 

Capitol Mall, Sacramento, CA 95814. 

Please submit any new information, 

materials, comments, or questions 

concerning this finding to the above 

street address. 

FOR FURTHER INFORMATION CONTACT: 

Mike Chotkowski, Field Supervisor, San 

Francisco Bay-Delta Fish and Wildlife 

Office (see ADDRESSES); by telephone at 

916–930–5603; or by facsimile at 916– 

930–5654 mailto:. If you use a 

telecommunications device for the deaf 

(TDD), please call the Federal 

Information Relay Service (FIRS) at 

800–877–8339. 

SUPPLEMENTARY INFORMATION: 

Background 

Section 4(b)(3)(B) of the Endangered 

Species Act of 1973, as amended (Act) 

(16 U.S.C. 1531 et seq.), requires that, 

for any petition to revise the Federal 

Lists of Endangered and Threatened 

Wildlife and Plants that contains 

substantial scientific or commercial 

information that listing the species may 

be warranted, we make a finding within 

12 months of the date of receipt of the 

petition. In this finding, we will 

determine that the petitioned action is: 

(1) Not warranted, (2) warranted, or (3) 

warranted, but the immediate proposal 

of a regulation implementing the 

petitioned action is precluded by other 

pending proposals to determine whether 

species are endangered or threatened, 

and expeditious progress is being made 

to add or remove qualified species from 

the Federal Lists of Endangered and 

Threatened Wildlife and Plants. Section 

4(b)(3)(C) of the Act requires that we 

treat a petition for which the requested 

action is found to be warranted but 

precluded as though resubmitted on the 

date of such finding, that is, requiring a 

subsequent finding to be made within 

12 months. We must publish these 12- 

month findings in the Federal Register. 

Previous Federal Actions 

On November 5, 1992, we received a 

petition from Mr. Gregory A. Thomas of 

the Natural Heritage Institute and eight 

co-petitioners to add the longfin smelt 

(Spirinchus thaleichthys) to the List of 

Endangered and Threatened Wildlife 

and designate critical habitat in the 

Sacramento and San Joaquin Rivers and 

estuary. On July 6, 1993, we published 

a 90-day finding (58 FR 36184) in the 

Federal Register that the petition 

contained substantial information 

indicating the requested action may be 

warranted, and that we would proceed 

with a status review of the longfin 

smelt. On January 6, 1994, we published 

a notice of a 12-month finding (59 FR 

869) on the petition to list the longfin 

smelt. We determined that the 

petitioned action was not warranted, 

based on the lack of population trend 

data for estuaries in Oregon and 

Washington, although the southernmost 

populations were found to be declining. 

Furthermore, we found the SacramentoSan Joaquin River estuary population of 

longfin smelt was not a distinct 

population segment (DPS) because we 

determined that the population was not 

biologically significant to the species as 

a whole, and did not appear to be 

sufficiently reproductively isolated. 

On August 8, 2007, we received a 

petition from the Bay Institute, the 

Center for Biological Diversity, and the 

Natural Resources Defense Council to 

list the San Francisco Bay-Delta 

(hereafter referred to as the Bay-Delta) 

population of the longfin smelt as a DPS 

and designate critical habitat for the 

DPS concurrent with the listing. On 

May 6, 2008, we published a 90-day 

finding (73 FR 24911) in which we 

concluded that the petition provided 

substantial information indicating that 

listing the Bay-Delta population of the 

longfin smelt as a DPS may be 

warranted, and we initiated a status 

review. On April 9, 2009, we published 

a notice of a 12-month finding (74 FR 

16169) on the August 8, 2007, petition. 

We determined that the Bay-Delta 

population of the longfin smelt did not 

meet the discreteness element of our 

DPS policy and, therefore, was not a 

valid DPS. We therefore determined that 

the Bay-Delta population of the longfin 

smelt was not a listable entity under the 

Act. 

On November 13, 2009, the Center for 

Biological Diversity filed a complaint in 

U.S. District Court for the Northern 

District of California, challenging the 

Service on the merits of the 2009 

determination. On February 2, 2011, the 

Service entered into a settlement 

agreement with the Center for Biological 

Diversity and agreed to conduct a 

rangewide status review and prepare a 

12-month finding to be published by 

September 30, 2011. In the event that 

the Service determined in the course of 

the status review that the longfin smelt 

does not warrant listing as endangered 

or threatened over its entire range, the 

Service agreed to consider whether any 

population of longfin smelt qualifies as 

a DPS. In considering whether any 

population of longfin smelt qualifies as 

a DPS, the Service agreed to reconsider 

whether the Bay-Delta population of the 

longfin smelt constitutes a DPS. At the 

request of the Service, Department of 

Justice requested an extension from the 

Court to allow for a more 

comprehensive review of new 

information pertaining to the longfin 

smelt and to seek the assistance of two 

expert panels to assist us with that 

review. The plaintiffs filed a motion of 

non-opposition, and on October 3, 2011, 

the court granted an extension to March 

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23, 2012 for the publication of a new 12- 

month finding. 

Species Information 

Species Description and Taxonomy 

Longfin smelt measure 9–11 

centimeters (cm) (3.5–4.3 inches (in)) 

standard length, although third-year 

females may grow up to 15 cm (5.9 in). 

The sides and lining of the gut cavity 

appear translucent silver, the back has 

an olive to iridescent pinkish hue, and 

mature males are usually darker in color 

than females. Longfin smelt can be 

distinguished from other smelts by their 

long pectoral fins, weak or absent 

striations on their opercular (covering 

the gills) bones, incomplete lateral line, 

low numbers of scales in the lateral 

series (54 to 65), long maxillary bones 

(in adults, these bones extend past mideye, just short of the posterior margin of 

the eye), and lower jaw extending 

anterior of the upper jaw (Mcallister 

1963, p. 10; Miller and Lea 1972, pp. 

158–160; Moyle 2002, pp. 234–236). 

The longfin smelt belongs to the true 

smelt family Osmeridae and is one of 

three species in the Spirinchus genus; 

the night smelt (Spirinchus starksi) also 

occurs in California, and the shishamo 

(Spirinchus lanceolatus) occurs in 

northern Japan (McAllister 1963, pp. 10, 

15). Because of its distinctive physical 

characteristics, the Bay-Delta population 

of longfin smelt was once described as 

a species separate from more northern 

populations (Moyle 2002, p. 235). 

McAllister (1963, p. 12) merged the two 

species S. thaleichthys and S. dilatus 

because the difference in morphological 

characters represented a gradual change 

along the north-south distribution rather 

than a discrete set. Stanley et al. (1995, 

p. 395) found that individuals from the 

Bay-Delta population and Lake 

Washington population differed 

significantly in allele (proteins used as 

genetic markers) frequencies at several 

loci (gene locations), although the 

authors also stated that the overall 

genetic dissimilarity was within the 

range of other conspecific fish species. 

They concluded that longfin smelt from 

Lake Washington and the Bay-Delta are 

conspecific (of the same species) despite 

the large geographic separation. 

Delta smelt and longfin smelt hybrids 

have been observed in the Bay-Delta 

estuary, although these offspring are not 

thought to be fertile because delta smelt 

and longfin smelt are not closely related 

taxonomically or genetically (California 

Department of Fish and Game (CDFG) 

2001, p. 473). 

Biology 

Nearly all information available on 

longfin smelt biology comes from either 

the Bay-Delta population or the Lake 

Washington population. Longfin smelt 

generally spawn in freshwater and then 

move downstream to brackish water to 

rear. The life cycle of most longfin smelt 

generally requires estuarine conditions 

(CDFG 2009, p. 1). 

Bay-Delta Population 

Longfin smelt are considered pelagic 

and anadromous (Moyle 2002, p. 236), 

although anadromy in longfin smelt is 

poorly understood, and certain 

populations are not anadromous and 

complete their entire life cycle in 

freshwater lakes and streams (see Lake 

Washington Population section below). 

Within the Bay-Delta, the term pelagic 

refers to organisms that occur in open 

water away from the bottom of the water 

column and away from the shore. 

Juvenile and adult longfin smelt have 

been found throughout the year in 

salinities ranging from pure freshwater 

to pure seawater, although once past the 

juvenile stage, they are typically 

collected in waters with salinities 

ranging from 14 to 28 parts per 

thousand (ppt) (Baxter 1999, pp. 189– 

192). Longfin smelt are thought to be 

restricted by high water temperatures, 

generally greater than 22 degrees Celsius 

(°C) (71 degrees Fahrenheit (°F)) (Baxter 

et. al. 2010, p. 68), and will move down 

the estuary (seaward) and into deeper 

water during the summer months, when 

water temperatures in the Bay-Delta are 

higher. Within the Bay-Delta, adult 

longfin smelt occupy water at 

temperatures from 16 to 20 °C (61 to 68 

°F), with spawning occurring in water 

with temperatures from 5.6 to 14.5 °C 

(41 to 58 °F) (Wang 1986, pp. 6–9). 

Longfin smelt usually live for 2 years, 

spawn, and then die, although some 

individuals may spawn as 1- or 3-yearold fish before dying (Moyle 2002, p. 

36). In the Bay-Delta, longfin smelt are 

believed to spawn primarily in 

freshwater in the lower reaches of the 

Sacramento River and San Joaquin 

River. Longfin smelt congregate in deep 

waters in the vicinity of the low salinity 

zone (LSZ) near X2 (see definition 

below) during the spawning period, and 

it is thought that they make short runs 

upstream, possibly at night, to spawn 

from these locations (CDFG 2009, p. 12; 

Rosenfield 2010, p. 8). The LSZ is the 

area where salinities range from 0.5 to 

6 practical salinity units (psu) within 

the Bay-Delta (Kimmerer 1998, p. 1). 

Salinity in psu is determined by 

electrical conductivity of a solution, 

whereas salinity in parts per thousand 

(ppt) is determined as the weight of salts 

in a solution. For use in this document, 

the two measurements are essentially 

equivalent. X2 is defined as the distance 

in kilometers up the axis of the estuary 

(to the east) from the Golden Gate 

Bridge to the location where the daily 

average near-bottom salinity is 2 psu 

(Jassby et al. 1995, p. 274; Dege and 

Brown 2004, p. 51). 

Longfin smelt in the Bay-Delta may 

spawn as early as November and as late 

as June, although spawning typically 

occurs from January to April (CDFG 

2009, p. 10; Moyle 2002, p. 36). Longfin 

smelt have been observed in their 

winter and spring spawning period as 

far upstream as Isleton in the 

Sacramento River, Santa Clara shoal in 

the San Joaquin system, Hog Slough off 

the South-Fork Mokelumne River, and 

in Old River south of Indian Slough 

(CDFG 2009a, p. 7; Radtke 1966, pp. 

115–119). 

Exact spawning locations in the Delta 

are unknown and may vary from year to 

year in location, depending on 

environmental conditions. However, it 

seems likely that spawning locations 

consist of the overlap of appropriate 

conditions of flow, temperature, and 

salinity with appropriate substrate 

(Rosenfield 2010, p. 8). Longfin smelt 

are known to spawn over sandy 

substrates in Lake Washington and 

likely prefer similar substrates for 

spawning in the Delta (Baxter et. al. 

2010, p. 62; Sibley and Brocksmith 

1995, pp. 32–74). Baxter found that 

female longfin smelt produced between 

1,900 and 18,000 eggs, with fecundity 

greater in fish with greater lengths 

(CDFG 2009, p. 11). At 7 °C (44.6 °F), 

embryos hatch in 40 days (Dryfoos 1965, 

p. 42); however, incubation time 

decreases with increased water 

temperature. At 8–9.5 °C (46.4–49.1 °F), 

embryos hatch at 29 days (Sibley and 

Brocksmith 1995, pp. 32–74). 

Larval longfin smelt less than 12 

millimeters (mm) (0.5 in) in length are 

buoyant because they have not yet 

developed an air bladder; as a result, 

they occupy the upper one-third of the 

water column. After hatching, they 

quickly make their way to the LSZ via 

river currents (CDFG 2009, p. 8; Baxter 

2011a, pers comm.). Longfin smelt 

develop an air bladder at approximately 

12–15 mm (0.5–0.6 in.) in length and are 

able to migrate vertically in the water 

column. At this time, they shift habitat 

and begin living in the bottom twothirds of the water column (CDFG 2009, 

p. 8; Baxter 2008, p. 1). 

Longfin smelt larvae can tolerate 

salinities of 2–6 psu within days of 

hatching, and can tolerate salinities up 

to 8 psu within weeks of hatching 

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(Baxter 2011a, pers. comm.). However, 

very few larvae (individuals less than 20 

mm in length) are found in salinities 

greater than 8 psu, and it takes almost 

3 months for longfin smelt to reach 

juvenile stage. A fraction of juvenile 

longfin smelt individuals are believed to 

tolerate full marine salinities (greater 

than 8 psu) (Baxter 2011a, pers. comm.). 

Longfin smelt are dispersed broadly 

in the Bay-Delta by high flows and 

currents, which facilitate transport of 

larvae and juveniles long distances. 

Longfin smelt larvae are dispersed 

farther downstream during high 

freshwater flows (Dege and Brown 2004, 

p. 59). They spend approximately 21 

months of their 24-month life cycle in 

brackish or marine waters (Baxter 1999, 

pp. 2–14; Dege and Brown 2004, pp. 58– 

60). 

In the Bay-Delta, most longfin smelt 

spend their first year in Suisun Bay and 

Marsh, although surveys conducted by 

the City of San Francisco collected some 

first-year longfin in coastal waters 

(Baxter 2011c, pers. comm.; City of San 

Francisco 1995, no pagination). The 

remainder of their life is spent in the 

San Francisco Bay or the Gulf of 

Farallones (Moyle 2008, p. 366; City of 

San Francisco 1995, no pagination). 

Rosenfield and Baxter (2007, pp. 1587, 

1590) inferred based on monthly survey 

results that the majority of longfin smelt 

from the Bay-Delta were migrating out 

of the estuary after the first winter of 

their life cycle and returning during late 

fall to winter of their second year. They 

noted that migration out of the estuary 

into nearby coastal waters is consistent 

with captures of longfin smelt in the 

coastal waters of the Gulf of Farallones. 

It is possible that some longfin smelt 

may stay in the ocean and not re-enter 

freshwater to spawn until the end of 

their third year of life (Baxter 2011d, 

pers. comm.). Moyle (2010, p. 8) states 

that longfin smelt that migrate out of 

and back into the Bay-Delta estuary may 

primarily be feeding on the rich 

planktonic food supply in the Gulf of 

Farallones. Rosenfield and Baxter (2007, 

p. 1290) hypothesize that the movement 

of longfin smelt into the ocean or deeper 

water habitat in summer months is at 

least partly a behavioral response to 

warm water temperatures found during 

summer and early fall in the shallows of 

south San Francisco Bay and San Pablo 

Bay (Rosenfield and Baxter 2007, p. 

1590). 

In the Bay-Delta, calanoid copepods 

such as Pseudodiatomus forbesi and 

Eurytemora sp., as well as the cyclopoid 

copepod Acanthocyclops vernali (no 

common names), are the primary prey of 

longfin smelt during the first few 

months of their lives (approximately 

January through May) (Slater 2009b, 

slide 45). Copepods are a type of 

zooplankton (organisms drifting in the 

water column of oceans, seas, and 

bodies of fresh water). The longfin 

smelt’s diet shifts to include mysids 

such as opossum shrimp (Neomysis 

mercedis) and other small crustaceans 

(Acanthomysis sp.) as soon as they are 

large enough (20–30 mm (0.78–1.18 in)) 

to consume these larger prey items, 

sometime during the summer months of 

the first year of their lives (CDFG 2009, 

p. 12). Upstream of San Pablo Bay, 

mysids and amphipods form 80–95 

percent or more of the juvenile longfin 

smelt diet by weight from July through 

September (Slater 2009, unpublished 

data). Longfin smelt occurrence is likely 

associated with the occurrence of their 

prey, and both of these invertebrate 

groups occur near the bottom of the 

water column during the day under 

clear water marine conditions. 

Lake Washington Population 

The Lake Washington population near 

Seattle, Washington is considered a 

landlocked population of longfin smelt, 

as are the populations of longfin smelt 

in Harrison and Pitt Lakes in British 

Columbia east of Vancouver (Chigbu 

and Sibley 1994, p. 1). These 

populations are not anadromous and 

complete their entire life cycle in 

freshwater. Young longfin smelt feed 

primarily on the copepods Diaptomus, 

Diaphanosoma, and Epischura, with 

older fish switching over to mysids 

(Wydoski and Whitney 2003, p. 105). 

Chigbu and Sibley (1994, pp. 11–14) 

found that mysids dominate the diets of 

longfin smelt in their second year of life 

(age-1), while amphipods, copepods, 

and daphnia also contributed 

substantially to the longfin smelt’s diet. 

A strong spawning run of longfin smelt 

occurs on even years in Lake 

Washington, with weak runs on odd 

years. They spawn at night in the lower 

reaches of at least five streams that flow 

into Lake Washington. Water 

temperatures during spawning were 

4.4 °C (40 °F) to 7.2 °C (45 °F) (Wydoski 

and Whitney 2003, p. 105). Chigbu and 

Sibley (1994, p. 9) found that female 

longfin smelt produced between 6,000 

and 24,000 eggs, while Wydoski and 

Whitney (2003, p. 105) found that 

longfin smelt produced between 1,455 

and 1,655 eggs. The reason for the large 

difference between the observations of 

these two studies is not known. 

Habitat 

Longfin smelt have been collected in 

estuaries from the Bay-Delta (33° N 

latitude) to Prince William Sound (62° 

N latitude), a distance of approximately 

1,745 nautical miles (Figure 1). Mean 

annual water temperatures range from 

2.4 °C (36.3 °F) in Anchorage to 14.1 °C 

(57.3 °F) in San Francisco (NOAA 

2011a). The different estuary types that 

the longfin smelt is found in and the 

range of variability of environments 

where the species has been observed 

will be discussed below. 

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The origin and geomorphology of 

West Coast estuaries result from 

geologic forces driven by plate tectonics 

and have been modified by glaciations 

and sea level rise (Emmett et al. 2000, 

pp. 766–767). Major classifications of 

estuaries include fjord, drowned-river 

valley, lagoon, and bar-built. Fjords 

typically are long, narrow, steep-sided 

valleys created by glaciation, with 

moderately high freshwater inflow but 

little mixing with seawater due to the 

formation of a sill at the mouth (NOAA 

2011b). Fjords generally have one large 

tributary river and numerous small 

streams (Emmett et al. 2000, p. 768). 

Drowned-river valleys, also termed 

coastal plain estuaries, are found 

primarily in British Columbia, 

Washington, and Oregon, and are the 

dominant type along the west coast, 

occurring as a result of rising sea levels 

following the last ice age. Lagoons, 

primarily found in California, occur 

where coastal river systems that are 

closed to the sea by sand spits for much 

of the year are breached during the 

winter (Emmett et al. 2000, p. 768). The 

rarest type of estuary is the bar-built, 

which is formed by a bar and semienclosed body of water (Emmett et al. 

2000, p. 768). Estuaries have also been 

classified by physical or environmental 


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variables into Northern Riverine, 

Southern California, Northern Estuarine, 

Central Marine, Fjord, and Coastal 

Northwest Groups (Monaco et al. 1992, 

p. 253). Longfin smelt have been 

collected from estuaries of all types and 

classifications. 

The Bay-Delta is the largest estuary on 

the West Coast of the United States 

(Sommer et al. 2007, p. 271). The 

modern Bay-Delta bears only a 

superficial resemblance to the historical 

Bay-Delta. The Bay-Delta supports an 

estuary covering approximately 1,235 

square kilometers (km2) (477 square 

miles (mi2)) (Rosenfield and Baxter 

2007, p. 1577), which receives almost 

half of California’s runoff (Lehman 

2004, p. 313). The historical island 

marshes surrounded by low natural 

levees are now intensively farmed and 

protected by large, manmade structures 

(Moyle 2002, p. 32). The watershed, 

which drains approximately 40 percent 

of the land area of California, has been 

heavily altered by dams and diversions, 

and nonnative species now dominate, 

both in terms of numbers of species and 

numbers of individuals (Kimmerer 

2004, pp. 7–9). The Bay Institute has 

estimated that intertidal wetlands in the 

Delta have been diked and leveed so 

extensively that approximately 95 

percent of the 141,640 hectares (ha) 

(350,000 acres (ac)) of tidal wetlands 

that existed in 1850 are gone (The Bay 

Institute 1998, p. 17). 

The physical and biological 

characteristics of the estuary define 

longfin smelt habitat. The Bay-Delta is 

unique in that it contains significant 

amounts of tidal freshwater (34 km2 (13 

mi2)) and mixing zone (194 km2 (75 

mi2)) habitat (Monaco et al. 1992, pp. 

254–255, 258). San Francisco Bay is 

relatively shallow and consists of a 

northern bay that receives freshwater 

inflow from the Sacramento-San Joaquin 

system and a southern bay that receives 

little freshwater input (Largier 1996, p. 

69). Dominant fish species are highly 

salt-tolerant and include the 

commercially important Pacific sardine 

(Sardinops sagax) and rockfish 

(Sebastes spp.). Major habitat types 

include riverine and tidal wetlands, 

mud flat, and salt marsh, with 

substantial areas of diked wetland 

managed for hunting. The sandy 

substrates that longfin smelt are 

presumed to use for spawning are 

abundant in the Delta. 

The Russian River collects water from 

a drainage area of approximately 3,846 

km2 (1,485 mi2), has an average annual 

discharge of 1.6 million acre-feet, and is 

approximately 129 km (80 mi) in length 

(Langridge et al. 2006, p. 4). Little 

information is available on potential 

spawning and rearing habitat for longfin 

smelt, but it is likely to be both small 

and ephemeral because spawning and 

rearing habitat is highly dependent 

upon freshwater inflow, and there may 

be insufficient freshwater flows for 

spawning and rearing in some years 

(Moyle 2010, p. 5). A berm encloses the 

mouth of the Russian River during 

certain times of the year, essentially 

cutting it off from the coastal ocean. 

This results in a lack of connectivity 

with the ocean that could be important 

during dry years. However, in most 

years the berm is breached by 

freshwater flows, which allows longfin 

smelt to enter the Russian River and 

spawn. 

The Eel River drains an area of 3,684 

mi2 (9,542 km2) and is the third largest 

river in California. Wetlands and tidal 

areas have been reduced 60 to 90 

percent since the 1800s (Cannata and 

Hassler 1995, p. 1), resulting in changes 

in tidal influence and a reduction in 

channel connectivity (Downie 2010, p. 

15). The estuary is characterized by a 

small area where freshwater and 

saltwater mix (Monaco et al. 1992, p. 

258) and thus provides only limited 

potential longfin rearing habitat. 

Humboldt Bay is located only 26 km 

(16 mi) north of the Eel River and is 

approximately 260 mi (418 km) north of 

the Bay-Delta. Humboldt Bay is the 

second largest coastal estuary in 

California after the Bay-Delta. However, 

true estuarine conditions rarely occur in 

Humboldt Bay because it receives 

limited freshwater input and 

experiences little mixing of freshwater 

and saltwater (Pequegnat and Butler 

1982, p. 39). 

The Klamath Basin has been 

extensively modified by levees, dikes, 

dams, and the draining of natural water 

bodies since the U.S. Bureau of 

Reclamation’s Klamath Project, 

designed to improve the region’s ability 

to support agriculture, began in 1905. 

These changes to the system have 

altered the biota of the basin (NRC 2008, 

p. 16). Over the years, loss of thousands 

of acres of connected wetlands and open 

water in the Klamath River Basin has 

greatly reduced habitat value, likely 

depleting the ability of this area to cycle 

nutrients and affecting water quality 

(USFWS 2008, p. 55). The river drains 

a vast area of 10 million ac (4 million 

ha). Although a large river, the Klamath 

River estuary is characterized by small 

tidal freshwater and mixing zones 

(Monaco et al. 1992, p. 258) and thus 

provides limited potential longfin smelt 

rearing habitat. 

Yaquina Bay is located on the midcoastal region of Oregon, 201 km (125 

mi) south of the Columbia River and 348 

km (216 mi) north of the California 

border. Wetlands encompass 548 ha 

(1,353 ac), including 216 ha (534 ac) of 

mud flats and 331 ha (819 ac) of tidal 

marshes (Yaquina Bay Geographic 

Response Plan 2005, p. 2.1). Forty-eight 

percent of the estuary is intertidal 

(Brown et al. 2007, p. 6). The estuary 

has been modified greatly, being 

alternately dredged and filled at 

different locations as a result of 

development. Dredging, industrial, and 

residential uses have reduced fish 

habitat and water quality in the bay. 

Dredging disturbs sediment, resulting in 

increased turbidity and reduced 

sunlight penetration, which can impact 

native eelgrasses and the benthic 

species dependent eelgrass beds for 

breeding, spawning, and shelter 

(Oberrecht 2011, pp. 1–8). 

On the Columbia River, dams, dikes, 

maintenance dredging, and urbanization 

have all contributed to habitat loss and 

alterations that have negatively affected 

fish and wildlife populations (Lower 

Columbia River Estuary Partnership 

2011, p. 1). It is estimated that as much 

as 43 percent of estuarine tidal marshes 

and 77 percent of tidal swamps in the 

river estuary available for fish species 

have been lost since 1870 (Columbia 

River Estuary Study Taskforce 2006, pp. 

1–30). Sixty square miles of peripheral 

tidal habitat have been lost to diking, 

filling, and conversion to upland habitat 

for industrial and agricultural use since 

1870 (Columbia River Estuary Study 

Taskforce 2006, p. 1). Prior to 

construction of dams, estuary islands 

and much of the floodplain were 

inundated throughout the year, 

beginning in December and again in 

May or June. Dam operations on the 

Columbia River’s main stem and major 

tributaries have substantially reduced 

peak river flows. Dikes and levees have 

all but eliminated flooding in many lowlying areas. Dredging of shipping 

channels has caused loss of wetlands 

and altered shoreline configuration. 

Dredging has resulted in large sediment 

reductions upstream, and the dredged 

sediments have created islands 

downstream. This has likely reduced 

spawning habitat and sheltering sites for 

fish (OWJP 1991, pp. 1–24; Lower 

Columbia Fish Recovery Board 2004a, 

pp. 1–192). 

Puget Sound is a large saltwater 

estuary of interconnected flooded 

glacial valleys located at the northwest 

corner of the State of Washington. Puget 

Sound is about 161 km (100 mi) long, 

covers about 264,179 ha (652,800 ac), 

and has over 2,092 km (1,300 mi) of 

shoreline. Fed by streams and rivers 

from the Olympic and Cascade 

Mountains, waters flow out to the 

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Pacific Ocean through the Strait of Juan 

de Fuca (Lincoln 2000, p. 1). The basin 

consists of eight major habitat types, the 

largest of which is kelp and eelgrass, but 

also includes wetlands, mudflats, and 

sandflats. Puget Sound consists of five 

regions, each with its own physical and 

biological characteristics. Urban and 

industrial development borders the 

main basin, which is bounded by Port 

Townsend on the north and the Narrows 

(Tacoma) on the south. Approximately 

30 percent of freshwater inflow to the 

main basin is from the Skagit River, 

which drains an area of approximately 

8,011 km2 (3,093 mi2). Sills at 

Admiralty Inlet and the Narrows 

influence circulation. Puget Sound is 

highly productive. The fish community 

includes many commercially important 

species, such as Pacific herring, Pacific 

salmon, and several species of rockfish 

(NOAA 2011c, p. 11). There are 10 

major dams and thousands of small 

water diversions in the Puget Sound 

system (Puget Sound Partnership 2008b, 

p. 21). Human activities in the region 

have resulted in the loss of 75 percent 

of the saltwater marsh habitat and 90 

percent of the estuarine and riverine 

wetlands (Puget Sound Partnership 

2008b, p. 21). 

The coastline of British Columbia has 

been shaped by plate tectonics and 

extensive glaciations. Particularly in 

summer, prevailing winds drive coastal 

upwelling, which results in a highly 

productive food chain. The tidal 

amplitude is 3–5 meters (m) (9.8–16.4 ft) 

in most areas, and numerous large and 

small rivers provide freshwater inflow. 

Biological communities are diverse and 

highly variable, including coastal 

wetlands, kelp beds, and seaweed beds 

that support a diverse marine fauna 

(Dale 1997, pp. 13–15). Nearshore areas 

of British Columbia are characterized by 

steep to moderately sloping fjords, 20– 

50 m (65–164 ft) in depth, with 

salinities ranging from 18 to 28 ppt 

(AXYS Environmental Consulting 2001, 

pp. 5, 11, 20). Bar-built estuaries that are 

semi-enclosed by an ocean-built bar 

occur on the west coast of Vancouver 

Island and the Queen Charlotte Islands 

(Emmett et al. 2000, pp. 769–770). 

Oxygen depletion is common in fjords 

(Emmett et al. 2000, p. 776), but because 

they are anadromous, longfin smelt 

would presumably be able to avoid 

those conditions. However, if depletion 

were to occur during spawning or 

rearing, recruitment could be affected. 

The Fraser River, at approximately 

1,375 miles (2,213 km), is the longest 

river in British Columbia and the tenth 

longest river in Canada. The Fraser 

River drains an area of 220,000 km2 and 

flows to the Strait of Georgia at the City 

of Vancouver before it drains into the 

Pacific Ocean. Diking and drainage in 

the lower basin area have reduced the 

extent of estuarine wetlands that are 

important to the longfin smelt and other 

fishes that utilize these areas (Blomquist 

2005, p. 8). 

Habitat types common in Alaskan 

estuaries include eel grass beds, 

understory kelp, sand and gravel beds, 

and bedrock outcrops (NOAA 2011d). 

Shallow nearshore areas provide a 

mosaic of habitat types that support a 

variety of fishes (NOAA 2005, p. 59). In 

southwestern Alaska, the related 

osmerid species capelin (Mallotus 

villosus) was found to occur in sandand-gravel habitats, and the surf smelt 

(Hypomesus pretiosus) was found to 

occur in bedrock habitats (NOAA 2005, 

pp. 27, 29). As in British Columbia, if 

oxygen depletion occurs in fjord 

habitats during spawning or rearing, 

longfin smelt recruitment could be 

affected. 

Cook Inlet is a large mainland 

Alaskan estuary located in the northern 

Gulf of Alaska. Cook Inlet is 

approximately 290 km (180 miles) long. 

The watershed covers about 100,000 

km2 of southern Alaska (USACE 2011, 

p. 1). 

Distribution 

Longfin smelt are widely distributed 

along 3,541 km (2,200 mi) of Pacific 

coastline from the Bay-Delta to Cook 

Inlet, Alaska (Table 1). We found no 

evidence of range contraction; the 

current distribution of longfin smelt 

appears to be similar to its historical 

distribution. 

TABLE 1—KNOWN OCCURRENCES OF LONGFIN SMELT

State Location Reference 

California .............................................. Monterey Bay .......................................................... Eschmeyer 1983, p. 82; Wang 1986, pp. 6–10). 

Bay-Delta ................................................................. Eschmeyer 1983, p. 82; Wang 1986, pp. 6–10. 

Offshore Bay-Delta .................................................. City of San Francisco 1993, p. 5–8. 

Russian River Estuary ............................................ Cook 2010, pers. comm. 

Van Duzen River ..................................................... Moyle 2002, p. 235. 

McNulty Slough of Eel River ................................... CDFG 2010, unpublished data. 

Offshore Humboldt Bay ........................................... Quirollo 1994, pers. comm. 

Humboldt Bay and tributaries ................................. CDFG 2010, unpublished data. 

Mad River ................................................................ Moyle 2002, p. 235. 

Klamath River .......................................................... Kisanuki et al. 1991, p. 72, CDFG 2009, p. 5. 

Lake Earl ................................................................. D. McLeod field note 1989 

(Cannata and Downie 2009). 

Oregon ................................................. Coos Bay ................................................................. Veroujean 1994, p. 1. 

Yaquina Bay ............................................................ ODFW 2011, pp. 1–3, ANHP 2006, p. 3. 

Tillamook Bay .......................................................... Ellis 2002, p. 17. 

Columbia River Estuary .......................................... ODFW 2011, pp. 1–3. 

Washington .......................................... Willapa Bay ............................................................. WDFW 2011, pp. 1–3. 

Grays Harbor ........................................................... U.S. Army Corps of Engineers 2000, p. 2. 

Puget Sound Basin ................................................. Miller and Borton 1980, p. 17.4. 

Lake Washington .................................................... Chigbu and Sibley 1994, p. 1. 

British Columbia ................................... Fraser River ............................................................ Fishbase 2011a, p. 1; Fishbase 2011b, p. 1. 

Pitt Lake .................................................................. Taylor 2011, pers. comm. 

Harrison Lake .......................................................... Page and Burr 1991, p. 57. 

Vancouver ............................................................... Hart 1973, p. 147. 

Prince Rupert .......................................................... Hart 1973, p. 147. 

Skeena Estuary ....................................................... Kelson 2011, pers. comm. 

Alaska .................................................. Dixon Entrance ........................................................ Alaska Natural Heritage Program 2006, p. 3. 

Sitka National Historical Park ................................. NPS 2011, p. 1. 

Glacier Bay .............................................................. Arimitsu 2003, pp. 35, 41. 

Klondike Gold Rush National Historical Park ......... NPS 2011, p. 1. 

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TABLE 1—KNOWN OCCURRENCES OF LONGFIN SMELT—Continued 

State Location Reference 

Yakutat Bay ............................................................. Alaska Natural Heritage Program 2006, p. 3. 

Wrangell-St. Elias National Park ............................. Arimitsu 2003, pp. 35, 41, NPS 2011, p. 1. 

Cook Inlet ................................................................ NOAA 2010b, p. 4, NOAA 2010a, p. 8. 

Kachemak Bay ........................................................ Abookire et al. 2000, NPS 2011, p. 1. 

Hinchinbrook Island ................................................. Alaska Natural Heritage Program 2006, p. 3. 

Lake Clark National Park and Preserve ................. NPS 2011, p. 1. 

Prince William Sound .............................................. Alaska Natural Heritage Program 2006, p. 3. 

California 

The southernmost known population 

of longfin smelt is the Bay-Delta estuary, 

and longfin smelt occupy different 

habitats of the estuary at various stages 

in their life cycle (See Habitat section 

above). Eschmeyer (1983, p. 82) 

reported the southern extent of the 

range as Monterey Bay, and Wang (1986, 

pp. 6–10) reported that an individual 

longfin smelt had been captured at Moss 

Landing in Monterey Bay in 1980. Most 

sources, however, identify the Bay-Delta 

as the southern extent of the species’ 

range (Moyle 2002, p. 235). 

Small numbers of longfin were 

collected within the Russian River 

estuary each year between 1997 and 

2000 (SCWA 2001, p. 18). No surveys 

were conducted in 2001 or 2002 (Cook 

2011, pers. comm.). Recent surveys 

(since 2003) in the Russian River 

estuary conducted by Sonoma County 

Water Agency have not collected longfin 

smelt; however, in 2003, trawling 

surveys were replaced by beach seining, 

a type of survey less likely to capture a 

pelagic fish species such as the longfin 

smelt. Longfin smelt breeding has not 

been documented at the Russian River 

(Baxter 2011b, pers. comm.), and 

because of its limited size, the Russian 

River estuary is not believed to be 

capable of supporting a self-sustaining 

longfin smelt population (The Bay 

Institute et al. 2007, p. ii; Moyle 2010, 

p. 5). 

Longfin smelt were observed 

spawning in the Eel River estuary in 

1974 (Puckett 1977, p. 19). Although 

longfin were observed in the Eel River 

in 2008 and 2009 (Cannata and Downie 

2009), it is unknown whether or not 

they currently spawn there. Humboldt 

Bay is located 420 km (260 mi) north of 

the Bay-Delta. Longfin smelt were 

collected in Humboldt Bay or its 

tributaries every year from 2003 to 2009, 

with the exception of 2004 (CDFG 2010, 

unpublished data). Longfin smelt also 

have been observed in coastal waters 

adjacent to Humboldt Bay (Quirollo 

1994, pers. comm.). The Humboldt Bay 

population is thought to be the nearest 

known breeding population to the BayDelta (Baxter 2011b, pers. comm.). 

Longfin smelt were collected 

consistently in the Klamath River 

estuary between 1979 and 1989 

(Kisanuki et al. 1991, p. 72), and one 

longfin smelt was collected in the 

Klamath River in 2001 (CDFG 2009, 

p. 5). 

Oregon 

In Oregon, there are historical records 

of longfin smelt in Tillamook Bay, 

Columbia River, Coos Bay, and Yaquina 

Bay (ANHP 2006, p. 3). One individual 

was detected in Tillamook Bay in 2000 

(Ellis 2002, p. 17). Williams et al. (2004, 

p. 30) collected 308 longfin in the 

Columbia River estuary in 2004. Longfin 

smelt were reported in the Columbia 

River estuary, the coastal waters 

adjacent to the Columbia River, and in 

Yaquina Bay in 2009 (Nesbit 2011, pers. 

comm.). In Coos Bay, longfin smelt were 

detected in low numbers in the early 

1980s. However, longfin smelt do not 

appear to be common in Coos Bay and 

were not detected during sampling that 

occurred in the 1970s and the late 1980s 

(Veroujean 1994, no pagination). 

Washington 

In Washington, within the Puget 

Sound Basin, longfin smelt are known 

to occur in the Nooksack River, 

Bellingham Bay, Snohomish River, 

Duwamish River, Skagit Bay, Strait of 

San Juan de Fuca, Twin River, and 

Pysht River (Table 1). Longfin smelt are 

known to occur in nearby Bellingham 

Bay (Penttila 2007, p. 4). Longfin smelt 

were collected in the Snohomish River 

estuary during extensive beach seine 

and fyke trapping in 2009 (Rice 2010, 

pers. comm.). Longfin smelt were 

captured (reported as non-target) in 

high-rise otter trawls in the lower 

Duwamish River (Anchor and King 

County 2007, p. 11). Longfin smelt are 

common in the Strait of San Juan de 

Fuca (Penttila 2007, p. 4). Miller et al. 

(1980, p. 28) found longfin smelt to be 

the second most common species in 

tow-net surveys conducted in the Strait 

of San Juan de Fuca. Most fish caught 

in these surveys were young of the year 

and were found near the Twin and 

Pysht Rivers, both of which may have 

suitable spawning grounds (Miller et al. 

1980, p. 28). Occurrences of longfin 

smelt within northern Puget Sound and 

the Strait of Georgia may reflect the 

abundance and distribution of the 

anadromous populations from the 

Fraser River in British Columbia 

(Washington Department of Fish and 

Wildlife 2011, pp. 1–3). Currently, the 

National Park Service states that longfin 

smelt are probably present within 

Olympic National Park (NPS 2011, p. 1). 

Longfin smelt appear to be common in 

Grays Harbor (U.S. Army Corps of 

Engineers 2000, p. 2). Longfin smelt 

have been infrequently documented in 

the upper Chehalis estuary at 

Cosmopolis; however, when they do 

occur, they have been reported as 

abundant (Anderson 2011). Ocean 

trawls off Willapa Bay have collected 

longfin smelt, although no spawning 

population has been identified in the 

basin (Anderson 2011). 

A resident, freshwater population of 

longfin smelt occurs in Lake 

Washington (Chigbu and Sibley 1994, p. 

1). First caught in 1959, it is believed 

that the longfin smelt either were 

introduced to the lake or became 

trapped during canal construction 

(Chigbu et al. 1998, p. 180). In the 

1960s, the abundance of longfin smelt in 

Lake Washington was low but increased 

to higher levels in the 1980s (Chigbu 

and Sibley 1994, p. 4). 

British Columbia 

Longfin smelt populations occur in 

Pitt Lake and Harrison Lake in British 

Columbia (Page and Burr 1991, p. 57; 

Taylor 2011, pers. comm.); these 

populations are believed to be resident 

fish that are not anadromous (that is, 

they are thought to complete their entire 

life cycle in freshwater). Pitt Lake is 

located approximately 64 river km (40 

mi) up the Fraser and Pitt Rivers, and 

Harrison Lake is located approximately 

121 river km (75 mi) up the Fraser and 

Harrison Rivers. Longfin smelt are 

known to occur within the Fraser River 

near Vancouver (Hart 1973, p. 147; 

Fishbase 2011a, p. 1; Fishbase 2011b, p. 

1). Longfin smelt are also known to 

occur in the Skeena River estuary near 

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Prince Rupert (Hart 1973, p. 147; Kelson 

2011, pers. comm.; Gottesfeld 2002, p. 

54). 

Alaska 

In Alaska, longfin smelt are known 

from Hinchinbrook Island, Prince 

William Sound, Dixon Entrance, 

Yakutat Bay, and Cook Inlet (Alaska 

Natural Heritage Program 2006, p. 3). In 

nearly 1,000 recent beach seine surveys 

in Alaska, longfin smelt have only been 

caught off Fire Island in upper Cook 

Inlet in 2009 and 2010 (NOAA 2010b, 

p. 4; Johnson 2010, pers. comm.; Wing 

2010, pers. comm.). However, as stated 

earlier, longfin smelt are unlikely to be 

caught in beach seine surveys because 

they are a pelagic species and do not 

typically occur near shore where beach 

seine surveys take place. Surveys in 

Prince William Sound did not collect 

longfin smelt in 2006 or 2007 (NOAA 

2011, p. 1). Longfin smelt were collected 

in Wrangell-St. Elias National Park and 

Glacier Bay in 2001 and 2002 (Arimitsu 

2003, pp. 35, 41). Longfin were 

collected in Kachemak Bay in 1996– 

1998 seine and trawling surveys 

(Abookire et al. 2000). The NPS was not 

able to confirm presence or absence in 

Lake Clark National Park and Preserve. 

The NPS concludes that presence is 

probable in Glacier Bay National Park 

and Preserve, Klondike Gold Rush 

National Historical Park, Sitka National 

Historical Park, and Wrangell-St. Elias 

National Park and Preserve (NPS 2011, 

p. 1). 

Abundance 

In most locations throughout their 

range, longfin smelt populations have 

not been monitored. Within the BayDelta, longfin smelt are consistently 

collected in the monitoring surveys that 

have been conducted by CDFG as far 

back as the late 1960s. We know of no 

similar monitoring data for other longfin 

smelt populations. CDFG did report 

catches of longfin smelt in Humboldt 

Bay from surveys conducted between 

2003 and 2009; small numbers of 

longfin were collected each of the years 

except 2004 (CDFG 2010, unpublished 

data). Moyle (2002, p. 237; 2010, p. 4) 

noted that the longfin smelt population 

in Humboldt Bay appeared to have 

declined between the 1970s and 2002, 

but survey data are not available from 

that time. 

Longfin smelt numbers in the BayDelta have declined significantly since 

the 1980s (Moyle 2002, p. 237; 

Rosenfield and Baxter 2007, p. 1590; 

Baxter et. al. 2010, pp. 61–64). 

Rosenfield and Baxter (2007, pp. 1577– 

1592) examined abundance trends in 

longfin smelt using three long-term data 

sets (1980–2004) and detected a 

significant decline in the Bay-Delta 

longfin smelt population. They 

confirmed the positive correlation 

between longfin smelt abundance and 

freshwater flow that had been 

previously documented by others 

(Stevens and Miller 1983, p. 432; Baxter 

et al. 1999, p. 185; Kimmerer 2002b, p. 

47), noting that abundances of both 

adults and juveniles were significantly 

lower during the 1987–1994 drought 

than during either the pre- or postdrought periods (Rosenfield and Baxter 

2007, pp. 1583–1584). 

Despite the correlation between 

drought and low population in the 

1980s and 90s, the declines in the first 

decade of this century appear to be 

caused in part by additional factors. 

Abundance of longfin smelt has 

remained very low since 2000, even 

though freshwater flows increased 

during several of these years (Baxter et 

al. 2010, p. 62). Abundance indices 

derived from the Fall Midwater Trawl 

(FMWT), Bay Study Midwater Trawl 

(BSMT), and Bay Study Otter Trawl 

(BSOT) all show marked declines in 

Bay-Delta longfin smelt populations 

from 2002 to 2009 (Messineo et al. 2010, 

p. 57). Longfin smelt abundance over 

the last decade is the lowest recorded in 

the 40-year history of CDFG’s FMWT 

monitoring surveys. Scientists became 

concerned over the simultaneous 

population declines since the early 

2000s of longfin smelt and three other 

Bay-Delta pelagic fish species—delta 

smelt (Hypomesus transpacificus), 

striped bass (Morone saxatilis), and 

threadfin shad (Dorosoma petenense) 

(Sommer et al. 2007, p. 273). The 

declines of longfin smelt and these other 

pelagic fish species in the Bay-Delta 

since the early 2000s has come to be 

known as the Pelagic Organism Decline, 

and considerable research efforts have 

been initiated since 2005, to better 

understand causal mechanisms 

underlying the declines (Sommer et al. 

2007, pp. 270–277; MacNally et al. 

2010, pp. 1417–1430; Thomson et al. 

2010, pp. 1431–1448). The population 

did increase in the 2011 FMWT index 

to 477 (Contreras 2011, p. 2), probably 

a response to an exceptionally wet year. 

The FMWT index of abundance in the 

Bay-Delta shows great annual variation 

in abundance but a severe decline over 

the past 40 years (Figure 2). The 

establishment of the overbite clam 

(Corbula amurensis) in the Bay-Delta in 

1987 is believed to have contributed to 

the population decline of longfin smelt 

(See Factor E: Introduced Species, 

below), as well as to the declining 

abundance of other pelagic fish species 

in the Bay-Delta (Sommer et al. 2007, p. 

274). Figure 2 shows low values of the 

abundance index for longfin smelt 

during drought years (1976–1977 and 

1986–1992) and low values overall since 

the time that the overbite clam became 

established in the estuary. 

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Using data from 1975–2004 from the 

FMWT survey, Rosenfield and Baxter 

2007 (p. 1589) found that longfin smelt 

exhibit a significant stock-recruitment 

relationship—abundance of juvenile 

(age-0) fish is directly related to the 

abundance of adult (age-1) fish from the 

previous year. They found that the 

abundance of juvenile fish declined by 

90 percent during the time period 

analyzed. Rosenfield and Baxter (2007, 

p. 1589) also found a decline in age-1 

individuals that was significant even 

after accounting for the decline in the 

age-0 population. If unfavorable 

environmental conditions persist for 

one or more years, recruitment into the 

population could be suppressed, 

affecting the species’ ability to recover 

to their previous abundance. The 

current low abundance of adult longfin 

smelt within the Bay-Delta could reduce 

the ability of the species to persist in the 

presence of various threats. 

Conservation Actions 

Bay-Delta 

The CALFED program existed as a 

multi-purpose (water supply, flood 

protection, and conservation) program 

with significant ecosystem restoration 

and enhancement elements. 

Implemented by the California BayDelta Authority, the program brought 

together more than 20 State and Federal 

agencies to develop a long-term 

comprehensive plan to restore 

ecological health and improve water 

management for all beneficial uses in 

the Bay-Delta system. The program 

specifically addressed ecosystem 

quality, water quality, water supply, and 

levee system integrity. The California 

Bay-Delta Authority was replaced in 

2009 by the Delta Stewardship Council, 

but many of its programs continue to be 

implemented and are now housed 

within the CALFED program’s former 

member agencies. 

The CALFED Ecosystem Restoration 

Program (ERP) developed a strategic 

plan for implementing an ecosystembased approach for achieving 

conservation targets (CALFED 2000a, 

pp. 1–3). The CDFG is the primary 

implementing agency for the ERP. The 

goal of ERP in improving conditions for 

longfin smelt will carry forward, 

irrespective of the species Federal 

listing status. CALFED had an explicit 

goal to balance the water supply 

program elements with the restoration 

of the Bay-Delta and tributary 

ecosystems and recovery of the longfin 

smelt and other species. Because 

achieving the diverse goals of the 

program is iterative and subject to 

annual funding by diverse agencies, the 

CALFED agencies have committed to 

maintaining balanced implementation 

of the program within an adaptive 

management framework. The intention 

of this framework is that the storage, 


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conveyance, and levee program 

elements would be implemented in 

such a way that the longfin smelt’s 

status would be maintained and 

eventually improved. 

CALFED identified 54 species 

enhancement conservation measures for 

longfin smelt, more than half of which 

have been completed (CALFED 

Ecosystem Restoration Project 2011, 

entire). One such restoration action at 

Liberty Island at the southern end of the 

Yolo Bypass (a flood control project) has 

likely benefitted longfin smelt. After 

years of active agricultural production 

on Liberty Island, the levees were 

breached in 1997, and the island was 

allowed to return to a more natural state 

(Wilder 2010, slide 4). Wildlands 

Corporation has recently completed a 

restoration project removing several 

levees surrounding Liberty Island and 

creating 186 acres of various habitats for 

fish (Wildlands 2011, p. 1). Longfin 

smelt are utilizing the flooded island, 

and were collected in a number of 

surveys between 2003 and 2005 (Liberty 

Island Monitoring Program 2005, pp. 

42–44; Marshall et al. 2006, p. 1). 

The Bay-Delta Conservation Plan 

(BDCP), an effort to help provide 

restoration of the Bay-Delta ecosystem 

and reliable water supplies, is currently 

in preparation by a collaborative of 

water agencies, resource agencies, and 

environmental groups. The BDCP is 

intended to provide a basis for 

permitting take of listed species under 

sections 7 and 10 of the Act and the 

California Natural Communities 

Conservation Planning Act, and would 

provide a comprehensive habitat 

conservation and restoration plan for 

the Bay-Delta, as well as a new funding 

source. The BDCP shares many of the 

same goals outlined in the 2000 

CALFED Record of Decision (CALFED 

2000) but would not specifically address 

all listed-species issues. The BDCP 

would, however, target many of the 

threats to current and future listed 

species and could contribute to species 

recovery. However, the BDCP, if 

completed, would not be initiated until 

at least 2013 or later. The plan’s 

implementation is anticipated to extend 

through 2060. 

Humboldt Bay 

The Humboldt Bay Watershed 

Advisory Committee has completed the 

Humboldt Bay Salmon and Steelhead 

Conservation Plan with funding from 

CDFG, National Oceanographic 

Atmospheric Administration (NOAA), 

and the California State Coastal 

Conservancy with the purpose of 

protecting and restoring salmon habitat 

in Humboldt Bay through cooperative 

planning (Humboldt Bay Watershed 

Advisory Committee 2005, pp. 1–2). 

Many of the habitat restoration activities 

proposed may benefit longfin smelt, 

including restoration in freshwater 

streams and brackish sloughs. The 

Natural Resource Services has designed 

an enhancement program that is based 

on the Humboldt Bay Salmon and 

Steelhead Conservation Plan. Natural 

Resource Services has completed a tidal 

marsh enhancement project on 

Freshwater Creek and has other projects 

in the design stage (Don Allen 2011, 

pers. comm.). The Natural Resource 

Services is a division of the Redwood 

Community Action Agency dedicated to 

improving the health of northern 

California communities and the 

watersheds that they depend on (NRS 

2011, p. 1). These types of restoration 

efforts are current and ongoing and may 

benefit longfin smelt by increasing 

access to intertidal areas within 

Humboldt Bay. 

Puget Sound 

The Puget Sound Partnership is a 

Washington State Agency created in 

2007, to oversee the restoration and 

protection of Puget Sound. The Puget 

Sound Partnership created an Action 

Agenda that identifies and prioritizes 

work needed to protect and restore 

Puget Sound (Puget Sound Partnership 

2008b, p. 2). Protection actions 

including local watershed planning, 

shoreline management planning, and 

citizen involvement through groups 

such as beach watchers and shore 

stewards are among the current 

restoration efforts in Puget Sound 

watershed (Puget Sound Partnership 

2008a, pp. 1–2). These measures are 

expected to benefit longfin smelt by 

protecting and restoring habitat through 

legislative approval and funding for 

land acquisition for protection and 

restoration of ecologically important 

lands and habitats and by adding lands 

to State Aquatic Reserves program 

(Puget Sound Partnership 2008a, 

pp. 1–2). 

Alaska 

State and Federal land ownership 

affords protection for vast distances of 

shoreline within Glacier Bay and 

Wrangell-St. Elias National Parks, 

Tongass National Forest, and State 

landholdings. Kachemak Bay, located 

near the mouth of lower Cook Inlet, is 

a National Estuarine Research Reserve 

regarded as extremely important for 

marine biodiversity conservation (ADFG 

2006, pp. 133–134). Alaska’s only State 

wilderness park, Kachemak Bay State 

Park, is also located in Kachemak Bay 

(ADNR 2011, p. 1). Yakutat Bay lies 

between peninsular and mainland 

Alaska and is bordered by Wrangell-St. 

Elias National Park to the northwest and 

Tongass National Forest. The Federal 

lands surrounding Yakutat Bay protect 

it from the effects of development. The 

Tongass National Forest management 

plan requires that logging activities be 

distanced from estuarine and riparian 

edges (ADFG 2006, p. 107). As a species 

group, the osmerids are identified in 

Alaska’s Comprehensive Wildlife 

Conservation Strategy as Species of 

Greatest Conservation Need (ADFG 

2006, pp. 140–143). The Conservation 

Action Plan for anadromous smelts 

identifies objectives, issues, and 

conservation actions to address 

information gaps. Determining life 

history, trophic ecology, instream flow 

and habitat needs, and monitoring 

protocols are included as measures that 

need to be undertaken as part of 

Alaska’s Conservation Strategy to 

identify conservation status and needs 

of anadromous smelt including longfin. 

Summary of Information Pertaining to 

the Five Factors 

Section 4 of the Act (16 U.S.C. 1533) 

and implementing regulations (50 CFR 

part 424) set forth procedures for adding 

species to, removing species from, or 

reclassifying species on the Federal 

Lists of Endangered and Threatened 

Wildlife and Plants. Under section 

4(a)(1) of the Act, a species may be 

determined to be endangered or 

threatened based on any of the 

following five factors: 

(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. 

In making these findings, information 

pertaining to each species in relation to 

the five factors provided in section 

4(a)(1) of the Act is discussed below. In 

considering what factors might 

constitute threats to a species, we must 

look beyond the exposure of the species 

to a particular factor to evaluate whether 

the species may respond to the factor in 

a way that causes actual impacts to the 

species. If there is exposure to a factor 

and the species responds negatively, the 

factor may be a threat, and during the 

status review, we attempt to determine 

how significant a threat it is. The threat 

is significant if it drives or contributes 

to the risk of extinction of the species 

such that the species warrants listing as 

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endangered or threatened as those terms 

are defined by the Act. However, the 

identification of factors that could 

impact a species negatively may not be 

sufficient to compel a finding that the 

species warrants listing. The 

information must include evidence 

sufficient to suggest that the potential 

threat has the capacity (i.e., it should be 

of sufficient magnitude and extent) to 

affect the species’ status such that it 

meets the definition of endangered or 

threatened under the Act. 

In making our 12-month finding on 

the petition, we considered and 

evaluated the best available scientific 

and commercial information. Much of 

the scientific and commercial 

information available on potential 

threats to longfin smelt comes from 

information on the Bay-Delta, and 

therefore the threats analysis is largely 

focused on the Bay-Delta longfin smelt 

population. 

Factor A. The Present or Threatened 

Destruction, Modification, or 

Curtailment of Its Habitat or Range 

Potential threats to longfin smelt 

habitat include the effects of reduced 

freshwater flow, climate change, and 

channel disturbance. Nearly all 

information available on Factor A 

threats to longfin smelt come from the 

Bay-Delta estuary. Therefore, our 

analysis below focuses on habitat 

impacts to the Bay-Delta population. 

Reduced Freshwater Flow 

Most longfin smelt populations, other 

than those in a few freshwater lakes in 

Washington and British Columbia, are 

known from estuaries. Estuaries are 

complex ecosystems with boundaries 

between freshwater, brackish water, and 

saltwater that vary in time and space. 

Drought and water diversions affect 

these boundaries by altering the 

amounts and timing of freshwater flow 

into and within the estuary. These 

altered freshwater flows affect the 

physical and biological characteristics 

of the estuary, and the physical and 

biological characteristics of the estuary 

define longfin smelt habitat. 

Many environmental attributes 

respond to variance in freshwater flow 

into the estuary, including patterns of 

flooding and drought, nutrient loading, 

sediment loading (turbidity), 

concentration of organic matter and 

planktonic biota, physical changes in 

the movement and compression of the 

salt field, and changes in the 

hydrodynamic environment (Kimmerer 

2002a, p. 40). The San Francisco Estuary 

exhibits one of the strongest and most 

consistent responses of biota to flow 

among large estuaries (Kimmerer 2004, 

p. 14). 

Reduced freshwater flows into 

estuaries may affect fish and other 

estuarine biota in multiple ways. Effects 

may include: (1) Decreased nutrient 

loading, resulting in decreased primary 

productivity; (2) decreased stratification 

of the salinity field, resulting in 

decreased primary productivity; (3) 

decreased organic matter loading and 

deposition into the estuary; (4) reduced 

migration cues; (5) decreased sediment 

loading and turbidity, which may affect 

both feeding efficiency and predation 

rates; (6) reduced dilution of 

contaminants; (7) impaired transport to 

rearing areas (e.g., low-salinity zones); 

and (8) reduction in physical area of, or 

access to, suitable spawning or rearing 

habitat (Kimmerer 2002b, p. 1280). 

Bay-Delta Population 

Freshwater flow is strongly related to 

the natural hydrologic cycles of drought 

and flood. In the Bay-Delta estuary, 

increased Delta outflow during the 

winter and spring is the largest factor 

positively affecting longfin smelt 

abundance (Stevens and Miller 1983, 

pp. 431–432; Jassby et al. 1995; Sommer 

et al. 2007, p. 274; Thomson et al. 2010, 

pp. 1439–1440). During high outflow 

periods, larvae presumably benefit from 

increased transport and dispersal 

downstream, increased food production, 

reduced predation through increased 

turbidity, and reduced loss to 

entrainment due to a westward shift in 

the boundary of spawning habitat and 

strong downstream transport of larvae 

(CFDG 1992; Hieb and Baxter 1993; 

CDFG 2009a). Conversely, during low 

outflow periods, negative effects of 

reduced transport and dispersal, 

reduced turbidity, and potentially 

increased loss of larvae to predation and 

increased loss at the export facilities 

result in lower young-of-the-year 

recruitment. Despite numerous studies 

of longfin smelt abundance and flow in 

the Bay-Delta, the underlying causal 

mechanisms are still not fully 

understood (Baxter et al. 2010, p. 69; 

Rosenfield 2010, p. 9). 

As California’s population has grown, 

demands for reliable water supplies and 

flood protection have grown. In 

response, State and Federal agencies 

built dams and canals, and captured 

water in reservoirs, to increase capacity 

for water storage and conveyance 

resulting in one of the largest manmade 

water systems in the world (Nichols et 

al. 1986, p. 569). Operation of this 

system has altered the seasonal pattern 

of freshwater flows in the watershed. 

Storage in the upper watershed of peak 

runoff and release of the captured water 

for irrigation and urban needs during 

subsequent low flow periods result in a 

broader, flatter hydrograph with less 

seasonal variability in freshwater flows 

into the estuary (Kimmerer 2004, p. 15). 

In addition to the system of dams and 

canals built throughout the Sacramento 

River-San Joaquin River basin, the BayDelta is unique in having a large water 

diversion system located within the 

estuary (Kimmerer 2002b, p. 1279). The 

State Water Project (SWP) and Central 

Valley Project (CVP) operate two water 

export facilities in the Delta (Sommer et 

al. 2007, p. 272). Project operation and 

management is dependent upon 

upstream water supply and export area 

demands. Despite the size of the water 

storage and diversion projects, much of 

the interannual variability in Delta 

hydrology is due to variability in 

precipitation from year to year. Annual 

inflow from the watershed to the Delta 

is strongly correlated to unimpaired 

flow (runoff that would hypothetically 

occur if upstream dams and diversions 

were not in existence), mainly due to 

the effects of high-flow events 

(Kimmerer 2004, p. 15). Water 

operations are regulated in part by the 

California State Water Resources 

Control Board (SWRCB) according to the 

Water Quality Control Plan (WQCP) 

(SWRCB 2000, entire). The WQCP limits 

Delta water exports in relation to Delta 

inflow (the Export/Inflow, or E/I ratio). 

It is important to note that in the case 

of the Bay-Delta, freshwater flow is 

expressed as both Delta inflow (from the 

rivers into the Delta) and as Delta 

outflow (from the Delta into the lower 

estuary), which are closely correlated, 

but not equivalent. Freshwater flow into 

the Delta affects the location of the low 

salinity zone and X2 within the estuary. 

Because longfin smelt spawn in 

freshwater, they must migrate farther 

upstream to spawn as flow reductions 

alter the position of X2 and the lowsalinity zone moves upstream (CDFG 

2009, p. 17). Longer migration distances 

into the Bay-Delta make longfin smelt 

more susceptible to entrainment in the 

State and Federal water pumps (see 

Factor E: Entrainment Losses). In 

periods with greater freshwater flow 

into the Delta, X2 is pushed farther 

downstream (seaward); in periods with 

low flows, X2 is positioned farther 

landward (upstream) in the estuary and 

into the Delta. Not only is longfin smelt 

abundance in the Bay-Delta strongly 

correlated with Delta inflow and X2, but 

the spatial distribution of longfin smelt 

larvae is also strongly associated with 

X2 (Dege and Brown 2004, pp. 58–60; 

Baxter et al. 2010, p. 61). As longfin 

hatch into larvae, they move from the 

areas where they are spawned and 

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orient themselves just downstream of 

X2 (Dege and Brown 2004, pp. 58–60). 

Larval (winter-spring) habitat varies 

with outflow and with the location of 

X2 (CDFG 2009, p. 12), and has been 

reduced since the 1990s due to a general 

upstream shift in the location of X2 

(Hilts 2012, unpublished data). The 

amount of rearing habitat (salinity 

between 0.1 and 18 ppt) is also 

presumed to vary with the location of 

X2 (Baxter et al. 2010, p. 64). However, 

as previously stated, the location of X2 

is of particular importance to the 

distribution of newly-hatched larvae 

and spawning adults. The influence of 

water project operations from November 

through April, when spawning adults 

and newly-hatched larvae are oriented 

to X2, is greater in drier years than in 

wetter years (Knowles 2002, p. 7). 

Research on declines of longfin smelt 

and other pelagic fish species in the 

Bay-Delta since 2002 (referred to as 

Pelagic Organism Decline—see 

Abundance section, above) have most 

recently been summarized in the 

Interagency Ecological Program’s 2010 

Pelagic Organism Decline Work Plan 

and Synthesis of Results (Baxter et al. 

2010, pp. 61–69). While Baxter et al. 

(2010, pp. 17–19) acknowledge 

significant uncertainties about the 

causal mechanisms underlying the 

Pelagic Organism Decline, they have 

identified reduced Delta freshwater 

flows as one of several key factors that 

they believe contribute to recent 

declines in the abundance of longfin 

smelt (Baxter et al. 2010, pp. 61–69, 

Figure 5). 

Other Populations 

Information on effects of reduced 

freshwater flows on longfin smelt 

populations other than the Bay-Delta 

population are lacking. Dams and 

reservoirs are located in the inland 

water basins of most of the estuaries 

where longfin smelt occur. Some of 

these systems are large and consist of 

multiple dams and diversions (e.g., 

Klamath River basin, Columbia River 

basin). Water diversion systems with 

dams, canals, and water pipelines 

located upstream of the estuary may 

affect longfin smelt aquatic habitat by 

reducing freshwater flows into the 

estuary—especially if water is diverted 

out of the drainage basin—and altering 

the timing of freshwater flows into the 

estuary. 

Climate Change 

‘‘Climate’’ refers to an area’s long-term 

average weather statistics (typically for 

at least 20- or 30-year periods), 

including the mean and variation of 

surface variables such as temperature, 

precipitation, and wind, whereas 

‘‘climate change’’ refers to a change in 

the mean and/or variability of climate 

properties that persists for an extended 

period (typically decades or longer), 

whether due to natural processes or 

human activity (Intergovernmental 

Panel on Climate Change (IPCC) 2007a, 

p. 78). Although changes in climate 

occur continuously over geological time, 

changes are now occurring at an 

accelerated rate. For example, at 

continental, regional, and ocean basin 

scales, recent observed changes in longterm trends include: a substantial 

increase in precipitation in eastern parts 

of North American and South America, 

northern Europe, and northern and 

central Asia, and an increase in intense 

tropical cyclone activity in the North 

Atlantic since about 1970 (IPCC 2007a, 

p. 30); and an increase in annual 

average temperature of more than 2 °F 

(1.1 °C) across the United States since 

1960 (Global Climate Change Impacts in 

the United States (GCCIUS) 2009, p. 27). 

Examples of observed changes in the 

physical environment include: an 

increase in global average sea level, and 

declines in mountain glaciers and 

average snow cover in both the northern 

and southern hemispheres (IPCC 2007a, 

p. 30); substantial and accelerating 

reductions in arctic sea-ice (e.g., Comiso 

et al. 2008, p. 1); and a variety of 

changes in ecosystem processes, the 

distribution of species, and the timing of 

seasonal events (e.g., GCCIUS 2009, pp. 

79–88). 

The IPCC used Atmosphere-Ocean 

General Circulation Models and various 

greenhouse gas emissions scenarios to 

make projections of climate change 

globally and for broad regions through 

the 21st century (Meehl et al. 2007, p. 

753; Randall et al. 2007, pp. 596–599), 

and reported these projections using a 

framework for characterizing certainty 

(Solomon et al. 2007, pp. 22–23). 

Examples include: (1) It is virtually 

certain there will be warmer and more 

frequent hot days and nights over most 

of the earth’s land areas; (2) it is very 

likely there will be increased frequency 

of warm spells and heat waves over 

most land areas, and the frequency of 

heavy precipitation events will increase 

over most areas; and (3) it is likely that 

increases will occur in the incidence of 

extreme high sea level (excludes 

tsunamis), intense tropical cyclone 

activity, and the area affected by 

droughts (IPCC 2007b, p. 8, Table 

SPM.2). More recent analyses using a 

different global model and comparing 

other emissions scenarios resulted in 

similar projections of global temperature 

change across the different approaches 

(Prinn et al. 2011, pp. 527, 529). 

All models (not just those involving 

climate change) have some uncertainty 

associated with projections due to 

assumptions used, data available, and 

features of the models; with regard to 

climate change this includes factors 

such as assumptions related to 

emissions scenarios, internal climate 

variability, and differences among 

models. Despite this, however, under all 

global models and emissions scenarios, 

the overall projected trajectory of 

surface air temperature is one of 

increased warming compared to current 

conditions (Meehl et al. 2007, p. 762; 

Prinn et al. 2011, p. 527). Climate 

models, emissions scenarios, and 

associated assumptions, data, and 

analytical techniques will continue to 

be refined, as will interpretations of 

projections, as more information 

becomes available. For instance, some 

changes in conditions are occurring 

more rapidly than initially projected, 

such as melting of arctic sea ice (Comiso 

et al. 2008, p. 1; Polyak et al. 2010, p. 

1797), and since 2000 the observed 

emissions of greenhouse gases, which 

are a key influence on climate change, 

have been occurring at the mid- to 

higher levels of the various emissions 

scenarios developed in the late 1990s 

and used by the IPPC for making 

projections (e.g., Raupach et al. 2007, 

Figure 1, p. 10289; Manning et al. 2010, 

Figure 1, p. 377; Pielke et al. 2008, 

entire). Also, the best scientific and 

commercial data available indicate that 

average global surface air temperature is 

increasing and that several climaterelated changes are occurring and will 

continue for many decades even if 

emissions are stabilized soon (e.g. 

Meehl et al. 2007, pp. 822–829; Church 

et al. 2010, pp. 411–412; Gillett et al. 

2011, entire). 

Changes in climate can have a variety 

of direct and indirect impacts on 

species, and can exacerbate the effects 

of other threats. Rather than assessing 

‘‘climate change’’ as a single threat in 

and of itself, we examine the potential 

consequences to species and their 

habitats that arise from changes in 

environmental conditions associated 

with various aspects of climate change. 

For example, climate-related changes to 

habitats, predator-prey relationships, 

disease and disease vectors, or 

conditions that exceed the physiological 

tolerances of a species, occurring 

individually or in combination, may 

affect the status of a species. 

Vulnerability to climate change impacts 

is a function of sensitivity to those 

changes, exposure to those changes, and 

adaptive capacity (IPCC 2007, p. 89; 

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Glick et al. 2011, pp. 19–22). As 

described above, in evaluating the status 

of a species, the Service uses the best 

scientific and commercial data 

available, and this includes 

consideration of direct and indirect 

effects of climate change. As is the case 

with all potential threats, if a species is 

currently affected or is expected to be 

affected by one or more climate-related 

impacts, this does not necessarily mean 

the species is an endangered or 

threatened species as defined under the 

Act. If a species is listed as endangered 

or threatened, this knowledge regarding 

its vulnerability to, and impacts from, 

climate-associated changes in 

environmental conditions can be used 

to help devise appropriate strategies for 

its recovery. 

The effects of climate change do not 

act in isolation, but act in combination 

with existing threats to species and 

systems. We considered the potential 

effects of climate change on the longfin 

smelt based on projections derived from 

various modeling scenarios. 

Temperature increases are likely to lead 

to a continued rise in sea level, further 

increasing salinity within longfin smelt 

estuarine rearing habitat and likely 

shifting spawning and early rearing 

upstream as the boundary of fresh and 

brackish water moves upstream (Baxter 

2011, pers. comm.). Reduced snowpack, 

earlier melting of the snowpack, and 

increased water temperatures will likely 

alter freshwater flows, possibly shifting 

and condensing the timing of longfin 

smelt spawning (Baxter 2011, pers. 

comm.). 

Effects of climate change could be 

particularly profound for aquatic 

ecosystems and include increased water 

temperatures and altered hydrology, 

along with changes in the extent, 

frequency, and magnitude of extreme 

events such as droughts, floods, and 

wildfires (Reiman and Isaak 2010, p. 1). 

Numerous climate models predict 

changes in precipitation frequency and 

pattern in the western United States 

(IPCC 2007b, p. 8). Projections indicate 

that temperature and precipitation 

changes will diminish snowpack, 

changing the availability of natural 

water supplies (USBR 2011, p. 143). 

Warming may result in more 

precipitation falling as rain and less 

storage as snow. This would result in 

increased rain-on-snow events and 

increase winter runoff as spring runoff 

decreases (USBR 2011, p. 147). Earlier 

seasonal warming increases the 

likelihood of rain-on-snow events, 

which are associated with mid-winter 

floods. Smaller snowpacks that melt 

earlier in the year result in increased 

drought frequency and severity (Rieman 

and Isaak 2010, p. 6). These changes 

may lead to increased flood and drought 

risk during the 21st century (USBR 

2011, p. 149). 

It is uncertain how a change in the 

timing and duration of freshwater flows 

will affect longfin smelt. The melting of 

the snowpack earlier in the year could 

result in higher flows in January and 

February, which are peak spawning and 

hatching months for longfin smelt. This 

would reduce adult migration distance 

and increase areas of freshwater 

spawning habitat during these months, 

potentially creating better spawning and 

larval rearing conditions. Associated 

higher turbidity may reduce predation 

on longfin smelt adults and larvae 

(Baxter 2011, pers. comm.). However, if 

high flows last only a short period, 

benefits may be negated by poorer 

conditions before and after the high 

flows. As the freshwater boundary 

moves farther inland into the Delta with 

increasing sea level (see below) and 

reduced flows, adults will need to 

migrate farther into the Delta to spawn, 

increasing the risk of predation and the 

potential for entrainment into water 

export facilities and diversions for both 

themselves and their progeny. 

Global sea level rose at an average rate 

of 1.8 mm (0.07 in) per year from 1961 

to 2003, and at an average rate of 3.1 

mm (0.12 in) per year from 1993 to 2003 

(IPCC 2007a, p. 49). The IPCC (2007b, p. 

13) report estimates that sea levels could 

rise by 0.18 to 0.58 m (0.6 to 1.9 ft) by 

2100; however, Rahmstorf (2007, p. 369) 

indicated that global sea level rise could 

increase by over 1.2 m (4 ft) in that time 

period (CEC 2009, p. 49). Even if 

emissions could be halted today, the 

oceans would continue to rise and 

expand for centuries due to their 

capacity to store heat (CEC 2009, pp. 

49–50). In the Bay-Delta, higher tides 

combined with more severe drought and 

flooding events are likely to increase the 

likelihood of levee failure, possibly 

resulting in major alterations of the 

environmental conditions (Moyle 2008, 

pp. 362–363). It is reasonable to 

conclude that more severe drought and 

flooding events will also occur in other 

estuaries where the longfin smelt 

occurs. Sea level rise is likely to 

increase the frequency and range of 

saltwater intrusion. Salinity within the 

northern San Francisco Bay is projected 

to rise 4.5 psu by the end of the century 

(Cloern et al. 2011, p. 7). Elevated 

salinity levels could push the position 

of X2 farther up the estuary and could 

result in increased distances that longfin 

smelt must migrate to reach spawning 

habitats. Elevated sea levels could result 

in greater sedimentation, erosion, 

coastal flooding, and permanent 

inundation of low-lying natural 

ecosystems (CDFG 2009, p. 30). 

Typically, longfin smelt spawning in 

the Bay-Delta occurs at water 

temperatures between 7.0 and 14.5 °C 

(44.6–58.2 °F), although spawning has 

been observed at lower temperatures in 

other areas, such as Lake Washington 

(Moyle 2002, p. 236). Mean annual 

water temperatures within the upper 

Sacramento River portion of the BayDelta estuary are expected to approach 

or exceed 14 °C during the second half 

of this century (Cloern et al. 2011, p. 7). 

Increased water temperatures could 

compress the late-fall to early-spring 

spawning period and could result in 

shorter egg incubation time. Longfin 

smelt are adapted to hatching in cold, 

relatively unproductive waters where 

they grow slowly until ample food 

resources are available in spring. 

Warmer water during winter would 

likely result in increased metabolism of 

larvae, which may result in increased 

food needs for maintenance and growth 

and create a mismatch between food 

needs and availability (Baxter 2011, 

pers. comm.). If increased water 

temperatures compress the spawning 

period and lead to more synchronized 

hatching during winter, then prevailing 

low sunlight and low food resources 

could result in greater intra-specific 

(within species) competition (Baxter 

2011, pers. comm.). Moreover, 

increasing water temperatures might 

also lead to earlier spawning and 

hatching of other fishes, and to greater 

inter-specific (between species) 

competition. 

Although climate change and sea 

level rise are projected to result in 

continued increases in water 

temperature and salinity, longfin smelt 

is considered euryhaline (tolerant of a 

wide range of salinities) (Moyle 2002, p. 

236; Rosenfield and Baxter 2007 p. 

1578) and is known to move between 

different parts of the estuary that vary 

greatly in temperature and salinity. 

Being able to move between aquatic 

habitats that vary greatly in water 

temperature and salinity may reduce the 

potential impacts of climate change and 

sea level rise to some degree. 

Channel Disturbances 

Dredging and other channel 

disturbances potentially degrade 

spawning habitat and cause entrainment 

loss of individual fish and eggs; disposal 

of dredge spoils also can create large 

sediment plumes that expose fish to gillclogging sediments and possibly to 

decreased oxygen availability (LevineFricke 2004, p. 56). Longfin smelt is a 

pelagic species (living away from the 

bottom of the water column and 

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shoreline), and thus less likely to be 

directly affected by dredging, sand and 

gravel mining, and other disturbances to 

the channel bed compared to bottomdwelling fish species. Longfin smelt are 

likely most vulnerable to entrainment 

by dredging during spawning and egg 

incubation because eggs are deposited 

and develop on channel bottom 

substrates (CDFG 2009, p. 27). Egg 

development takes approximately 40 

days (Moyle 2002, p. 236). 

We have found no information 

documenting population impacts of 

dredging or sand and gravel mining on 

longfin smelt. Channel maintenance 

dredging occurs regularly within the 

Bay-Delta and other estuaries that serve 

as shipping channels (e.g., Humboldt 

Bay, Coos Bay, Yaquina Bay, Columbia 

River). In their 2009 status review on 

longfin smelt, CDFG concluded that 

effects of regular maintenance dredging 

and sand mining within the Bay-Delta 

estuary on longfin smelt were expected 

to be small and localized (CDFG 2009, 

p. 26). They reviewed two studies on 

entrainment effects of channel dredging, 

and each study found that no longfin 

smelt were entrained during dredging 

(fish that were entrained were primarily 

bottom-dwelling species). 

There is currently a proposal to 

deepen and selectively widen the 

Sacramento Deep Water Ship Channel 

and the lower portion of the Sacramento 

River in the Bay-Delta. This dredging 

project would remove between 6.1–7.6 

million cubic meters (8 and 10 million 

cubic yards) of material from the 

channel and Sacramento River and 

extend for 74 km (45.8 mi) (USACE 

2011a, entire). Potential effects of this 

new project to longfin smelt include 

mortality through loss of spawning 

substrate, habitat modification, and a 

shift in spawning and rearing habitat. 

The project also has potential to alter 

breeding and foraging behavior of the 

Bay-Delta longfin smelt population. 

However, this project is only a proposal 

at this time and is not certain to occur. 

Potential effects of the proposed project 

are currently under evaluation. 

Summary of Factor A 

Although we find that reduced 

freshwater flows are currently a threat to 

the Bay-Delta longfin smelt population, 

it is difficult to make inferences on the 

effects of reduced freshwater flows to 

longfin smelt populations throughout 

the species range. Because the Bay-Delta 

system includes one of the largest man 

made water system in the world, it 

would be impractical to compare 

diversions and alterations in other 

estuaries to diversions and alterations in 

the Bay-Delta. The effects of water 

development in the Bay-Delta are 

unique to the physical, geologic, and 

hydrologic environment of the estuary. 

Reduced flow from diversions and dams 

in other estuaries is not expected to be 

as significant as the reduced flows that 

have been shown in the Bay-Delta 

because less water is exported from 

other estuaries. We have no information 

to show that reduced freshwater flow is 

a threat to longfin smelt in other 

estuaries. Therefore, we conclude that 

while reduced flow is a threat to the 

Bay-Delta population of longfin smelt, 

the best available science does not 

indicate that the lack of freshwater flow 

is a threat to the species in other parts 

of its range. 

Climate change will likely affect 

longfin smelt in multiple ways, but 

longfin smelt are able to move between 

a wide range of aquatic environments 

that vary greatly in water temperature 

and salinity. These behavioral and 

physiological characteristics of the 

species may help it adapt to effects of 

climate change. We conclude at this 

time that the best available information 

does not indicate that climate change 

threatens the continued existence of 

longfin smelt across its range. 

Channel disturbances may have 

localized impacts to longfin smelt 

habitat suitability, but the best available 

information does not indicate that they 

pose significant threats to the species 

throughout its range. 

Based on the best available scientific 

information, we conclude that reduced 

freshwater flows, climate change, and 

channel disturbances are not significant 

current or future threats to longfin smelt 

across its range except in the Bay-Delta, 

where reduced freshwater flow is a 

threat. 

Factor B. Overutilization for 

Commercial, Recreational, Scientific, or 

Educational Purposes 

Recreational and Commercial Fishing 

In California, longfin smelt was listed 

as a threatened species under the State’s 

Endangered Species Act in 2009. This 

status makes take of longfin smelt 

illegal, unless authorized by an 

incidental take permit or other take 

authorization. However, longfin smelt 

are caught as bycatch in small bay 

shrimp trawl fishery and bait fishing 

(anchovies and sardines) operations in 

South San Francisco Bay, San Pablo 

Bay, and Carquinez Strait (CDFG 2009a, 

p. 1). CDFG (2009d, pp. 6, 9) estimated 

the total longfin smelt bycatch from 

shrimping in 1989 and 1990 at 15,539 

fish, and in 2004 at 18,815–30,574 fish. 

CDFG noted in 2009 that the bay shrimp 

trawl fishery industry had declined 

since 2004 (CDFG 2009d, p. 3). No 

shrimp fishery currently takes place in 

Humboldt Bay (Mello 2011, pers. 

comm.). 

In Oregon, smelt species may not be 

targeted in commercial fisheries, and if 

taken incidentally, smelt catch cannot 

exceed 1 percent of the total weight 

landed (ODFW 2011, p. 17). Rules limit 

in which estuaries bait fishing for 

herring, sardines, anchovies, and shad 

may occur. In Oregon, there is currently 

no known shrimping taking place 

within the estuaries where the longfin 

smelt might be found. Although a 

limited entry roe herring fishery is 

allowed in Yaquina Bay, no landings 

have occurred there since 2003, because 

biomass estimates have generally been 

too low to make the fishery 

economically viable (Krutzikowsky 

2011, pers. comm.). Anchovy fishing is 

allowed in Tillamook Bay, Yaquina Bay, 

and Coos Bay, but because there is 

currently no anchovy fishing occurring 

in these areas (Krutzikowsky 2011, pers. 

comm.), longfin smelt are not taken as 

bycatch. Records for commercial 

landings in Oregon show a total of 9.1 

kilograms (kg) (20 pounds (lb)) landed 

from 2005 to 2010 for smelt species 

other than eulachon. Recreational 

fishing for smelt species is allowed only 

in marine waters (Oregon Sport Fishing 

Regulations, p. 11). 

The State of Washington includes 

longfin smelt in a class of fish referred 

to as forage fish (small schooling fish 

that are major food items for many 

species of fish, birds, and marine 

mammals) (Bargmann 1998, p. 1). Both 

recreational and commercial fisheries 

exist for forage fish in Washington, but 

the recreational fishery is much smaller 

than the commercial fishery. A sport 

fishing license is not needed to catch 

smelt. Smelt can be harvested 

recreationally using a dip net or jig. Dip 

net fishing for longfin smelt is allowed 

in the Nooksack River and there are 

approximately two hundred trips a year 

made to fish for longfin smelt in this 

area (O’Toole 2011, pers. comm.). It is 

unlawful to use a herring or smelt rake. 

Sport and tribal commercial fisheries 

have been reported to occur on the 

Nooksack River longfin smelt stock 

(Bargmann 1998, p. 37). Longfin smelt 

may be caught incidentally in a 

medium-sized shore or pier-based 

recreational fishery for surf smelt in 

Puget Sound. 

There is currently no commercial 

fishing regulation specific to longfin 

smelt in Washington (Paulson 2011, 

pers. comm.). The daily limit for smelt 

is 4.5 kg (10 lb) and, like Oregon, is 

counted as an aggregate, which can 

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and anchovies (WDFW 2011, p. 27). 

There is a robust commercial herring 

fishery in Washington that takes 

approximately 450 metric tons (500 

tons) of fish per year (for sport bait) and 

a commercial surf smelt fishery that 

takes approximately 450,000 kg 

(100,000 lb) of fish per year (for human 

consumption). Longfin smelt bycatch in 

both of these fisheries is low. Anchovy 

fishing in Washington primarily takes 

place in Grays Harbor and the mouth of 

the Columbia River (O’Toole 2011, pers. 

comm.). 

In British Columbia, take of smelt 

from recreational fishing is limited to 20 

kilograms (kg) (44 lb) per day and 40 kg 

(88 lb) of total catch in possession. The 

fishing season takes place from April 1 

to June 14 (Department of Fisheries and 

Oceans Canada 2011a, p. 47). A 

commercial fishing industry targeting 

surf smelt may incidentally take longfin 

smelt (Department of Fisheries and 

Oceans Canada 2011b, p. 1). British 

Columbia supports a year-round shrimp 

fishery in Prince Rupert and Chatham 

Sound. Sardine and shrimp fishing 

occurs near Vancouver. 

In Alaska, a commercial fishery for 

smelt, which includes eulachon, was 

reopened in 2005. This fishery is 

restricted to the brackish waters of Cook 

Inlet, from May 1 to June 30. The total 

annual harvest of eulachon and longfin 

smelt may not exceed 90 metric tons 

(100 tons) of smelt. However, longfin 

smelt are unlikely to be specifically 

targeted in this fishery due to their 

small numbers in relation to eulachon 

in the region (Shields 2005, p. 4). Sport 

fishing is limited to salt water, where 

herring and smelt may be taken (Alaska 

Department of Fish and Game (ADFG) 

2010, p. 1). In Prince William Sound, 

the herring fishery has closed due to 

low abundance of herring. 

Monitoring Surveys 

Fisheries monitoring surveys are 

conducted by NOAA’s National Marine 

Fisheries Service, the Service and by 

State and local agencies in water bodies 

inhabited by longfin smelt throughout 

their range. Most of these surveys target 

other species, primarily salmonids, and 

rarely collect longfin smelt outside of 

the Bay-Delta area. 

Within the Bay-Delta, longfin smelt 

are regularly captured in monitoring 

surveys. The Interagency Ecological 

Program (IEP) implements scientific 

research in the Bay-Delta. Although the 

focus of its studies and the level of effort 

have changed over time, in general, 

their surveys have been directed at 

researching the Pelagic Organism 

Decline in the Bay-Delta. Between the 

years of 1987 to 2011, combined take of 

longfin smelt less than 20 mm (0.8 in) 

in length ranged from 2,405 to 158,588 

annually. All of these fish were 

preserved for research or assumed to die 

in processing. During the same time 

period, combined take for juveniles and 

adults (fish greater than or equal to 20 

mm (0.8 in)) ranged from 461 to 68,974 

annually (IEP 2011, no pagination). 

Although mortality is unknown, the 

majority of these fish likely do not 

survive. The Chipps Island survey, 

which is conducted by the Service, has 

captured an average of 2,697 longfin 

smelt per year during the past 10 years. 

Biologists attempt to release these fish 

unharmed, but at least 5,154 longfin 

smelt were known to have died during 

the Chipps Island survey between 2001 

and 2008 (Service 2010, entire). 

Survey methods have been modified 

recently to minimize potential impacts 

to delta smelt, a related species that also 

occurs in the Bay-Delta (75 FR 17669; 

April 7, 2010). These modifications are 

likely to result in reduced impacts to 

longfin smelt also. The Service conducts 

other surveys in the Bay-Delta to 

monitor salmon populations (Mossdale 

trawl, Sacramento trawl, beach seine 

surveys), but few longfin smelt are 

captured during these surveys. Mortality 

due to monitoring surveys was not 

identified by the Interagency Ecological 

Program in its most recent synthesis of 

results as a factor in the decline of 

longfin smelt and other pelagic fish 

species in the Bay-Delta since the early 

2000s (Baxter et al. 2010, pp. 19–53, 61– 

69). 

Summary of Factor B 

The species is incidentally caught in 

commercial shrimp and bait fishing 

operations throughout much of its 

range, but the bycatch numbers are 

usually low. In California, take of 

longfin smelt is illegal without 

authorization because the species is 

listed as threatened under the California 

Endangered Species Act. Because of its 

small size, it is not targeted by 

recreational angling, although it is 

certainly caught and used as bait for 

other larger recreational fish species. 

Monitoring surveys have resulted in 

high numbers of longfin smelt mortality 

in the Bay-Delta in the past, but efforts 

being made to reduce survey mortality 

for delta smelt, such as reductions in 

tow times, likely have also benefitted 

longfin smelt. The scientific collection 

surveys being conducted in the BayDelta are limited to research designed to 

benefit the species, and mortality from 

monitoring surveys has not been 

identified as a factor in the longfin 

smelt’s recent population decline. We 

have no information indicating that 

mortality from monitoring surveys 

threatens any populations within the 

species’ range. We conclude that 

overutilization due to commercial, 

recreational, or scientific take is not a 

significant current or future threat to the 

longfin smelt throughout its range. 

Factor C. Disease or Predation 

Disease 

All the information we found on 

disease in longfin populations 

originated from studies in the Bay-Delta. 

Two investigations published in 2006 

and 2008 by the California-Nevada Fish 

Health Center detected no significant 

health problems in juvenile longfin 

smelt in the Bay-Delta (Foott and Stone 

2008, pp. 15–16). The low observed rate 

of parasitic infection did not appear to 

affect the health of the fish, as indicated 

by the lack of associated tissue damage 

or inflammation (Foott and Stone 2008, 

p. 15). The only additional 

documentation of relevant wild fish 

disease in the Bay-Delta was a severe 

intestinal infection by a new species of 

myxozoan observed in nonnative 

juvenile yellowfin goby (Acanthogobius 

flavimanus) from Suisun Marsh (Baxa et 

al. in prep cited in Baxter et al. 2008, 

p. 16). The nonnative gobies could act 

as potential vectors of the parasite to 

other susceptible species in the BayDelta. It is unknown whether this or 

similar infections are affecting the 

health of longfin smelt. 

The south Delta is fed by water from 

the San Joaquin River, where pesticides 

(e.g., chlorpyrifos, carbofuran, and 

diazinon), salts (e.g., sodium sulfates), 

trace elements (boron and selenium), 

and high levels of total dissolved solids 

are prevalent due to agricultural runoff 

(64 FR 5963; February 8, 1999). 

Pesticides and other toxic chemicals 

may adversely affect the immune system 

of longfin smelt and other fish in the 

Bay-Delta and other estuaries, but we 

found no information documenting such 

effects (see Factor E: Contaminants, 

below). 

Predation 

As a forage species, longfin smelt are 

preyed upon by a variety of fishes, 

birds, and mammals (Barnhart et al. 

1992, p. 44). However, we found little 

information on predation of longfin 

smelt other than information for the 

Bay-Delta population and Lake 

Washington population. The striped 

bass (Morone saxatilis) is a potential 

predator of longfin smelt in the BayDelta. Striped bass were introduced into 

the Bay-Delta in 1879 and quickly 

became abundant throughout the 

estuary. However, their numbers have 

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declined substantially over the last 40 

years (Thomson et al. 2010, p. 1440), 

and they are one of the four species 

studied under Pelagic Organism Decline 

investigations (Baxter et al. 2010, p. 16). 

Numbers of largemouth bass 

(Micropterus dolomieui), another 

introduced species in the Bay-Delta, 

have increased in the Delta over the past 

few decades (Brown and Michniuk 

2007, p. 196). Largemouth bass, 

however, occur in shallow freshwater 

habitats, closer to shore than the pelagic 

longfin smelt, and do not typically cooccur with longfin smelt. Baxter et al. 

(2010, p. 40) reported that no longfin 

smelt have been found in largemouth 

bass stomachs sampled in a recent study 

of largemouth bass diet. Moyle (2002, p. 

238) believed that inland silverside 

(Menidia beryllina), another nonnative 

predatory fish, may be an important 

predator on longfin smelt eggs, larvae, 

juveniles, and adults. Rosenfield (2010, 

p. 18) acknowledged that they are likely 

major predators of longfin smelt eggs 

and larvae but thought it unlikely that 

they were an important predator on 

juveniles and subadults because inland 

silversides prefer shallow water habitats 

whereas juvenile and subadult longfin 

smelt do not. 

In the Bay-Delta, predation of longfin 

smelt may be high in the Clifton Court 

Forebay, where the SWP water export 

pumping plant is located (Moyle 2002, 

p. 238; Baxter et al. 2010, p. 42). 

However, once they are entrained in the 

Clifton Court Forebay, longfin smelt 

mortality would be high anyway due to 

high water temperatures in the forebay 

(CDFG 2009b, p. 4) and entrainment 

into the SWP water export pumping 

plant. In addition to elevated predation 

levels in the Clifton Court Forebay, 

predation also is concentrated at sites 

where fish salvaged from the SWP and 

CVP export facilities are released (Moyle 

2002, p. 238). However, few longfin 

smelt survive the salvage and transport 

process (see Factor E: Entrainment 

Losses, below) and therefore predation 

is not expected to be an important factor 

at drop-off sites. Reduced freshwater 

flows may result in lower turbidity and 

increased water clarity (see Factor A, 

above), which may contribute to 

increased risk of predation (Baxter et al. 

2010, p. 64). 

In Lake Washington, longfin are 

preyed upon by prickly sculpin (Cottus 

asper) (Tabor et al. 2007, p. 1085) and 

cutthroat trout (Oncorhynchus clarki) 

(Norwak et al. 2004, p. 632; Beauchamp 

et al. 1992, p. 156). Cutthroat trout have 

displaced the northern pikeminnow as 

the most important predator in Lake 

Washington and may be having an effect 

on other components of the ecosystem, 

including longfin smelt populations 

(Norwak et al. 2004, pp. 633–634). 

Summary of Factor C 

Similar to other threats, very little 

information is available about disease or 

predation threats to longfin smelt 

populations outside of the Bay-Delta. 

We found no information that disease is 

a threat to the longfin smelt throughout 

its range. Longfin smelt is a small fish 

that is preyed upon by a wide variety of 

fish, birds, and mammals, but we found 

no information documenting predation 

as a threat to the species rangewide. 

Predation, along with mortality from 

entrainment (see Factor E: Entrainment 

Losses, below), has been identified as a 

top-down effect that may be 

contributing to recent declines of 

longfin smelt and other pelagic fish 

species in the Bay-Delta estuary (Pelagic 

Organism Decline) (Sommer et al. 2007, 

p. 275). However, factors contributing to 

the Pelagic Organism Decline are 

numerous and complex, and the 

combination of underlying causal 

mechanisms remains uncertain (Baxter 

et al. 2010, pp. 61–69). Therefore, based 

on our review of the best available 

scientific and commercial information, 

we conclude that disease or predation 

are not significant current or future 

threats to the longfin smelt throughout 

its range. 

Factor D. The Inadequacy of Existing 

Regulatory Mechanisms 

Federal Laws 

A number of federal environmental 

laws and regulations exist that may 

provide some protection for longfin 

smelt: the National Environmental 

Policy Act, the Central Valley Project 

Improvement Act, and the Clean Water 

Act. 

National Environmental Policy Act 

The National Environmental Policy 

Act (NEPA) (42 U.S.C. 4321 et seq.) 

requires all Federal agencies to formally 

document, consider, and publicly 

disclose the environmental impacts of 

major Federal actions and management 

decisions significantly affecting the 

human environment. NEPA 

documentation is provided in an 

environmental impact statement, an 

environmental assessment, or a 

categorical exclusion, and may be 

subject to administrative or judicial 

appeal. However, the Federal agency is 

not required to select an alternative 

having the least significant 

environmental impacts, and may select 

an action that will adversely affect 

sensitive species provided that these 

effects are known and identified in a 

NEPA document. Therefore, we do not 

consider the NEPA process in itself is to 

be a regulatory mechanism that is 

certain to provide significant protection 

for the longfin smelt. 

Central Valley Project Improvement Act 

The Central Valley Project 

Improvement Act (Pub. L. 102–575) 

(CVPIA) amends the previous Central 

Valley Project authorizations to include 

fish and wildlife protection, restoration, 

and mitigation as project purposes 

having equal priority with irrigation and 

domestic uses, and fish and wildlife 

enhancement as having an equal 

priority with power generation (Pub. L. 

102–575, October 30, 1992; Bureau of 

Reclamation 2009). Included in CVPIA 

section 3406 (b)(2) was a provision to 

dedicate 800,000 acre-feet of Central 

Valley Project yield annually (referred 

to as ‘‘(b)(2) water’’) for fish, wildlife, 

and habitat restoration. Since 1993, 

(b)(2) water has been used and 

supplemented with acquired 

environmental water (Environmental 

Water Account and CVPIA section 3406 

(b)(3) water) to increase stream flows 

and reduce Central Valley Project export 

pumping in the Delta. These 

management actions were taken to 

contribute to the CVPIA salmonid 

population doubling goals and to 

protect Delta smelt and their habitat 

(Guinee 2011, pers. comm.). As 

discussed above, (see Biology and 

Factor A discussions), increased 

freshwater flows have been shown to be 

positively correlated with longfin smelt 

abundance; therefore, these 

management actions, although targeted 

towards other species, should also 

benefit longfin smelt. 

Clean Water Act 

Established in 1977, the Clean Water 

Act (33 U.S.C. 1251 et seq.) is the 

primary Federal law in the United 

States regulating water pollution. It 

employs a variety of regulatory and nonregulatory means to reduce direct water 

quality impacts and manage polluted 

runoff. The Clean Water Act provides 

the basis for the National Pollutant 

Discharge Elimination System (NPDES) 

and gives the Environmental Protection 

Agency (EPA) the authority to set 

effluent limits and require any entity 

discharging pollutants to obtain a 

NPDES permit. The EPA is authorized 

through the Clean Water Act to delegate 

the authority to issue NPDES permits to 

State governments and has done so in 

California. In States that have been 

authorized to implement Clean Water 

Act programs, EPA retains oversight 

responsibilities. Water bodies that do 

not meet applicable water quality 

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standards are placed on the section 

303(d) list of impaired water bodies, and 

the State is required to develop 

appropriate total maximum daily loads 

(TMDL) for the water body. A TMDL is 

a calculation of the maximum amount of 

a pollutant that a water body can receive 

and still meet water quality standards. 

At present, TMDLs are not in place in 

all impaired watersheds in which 

longfin smelt are known to occur. The 

Clean Water Act has not effectively 

limited ammonia input into the system, 

and ammonia has been shown to 

negatively affect the longfin smelt’s food 

supply. 

State Laws 

The State of California has a number 

of environmental laws and regulations 

which may provide some protection for 

longfin smelt: California Endangered 

Species Act, California Environmental 

Quality Act, California Marine Invasive 

Species Act, Porter-Cologne Water 

Quality Control Act, and regulatory 

prohibitions on streambed alterations. 

California Endangered Species Act 

Longfin smelt was listed as threatened 

under the California Endangered 

Species Act (CESA) (California Fish and 

Game Code 2050 et seq.) in 2009. The 

CESA prohibits unpermitted possession, 

purchase, sale, or take of listed species. 

However, the CESA definition of take 

does not include harm, which under the 

Act’s implementing regulations includes 

significant modification or degradation 

of habitat that actually kills or injures 

wildlife by significantly impairing 

essential behavioral patterns (50 CFR 

17.3). CESA allows take of species for 

otherwise lawful projects through use of 

an incidental take permit. An incidental 

take permit requires that impacts be 

minimized and fully mitigated (CESA 

sections 2081 (b) and (c)). Furthermore, 

CESA requires that the issuance of the 

permit will not jeopardize the continued 

existence of a State-listed species. The 

CESA does require consultation 

between CDFG and other State agencies 

to ensure that activities of State agencies 

will not jeopardize the continued 

existence of State-listed species (CERES 

2009, p. 1). Longfin Smelt Incidental 

Take Permit No. 2081–2009–001–03 

specifies that the Smelt Working Group, 

which was created under the Service’s 

2008 delta smelt biological opinion 

(Service 2008, p. 30), provide 

recommendations for export pumping 

reduction to CDFG if any of several 

criteria is reached. One of the criteria is 

that total salvage of adult longfin smelt 

(fish greater than or equal to 80 mm in 

length) at the State Water Project and 

Central Valley Project export pumps 

between December and February may 

not exceed five times the Fall Midwater 

Trawl longfin smelt annual abundance 

index. Also, if longfin abundance is low 

and surveys indicate that adults are 

distributed close to the export pumps, 

the Smelt Working Group may consider 

making recommendations for Old and 

Middle River Flows that would reduce 

pumping (CDFG 2009c, pp. 1–34; Smelt 

Working Group 2011, p. 4). 

California Environmental Quality Act 

The California Environmental Quality 

Act ((CEQA) (Public Resources Code 

section 21000 et seq.)) requires review 

of any project that is undertaken, 

funded, or permitted by the State of 

California or a local government agency. 

If significant effects are identified, the 

lead agency has the option of requiring 

mitigation through changes in the 

project or to decide that overriding 

considerations make mitigation 

infeasible (CEQA sec. 21002). In the 

latter case, projects may be approved 

that cause significant environmental 

damage, such as destruction of listed 

endangered species or their habitat. 

Protection of listed species through 

CEQA is, therefore, dependent on the 

discretion of the lead agency. The CEQA 

review process ensures that a full 

environmental review is undertaken 

prior to the permitting of any project 

within longfin smelt habitat. 

California Marine Invasive Species Act 

The California Marine Invasive 

Species Act (AB 433) was passed in 

2003. This 2003 act requires ballast 

water management for all vessels that 

intend to discharge ballast water in 

California waters. All qualifying vessels 

coming from ports within the Pacific 

Coast region must conduct an exchange 

in waters at least 50 nautical mi offshore 

and 200 m (656 ft) deep or retain all 

ballast water and associated sediments. 

To determine the effectiveness of the 

management provisions of this 2003 act, 

the legislation also requires State 

agencies to conduct a series of biological 

surveys to monitor new introductions to 

coastal and estuarine waters. These 

measures should further minimize the 

introduction of new invasive species 

into California’s coastal waters that 

could be a threat to the longfin smelt. 

The Coastal Ecosystems Protection Act 

of 2006 deleted a sunset provision of the 

Marine Invasive Species Act, making 

the program permanent. 

Porter-Cologne Water Quality Control 

Act 

The Porter-Cologne Water Quality 

Control Act (California Water Code 

13000 et seq.) is a California State law 

that establishes the State Water 

Resources Control Board (SWRCB) and 

nine Regional Water Quality Control 

Boards that are responsible for the 

regulation of activities and factors that 

could degrade California water quality 

and for the allocation of surface water 

rights (California Water Code Division 

7). In 1995, the SWRCB developed the 

Bay-Delta Water Quality Control Plan 

that established water quality objectives 

for the Delta. This plan is currently 

implemented by Water Rights Decision 

1641, which imposes flow and water 

quality standards on State and Federal 

water export facilities to assure 

protection of beneficial uses in the Delta 

(USFWS 2008, pp. 21–27). The various 

flow objectives and export restraints 

were designed, in part, to protect 

fisheries. These objectives include 

specific freshwater flow requirements 

throughout the year, specific water 

export restraints in the spring, and 

water export limits based on a 

percentage of estuary inflow throughout 

the year. The water quality objectives 

were designed to protect agricultural, 

municipal, industrial, and fishery uses; 

they vary throughout the year and by 

the wetness of the year. 

In December 2010, the California 

Central Valley Regional Water Quality 

Control Board (Regional Board) adopted 

a new National Pollutant Discharge and 

Elimination System (NPDES) permit for 

the Sacramento Regional Wastewater 

Treatment Plant to address ammonia 

loading to the Sacramento River and the 

Delta. In January 2011, the Sacramento 

Regional County Sanitation District 

petitioned the Regional Board for a 

review of the permit, which may require 

a year or more. There is currently no 

TMDL in place for ammonia discharge 

into the Sacramento watershed. The 

EPA is currently updating freshwater 

ammonia criteria that will include new 

discharge limits on ammonia (EPA 

2009, pp. 1–46). Ammonia has been 

shown to have negative effects on prey 

items that longfin smelt rely upon (see 

Factor E: Contaminants, below). This 

regulation does not adequately mitigate 

potential negative effects to longfin 

smelt from ammonia in the Bay-Delta. 

Streambed Alteration 

In California, section 1600 et seq. of 

the California Fish and Game Code 

authorizes CDFG to regulate streambed 

alteration. The CDFG must be notified of 

and approve any work that substantially 

diverts, alters, or obstructs the natural 

flow or that substantially changes the 

bed, channel, or banks of any river, 

stream, or lake. If an existing fish or 

wildlife resource, including longfin 

smelt, may be substantially adversely 

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affected by a project, the project 

proponent must submit proposals to 

protect the species to the CDFG at least 

90 days before the start of the project. 

However, these proposals are subject to 

agreement by the project proponent. If 

CDFG deems proposed measures to be 

inadequate, a third party arbitration may 

be initiated. However, projects that 

cause significant environmental damage 

such as destruction of species and their 

habitat including longfin smelt may be 

approved because the CDFG has no 

authority to deny requests for streambed 

alteration. 

Oregon Environmental Regulations 

Oregon classifies longfin smelt as a 

native migratory fish under Oregon 

Administrative Rule (Division 412, 635– 

412–0005). Operators of artificial 

obstructions located in waters in which 

any native migratory fish are currently 

or were historically present must 

provide for fish passage requirements 

during installation, replacement, or 

abandonment of artificial obstructions 

(ODFW 2011, p. 1). This State law helps 

ensure passage of migratory longfin 

smelt between rearing and spawning 

habitat. 

Washington Environmental Regulations 

Washington’s State Environmental 

Policy Act (RCW 43.21C) provides a 

process similar to CEQA and is 

applicable to every State and local 

agency in Washington State. This law 

requires State and local governments to 

consider impacts to the environment 

and include public participation in 

project planning and decision making 

(Washington Division of Wildlife 2011, 

p. 1). Project proponents must submit a 

proposal for their project to the 

appropriate city, county, or State lead 

agency where the project is taking place. 

The lead agency then makes a 

determination of whether or not the 

project will have significantly adverse 

environmental impacts. The lead agency 

then may require the applicant to 

change the proposal to minimize 

environmental impacts or in rare cases 

may deny the application (Washington 

State Department of Ecology (WSDE) 

2002, pp. 1–2). 

Alaska Environmental Regulations 

The Anadromous Fish Act (AS 

16.05.871–.901) requires that anyone 

desiring to alter a streambed or 

waterbody first obtain a permit from the 

Alaska Department of Fish and Game 

(ADFG). Regulated activities include 

construction, road crossings, gravel 

mining, water withdrawal, stream 

realignment, and bank stabilization. 

Although there are no minimization or 

mitigation components to this law, the 

ADFG commissioner has the ability to 

deny a permit if he or she finds the 

plans and specifications are insufficient 

for the proper protection of anadromous 

fish. The Fishway or Fish Passage Act 

(AS 15.05.841) requires that activities 

within or crossing a stream obtain 

permission from ADFG if they will 

impede the passage of resident or 

anadromous fish. This provides some 

degree of protection for longfin smelt, 

which is categorized as an anadromous 

fish in the State of Alaska. 

Canadian Environmental Regulations 

The Canadian Environmental 

Assessment Act (S.C. 1992, c. 37) was 

passed by the Canadian Parliament in 

1992. The Act requires Federal 

departments to conduct environmental 

assessments for proposals where the 

government is the proposer or the 

project involves Federal funding or 

permitting. The Canadian 

Environmental Protection Act of 1999 is 

intended to prevent pollution, protect 

the environment and human health, and 

contribute to promoting sustainable 

development. Canada has the Canadian 

Environmental Protection Act (CEPA), 

which is equivalent to the United States’ 

NEPA. It was enacted to protect 

Canada’s natural resources through 

pollution prevention and sustainable 

development. This provides some level 

of protection for longfin smelt from 

pollution and habitat degradation. The 

longfin smelt is not currently a 

protected species under the Species at 

Risk Act (SARA) of 2002 (S.C. 2002 c. 

29; SARA). SARA is similar to the 

United States’ Endangered Species Act. 

If the longfin smelt were determined by 

the Canadian government to need 

protection in the future, it could be 

listed under SARA. 

Summary of Factor D 

We evaluate existing regulatory 

mechanisms that have an effect on 

threats that we have identified 

elsewhere in the threats analysis. We do 

not evaluate the lack of a regulatory 

mechanism that may address a 

particular threat if that regulatory 

mechanism does not exist. We find that 

the threats to the longfin smelt and its 

habitat on Federal, State, and private 

lands on a range-wide basis are minimal 

(Factors A, B, C and E). Existing federal 

regulatory mechanisms provide a degree 

of protection for longfin smelt from 

these threats. Therefore, we find that 

regulatory mechanisms provide 

adequate protections to longfin smelt 

and its habitat throughout its range. 

Factor E. Other Natural or Manmade 

Factors Affecting Its Continued 

Existence 

Other natural or manmade factors 

potentially affecting the continued 

existence of longfin smelt include 

entrainment losses from water 

diversions, introduced species, and 

contaminants. 

Entrainment Losses 

The only information we found on 

entrainment losses of longfin smelt 

comes from the Bay-Delta population. 

Entrainment occurs when fish are 

drawn toward water diversions, where 

they are typically trapped or killed. In 

the Bay-Delta, water is diverted and fish 

potentially entrained at four major water 

export facilities within the Delta, two 

power plants, and numerous small 

water diversions throughout the Delta 

for agriculture and in Suisun Marsh for 

waterfowl habitat. In their 2009 status 

review of longfin smelt, CDFG (2009, 

pp. 19–26) summarized entrainment 

losses at these water diversions. 

Water Export Facilities 

The four State and Federal water 

export facilities (pumping stations) in 

the Delta are the State Water Project 

(SWP) facility in the south Delta, the 

Central Valley Project (CVP) in the 

south Delta, the Contra Costa facility in 

the south Delta, and the North Bay 

Aqueduct facility in the north Delta. 

The SWP and CVP facilities pump the 

majority of the water exported from the 

Delta. Average annual volumes of water 

exported from these facilities between 

1995 and 2005 were 3.60 km3 at the 

SWP facility, 3.10 km3 at the CVP 

facility, 0.15 km3 at the Contra Costa 

facility, and 0.05 km3 at the North Bay 

Aqueduct facility (Sommer et al. 2007, 

p. 272). Depending on upstream flow 

through the Delta, operation of the SWP 

and CVP facilities often causes reverse 

flows in the river channels leading to 

them; longfin smelt that occupy these 

channels during certain times of the 

year may be entrained by these reverse 

flows. The SWP and CVP water export 

facilities are equipped with their own 

fish collection facilities that divert 

entrained fish into holding pens using 

louver-bypass systems to protect them 

from being killed in the pumps. The fish 

collected at the facilities are referred to 

as ‘‘salvaged,’’ and are loaded onto 

tanker trucks and returned to the 

western Delta downstream (Aasen 2009, 

p. 36). The movement of fish can result 

in mortality due to overcrowding in the 

tanks, stress, moving procedures, or 

predation at locations where the fish are 

released. Salvage is an index of 

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entrainment, not an estimate, and is 

much smaller than total entrainment 

(Castillo et al. in review). Of spawning 

age fish (age-1 and age-2), which 

contribute most to longfin smelt 

population dynamics in the Bay-Delta, 

the total number of longfin smelt 

salvaged at both pumps between 1993 

and 2007 was 1,133 (CDFG 2009, 

Attachment 3, p. 2). 

Fish entering the intake channel of 

the CVP or the radial gates of the 

31,000-acre Clifton Court Forebay 

reservoir (SWP) are considered 

entrained (Fujimura 2009, p. 5; CDFG 

2009b, p. 2). Most longfin smelt that 

become entrained in Clifton Court 

Forebay are unable to escape (CDFG 

2009b, p. 4). The number of fish 

entrained at the SWP and CVP facilities 

has never been determined directly, but 

entrainment losses have been estimated 

indirectly using data from research and 

monitoring efforts. The magnitude of 

entrainment of larval longfin smelt is 

unknown because only fish greater than 

20 mm in length are salvaged at the two 

facilities (Baxter et al. 2008, p. 21). In 

years with low freshwater flows, 

approximately half of the longfin smelt 

larvae and early juveniles may remain 

for weeks within the Sacramento-San 

Joaquin Delta (Dege and Brown 2004), 

where model simulations indicate they 

are vulnerable to entrainment into State 

Water Project, Central Valley Project, 

and other diversions (Kimmerer and 

Nobriga 2008, CDFG 2009a, p. 8). 

Entrainment is no longer considered a 

major threat to longfin smelt in the BayDelta because of current regulations. 

Efforts to reduce delta smelt 

entrainment loss through the 

implementation of the 2008 delta smelt 

biological opinion and the listing of 

longfin smelt under the CESA have 

likely reduced longfin smelt 

entrainment losses. The high rate of 

entrainment that occurred in 2002 that 

threatened the Bay Delta longfin smelt 

population is unlikely to recur, and 

would no longer be allowed under 

today’s regulations because limits on 

longfin smelt take due to CESA 

regulations (see Factor D discussion, 

below) would trigger reductions in the 

magnitude of reverse flows. 

Power Plants 

Two power plants located near the 

confluence of the Sacramento and San 

Joaquin Rivers, the Contra Costa 

Generating Station and the Pittsburg 

Generating Station, pose an entrainment 

risk to longfin smelt. Past entrainment 

losses of delta smelt at these two 

facilities were significant and 

considered a threat to delta smelt (75 FR 

17671; April 7, 2010). Power plant 

operations have been substantially 

reduced since the late 1970s, when high 

entrainment and impingement were 

documented (CDFG 2009, p. 24); the 

power plants are now either kept offline 

or operating at very low levels, except 

as necessary to meet peak power needs. 

From 2007–2010, capacity utilization of 

these units averaged only 2.3 percent of 

maximum capacity. No longfin smelt 

were detected during impingement 

sampling conducted between May of 

2010 and April of 2011 to monitor 

entrainment losses at the two power 

plants (Tenera Environmental 2011, 

entire). The company that owns the two 

power plants has committed to retiring 

one of the two power stations in 2013 

(Contra Costa Generating Station) and 

has made this commitment enforceable 

through amendments to its Clean Air 

Act Title V permit (Raifsnider 2011, 

pers. comm.). 

Agricultural Diversions 

Water is diverted at numerous sites 

throughout the Bay-Delta for 

agricultural irrigation. Herren and 

Kawasaki (2001) reported over 2,200 

such water diversions within the Delta, 

but CDFG (2009, p. 25) notes that 

number may be high because Herren 

and Kawasaki (2001) did not accurately 

distinguish intake siphons and pumps 

from discharge pipes. CALFED’s 

Ecosystem Restoration Program (ERP) 

includes a program to screen remaining 

unscreened small agricultural 

diversions in the Delta and the 

Sacramento and San Joaquin Rivers. The 

purpose of screening fish diversions is 

to prevent entrainment losses; however, 

very little information is available on 

the efficacy of screening these 

diversions (Moyle and Israel 2005, p. 

20). Agricultural operations begin to 

divert water in March and April, and 

many longfin smelt have begun leaving 

the Delta by this time. Water diversions 

are primarily located on the edge of 

channels and along river banks. Longfin 

smelt are a pelagic fish species and tend 

to occupy the middle of the channel and 

the middle of the water column, where 

they are unlikely to be vulnerable to 

entrainment into these diversions. 

Suisun Marsh Diversions 

There are 366 diversions in Suisun 

Marsh used to enhance waterfowl 

habitat (USFWS 2008, p. 172). Water is 

pumped at these diversions between 

October and May. Longfin larvae are 

abundant in the Marsh from February 

through April, while adults are 

abundant from October to February 

(Meng and Mattern 2001, p. 756; 

Rosenfield and Baxter 2007, p. 1588). 

During a 2-year study sampling 2.3 

million m3 (81.2 million ft3) of water 

entering intakes, entrainment was found 

to be low, capturing only 124 adult 

longfin and 160 larvae (Enos et al. 2007, 

p. 16). Restrictions on pumping have 

been put in place to protect delta smelt 

and salmon. These restrictions likely 

also benefit longfin smelt. 

Introduced Species 

Nonnative introduced species (both 

plants and animals) are common in 

many of the estuaries within the range 

of the longfin smelt. Introduced species 

can significantly alter food webs in 

aquatic ecosystems. Introduced animal 

species can adversely affect longfin 

smelt through predation (see Factor C 

discussion, above) or competition. 

Although introduced species are 

common within many of the estuaries 

occupied by longfin smelt, most of the 

information we found on effects of 

introduced species on longfin smelt was 

for the Bay-Delta population. 

Bay-Delta Population 

The Bay-Delta is considered one of 

the most highly invaded estuaries in the 

world (Sommer et al. 2007, p. 272). 

Longfin smelt abundance in the BayDelta has remained low since the mid1980s (see Abundance section, above). 

This long-term decline has been at least 

partially attributed to effects of the 

introduced overbite clam (Kimmerer 

2002a, p. 47; Sommer et al. 2007, p. 274; 

Rosenfield and Baxter 2007, p. 1589; 

Baxter et al. 2010, pp. 61–62). The 

overbite clam has impacted zooplankton 

abundance and species composition by 

grazing on the phytoplankton that 

comprise part of the zooplankton’s food 

base (Orsi and Mecum 1996, pp. 384– 

386) and by grazing on larval stages of 

certain zooplankton like Eurytemora 

affinis (no common name) (Kimmerer 

2002, p. 51; Sommer et al. 2007, pp. 

274–276). Longfin smelt recruitment 

(replacement of individuals by the next 

generation) has steadily declined since 

1987, even after adjusting for Delta 

freshwater flows (Nobriga 2010, slide 5). 

These data suggest that changes in the 

estuary’s food web following 

introduction of the overbite clam may 

have had substantial and long-term 

impacts on longfin smelt population 

dynamics in the Bay-Delta. 

Numerous other invasive plant and 

animal species have been introduced 

into the Bay-Delta, and ecosystem 

disruptions will undoubtedly continue 

as new species are introduced. Sommer 

et al. (2007, p. 272) note that the quagga 

mussel (Dreissna bugensis) was 

discovered in southern California in late 

2006, and that it could become 

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established in the Bay-Delta and cause 

substantial ecosystem disruption. 

Other Populations 

The Eel River is undergoing a shift 

from native anadromous to resident 

introduced fish species. Of particular 

importance are the California roach 

(Hesperoleucus symmetricus) and the 

Sacramento pikeminnow (Ptychocheilus 

grandis) (Brown and Moyle 1997, p. 

274). The Sacramento pikeminnow is 

known to cause shifts in spatial 

distribution of native species (Brown & 

Moyle 1991, p. 856). The Sacramento 

pikeminnow preys on native fishes, 

particularly emigrating juvenile 

salmonids (Moyle 2002, p. 156) and 

likely preys upon the longfin smelt 

when present. 

In Humboldt Bay, one study recorded 

73 nonnative species, with another 13 

species of uncertain status (Boyd 2002, 

pp. 89–91). Many of the nonnative 

species, most of which are invertebrates, 

have been present in the Bay for over 

100 years, although some introductions 

have also occurred more recently (Boyd 

2002, pp. 89–91). It is possible that the 

presence of some of these introduced 

species have resulted in changes to the 

food web resulting in changes to longfin 

smelt food availability in Humboldt 

Bay, as has occurred in the Bay-Delta. 

However, there are no data with which 

to evaluate this hypothesis. Commercial 

oyster culturing in Humboldt Bay began 

in 1955 (Barrett 1963, p. 38). Oyster 

culture beds within the bay are located 

in areas that are favorable to eelgrass 

(Zostera marina), and the harvesting of 

oysters in these beds has resulted in a 

reduction of and damage to native 

eelgrass in Humboldt Bay (Trianni 1996, 

p. 4; Rummrill and Poulton 2004, p. 2). 

Longfin smelt are known to feed on 

fauna found on native eelgrass, and 

therefore loss of eelgrass communities 

could result in lower levels of longfin 

smelt prey, possibly resulting in 

decreased longfin smelt survival. 

Over 100 species of nonnative, 

invasive aquatic plants and animals 

have been documented in the Yaquina 

Bay estuary in Oregon (Oregon State 

University 2011, p. 1). One of the plants 

that has become established is Zostera 

japonica, a seagrass that was introduced 

to Yaquina Bay as live packing material 

for Japanese oysters. It poses a 

competitive threat to the native eelgrass 

(Brown et al. 2007, p. 9), and longfin 

smelt are known to feed on fauna found 

on native eelgrass (Phillips 1984, pp. 1– 

85). Invasive fish species in Yaquina 

Bay include American shad (Alosa 

sapidissima), common carp (Cyprinus 

carpio), bass (Micropterus spp.), and 

walleye (Sander vitreum). 

Numerous nonnative, invasive plant 

and animal species have established 

populations within the Columbia River 

estuary. Nonnative, invasive plants and 

fish are the largest taxa to inhabit the 

estuary, followed by mollusks and 

crustaceans (Sanderson et al. 2009, pp. 

245–256). American shad was 

introduced in the Columbia River soon 

after 1871 (Petersen et al. 2011, pp. 1– 

42). The spawning adult shad 

population in the Columbia River is 

more than 5,000,000 individuals, the 

largest anywhere (Petersen et al. 2011, 

pp. 1–42). Shad may have large, 

negative effects on Columbia River 

ecosystems, as adult and juvenile shad 

prey on zooplankton, thereby reducing 

the availability of prey for other fish 

species (Sanderson et al. 2009, pp. 245– 

256). Also present in the lower 

Columbia River are channel catfish 

(Ictalurus punctatus), striped bass, 

smallmouth bass (Microperterus 

dolomieui), largemouth bass 

(Micropterus salmoides), and walleye 

(Sander vitreus). These nonnative fishes 

are aggressive predators and have likely 

substantially altered food webs in the 

Columbia River estuary (Sanderson et 

al. 2009, pp. 245–256). The Eurasian 

water milfoil (Myriophyllum spicatum) 

may have been introduced into the 

lower Columbia River by ballast water 

from European ships in the 1800s 

(Aiken et al. 1979, pp. 201–215). It 

forms dense mats of vegetation and 

results in reduced dissolved oxygen 

concentrations as the plants decompose, 

altering aquatic ecosystem chemistry 

and function (Cronin et al. 2006, pp. 37– 

43; Unmuth et al. 2000, pp. 497–503), 

which could potentially restrict longfin 

smelt distribution in the region. 

Hundreds of invasive plants and 

animals have found their way into Puget 

Sound through importation of soils, 

plants, fruits, and seeds; through boat 

hulls and ship ballast water discharge; 

and through intentional human releases. 

Invasive tunicate species that reproduce 

quickly and cover docks and boat hulls 

are also present in the sound (Puget 

Sound Partnership 2008b, p. 26). 

Contaminants 

Bay-Delta 

Similar to other potential threats to 

longfin smelt, most of the information 

available is for the Bay-Delta. In 2009, 

over 15 million pounds of pesticides 

were applied within the five-county 

Bay-Delta area (California Department of 

Pesticide Regulation 2011, p. 1). 

Toxicity to invertebrates has been noted 

in water and sediments from the Delta 

and associated watersheds (e.g., Werner 

et al. 2000, pp. 218, 223). Fish exposed 

to agricultural drainage water from the 

San Joaquin River watershed can exhibit 

body burdens of selenium exceeding the 

level at which reproductive failure and 

increased juvenile mortality occur (Saiki 

et al. 2001, p. 629). Toxicity studies 

specific to longfin smelt are not 

available, but data do exist for other fish 

species such as the delta smelt, a related 

species. Longfin smelt could be 

similarly affected by contaminants as 

some life stages utilize similar habitat 

and prey resources, and longfin smelt 

have a physiology similar to delta smelt. 

Kuivila and Moon (2004, p. 239) found 

that peak densities of larval and juvenile 

delta smelt sometimes coincided in time 

and space with elevated concentrations 

of dissolved pesticides in the spring. 

These periods of co-occurrence lasted 

for up to 2 to 3 weeks. Concentrations 

of individual pesticides were low and 

much less than would be expected to 

cause acute mortality; however, the 

effects of exposure to the complex 

mixtures of pesticides are unknown. 

Bay-Delta waters are listed as 

impaired for several legacy and 

currently used pesticides under the 

Clean Water Act section 303(d) 

(California Department of Pesticide 

Regulation 2011, p. 1). Concentrations 

of dissolved pesticides vary in the Delta 

both temporally and spatially (Kuivila 

2000, p. 1). Several areas of the Delta, 

particularly the San Joaquin River and 

its tributaries, are impaired due to 

elevated levels of diazinon and 

chlorpyrifos, which are toxic at low 

concentrations to some aquatic 

organisms (MacCoy et al. 1995, pp. 21– 

30). Several studies have demonstrated 

the acute and chronic toxicity of two 

common dormant-spray insecticides, 

diazinon and esfenvalerate, in fish 

species (Barry et al. 1995, p. 273; 

Goodman et al. 1979, p. 479; Holdway 

et al.; 1994, p. 169; Scholz et al. 2000, 

p. 1911; Tanner and Knuth 1996, 

p. 244). 

Pyrethroid pesticides are of particular 

concern because of their widespread 

use, and their tendency to be genotoxic 

(DNA damaging) to fishes at low doses 

(in the range of micrograms per liter) 

(Campana et al. 1999, p. 159). The 

pyrethroid esfenvalerate is associated 

with delayed spawning and reduced 

larval survival of bluegill sunfish 

(Lepomis macrochirus) (Tanner and 

Knuth 1996, pp. 246–250) and increased 

susceptibility of juvenile Chinook 

salmon (Oncorhynchus tshawytscha) to 

disease (Clifford et al. 2005, pp. 1770– 

1771). In addition, synthetic pyrethroids 

may interfere with nerve cell function, 

which could eventually result in 

paralysis (Bradbury and Coats 1989, pp. 

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377–378; Shafer and Meyer 2004, pp. 

304–305). 

Weston and Lydy (2010, p. 1835) 

found the largest source of pyrethroids 

flowing into the Delta to be coming from 

the Sacramento Regional Water 

Treatment Plant (SRWTP), where only 

secondary treatment occurs. Their data 

not only indicate the presence of these 

contaminants, but the concentrations 

found exceeded acute toxicity 

thresholds for the amphipod Hyalella 

azteca. This is of substantial concern 

because the use of insecticides in the 

urban environment had not before been 

considered the primary source of 

insecticides flowing into the Delta. 

Furthermore, this was not the case for 

the Stockton Waste Water Treatment 

facility, where tertiary treatment occurs, 

suggesting that the tertiary treatment 

that occurs at the Stockton facility could 

minimize or eliminate toxic effluent 

being dispersed from wastewater 

facilities (Baxter et.al. 2010, p. 33). 

Several studies were initiated in 2005 

to address the possible role of 

contaminants and disease in the 

declines of Bay-Delta fish and other 

aquatic species. The primary study 

consists of twice-monthly monitoring of 

ambient water toxicity at 15 sites in the 

Bay-Delta and Suisun Bay (Baxter et al. 

2010, pp. 16, 17, 30). Significant 

mortality of amphipods was observed in 

5.6 percent of samples collected in 

2006–2007 and 0.5 percent of samples 

collected in 2008–2009. Werner et al. 

(2010b, p. 3) found that larval delta 

smelt were between 1.8 and 11 times 

more sensitive than fathead minnows 

(Pimephales promelas) to copper, 

ammonia, and all insecticides except 

permethrin. Aquatic insects in which 

the longfin smelt relies upon for food 

have been shown to be sensitive to 

ammonia. H. azteca was the most 

sensitive to all pyrethroids tested, while 

E. affinis and C. Dubia were the most 

sensitive to ammonia (Werner et al. 

2010b, pp. 18, 23). Pyrethroids are of 

particular interest because use of these 

insecticides has increased within the 

Bay-Delta watershed as use of 

organophosphate insecticides has 

declined. Longfin smelt are probably 

most vulnerable to the effects of toxic 

substances during the winter and 

spring, when their early life stages occur 

in the Delta and Suisun and San Pablo 

Bays, where they are closer to point and 

non-point inputs of contaminants from 

runoff. 

The largest source of ammonia 

entering the Delta ecosystem is the 

Sacramento Regional Wastewater 

Treatment Plant (SRWTP), which 

accounts for 90 percent of the total 

ammonia load released into the Delta. 

Ammonia is un-ionized and has the 

chemical formula NH3. Ammonium is 

ionized and has the formula NH4

+. The 

major factors determining the 

proportion of ammonia or ammonium in 

water are water pH and temperature. 

This is important, as NH3 ammonia is 

the form that can be directly toxic to 

aquatic organisms, and NH4

+

ammonium is the form documented to 

interfere with uptake of nitrates by 

phytoplankton (Dugdale et al. 2007, p. 

17; Jassby 2008, p. 3). 

Effects of elevated ammonia levels on 

fish range from irritation of skin, gills, 

and eyes to reduced swimming ability 

and mortality (Wicks et al. 2002, p. 67). 

Delta smelt have been shown to be 

directly sensitive to ammonia at the 

larval and juvenile stages (Werner et al. 

2008, pp. 85–88). Longfin smelt could 

similarly be affected by ammonia as 

they utilize similar habitat and prey 

resources and have a physiology similar 

to delta smelt. Ammonia also can be 

toxic to several species of copepods 

important to larval and juvenile fishes 

(Werner et al. 2010, pp. 78–79; Teh et 

al. 2011, pp. 25–27). 

In addition to direct effects on fish, 

ammonia in the form of ammonium has 

been shown to alter the food web by 

adversely impacting phytoplankton and 

zooplankton dynamics in the estuary 

ecosystem. Historical data show that 

decreases in Suisun Bay phytoplankton 

biomass coincide with increased 

ammonia discharge by the SRWTP 

(Parker et al. 2004, p. 7; Dugdale et al. 

2011, p. 1). Phytoplankton preferentially 

take up ammonium over nitrate when it 

is present in the water. Ammonium is 

insufficient to provide for growth in 

phytoplankton, and uptake of 

ammonium to the exclusion of nitrate 

results in decreases in phytoplankton 

biomass (Dugdale et al. 2007, p. 23). 

Therefore, ammonium impairs primary 

productivity by reducing nitrate uptake 

in phytoplankton. Ammonium’s 

negative effect on the food web has been 

documented in the longfin smelt rearing 

areas of San Francisco Bay and Suisun 

Bay (Dugdale et al. 2007, pp. 26–28). 

Decreased primary productivity results 

in less food available to longfin smelt 

and other fish in these bays. 

Several streams that flow into the 

Bay-Delta are listed as impaired because 

of high concentrations of metals such as 

cadmium, copper, lead, and zinc. Metal 

concentrations have been found to be 

toxic to fish in the upper Sacramento 

River near and downstream from 

Redding (Alpers et al. 2000a, p. 4; 

2000b, p. 5). Elevated levels of metals 

such as copper in streambed sediment 

continue to occur in the upper 

Sacramento River Basin downstream 

from Redding (MacCoy and Domagalski 

1999, p. 35). Copper and other metals 

may affect aquatic organisms in upper 

portions of contributing watersheds of 

the Delta. Mercury and its bioavailable 

form (methylmercury) are distributed 

throughout the estuary, although 

unevenly. Mercury has been known to 

bioaccumulate and cause neurological 

effects in some fish species, but it has 

not been associated with the Pelagic 

Organism Decline (Baxter et al. 2010, p. 

28). No specific information is available 

on the effects of mercury exposures to 

longfin smelt. Selenium, introduced 

into the estuary primarily from 

agricultural irrigation runoff via the San 

Joaquin River drainage and oil 

refineries, has been implicated in toxic 

and reproductive effects in fish and 

wildlife (Baxter 2010 et al., p. 28; 

Linville et al. 2002, p. 52). Selenium 

exposure has been shown to have effects 

on some benthic foraging species; 

however there is no evidence that 

selenium exposure is contributing to the 

decline of longfin smelt or other pelagic 

species in the Bay-Delta (Baxter et al. 

2010, p. 28). 

Large blooms of toxic Microcystis 

aeruginosa (blue-green algae) were first 

documented in the Bay-Delta during the 

summer of 1999 (Lehman et al. 2005, p. 

87). M. aeruginosa forms large colonies 

throughout most of the Delta and 

increasingly down into eastern Suisun 

Bay (Lehman et al. 2005, p. 92). Blooms 

typically occur when water 

temperatures are above 20 °C (68 °F) 

(Lehman et al. 2005, p. 87). Preliminary 

evidence indicates that the toxins 

produced by local blooms are not 

directly toxic to fishes at current 

concentrations (Baxter et al. 2010, p. 

10). However, the copepods that the 

related delta smelt eat are particularly 

susceptible to those toxins (Ger 2008, 

pp. 12, 13). Microcystis blooms may also 

decrease dissolved oxygen to lethal 

levels for fish (Lehman et al. 2005, p. 

97). Blooms typically occur between late 

spring and early fall when the majority 

of longfin smelt occur farther 

downstream, so effects are expected to 

be minimal. 

Other Populations 

As in the Bay-Delta, pesticide and 

metals contamination occurs in Yaquina 

Bay, the Columbia River, and the Fraser 

River (Johnson et al. 2007, p. 1; Lower 

Columbia River Estuary Partnership 

(LCREP) 2011, p. 1; Blomquist, 2005, p. 

8). Ammonia contamination occurs in 

the Klamath River (Oregon Department 

of Environmental Quality (ODEQ) 2011, 

p. 1) and Cook Inlet (ADEC 2011a, p. 1), 

and toxic algal blooms occur in the 

Klamath River (California State Water 

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Resources Control Board (CSWRCB) 

2010, p. 1) and Yaquina Bay (ODEQ 

Water Quality Assessment Online 

Database 2011). 

Industrial contaminants such as 

dioxins, polychlorinated biphenyls 

(PCBs), and polyaromatic hydrocarbons 

(PAHs) occur in Humboldt Bay 

(NCRWQCB 2010 pp. 3–4), Yaquina Bay 

(Johnson et al. 2007, p. 1), the Columbia 

River (LCREP 2011, p. 1), Puget Sound 

(Puget Sound Partnership 2008b, p. 21), 

and the Fraser River (British Columbia 

Ministry of Environment 2001, pp. 5–6; 

Blomquist, 2005, p. 8). Suspended 

sediment is a contaminant in the Eel 

River (Downie 2010, p. 10), Humboldt 

Bay (NCRWQCB 2010 pp. 3–4), Yaquina 

Bay (ODEQ Water Quality Assessment 

Online Database 2011), and Puget 

Sound (WA Department Ecology 2008, 

p. 1). Nutrient enrichment and low 

levels of dissolved oxygen occur in the 

Klamath River (CSWRCB 2010, p.1), 

Yaquina Bay (Bricker et al. 1999, pp. 1– 

71), and Fraser River (British Columbia 

Ministry of Environment 2001, pp. 5–6). 

Fecal coliform and other forms of 

bacteria contaminate Yaquina Bay, 

Puget Sound, the Fraser River, and Cook 

Inlet (Brown et al 2007, pp. 16–17, WA 

Department Ecology 2008, p. 1, 

Blomquist, 2005, p. 8, ADEC 2011a, 

p. 1). 

Oregon and Washington States have 

listed multiple reaches of the Lower 

Columbia River on their Federal Clean 

Water Act 303(d) lists, due to total 

dissolved gas levels exceeding State 

water quality standards. This occurs at 

several dams on these rivers where 

water flowing over the spillway of a 

dam creates air bubbles. When these are 

carried to depth in the dam’s stilling 

basin, the higher hydrostatic pressure 

forces air from the bubbles into solution. 

The result is water supersaturated with 

dissolved nitrogen, oxygen, and the 

other constituents of air (ODEQ 2002, p. 

ix). High total dissolved gas levels can 

cause gas bubble trauma in fish, which 

can result in injury or mortality to fish 

species (ODEQ 2002, pp. 1–150). 

Summary of Contaminants 

Most fish including longfin smelt can 

be sensitive to adverse effects from 

contaminants in their larval or juvenile 

stages. Adverse effects to longfin smelt 

would be more likely to occur where 

sources of contaminants occur in close 

proximity to spawning and rearing 

habitats (brackish or fresh waters). 

Laboratory studies have shown certain 

contaminants to potentially have 

adverse effects on individual delta 

smelt, a related species. Field studies 

have shown that the contaminants of 

concern are elevated in some of the 

estuaries throughout the species’ range, 

including the Bay-Delta. 

Summary of Factor E 

We evaluated whether entrainment 

losses, introduced species, and 

contaminants threaten the longfin smelt 

throughout its range. Longfin smelt is 

broadly distributed across a wide 

variety of estuaries from central 

California to Alaska, and there is no 

monitoring data documenting a 

population decline other than the 

population decline in the Bay-Delta. 

Because the Bay-Delta system is one 

of the largest man made water systems 

in the world, it would be impractical to 

compare diversions and alterations in 

other estuaries to diversions and 

alterations in the Bay-Delta. The effects 

of entrainment in the Bay-Delta are 

unique to the estuary because of the 

large water diversions. Because 

diversions in other estuaries are much 

smaller, we expect that the effects from 

these diversions would be minimal in 

relation to the effects in the Bay-Delta. 

We have no information to show that 

entrainment is a threat to longfin smelt 

throughout its range. 

Introduced species and contaminants 

are threats to the Bay-Delta long smelt 

population, but there is no information 

indicating that they are threats to the 

species in other parts of its range. 

Although invasive species are present in 

other estuaries, none have been 

documented to be having an effect on 

the longfin smelt food supply like the 

overbite clam has had. Similarly, 

although contaminants are present in 

other estuaries where the longfin smelt 

resides, none have been shown to have 

effects on the longfin smelt food supply 

like ammonia in the Bay-Delta has been 

shown to have. 

Finding 

As required by the Act, we considered 

the five factors in assessing whether the 

longfin smelt is endangered or 

threatened throughout all of its range. 

We have carefully examined the best 

scientific and commercial information 

available regarding the past, present, 

and future threats faced by the longfin 

smelt. We reviewed the petition, 

information available in our files, other 

available published and unpublished 

information, and we consulted with 

recognized longfin experts and other 

Federal and State agencies. 

Little information is available on 

longfin smelt populations other than the 

Bay-Delta and Lake Washington 

populations. Smelt caught along the 

Pacific Coast are rarely identified to 

species. Therefore, information on 

longfin smelt distribution and 

abundance outside the Bay-Delta is 

limited. Although monitoring data 

indicate a significant decline in the 

abundance of longfin smelt in the BayDelta, population monitoring for other 

populations is not available. Estuaries 

are complex ecosystems, and different 

estuaries within the longfin smelt’s 

range vary greatly in their 

environmental characteristics and in 

how they are managed. For example, in 

no estuary within the range of the 

longfin smelt, other than the Bay-Delta, 

are large volumes (up to 35 percent of 

freshwater inflow between February and 

June, and up to 65 percent of inflow 

between July and January) of freshwater 

pumped directly out of the estuary. 

Under Factor A, channel disturbances 

may have localized impacts to longfin 

smelt habitat suitability. However, we 

conclude that these activities are not 

significant threats to longfin smelt 

throughout its range. Climate change 

will likely affect longfin smelt in 

multiple ways, but longfin smelt are 

able to move between a wide range of 

aquatic environments that vary greatly 

in water temperature and salinity, and 

these behavioral and physiological 

characteristics of the species may help 

it adapt to the effects of climate change. 

We conclude that the best available 

information does not indicate that 

climate change threatens the continued 

existence of longfin smelt across its 

range. We conclude that reduced 

freshwater flows are a threat to the BayDelta longfin smelt population, but not 

to the species in the rest of its range. 

The Bay-Delta is unique among 

estuaries occupied by longfin smelt 

because large volumes of freshwater are 

exported away from the estuary on an 

annual basis. In addition, it is difficult 

to extrapolate from the Bay-Delta to 

other estuaries because the effects of 

water management in the Bay-Delta are 

likely unique to the physical, geologic, 

and hydrologic environment of that 

estuary. We conclude that the best 

scientific information available 

indicates that continued existence of the 

longfin smelt is not threatened in any 

part of its range outside of the Bay-Delta 

by the present or threatened destruction, 

modification, or curtailment of its 

habitat or range now or in the 

foreseeable future 

Under Factor B, we evaluated 

potential threats from recreational and 

commercial fishing and from monitoring 

surveys on longfin smelt. Longfin smelt 

are protected from intentional take in 

California because the species is listed 

as threatened under CESA. Efforts have 

been made to reduce mortality of 

longfin smelt as bycatch in a bay shrimp 

trawl commercial fishery and in 

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monitoring surveys in the Bay-Delta. 

Longfin smelt is caught as part of 

recreational or commercial fisheries in 

Oregon, Washington, British Columbia, 

and Alaska, but numbers of fish caught 

are considered low, and we found no 

evidence that fisheries harvest was 

causing population declines of longfin 

smelt. We conclude that overutilization 

is not a significant current or future 

threat to longfin smelt across its range. 

Under Factor C, we evaluated 

potential threats from disease and 

predation. We found no evidence of 

rangewide threats to the continued 

existence of the species due to disease 

or predation, now or in the foreseeable 

future. 

Under Factor D, we conclude that 

several Federal and State laws and 

regulations provide varying levels of 

protection for the longfin smelt 

throughout its range. Several of these 

regulatory mechanisms promote 

protection of longfin smelt habitat and 

provide tools to implement these habitat 

protections. We conclude that longfin 

smelt is not threatened throughout its 

range by inadequate regulatory 

mechanisms, now or in the foreseeable 

future. 

Under Factor E, we evaluated 

potential threats due to entrainment 

losses from water diversions, introduced 

species, and contaminants. Information 

indicates that introduced species are a 

threat to the Bay-Delta longfin smelt 

population and that ammonium may 

constitute a threat to the Bay-Delta 

longfin smelt population, but 

information does not indicate that 

entrainment losses, introduced species, 

or contaminants are threatening longfin 

smelt populations in other parts of its 

range, now or in the foreseeable future. 

Based upon our review of the best 

available scientific and commercial 

information pertaining to the five 

factors, we find that the threats are not 

of sufficient imminence, intensity, or 

magnitude to indicate that the longfin 

smelt is in danger of extinction 

(endangered), or likely to become 

endangered within the foreseeable 

future (threatened), throughout all of its 

range. Therefore, we find that listing the 

longfin smelt as an endangered or 

threatened species throughout all of its 

range is not warranted at this time. 

Distinct Vertebrate Population Segment 

Having found that the best available 

information does not indicate that the 

longfin smelt warrants listing 

rangewide, we now assess whether any 

distinct population segments of longfin 

smelt meet the definition of endangered 

or are likely to become endangered in 

the foreseeable future (threatened). 

Under the Services’ (joint policy of the 

Fish and Wildlife Service and National 

Marine Fisheries Service) DPS policy 

(61 FR 4722; February 7, 1996), three 

elements are considered in the decision 

concerning the establishment and 

classification of a possible DPS. These 

are applied similarly for additions to or 

removal from the Federal List of 

Endangered and Threatened Wildlife. 

These elements include: (1) The 

discreteness of a population 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, 

delisting, or reclassification (i.e., is the 

population segment endangered or 

threatened). We have identified one 

population that potentially meets all 

three elements of the 1996 DPS policy— 

the population that occurs in the BayDelta estuary. During the rangewide 

five-factor analysis, significant threats 

were identified only for the Bay-Delta 

population. Therefore, we determined 

that only the Bay-Delta population 

potentially meets the third element of 

the DPS. 

Discreteness 

Under the DPS policy, a population 

segment of a vertebrate taxon may be 

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. 

Marked Separation From Other 

Populations as a Consequence of 

Physical, Physiological, Ecological, or 

Behavioral Factors 

The limited swimming capabilities of 

the longfin smelt, existing ocean current 

patterns, and the great distances 

between the Bay-Delta and other known 

breeding populations make it unlikely 

that regular interchange occurs between 

the Bay-Delta and other longfin smelt 

breeding populations. Longfin smelt is a 

relatively short-lived species that 

completes its 2- to 3-year life cycle 

moving between freshwater spawning 

habitat in the Delta and brackish water 

rearing habitat downstream (seaward) in 

the estuary within Suisun Bay, San 

Pablo Bay, and central San Francisco 

Bay. At least a portion of the population 

also migrates into the near-coastal 

waters of the Gulf of Farallones 

(Rosenfield and Baxter 2007, p. 1590). 

Although its swimming capabilities 

have not been studied, it is a small fish 

believed to have a limited swimming 

capacity (Moyle 2010, pp. 5–6). How 

longfin smelt return to the Bay-Delta 

from the Gulf of Farallones is not known 

(Rosenfield and Baxter 2007, p.1590). 

The Bay-Delta population is the 

southernmost population of longfin 

smelt and is separated from other 

longfin smelt breeding populations by 

56 km (35 mi). The nearest location to 

the Bay-Delta where longfin smelt have 

been caught is the Russian River, 

located north of the Bay-Delta; however, 

little information is available for this 

population (see Distribution section, 

above). Due to limited freshwater flow 

into the estuary and interannual 

variation in freshwater flow, it is 

unlikely that the estuary provides 

sufficient potential spawning and 

rearing habitat to support a regularly 

breeding longfin smelt population 

(Moyle 2010, p. 4). 

The Eel River and Humboldt Bay are 

the next nearest locations where longfin 

smelt are known to occur, and they are 

located much farther to the north—Eel 

River is located 394 km (245 mi) north 

of the Bay-Delta, and Humboldt Bay is 

located 420 km (260 mi) north of the 

Bay-Delta. Moyle (2010, p. 4) considered 

Humboldt Bay to be the only other 

estuary in California potentially capable 

of supporting longfin smelt in most 

years. 

In our April 9, 2009, longfin smelt 

12-month finding (74 FR 16169), we 

concluded that the Bay-Delta population 

was not markedly separated from other 

populations and, therefore, did not meet 

the discreteness element of the 1996 

DPS policy. This conclusion was based 

in part on the assumption that ocean 

currents likely facilitated dispersal of 

anadromous longfin smelt to and from 

the Bay-Delta to other estuaries in 

numbers that could readily sustain the 

Bay-Delta population group if it was to 

be extirpated. Since 2009, we have 

obtained information relevant to 

assumptions that we made in the 2009 

12-month finding. Additional clarifying 

information comes in part from a 

declaration submitted to the U.S. 

District Court for the Northern District 

of California on June 29, 2010, by Dr. 

Peter Moyle, Professor of Fisheries 

Biology at the University of California at 

Davis (Moyle 2010, pp. 1–8). Moyle 

(2010, pp. 5–6) notes that he believes 

that we overestimated the swimming 

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capacity of longfin smelt in our 2009 12- 

month finding. Moyle (2010, p. 8) states 

that longfin smelt that migrate out of 

and back into the Bay-Delta estuary may 

primarily be feeding on the rich 

planktonic food supply in the Gulf of 

Farallones, and that this migration 

between the Bay-Delta and near coastal 

waters of the Gulf of Farallones does not 

indicate that longfin smelt are 

necessarily dispersing long distances to 

other estuaries to the north. 

At the time of our last finding, we did 

not have information available assessing 

the ability of longfin smelt to disperse 

northward from the Bay-Delta or 

southward to the Bay-Delta using 

currents in the Pacific Ocean. Since the 

time of our previous finding (74 FR 

16169; April 9, 2009), we have reviewed 

additional information on ocean 

currents in nearshore waters and over 

the continental shelf from 

approximately the Gulf of Farallones 

north to Coos Bay. We have evaluated 

the potential for longfin smelt to 

disperse northward from the Bay-Delta 

or southward to the Bay-Delta. On 

October 28, 2011, we convened a panel 

of experts to evaluate the potential of 

longfin smelt dispersal via ocean 

currents. Oceanographers on the panel 

were tasked with answering a series of 

questions on how ocean currents would 

affect longfin smelt potentially 

dispersing into or out of the Bay-Delta. 

Much of the following analysis was 

derived from that panel discussion. Our 

analysis relies upon ocean current 

information as it relates to what is 

known of longfin smelt biology and life 

history from the Bay-Delta population. 

Table 2 overlays longfin smelt life 

history with general ocean current 

patterns in central and northern 

California. However, the California 

Current System exhibits a high degree of 

seasonality as well as weekly variability. 

Currents are highly variable in fall and 

winter but tend to be predominately 

northward. Surface currents are 

northward during the storm season from 

December to March and transition to 

southward in March or April. Offshore 

of central California the surface currents 

remain generally southward during 

summer. However, despite the 

predominant southward surface current, 

northward currents are common at 

depths around 60 to 200 m along the 

continental slope at all times of the year. 

This deeper current is known as the 

California Undercurrent (Paduan 2011, 

pers. comm.) 

Eddies (clockwise water circulation 

areas) exist at various points between 

the Bay-Delta and Humboldt Bay at 

landmarks such as Point Arena and 

Cape Mendocino. These eddies vary in 

their distance from shore between 10 to 

100 km (6 to 62 mi) (Padaun 2011, pers. 

comm.). During the summer upwelling 

season, northerly winds drive a 

southward offshore flow of near-surface 

waters (Dever et al. 2006, p. 2109) and 

also set up a strong current over the 

continental shelf that is deflected 

offshore at capes such as Cape 

Mendocino, Point Arena, and Point 

Reyes (Magnell et al. 1990, p. 7; Largier 

2004, p. 107; Halle and Largier 2011, pp. 

1–24). Several studies have used drifters 

(flotation devices tracked by satellites) 

and pseudo-drifters (computersimulated satellite-tracked flotation 

devices) to evaluate currents in the 

California region of the Pacific Ocean. 

These studies indicate that the 


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circulation patterns located off Point 

Arena and Cape Mendocino limit 

dispersal (particularly southward) of 

flotation devices in the region (Sotka et 

al. 2004, p. 2150; Drake et al. 2011, pp. 

1–51; Halle and Largier 2011, posters). 

This limitation is important because 

Cape Mendocino and Point Arena are 

between the Bay-Delta and the nearest 

likely self-sustaining population of 

longfin smelt in Humboldt Bay. 

Longfin smelt are an euryhaline 

species, of which an unknown fraction 

of the population exhibits anadromy 

(Moyle 2002, p. 236; Rosenfield and 

Baxter 2007 p. 1578). Based on their 

small size and limited swimming 

ability, we expect that longfin smelt 

would be largely dependent on ocean 

currents to travel the large distance 

between the Bay-Delta and the 

Humboldt Bay. During wet years, newly 

spawned longfin smelt larvae may be 

flushed out to the ocean between 

December and March. It is unlikely that 

longfin smelt larvae can survive ocean 

transport because larvae are not known 

to tolerate salinities greater than 8 ppt 

(Baxter 2011b, pers. comm.), and surface 

salinities less than 8 ppt do not exist 

consistently in the ocean (Bograd and 

Paduan 2011, pers. comm.). 

A portion of the longfin smelt that 

spawn in the Bay-Delta make their way 

to the ocean once they are able to 

tolerate full marine salinities, sometime 

during the late spring or summer of 

their first year of life (age-0) (City of San 

Francisco and CH2MHill 1984 and 

1985, entire), and may remain there for 

18 months or longer before returning to 

the Bay-Delta to spawn (Baxter 2011c, 

pers. comm.). A larger portion of longfin 

smelt enter the coastal ocean during 

their second year of life (age-1) (City of 

San Francisco and CH2MHill 1984 and 

1985, entire) and remain there for 3 to 

7 months until they re-enter the BayDelta to spawn in early winter 

(Rosenfield and Baxter 2007, p 1590; 

Baxter 2011c, pers. comm.). Most of 

these age-1 longfin smelt move to 

coastal waters in July and August, 

possibly to escape warm water 

temperatures or to obtain food (Moyle 

2010, p. 8; Rosenfield and Baxter 2007, 

p. 1290). Some longfin smelt may live 

to 3 years of age and may remain in the 

coastal ocean until they are 3 years old. 

However, no 3-year old longfin smelt 

have been observed in the coastal ocean 

(Baxter 2011d, pers. comm.; Service 

2011, unpublished data). 

It is possible that some of these 

juvenile or adult longfin smelt could 

make their way into the Russian River, 

Eel River, or Humboldt Bay and 

supplement or sustain those 

populations by utilizing northward 

ocean currents (Padaun 2011, pers. 

comm.; Service 2011b, pp. 1–4), but 

there is no documentation of such longdistance coastal movements. The 

northward ocean currents are strongest 

and most reliable in winter, when 

satellite-tracked particles move between 

the Bay-Delta and Humboldt Bay in as 

little as 2 months (Service 2011, p. 3). 

Opportunities for longfin smelt 

dispersal utilizing ocean currents from 

northern estuaries to the Bay-Delta are 

more limited. Studies have revealed that 

currents near Cape Mendocino and 

Point arena would carry small objects to 

the west away from the coast (Padaun 

2011b, pers. comm.; Bograd 2011, pers. 

comm.). It is possible that longfin smelt 

in nearshore waters could travel south 

past these eddies if they stay close 

enough to shore. It is even possible that 

some longfin smelt may be moved closer 

to shore by the eddies (Bograd 2011, 

pers. comm.; Paduan 2011, pers. 

comm.). However, any longfin smelt 

that do travel south past the Cape 

Mendocino and Point Arena 

escarpments would be unlikely to reenter the Bay-Delta. These offshore 

ocean currents could displace any 

longfin smelt potentially moving south 

more than 100 km (62 mi) offshore of 

the Bay-Delta (Paduan 2011a, pers. 

comm.). Pathways that transport objects 

close to shore would be expected to be 

rare, if they exist at all (Padaun 2011b, 

pers. comm.; Bograd 2011, pers. comm.). 

So while we considered whether ocean 

currents may transport or facilitate 

movement of longfin smelt from 

northern estuaries to the Bay-Delta 

estuary, there is no information showing 

that such dispersal movement occurs. 

Using the best scientific data 

available, we compared longfin smelt 

biology and life history with the latest 

available ocean current data provided 

by oceanographers. We conclude that 

longfin smelt in the Bay-Delta 

population do not regularly breed or 

interact with longfin smelt in other 

breeding populations to the north and 

are therefore markedly separated from 

other longfin smelt populations. 

Under the 1996 DPS policy, the 

discreteness standard does not require 

absolute separation of a DPS from other 

members of its species, nor does the 

standard require absolute reproductive 

isolation (61 FR 4722). Because of the 

great distances between the Bay-Delta 

and known breeding populations to the 

north, the small size of the longfin 

smelt, and the low likelihood that ocean 

currents could facilitate longfin smelt 

movements between widely separated 

populations, we conclude that the BayDelta population is markedly separated 

from other longfin smelt populations 

and therefore discreet. 

Quantitative Measures of Genetic or 

Morphological Discontinuity 

The 1996 DPS policy states that 

quantitative measures of genetic or 

morphological discontinuity may 

provide evidence of marked separation 

and discreteness. Stanley et al. (1995, p. 

395) compared allozyme variation 

between longfin smelt from the BayDelta population and the Lake 

Washington population using 

electrophoresis. They found that 

individuals from the populations 

differed significantly in allele (portions 

of a chromosome that code for the same 

trait) frequencies at several loci (gene 

locations). However, the authors also 

stated that the overall genetic 

dissimilarity was within the range of 

other conspecific (of the same species) 

fish species, and concluded that longfin 

smelt from Lake Washington and the 

Bay-Delta are conspecific, despite the 

large geographic separation (Stanley et 

al. 1995, p. 395). This study provided 

evidence that the Bay-Delta population 

of longfin smelt differed in genetic 

characteristics from the Lake 

Washington population, but did not 

compare other populations rangewide to 

the Bay-Delta population. More 

recently, Israel et al. (2011, pp. 1–10) 

presented preliminary results from an 

ongoing study, but these results were 

inconclusive in providing evidence of 

whether the Bay-Delta population is 

markedly separated from other longfin 

smelt populations (Cope 2011, pers. 

comm.; Service 2011a, pp. 1–3). 

We conclude that the limited 

quantitative genetic and morphological 

information available does not provide 

additional evidence of marked 

separation of the Bay-Delta longfin 

smelt population beyond the evidence 

presented above under Marked 

Separation from Other Populations as a 

Consequence of Physical, Physiological, 

Ecological, or Behavioral Factors. 

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 

The Bay-Delta population of longfin 

smelt is not delimited by an 

international boundary. Therefore, we 

conclude that it does not meet the 

international governmental boundaries 

criterion for discreteness. 

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Conclusion for Discreteness 

Because of its limited swimming 

capabilities and because of the great 

distances between the Bay-Delta and 

known breeding populations to the 

north, we conclude that the Bay-Delta 

population is markedly separated from 

other longfin smelt populations, and 

thus meets the discreteness element of 

the 1996 DPS policy. The best available 

information indicates that longfin smelt 

from the Bay-Delta population complete 

their life cycle moving between 

freshwater, brackish water, and 

saltwater portions of the estuary and 

nearby coastal ocean waters in the Gulf 

of Farallones. The nearest known 

breeding population of longfin smelt is 

Humboldt Bay, 420 km (260 mi) north 

of the Bay-Delta. As a result, potential 

interchange between the Bay-Delta 

population and other longfin smelt 

breeding populations is limited. 

Although the best scientific information 

suggests that potential movement of 

longfin smelt northward from the BayDelta would be facilitated by ocean 

currents, potential movement from more 

northern estuaries south to the BayDelta would be more difficult and 

unlikely because of ocean currents. 

Based on our review of the best 

available scientific and commercial 

information available, we conclude that 

the Bay-Delta population of longfin 

smelt is markedly separated from other 

longfin smelt populations as a 

consequence of physical, physiological, 

ecological, or behavioral factors. 

Significance 

Since we have found that the BayDelta longfin smelt population meets 

the discreteness element of the 1996 

DPS policy, we now consider its 

biological and ecological significance in 

light of Congressional guidance that the 

authority to list DPSes be used 

‘‘sparingly’’ while encouraging the 

conservation of genetic diversity. In 

making this determination, we consider 

available scientific evidence of the 

discrete population segment’s 

importance to the taxon to which it 

belongs. As precise circumstances are 

likely to vary considerably from case to 

case, the DPS policy does not describe 

all the classes of information that might 

be used in determining the biological 

and ecological importance of a discrete 

population. However, the DPS policy 

describes four possible classes of 

information that provide evidence of a 

population segment’s biological and 

ecological importance to the taxon to 

which it belongs. As specified in the 

DPS policy, this consideration of the 

population segment’s significance may 

include, but is not limited to, the 

following: 

(1) Persistence of the discrete 

population segment in an ecological 

setting unusual or unique to the taxon; 

(2) Evidence that loss of the discrete 

population segment would result in a 

significant gap in the range of a taxon; 

(3) Evidence that the discrete 

population segment 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 discrete 

population segment differs markedly 

from other populations of the species in 

its genetic characteristics. 

A population segment needs to satisfy 

only one of these conditions to be 

considered significant. Furthermore, 

other information may be used as 

appropriate to provide evidence for 

significance. 

(1) Persistence of the discrete 

population segment in an ecological 

setting unusual or unique to the taxon. 

The Bay-Delta population is the 

southernmost breeding population in 

the range of the species. Populations at 

the edge of a species’ range may be 

important in species conservation 

because environmental conditions at the 

periphery of a species’ range can be 

different from environmental conditions 

nearer the center of a species’ range. 

Thus, populations at the edge of the 

taxon’s range may experience different 

natural selection pressures that promote 

divergent evolutionary adaptations 

(Scudder 1989, entire; Fraser 2000, 

entire). Lomolino and Channell (1998, 

p. 482) hypothesized that because 

peripheral populations should be 

adapted to a greater variety of 

environmental conditions, they may be 

better suited to deal with anthropogenic 

(human-caused) disturbances than 

populations in the central part of a 

species’ range; however, this hypothesis 

remains unproven. This could be 

especially important because of 

changing natural selection pressures 

associated with climate change. 

For example, increasing ocean 

temperatures is an environmental 

change to which the Bay-Delta 

population of longfin smelt may be 

uniquely adapted. Because it is the 

southern-most estuary within the 

species’ range, the Bay-Delta has 

warmer average water temperatures than 

estuaries in central and northern parts 

of the species’ range. As a result, the 

Bay-Delta longfin smelt population may 

have behavioral or physiological 

adaptations for coping with higher 

water temperatures that may come as a 

result of climate change (see discussion 

under Factor A: Climate Change). Baxter 

et al. (2010, p. 68) conclude that high 

water temperatures in the Bay-Delta 

influence spatial distribution of longfin 

smelt in the estuary. Rosenfield and 

Baxter (2007, p. 1290) hypothesize that 

the partial anadromy exhibited by the 

population (part of the population is 

believed to migrate out into the cooler, 

nearby coastal ocean waters in the Gulf 

of Farallones) and concentrations of 

longfin smelt in deeper water habitat in 

summer months is at least partly a 

behavioral response to warm water 

temperatures found during summer and 

early fall in the shallows of south San 

Francisco Bay and San Pablo Bay 

(Rosenfield and Baxter 2007, p. 1590). 

The Bay-Delta estuary, although 

greatly degraded, is the largest estuary 

on the Pacific Coast of the United States 

(Sommer et al. 2007, p. 271). Because of 

its large size and diverse habitat, it is 

capable of supporting a large longfin 

smelt population. Large populations are 

valuable in the conservation of species 

because of their lower extinction risks 

compared to small populations. 

Historically, longfin smelt is believed to 

have been one of the more abundant 

pelagic fishes in the Bay-Delta. The 

areal extent of tidal freshwater habitat in 

the Bay-Delta estuary exceeds that of 

other California estuaries by an order of 

magnitude (NOAA 2007, p. 1), 

providing not only more available 

spawning habitat but also important 

habitat diversity should conditions at 

any one location become unsuitable. 

The Bay-Delta contains significant 

amounts of tidal freshwater and mixing 

zone habitat (Monaco et al. 1992, p. 

255), which is crucial for spawning and 

rearing of juvenile longfin smelt. Other 

Pacific Coast estuaries where longfin 

smelt occur are predominately riverdominated estuaries (e.g., Russian River, 

Eel River, Klamath River, Columbia 

River), which have much smaller areas 

of low-salinity brackish water for 

longfin smelt rearing habitat. 

(2) Evidence that loss of the discrete 

population segment would result in a 

significant gap in the range of a taxon. 

Loss of the Bay-Delta population of 

longfin smelt would result in a 

significant gap in the range of the taxon 

because the nearest persistent longfin 

smelt breeding population to the BayDelta population is in Humboldt Bay, 

which is located approximately 420 km 

(260 mi) away. Loss of the Bay-Delta 

population would truncate the range of 

the species by hundreds of miles. 

(3) Evidence that the discrete 

population segment represents the only 

surviving natural occurrence of a taxon 

that may be more abundant elsewhere as 

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an introduced population outside its 

historic range. 

This factor does not apply to the BayDelta longfin smelt population because 

other naturally occurring populations 

are found within the species’ range. 

(4) Evidence that the discrete 

population segment differs markedly 

from other populations of the species in 

its genetic characteristics. 

As discussed above under 

Quantitative Measures of Genetic or 

Morphological Discontinuity, two 

studies have evaluated genetic 

characteristics of the Bay-Delta longfin 

smelt population. One study concluded 

that genetic characteristics of the BayDelta population differed from the Lake 

Washington population but did not 

compare any other populations (Stanley 

et al. 1995, pp. 390–396). Israel et al. 

(2011, pp. 1–10) presented preliminary 

results from an ongoing study, but these 

results are inconclusive in determining 

whether the Bay-Delta population 

differs markedly from other longfin 

smelt populations in its genetic 

characteristics. Therefore, although 

information indicates that the genetic 

characteristics of the Bay-Delta 

population differs from at least one 

other longfin smelt population (Lake 

Washington), there is no other 

information currently available 

indicating that the genetic 

characteristics of the Bay-Delta 

population differ markedly from other 

longfin smelt populations. 

Conclusion for Significance 

We conclude that the Bay-Delta 

population is biologically significant to 

the longfin smelt species because the 

population occurs in an ecological 

setting unusual or unique for the species 

and its loss would result in a significant 

truncation of the range of the species. 

The Bay-Delta longfin smelt population 

occurs at the southern edge of the 

species’ range and has likely 

experienced different natural selection 

pressures than those experienced by 

populations in middle portions of the 

species’ range. The population may 

therefore possess unique evolutionary 

adaptations important to the 

conservation of the species. The BayDelta also is unique because it is the 

largest estuary on the Pacific Coast of 

the United States. Because of its large 

size and diverse aquatic habitats, the 

Bay-Delta has the potential to support a 

large longfin smelt population and is 

thus potentially important in the 

conservation of the species. The BayDelta population also is significant to 

the taxon because the nearest known 

breeding population of longfin smelt is 

hundreds of miles away, so loss of the 

Bay-Delta population would 

significantly truncate the range of the 

species and result in a significant gap in 

the species’ range. Based on our review 

of the best available scientific and 

commercial information, we conclude 

that the Bay-Delta population meets the 

significance element of the 1996 DPS 

policy. 

Determination of Distinct Population 

Segment 

Because we have determined that the 

Bay-Delta population meets both the 

discreteness and significance elements 

of the 1996 DPS policy, we find that the 

Bay-Delta longfin smelt population is a 

valid DPS and thus is a listable entity 

under the Act. Therefore, we next 

evaluate its 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?). 

Distinct Population Segment FiveFactor Analysis 

Because the Bay-Delta population of 

longfin smelt meets the criteria for a 

DPS, we will now evaluate its status 

with regard to its potential for listing as 

endangered or threatened under the five 

factors enumerated in section 4(a) of the 

Act. Our evaluation of the Bay-Delta 

DPS of longfin smelt follows. 

Under Summary of Information 

Pertaining to the Five Factors, we 

evaluated threats to longfin smelt 

throughout its range. Much of this 

rangewide analysis focused on threats to 

the Bay-Delta population because so 

little information exists for other parts 

of the species’ range. Although the 

threats of lack of freshwater flow, 

contaminants, and invasive species do 

not rise to the level of being significant 

threats rangewide, the best available 

scientific and commercial data indicates 

that these threats are significant to the 

species within the Bay-Delta. We 

utilized the vast amounts of research 

that have been conducted within the 

Bay-Delta by the Interagency Ecological 

Program and University of California at 

Davis to make our determinations of 

threats in the Bay-Delta. 

Factor A. The Present or Threatened 

Destruction, Modification, or 

Curtailment of Its Habitat or Range 

Reduced Freshwater Flow 

As we discussed above in the 

rangewide analysis, a primary threat to 

the Bay-Delta longfin smelt is reduced 

freshwater flows. In the Bay-Delta, 

freshwater flow is strongly related to the 

natural hydrologic cycles of drought and 

flood. Studies of Bay-Delta longfin smelt 

have found that increased Delta outflow 

during the winter and spring is the 

largest factor positively affecting longfin 

smelt abundance (Stevens and Miller 

1983, pp. 431–432; Jassby et al. 1995, p. 

285; Sommer et al. 2007, p. 274; 

Thomson et al. 2010, pp. 1439–1440). 

During high outflow periods larvae are 

believed to benefit from increased 

transport and dispersal downstream, 

increased food production, reduced 

predation through increased turbidity, 

and reduced loss to entrainment due to 

a westward shift in the boundary of 

spawning habitat and strong 

downstream transport of larvae (CFDG 

1992, pp. 45–61; Hieb and Baxter 1993, 

pp. 106–107; CDFG 2009a, p. 18). 

Conversely, during low outflow periods, 

the negative effects of reduced transport 

and dispersal, reduced turbidity, and 

potentially increased loss of larvae to 

predation and increased loss at the 

export facilities result in lower youngof-the-year recruitment. Despite 

numerous studies of longfin smelt 

abundance and flow in the Bay-Delta, 

the underlying causal mechanisms are 

still not fully understood (Baxter et al. 

2010, p. 69; Rosenfield 2010, p. 9). 

As California’s population has grown, 

demands for reliable water supplies and 

flood protection have grown. In 

response, State and Federal agencies 

built dams and canals, and captured 

water in reservoirs, to increase capacity 

for water storage and conveyance 

resulting in one of the largest manmade 

water systems in the world (Nichols et 

al. 1986, p. 569). Operation of this 

system has altered the seasonal pattern 

of freshwater flows in the watershed. 

Storage in the upper watershed of peak 

runoff and release of the captured water 

for irrigation and urban needs during 

subsequent low flow periods result in a 

broader, flatter hydrograph with less 

seasonal variability in freshwater flows 

into the estuary (Kimmerer 2004, p. 15). 

In addition to the system of dams and 

canals built throughout the Sacramento 

River-San Joaquin River basin, the BayDelta is unique in having a large water 

diversion system located within the 

estuary (Kimmerer 2002b, p. 1279). The 

State Water Project (SWP) and Central 

Valley Project (CVP) operate two water 

export facilities in the Delta (Sommer et 

al. 2007, p. 272). Project operation and 

management is dependent upon 

upstream water supply and export area 

demands. Despite the size of the water 

storage and diversion projects, much of 

the interannual variability in Delta 

hydrology is due to variability in 

precipitation from year to year. Annual 

inflow from the watershed to the Delta 

is strongly correlated to unimpaired 

flow (runoff that would hypothetically 

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occur if upstream dams and diversions 

were not in existence), mainly due to 

the effects of high-flow events 

(Kimmerer 2004, p. 15). Water 

operations are regulated in part by the 

California State Water Resources 

Control Board (SWRCB) according to the 

Water Quality Control Plan (WQCP) 

(SWRCB 2000, entire). The WQCP limits 

Delta water exports in relation to Delta 

inflow (the Export/Inflow, or E/I ratio). 

It is important to note that in the case 

of the Bay-Delta, freshwater flow is 

expressed as both Delta inflow (from the 

rivers into the Delta) and as Delta 

outflow (from the Delta into the lower 

estuary), which are closely correlated, 

but not equivalent. Freshwater flow into 

the Delta affects the location of the low 

salinity zone and X2 within the estuary. 

As longfin smelt spawn in freshwater, 

they must migrate farther upstream to 

spawn as flow reductions alter the 

position of X2 and the low-salinity zone 

moves upstream (CDFG 2009, p. 17). 

Longer migration distances into the BayDelta make longfin smelt more 

susceptible to entrainment in the State 

and Federal water pumps (see Factor E: 

Entrainment Losses, below). In periods 

with greater freshwater flow into the 

Delta, X2 is pushed farther downstream 

(seaward); in periods with low flows, X2 

is positioned farther landward 

(upstream) in the estuary and into the 

Delta. Not only is longfin smelt 

abundance in the Bay-Delta strongly 

correlated with Delta inflow and X2, but 

the spatial distribution of longfin smelt 

larvae is also strongly associated with 

X2 (Dege and Brown 2004, pp. 58–60; 

Baxter et al. 2010, p. 61). As longfin 

hatch into larvae, they move from the 

areas where they are spawned and 

orient themselves just downstream of 

X2 (Dege and Brown 2004, pp. 58–60). 

Larval (winter-spring) habitat varies 

with outflow and with the location of 

X2 (CDFG 2009, p. 12), and has been 

reduced since the 1990s due to a general 

upstream shift in the location of X2 

(Hilts 2012, unpublished data). The 

amount of rearing habitat (salinity 

between 0.1 and 18 ppt) is also 

presumed to vary with the location of 

X2 (Baxter et al. 2010, p. 64). However, 

as previously stated, the location of X2 

is of particular importance to the 

distribution of newly-hatched larvae 

and spawning adults. The influence of 

water project operations from November 

through April, when spawning adults 

and newly-hatched larvae are oriented 

to X2, is greater in drier years than in 

wetter years (Knowles 2002, p. 7). 

In addition to the effects of reduced 

freshwater flow on habitat suitability for 

longfin smelt and other organisms in the 

Bay-Delta, one of the principal concerns 

over the biological impacts of these 

water export facilities has been 

entrainment of fish and other aquatic 

organisms. For a detailed discussion, 

see Factor E: Entrainment Losses, below. 

Given the observed negative 

association between the reduction of 

freshwater outflow and longfin smelt 

abundance, we consider the current 

reductions in freshwater outflow to pose 

a significant threat to the Bay-Delta DPS 

of longfin smelt. Based on the observed 

associations in the Bay-Delta between 

freshwater outflow and longfin 

abundance, the lack of effective control 

mechanisms, and projections of 

freshwater outflow fluctuations, we 

expect the degree of this threat to 

continue and likely increase within the 

foreseeable future. We conclude that 

lack of freshwater flow is a significant 

current and future threat to the BayDelta DPS of longfin smelt. 

Climate Change 

Climate change may affect the BayDelta DPS of longfin smelt habitat as a 

result of (1) Changes in the timing and 

availability of freshwater flow into the 

estuary due to reduced snowpack and 

earlier melting of the snowpack; (2) sea 

level rise and saltwater intrusion into 

the estuary; (3) effects associated with 

increased water temperatures; and (4) 

effects related to changes in frequency 

and intensity of storms, floods, and 

droughts. It is difficult to evaluate 

effects related to changes in the timing 

and availability of freshwater flow into 

the estuary due to reduced snowpack 

and earlier melting of the snowpack 

because these potential effects will 

likely be impacted to some extent 

through decisions on water management 

in the intensively managed Sacramento 

River-San Joaquin River water basin. 

Continued sea level rise will result in 

saltwater intrusion and landward 

displacement of the low-salinity zone, 

which would likely negatively affect 

longfin smelt habitat suitability. 

Increasing water temperatures would 

likely affect distribution and movement 

patterns of longfin smelt in the estuary; 

longfin smelt may be displaced to 

locations with deeper and cooler water 

temperatures. This displacement may 

result in decreased survival and 

productivity. Increased frequency and 

severity of storms, floods, and droughts 

could result in reduced longfin smelt 

habitat suitability, but it is difficult to 

estimate these effects because of 

uncertainty about the frequency and 

severity of these events. However, 

warming may result in more 

precipitation falling as rain and less 

storage as snow, increasing winter 

runoff as spring runoff decreases (USBR 

2011, p. 147). 

It is uncertain how a change in the 

timing and duration of freshwater flows 

will affect longfin smelt. Higher flows in 

January and February (peak spawning 

and hatching months) resulting from 

snow packs that melt sooner and rainon-snow events could potentially create 

better spawning and larval rearing 

conditions. This would reduce adult 

migration distance and increase areas of 

freshwater spawning habitat during 

these months. In addition, the higher 

turbidity associated with these flows 

may reduce predation on longfin smelt 

adults and larvae (Baxter 2011, pers. 

comm.). However, if high flows last only 

a short period, benefits may be negated 

by poorer conditions before and after 

the high flows. As the freshwater 

boundary moves farther inland into the 

Delta with increasing sea level (see 

below) and reduced flows, adults will 

need to migrate farther into the Delta to 

spawn, increasing the risk of predation 

and the potential for entrainment into 

water export facilities and diversions for 

both themselves and their progeny. 

Because of the uncertainties 

surrounding climate change and the 

potential for increased winter runoff 

that could benefit longfin smelt, we 

determined that there is not sufficient 

information to conclude that climate 

change threatens the continued 

existence of the Bay-Delta DPS of 

longfin smelt. 

Channel Disturbances 

Channel dredging in the Bay-Delta is 

an ongoing periodic disturbance of 

longfin smelt habitat, but most activity 

occurs in areas where longfin smelt are 

not likely to be present. We conclude 

that the effects of ongoing channel 

maintenance dredging are small and 

localized and do not rise to a level that 

would significantly affect the 

population as a whole. 

There is currently a proposal to 

deepen and selectively widen the 

Sacramento Deep Water Ship Channel 

and the lower portion of the Sacramento 

River in the Bay-Delta. This dredging 

project would remove between 6.1–7.6 

million cubic meters (8 and 10 million 

cubic yards) of material from the 

channel and Sacramento River and 

extend for 74 km (45.8 mi) (USACE 

2011a, entire). Potential effects of this 

new project to longfin smelt include 

mortality through loss of spawning 

substrate, habitat modification, and a 

shift in spawning and rearing habitat. 

The project also has potential to alter 

breeding and foraging behavior of the 

Bay-Delta longfin smelt population. 

However, this project is only a proposal 

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at this time and is not certain to occur. 

Potential effects of the proposed project 

are currently under evaluation. 

Summary of Factor A 

In summary, we conclude that the 

best available scientific and commercial 

information available indicates that the 

effects of reduced freshwater flows 

constitute a current and future threat to 

the Bay-Delta DPS of longfin smelt. We 

find that the Bay-Delta DPS of longfin 

smelt is currently threatened in part due 

to the present or threatened destruction, 

modification, or curtailment of its 

habitat or range due to reduced 

freshwater flow. 

Factor B. Overutilization for 

Commercial, Recreational, Scientific, or 

Educational Purposes 

Commercial and Recreational Take 

Because of its status as a threatened 

species under the California Endangered 

Species Act, take of longfin smelt in the 

Bay-Delta is illegal, unless authorized 

by an incidental take permit or other 

take authorization. However, longfin 

smelt are caught as bycatch in a small 

bay shrimp trawl commercial fishery 

that operates in South San Francisco 

Bay, San Pablo Bay, and Carquinez 

Strait (Hieb 2009, p. 1). CDFG (Hieb 

2009, pp. 6, 9) estimated the total 

longfin smelt bycatch from this fishery 

from 1989–1990 at 15,539 fish, and in 

2004 at 18,815–30,574 fish. CDFG noted 

in 2009 that they thought the bay 

shrimp trawl fishery had declined since 

2004 (Hieb, p. 3) and just recently 

reported the number of active shrimp 

permits at less than 10 (Hieb 2011, pers. 

comm.). 

Scientific Take 

Within the Bay-Delta, longfin smelt 

are regularly captured in monitoring 

surveys. The Interagency Ecological 

Program (IEP) implements scientific 

research in the Bay-Delta. Although the 

focus of its studies and the level of effort 

have changed over time, in general, 

their surveys have been directed at 

researching the Pelagic Organism 

Decline in the Bay-Delta. Between the 

years of 1987 to 2011, combined take of 

longfin smelt less than 20 mm (0.8 in) 

in length ranged from 2,405 to 158,588 

annually. All of these fish were 

preserved for research or assumed to die 

in processing. During the same time 

period, combined take for juveniles and 

adults (fish greater than or equal to 20 

mm (0.8 in)) ranged from 461 to 68,974 

annually (IEP 2011). Although mortality 

is unknown, the majority of these fish 

likely do not survive. The Chipps Island 

survey, which is conducted by the 

Service, has captured an average of 

2,697 longfin smelt per year during the 

past 10 years. Biologists attempt to 

release these fish unharmed, but at least 

5,154 longfin smelt were known to have 

died during the Chipps Island survey 

between 2001 and 2008 (Service 2010, 

entire). 

Incidental take from bycatch and 

monitoring surveys has not been 

identified as a possible factor related to 

recent longfin smelt population declines 

in the Bay-Delta (Baxter et al. 2010, pp. 

61–69). CDFG (2009, p. 32) 

recommended adaptively managing 

scientific collection of longfin smelt to 

avoid adverse population effects, and 

survey methods have been modified 

recently to minimize potential impacts 

to delta smelt (75 FR 17669; April 7, 

2010). These modifications likely have 

resulted in reduced impacts to longfin 

smelt. Based on the best scientific and 

commercial information, we conclude 

that the Bay-Delta DPS of longfin smelt 

is not currently threatened by 

overutilization for commercial, 

recreational, scientific, or educational 

purposes, nor do we anticipate 

overutilization posing a significant 

threat in the future. 

Factor C. Disease or Predation 

Disease 

Little information is available on 

incidence of disease in the Bay-Delta 

longfin smelt DPS. Larval and juvenile 

longfin smelt were collected from the 

Bay-Delta in 2006 and 2007 and 

analyzed for signs of disease and 

parasites (Foott and Stone 2006, entire; 

Foott and Stone 2007, entire). No 

significant health problem was detected 

in either year (Foott and Stone 2007, p. 

15). The south Delta is fed by water 

from the San Joaquin River, where 

pesticides (e.g., chlorpyrifos, 

carbofuran, and diazinon), salts (e.g., 

sodium sulfates), trace elements (boron 

and selenium), and high levels of total 

dissolved solids are prevalent due to 

agricultural runoff (64 FR 5963; 

February 8, 1999). Pesticides and other 

toxic chemicals may adversely affect the 

immune system of longfin smelt and 

other fish in the Bay-Delta and other 

estuaries, but we found no information 

documenting such effects. 

Predation 

Striped bass were introduced into the 

Bay-Delta in 1879 and quickly became 

abundant throughout the estuary. 

However, their numbers have declined 

substantially over the last 40 years 

(Thomson et al. 2010, p. 1440), and they 

are themselves one of the four species 

studied under Pelagic Organism Decline 

investigations (Baxter et al. 2010, p. 16). 

Numbers of largemouth bass, another 

introduced species in the Bay-Delta, 

have increased in the Delta over the past 

few decades (Brown and Michniuk 

2007, p. 195). Largemouth bass, 

however, occur in shallow freshwater 

habitats, closer to shore than the pelagic 

longfin smelt, and so do not tend to cooccur with longfin for much of their life 

history. Baxter et al. (2010, p. 40) 

reported that no longfin smelt have been 

found in largemouth bass stomachs 

sampled in a recent study of largemouth 

bass diet. Moyle (2002, p. 238) believed 

that inland silverside, another 

nonnative predatory fish, may be an 

important predator on longfin eggs and 

larvae, but Rosenfield et al. (2010, p. 18) 

believed that to be unlikely because 

inland silversides prefer shallow water 

habitats where juvenile and subadult 

longfin smelt are rare. 

In the Bay-Delta, predation of longfin 

smelt may be high in the Clifton Court 

Forebay, where the SWP water export 

pumping plant is located (Moyle 2002, 

p. 238; Baxter et al. 2010, p. 42). 

However, once they are entrained in the 

Clifton Court Forebay, longfin smelt 

mortality would be high anyway due to 

high water temperatures in the Forebay 

(CDFG 2009b, p. 4) and entrainment 

into the SWP water export pumping 

plant. In addition to elevated predation 

levels in the Clifton Court Forebay, 

predation also is concentrated at sites 

where fish salvaged from the SWP and 

CVP export facilities are released (Moyle 

2002, p. 238). However, few longfin 

smelt survive the salvage and transport 

process (see Factor E: Entrainment 

Losses, below), and therefore predation 

is not expected to be an important factor 

at drop off sites. As discussed above, 

reduced freshwater flows may result in 

lower turbidity and increased water 

clarity (see discussion under DPS’ 

Factor A), which may contribute to 

increased risk of predation (Baxter et al. 

2010, p. 64). 

Based on a review of the best 

available scientific and commercial 

information, we conclude that disease 

does not constitute a threat to the BayDelta longfin smelt DPS. Available 

information indicates that Bay-Delta 

longfin smelt experience elevated levels 

of predation near the water diversions at 

the SWP and CVP water export facilities 

in the south Delta and at the salvage 

release sites. Reduced freshwater flows 

resulting from water diversions result in 

increased water clarity, and increased 

water clarity may result in increased 

predation risks to longfin smelt. 

In summary, striped bass predation is 

in decline and largemouth bass 

predation is unlikely a threat because of 

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the minimal overlap in time and space 

of largemouth bass and longfin smelt. 

Therefore, the current rates of predation 

on longfin smelt are not expected to be 

having a substantial effect on the overall 

population level. Based on the best 

available scientific and commercial 

information, we conclude that neither 

disease nor predation are significant 

current or future threats to the Bay-Delta 

longfin smelt DPS. 

Factor D. The Inadequacy of Existing 

Regulatory Mechanisms 

Existing Federal and State regulatory 

mechanisms discussed under Factor D 

of the rangewide analysis that provide 

protections or reduce threats to the BayDelta DPS of longfin smelt include: 

California Endangered Species Act, 

Porter-Cologne Water Quality Control 

Act, California Marine Invasive Species 

Act, Central Valley Project Improvement 

Act, and Clean Water Act (including the 

National Pollutant Discharge 

Elimination System). Several of these 

regulatory mechanisms provide 

important protections for the Bay-Delta 

DPS of longfin smelt and act to reduce 

threats, such as reduction of freshwater 

outflow, the invasion of the overbite 

clam and ammonia discharges (See 

Factors A, above, and E, below). 

The longfin smelt was listed under 

the California Endangered Species Act 

as threatened throughout its range in 

California on March 5, 2009 (CDFG 

2009, p. V). CESA does allow take of 

species for otherwise lawful projects 

through use of an incidental take 

permit. A take permit requires that 

impacts be minimized and fully 

mitigated (CESA sections 2081 (b) and 

(c)). Furthermore, the CESA ensures 

through the issuance of a permit for a 

project that may affect longfin smelt or 

its habitat, that the project will not 

jeopardize the continued existence of a 

State-listed species. 

The Porter-Cologne Water Quality 

Control Act is the California State law 

that establishes the State Water 

Resources Control Board (SWRCB) and 

nine Regional Water Quality Control 

Boards that are responsible for the 

regulation of activities and factors that 

could degrade California water quality 

and for the allocation of surface water 

rights. The State Water Resources 

Control Board Water Rights Decision 

1641 (D–1641) imposes flow and water 

quality standards on the State and 

Federal water export facilities to assure 

protection of beneficial uses in the Delta 

(FWS 2008, pp. 21–27). The various 

flow objectives and export restraints are 

designed, in part, to protect fisheries. 

These objectives include specific 

outflow requirements throughout the 

year, specific water export restraints in 

the spring, and water export limits 

based on a percentage of estuary inflow 

throughout the year. The water quality 

objectives are designed to protect 

agricultural, municipal, industrial, and 

fishery uses; they vary throughout the 

year and by the wetness of the year. 

These protections have had limited 

effectiveness in providing adequate 

freshwater flows within the Delta. Lack 

of freshwater outflow continues to be 

the primary contributing factor to the 

decline of the longfin smelt in the BayDelta (see Factor A, above, for further 

discussion). 

The California Marine Invasive 

Species Act requires ballast water 

management for all vessels that intend 

to discharge ballast water in California 

waters. All qualifying vessels coming 

from ports within the Pacific Coast 

region must conduct an exchange in 

waters at least 50 nautical mi offshore 

and 200 m (656 ft) deep or retain all 

ballast water and associated sediments. 

To determine the effectiveness of the 

management provisions of the this State 

act, the legislation also requires State 

agencies to conduct a series of biological 

surveys to monitor new introductions to 

coastal and estuarine waters. These 

measures should further minimize the 

introduction of new invasive species 

into California’s coastal waters that 

could be a threat to the longfin smelt. 

The Central Valley Project 

Improvement Act amends the previous 

Central Valley Project authorizations to 

include fish and wildlife protection, 

restoration, and mitigation as project 

purposes having equal priority with 

irrigation and domestic uses, and fish 

and wildlife enhancement as having an 

equal priority with power generation. 

Included in CVPIA section 3406 (b)(2) 

was a provision to dedicate 800,000 

acre-feet of Central Valley Project yield 

annually (referred to as ‘‘(b)(2) water’’) 

for fish, wildlife, and habitat restoration. 

Since 1993, (b)(2) water has been used 

and supplemented with acquired 

environmental water (Environmental 

Water Account and CVPIA section 3406 

(b)(3) water) to increase stream flows 

and reduce Central Valley Project export 

pumping in the Delta. These 

management actions were taken to 

contribute to the CVPIA salmonid 

population doubling goals and to 

protect Delta smelt and their habitat 

(Guinee 2011, pers. comm.). As 

discussed above (under Biology and 

Factor A), increased freshwater flows 

have been shown to be positively 

correlated with longfin smelt 

abundance; therefore, these 

management actions, although targeted 

towards other species, should also 

benefit longfin smelt. 

The Clean Water Act (CWA) provides 

the basis for the National Pollutant 

Discharge Elimination System (NPDES). 

The CWA gives the EPA the authority to 

set effluent limits and requires any 

entity discharging pollutants to obtain a 

NPDES permit. The EPA is authorized 

through the CWA to delegate the 

authority to issue NPDES Permits to 

State governments. In States that have 

been authorized to implement CWA 

programs, the EPA still retains oversight 

responsibilities (EPA 2011, p. 1). 

California is one of these States to 

which the EPA has delegated CWA 

authority. The Porter-Cologne Water 

Quality Control Act established the 

California State Water Resources 

Control Board (SWRCB) and nine 

Regional Water Quality Control Boards 

that are now responsible for issuing 

these NPDES permits, including permits 

for the discharge of effluents such as 

ammonia. The SWRCB is responsible for 

regulating activities and factors that 

could degrade California water quality 

(California Water Code Division 7, 

section 13370–13389). 

The release of ammonia into the 

estuary is having detrimental effects on 

the Delta ecosystem and food chain (see 

Factor E, below). The release of 

ammonia is controlled primarily by the 

CWA (Federal law) and secondarily 

through the Porter-Cologne Water 

Quality Control Act (State law). EPA is 

currently updating freshwater discharge 

criteria that will include new limits on 

ammonia (EPA 2009, pp. 1–46). An 

NPDES permit for the Sacramento 

Regional Wastewater Treatment Plant, a 

major discharger, was prepared by the 

California Central Valley Regional Water 

Quality Control Board in the fall of 

2010, with new ammonia limitations 

intended to reduce loadings to the Delta. 

The permit is currently undergoing 

appeal, but it is likely that the new 

ammonia limits will take effect in 2020. 

Until that time, CWA protections for 

longfin smelt are limited, and do not 

reduce the current threat to longfin 

smelt. 

Summary of Factor D 

A number of Federal and State 

regulatory mechanisms exist that can 

provide some protections for the BayDelta DPS of longfin smelt. However, 

the continued decline in longfin smelt 

trend indicators suggests that existing 

regulatory mechanisms, as currently 

implemented, are not adequate to 

reduce threats to the species. Therefore, 

based on a review of the best scientific 

information available, we conclude that 

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existing regulatory mechanisms are not 

sufficient to protect the species. 

Factor E. Other Natural or Manmade 

Factors Affecting Its Continued 

Existence 

Other factors affecting the continued 

existence of the Bay-Delta DPS of 

longfin smelt are entrainment losses due 

to water diversions, introduced species, 

and contaminants (see Factor E of the 

Summary of Information Pertaining to 

the Five Factors section, above). 

Entrainment Losses Due to Water 

Diversions 

Entrainment losses at the SWP and 

CVP water export facilities are a known 

source of mortality of longfin smelt and 

other pelagic fish species in the Bay 

Delta, although the full magnitude of 

entrainment losses and population-level 

implications of these losses is still not 

fully understood. High entrainment 

losses of longfin smelt and other BayDelta pelagic fish between 2000 and 

2005 correspond with high volumes of 

water exports during winter (Baxter et 

al. 2010, p. 63). Baxter et al. (2010, p. 

62) hypothesize that entrainment is 

having an important effect on the 

longfin smelt population during winter, 

particularly during years with low 

freshwater flows when a higher 

proportion of the population may spawn 

farther upstream in the Delta. However, 

Baxter et al. (2010, p. 63) conclude that 

these losses have yet to be placed in a 

population context, and no conclusions 

can be drawn regarding their effects on 

recent longfin smelt abundance. CDFG 

(2009, p. 22) believes that efforts to 

reduce past delta smelt entrainment loss 

through the implementation of the 2008 

delta smelt biological opinion for SWP 

and CVP operations may have reduced 

longfin smelt entrainment losses, 

incidentally providing a benefit to the 

longfin smelt. These efforts to manage 

entrainment losses in drier years, when 

entrainment risk is greater, substantially 

reduce the threat of entrainment for 

longfin smelt. 

Estimates of entrainment have shown 

that it may have been a threat to the 

Bay-Delta longfin smelt DPS in the past. 

Fujimura (2009) estimated cumulative 

longfin smelt entrainment at the SWP 

facility between 1993 and 2008 at 

1,376,432 juveniles and 11,054 adults, 

and estimated that 97.6 percent of 

juveniles and 95 percent of adults 

entrained were lost. Fujimura (2009) 

estimated cumulative longfin 

entrainment at the CVP facility between 

1993 and 2008 at 224,606 juveniles and 

1,325 adults, and estimated that 85.2 

percent of the juveniles and 82.1 

percent of the adults entrained were 

lost. These estimated losses are 4 times 

higher than observed salvage at the CVP 

and 21 times higher than the actual 

salvage numbers at the SWP (Fujimura 

2009, p. 2). The estimated entrainment 

numbers were much higher than the 

actual salvage numbers at the SWP, due 

in large part to the high pre-screen 

losses in the Clifton Court Forebay 

(CDFG 2009a, p. 21). It should be noted 

that these estimates were calculated 

using equations and parameters devised 

for other species and may not accurately 

estimate longfin smelt losses. Further, 

estimates may be misleading because 

the majority of estimated losses 

occurred during the dry year of 2002 

(1.1 million juveniles estimated at the 

SWP) while during all other years 

estimated entrainment was below 

70,000 individuals. 

Entrainment is no longer considered a 

threat to longfin in the Bay-Delta 

because of current regulations. Efforts to 

reduce delta smelt entrainment loss 

through the implementation of the 2008 

delta smelt biological opinion and the 

listing of longfin smelt under the CESA 

have likely reduced longfin smelt 

entrainment losses. The high rate of 

entrainment that occurred in 2002 that 

threatened the Bay Delta longfin smelt 

DPS is very unlikely to recur, and 

would no longer be allowed under 

today’s regulations because limits on 

longfin smelt take due to CESA 

regulations (see DPS’ Factor D 

discussion, above) would trigger 

reductions in the magnitude of reverse 

flows. 

Although larval and adult longfin 

smelt are lost as a result of entrainment 

in the water export facilities in the 

Delta, we conclude that the risk of 

entrainment is generally greatest when 

X2 is upstream and export volumes 

from the CVP and SWP pumps are high. 

Therefore, we have determined that 

longfin smelt are not currently 

threatened by entrainment, nor do we 

anticipate longfin smelt will be 

threatened by entrainment in the future. 

Introduced Species 

In Suisun Bay, a key longfin smelt 

rearing area, phytoplankton biomass is 

influenced by the overbite or Amur 

River clam. A sharp decline in 

phytoplankton biomass occurred 

following the invasion of the estuary by 

this species, even though nutrients were 

not found to be limiting (Alpine and 

Cloern 1992, pp. 950–951). Abundance 

of zooplankton decreased across several 

taxa, and peaks that formerly occurred 

in time and space were absent, reduced 

or relocated after 1987 (Kimmerer and 

Orsi 1996, p. 412). The general decline 

in phytoplankton and zooplankton is 

likely affecting longfin smelt by 

decreasing food supply for their prey 

species, such as N. mercedis (Kimmerer 

and Orsi 1996, pp. 418–419). Models 

indicate that the longfin smelt 

abundance index has been on a steady 

linear decline since about the time of 

the invasion of the non-native overbite 

(or Amur) clam in 1987 (Rosenfield and 

Swanson 2010, p. 14). 

Given the observed negative 

association between the introduction of 

the overbite clam and longfin smelt 

abundance in the Bay-Delta and the 

documented decline of key longfin 

smelt prey items, we consider the 

current overbite clam population to 

pose a significant threat to the Bay-Delta 

DPS of longfin smelt. Based on the 

observed associations in the Bay-Delta 

between overbite clam invasion and 

longfin abundance and the lack of 

effective control mechanisms, we expect 

the degree of this threat will continue 

into the foreseeable future. The BayDelta has numerous other invasive 

species that have disrupted ecosystem 

dynamics; however, only the overbite 

clam has been shown to have an impact 

on the longfin smelt population. We 

consider the overbite clam to be a 

significant ongoing threat to the BayDelta longfin smelt population. 

Contaminants 

Extensive research on the role of 

contaminants in the Pelagic Organism 

Decline is currently being conducted 

(Baxter et al. 2010, pp. 28–36). Of 

potential concern are effects of high 

levels of mercury and other metals; high 

ammonium concentrations from 

municipal wastewater; potentially 

harmful cyanobacteria algal blooms; and 

pesticides, especially pyrethroid 

pesticides, which are heavily used in 

San Joaquin Valley agriculture. 

Contaminants may have direct toxic 

effects to longfin smelt and other pelagic 

fish and indirect effects as a result of 

impacts to prey abundance and 

composition. Ammonium has been 

shown to impact longfin smelt habitat 

by affecting primary production and 

prey abundance within the Bay-Delta 

(Dugdale et al. 2007, p. 26). While 

contaminants are suspected of playing a 

role in declines of pelagic fish species 

in the Bay-Delta (Baxter et al. 2010, p. 

28), contaminant effects remain 

unresolved. 

The largest source of ammonia 

entering the Delta ecosystem is the 

Sacramento Regional Wastewater 

Treatment Plant (SRWTP), which 

accounts for 90 percent of the total 

ammonia load released into the Delta. 

Ammonia is un-ionized and has the 

chemical formula NH3. Ammonium is 

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ionized and has the formula NH4

+. The 

major factors determining the 

proportion of ammonia or ammonium in 

water are water pH and temperature. 

This is important, as NH3 ammonia is 

the form that can be directly toxic to 

aquatic organisms, and NH4+ 

ammonium is the form documented to 

interfere with uptake of nitrates by 

phytoplankton (Dugdale et al. 2007, p. 

17; Jassby 2008, p. 3). 

In addition to potential direct effects 

on fish, ammonia in the form of 

ammonium has been shown to alter the 

food web by adversely impacting 

phytoplankton and zooplankton 

dynamics in the estuary ecosystem. 

Historical data suggest that decreases in 

Suisun Bay phytoplankton biomass 

coincide with increased ammonia 

discharge by the SRWTP (Parker et al. 

2004, p. 7; Dugdale et al. 2011, p. 1). 

Phytoplankton preferentially take up 

ammonium over nitrate when it is 

present in the water. Ammonium is 

insufficient to provide for growth in 

phytoplankton, and uptake of 

ammonium to the exclusion of nitrate 

results in decreases in phytoplankton 

biomass (Dugdale et al. 2007, p. 23). 

Therefore, ammonium impairs primary 

productivity by reducing nitrate uptake 

in phytoplankton. Ammonium’s 

negative effect on the food web has been 

documented in the longfin smelt rearing 

areas of San Francisco Bay and Suisun 

Bay (Dugdale et al. 2007, pp. 27–28). 

Decreased primary productivity results 

in less food available to longfin smelt 

and other fish in these bays. 

In summary, although no direct link 

has been made between contaminants 

and longfin smelt (Baxter et al. 2010, p. 

68), ammonium has been shown to have 

a direct effect on the food supply that 

the Bay-Delta longfin smelt DPS relies 

upon. Therefore, we conclude that high 

ammonium concentrations may be a 

significant current and future threat to 

the Bay-Delta DPS of longfin smelt. 

Summary of Factor E 

The best available information 

indicates that introduced species 

constitute a threat to the Bay-Delta DPS 

of longfin smelt and that and 

contaminants (high ammonium 

concentrations) may constitute a threat 

to the Bay-Delta DPS of longfin smelt. 

Entrainment is a potential threat to the 

DPS, but information currently available 

does not indicate that entrainment 

threatens the continued existence of the 

Bay-Delta longfin smelt population. 

Although entrainment results in 

mortality of longfin smelt, Baxter et al. 

(2010, p. 63) concluded that these losses 

have yet to be placed in a population 

context, and no conclusions can be 

drawn regarding their effects on recent 

longfin smelt abundance. Therefore, 

based on the best scientific evidence 

available, we conclude that the BayDelta longfin smelt DPS is threatened in 

part due to other natural or manmade 

factors including the nonnative overbite 

clam and high ammonium 

concentrations. 

Finding 

This status review identified threats 

to the Bay-Delta DPS of longfin smelt 

attributable to Factors A, D, and E, as 

well as interactions between these 

threats. The primary threat to the DPS 

is from reduced freshwater flows. 

Upstream dams and water storage 

exacerbated by water diversions, 

especially from the SWP and CVP water 

export facilities, result in reduced 

freshwater flows within the estuary, and 

these reductions in freshwater flows 

result in reduced habitat suitability for 

longfin smelt (Factor A). Freshwater 

flows, especially winter-spring flows, 

are significantly correlated with longfin 

smelt abundance—longfin smelt 

abundance is lower when winter-spring 

flows are lower. While freshwater flows 

have been shown to be significantly 

correlated with longfin smelt 

abundance, causal mechanisms 

underlying this correlation are still not 

fully understood and are the subject of 

ongoing research on the Pelagic 

Organism Decline. 

In addition to the threat caused by 

reduced freshwater flow into the BayDelta, and alteration of natural flow 

regimes resulting from water storage and 

diversion, there appear to be other 

factors contributing to the Pelagic 

Organism Decline (Baxter 2010 et al., p. 

69). Models indicate a steady linear 

decline in abundance of longfin smelt 

since about the time of the invasion of 

the nonnative overbite clam in 1987 

(Rosenfield and Swanson 2010, pp. 13– 

14; see Factor E: Introduced Species) in 

the Bay-Delta. However, not all aspects 

of the longfin smelt decline can be 

attributed to the overbite clam invasion, 

as a decline in abundance of prespawning adults in Suisun Marsh 

occurred before the invasion of the 

clam, and a partial rebound in longfin 

smelt abundance occurred in the early 

2000s (Rosenfield and Baxter 2007, 

p. 1589). 

The long-term decline in abundance 

of longfin smelt in the Bay-Delta has 

been partially attributed to reductions in 

food availability and disruptions of the 

Bay-Delta food web caused by 

establishment of the nonnative overbite 

clam in 1987 (Factor E) and ammonium 

concentrations (Factor E). Impacts of the 

overbite clam and ammonium on the 

Bay-Delta food web have been longlasting and are ongoing. We conclude 

that ongoing disruptions of the food web 

caused by the overbite clam are a threat 

to the continued existence of the BayDelta DPS of longfin smelt. We also 

conclude that high ammonium 

concentrations in the Bay-Delta may 

constitute a threat to the continued 

existence of the overbite clam. 

Multiple existing Federal and State 

regulatory mechanisms provide 

important protections for the Bay-Delta 

DPS of longfin smelt and act to reduce 

threats to the DPS. However, the 

continued decline in the abundance of 

the Bay-Delta longfin smelt DPS 

indicates that existing regulatory 

mechanisms, as currently implemented, 

are not adequate to sufficiently reduce 

threats identified in this finding. 

Therefore, we find that inadequate 

existing regulatory mechanisms 

contribute to threats faced by the BayDelta longfin smelt DPS. 

The threats identified are likely acting 

together to contribute to the decline of 

the population (Baxter et al. 2010, p. 

69). Reduced freshwater flows result in 

effects to longfin smelt habitat 

suitability, at the same time that the 

food web has been altered by introduced 

species and ammonium concentrations. 

It is possible that climate change could 

exacerbate these threats; however, due 

to uncertainties of how longfin smelt 

will respond to climate change effects, 

we cannot conclude that climate change 

will threaten the continued existence of 

the Bay-Delta longfin smelt DPS. The 

combined effects of reduced freshwater 

flows, the invasive overbite clam 

(reduced levels of phytoplankton and 

zooplankton that are important to the 

Bay-Delta food web), and high 

ammonium concentrations act to 

significantly reduce habitat suitability 

for longfin smelt. 

The best scientific and commercial 

information available indicates that the 

threats facing the Bay-Delta DPS of 

longfin smelt are of sufficient 

imminence, intensity and magnitude to 

threaten the continued existence of the 

species now or in the foreseeable future. 

Therefore, we find that listing the BayDelta longfin smelt DPS is warranted. 

We will make a determination on the 

status of the DPS as endangered or 

threatened when we prepare a proposed 

listing determination. However, as 

explained in more detail below, an 

immediate proposal of a regulation 

implementing this action is precluded 

by higher priority listing actions, and 

progress is being made to add or remove 

qualified species from the Lists of 

Endangered and Threatened Wildlife 

and Plants. 

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We reviewed the available 

information to determine if the existing 

and foreseeable threats render the 

species at risk of extinction now such 

that issuing an emergency regulation 

temporarily listing the species under 

section 4(b)(7) of the Act is warranted. 

We determined that issuing an 

emergency regulation temporarily 

listing the DPS is not warranted at this 

time because the threats are not of 

sufficient magnitude and imminence to 

pose an immediate threat to the 

continued existence of the DPS. 

However, if at any time we determine 

that issuing an emergency regulation 

temporarily listing the Bay-Delta DPS of 

longfin smelt is warranted, we will 

initiate this action at that time. 

Significant Portion of Its Range 

The Act defines ‘‘endangered species’’ 

as any species which is ‘‘in danger of 

extinction throughout all or a significant 

portion of its range,’’ and ‘‘threatened 

species’’ as any species which is ‘‘likely 

to become an endangered species within 

the foreseeable future throughout all or 

a significant portion of its range.’’ The 

definition of ‘‘species’’ is also relevant 

to this discussion. The Act defines 

‘‘species’’ as ‘‘any subspecies of fish or 

wildlife or plants, and any distinct 

population segment [DPS] of any 

species of vertebrate fish or wildlife 

which interbreeds when mature’’ (16 

U.S.C. 1532(16)). The phrase 

‘‘significant portion of its range’’ (SPR) 

is not defined by the statute, and we 

have never addressed in our regulations: 

(1) The consequences of a determination 

that a species is either endangered or 

likely to become so throughout a 

significant portion of its range, but not 

throughout all of its range; or (2) what 

qualifies a portion of a range as 

‘‘significant.’’ 

Two recent district court decisions 

have addressed whether the SPR 

language allows the Service to list or 

protect less than all members of a 

defined ‘‘species’’: Defenders of Wildlife 

v. Salazar, 729 F. Supp. 2d 1207 (D. 

Mont. 2010), concerning the Service’s 

delisting of the Northern Rocky 

Mountain gray wolf (74 FR 15123, April 

2, 2009); and WildEarth Guardians v. 

Salazar, 2010 U.S. Dist. LEXIS 105253 

(D. Ariz. September 30, 2010), 

concerning the Service’s 2008 finding 

on a petition to list the Gunnison’s 

prairie dog (73 FR 6660, February 5, 

2008). The Service had asserted in both 

of these determinations that it had 

authority, in effect, to protect only some 

members of a ‘‘species,’’ as defined by 

the Act (i.e., species, subspecies, or 

DPS), under the Act. Both courts ruled 

that the determinations were arbitrary 

and capricious on the grounds that this 

approach violated the plain and 

unambiguous language of the Act. The 

courts concluded that reading the SPR 

language to allow protecting only a 

portion of a species’ range is 

inconsistent with the Act’s definition of 

‘‘species.’’ The courts concluded that 

once a determination is made that a 

species (i.e., species, subspecies, or 

DPS) meets the definition of 

‘‘endangered species’’ or ‘‘threatened 

species,’’ it must be placed on the list 

in its entirety and the Act’s protections 

applied consistently to all members of 

that species (subject to modification of 

protections through special rules under 

sections 4(d) and 10(j) of the Act). 

Consistent with that interpretation, 

and for the purposes of this finding, we 

interpret the phrase ‘‘significant portion 

of its range’’ in the Act’s definitions of 

‘‘endangered species’’ and ‘‘threatened 

species’’ to provide an independent 

basis for listing; thus there are two 

situations (or factual bases) under which 

a species would qualify for listing: a 

species may be endangered or 

threatened throughout all of its range; or 

a species may be endangered or 

threatened in only a significant portion 

of its range. If a species is in danger of 

extinction throughout an SPR, it, the 

species, is an ‘‘endangered species.’’ 

The same analysis applies to 

‘‘threatened species.’’ Based on this 

interpretation and supported by existing 

case law, the consequence of finding 

that a species is endangered or 

threatened in only a significant portion 

of its range is that the entire species will 

be listed as endangered or threatened, 

respectively, and the Act’s protections 

will be applied across the species’ entire 

range. 

We conclude, for the purposes of this 

finding, that interpreting the SPR phrase 

as providing an independent basis for 

listing is the best interpretation of the 

Act because it is consistent with the 

purposes and the plain meaning of the 

key definitions of the Act; it does not 

conflict with established past agency 

practice (i.e., prior to the 2007 

Solicitor’s Opinion), as no consistent, 

long-term agency practice has been 

established; and it is consistent with the 

judicial opinions that have most closely 

examined this issue. Having concluded 

that the phrase ‘‘significant portion of 

its range’’ provides an independent 

basis for listing and protecting the entire 

species, we next turn to the meaning of 

‘‘significant’’ to determine the threshold 

for when such an independent basis for 

listing exists. 

Although there are potentially many 

ways to determine whether a portion of 

a species’ range is ‘‘significant,’’ we 

conclude, for the purposes of this 

finding, that the significance of the 

portion of the range should be 

determined based on its biological 

contribution to the conservation of the 

species. For this reason, we describe the 

threshold for ‘‘significant’’ in terms of 

an increase in the risk of extinction for 

the species. We conclude that a 

biologically based definition of 

‘‘significant’’ best conforms to the 

purposes of the Act, is consistent with 

judicial interpretations, and best 

ensures species’ conservation. Thus, for 

the purposes of this finding, and as 

explained further below, a portion of the 

range of a species is ‘‘significant’’ if its 

contribution to the viability of the 

species is so important that without that 

portion, the species would be in danger 

of extinction. 

We evaluate biological significance 

based on the principles of conservation 

biology using the concepts of 

redundancy, resiliency, and 

representation. Resiliency describes the 

characteristics of a species and its 

habitat that allow it to recover from 

periodic disturbance. Redundancy 

(having multiple populations 

distributed across the landscape) may be 

needed to provide a margin of safety for 

the species to withstand catastrophic 

events. Representation (the range of 

variation found in a species) ensures 

that the species’ adaptive capabilities 

are conserved. Redundancy, resiliency, 

and representation are not independent 

of each other, and some characteristic of 

a species or area may contribute to all 

three. For example, distribution across a 

wide variety of habitat types is an 

indicator of representation, but it may 

also indicate a broad geographic 

distribution contributing to redundancy 

(decreasing the chance that any one 

event affects the entire species), and the 

likelihood that some habitat types are 

less susceptible to certain threats, 

contributing to resiliency (the ability of 

the species to recover from disturbance). 

None of these concepts is intended to be 

mutually exclusive, and a portion of a 

species’ range may be determined to be 

‘‘significant’’ due to its contributions 

under any one or more of these 

concepts. 

For the purposes of this finding, we 

determine if a portion’s biological 

contribution is so important that the 

portion qualifies as ‘‘significant’’ by 

asking whether without that portion, the 

representation, redundancy, or 

resiliency of the species would be so 

impaired that the species would have an 

increased vulnerability to threats to the 

point that the overall species would be 

in danger of extinction (i.e., would be 

‘‘endangered’’). Conversely, we would 

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not consider the portion of the range at 

issue to be ‘‘significant’’ if there is 

sufficient resiliency, redundancy, and 

representation elsewhere in the species’ 

range that the species would not be in 

danger of extinction throughout its 

range if the population in that portion 

of the range in question became 

extirpated (extinct locally). 

We recognize that this definition of 

‘‘significant’’ (a portion of the range of 

a species is ‘‘significant’’ if its 

contribution to the viability of the 

species is so important that without that 

portion, the species would be in danger 

of extinction) establishes a threshold 

that is relatively high. On the one hand, 

given that the consequences of finding 

a species to be endangered or threatened 

in an SPR would be listing the species 

throughout its entire range, it is 

important to use a threshold for 

‘‘significant’’ that is robust. It would not 

be meaningful or appropriate to 

establish a very low threshold whereby 

a portion of the range can be considered 

‘‘significant’’ even if only a negligible 

increase in extinction risk would result 

from its loss. Because nearly any portion 

of a species’ range can be said to 

contribute some increment to a species’ 

viability, use of such a low threshold 

would require us to impose restrictions 

and expend conservation resources 

disproportionately to conservation 

benefit: listing would be rangewide, 

even if only a portion of the range of 

minor conservation importance to the 

species is imperiled. On the other hand, 

it would be inappropriate to establish a 

threshold for ‘‘significant’’ that is too 

high. This would be the case if the 

standard were, for example, that a 

portion of the range can be considered 

‘‘significant’’ only if threats in that 

portion result in the entire species’ 

being currently endangered or 

threatened. Such a high bar would not 

give the SPR phrase independent 

meaning, as the Ninth Circuit held in 

Defenders of Wildlife v. Norton, 258 

F.3d 1136 (9th Cir. 2001). 

The definition of ‘‘significant’’ used in 

this finding carefully balances these 

concerns. By setting a relatively high 

threshold, we minimize the degree to 

which restrictions will be imposed or 

resources expended that do not 

contribute substantially to species 

conservation. But we have not set the 

threshold so high that the phrase ‘‘in a 

significant portion of its range’’ loses 

independent meaning. Specifically, we 

have not set the threshold as high as it 

was under the interpretation presented 

by the Service in the Defenders 

litigation. Under that interpretation, the 

portion of the range would have to be 

so important that current imperilment 

there would mean that the species 

would be currently imperiled 

everywhere. Under the definition of 

‘‘significant’’ used in this finding, the 

portion of the range need not rise to 

such an exceptionally high level of 

biological significance. (We recognize 

that if the species is imperiled in a 

portion that rises to that level of 

biological significance, then we should 

conclude that the species is in fact 

imperiled throughout all of its range, 

and that we would not need to rely on 

the SPR language for such a listing.) 

Rather, under this interpretation we ask 

whether the species would be 

endangered everywhere without that 

portion, i.e., if that portion were 

completely extirpated. In other words, 

the portion of the range need not be so 

important that even the species being in 

danger of extinction in that portion 

would be sufficient to cause the species 

in the remainder of the range to be 

endangered; rather, the complete 

extirpation (in a hypothetical future) of 

the species in that portion would be 

required to cause the species in the 

remainder of the range to be 

endangered. 

The range of a species can 

theoretically be divided into portions in 

an infinite number of ways. However, 

there is no purpose to analyzing 

portions of the range that have no 

reasonable potential to be significant or 

to analyzing portions of the range in 

which there is no reasonable potential 

for the species to be endangered or 

threatened. To identify only those 

portions that warrant further 

consideration, we determine whether 

there is substantial information 

indicating that: (1) The portions may be 

‘‘significant,’’ and (2) the species may be 

in danger of extinction there or likely to 

become so within the foreseeable future. 

Depending on the biology of the species, 

its range, and the threats it faces, it 

might be more efficient for us to address 

the significance question first or the 

status question first. Thus, if we 

determine that a portion of the range is 

not ‘‘significant,’’ we do not need to 

determine whether the species is 

endangered or threatened there; if we 

determine that the species is not 

endangered or threatened in a portion of 

its range, we do not need to determine 

if that portion is ‘‘significant.’’ In 

practice, a key part of the determination 

that a species is in danger of extinction 

in a significant portion of its range is 

whether the threats are geographically 

concentrated in some way. If the threats 

to the species are essentially uniform 

throughout its range, no portion is likely 

to warrant further consideration. 

Moreover, if any concentration of 

threats to the species occurs only in 

portions of the species’ range that 

clearly would not meet the biologically 

based definition of ‘‘significant,’’ such 

portions will not warrant further 

consideration. 

We have determined that the longfin 

smelt does not face elevated threats in 

most portions of its range, and we have 

determined that the portion of the range 

that has concentrated threats (the BayDelta portion of the range) is a DPS. The 

rangewide five factor analysis for 

longfin smelt does not identify any 

portions of the species’ range outside of 

Bay-Delta where threats are 

concentrated. Potential threats to the 

species are by and large uniform 

throughout its range with the exception 

of the Bay-Delta. Therefore, we will not 

further consider the Bay-Delta DPS as an 

SPR. 

Listing Priority Number 

The Service adopted guidelines on 

September 21, 1983 (48 FR 43098) to 

establish a rational system for utilizing 

available resources for the highest 

priority species when adding species to 

the Lists of Endangered or Threatened 

Wildlife and Plants or reclassifying 

species listed as threatened to 

endangered status. The system places 

greatest importance on the immediacy 

and magnitude of threats, but also 

factors in the level of taxonomic 

distinctiveness by assigning priority in 

descending order to monotypic genera 

(genus with one species), full species, 

and subspecies (or equivalently, distinct 

population segments of vertebrates 

(DPS)). As a result of our analysis of the 

best available scientific and commercial 

information, we assign the Bay-Delta 

DPS of longfin smelt a listing priority 

number of 3, based on the high 

magnitude and immediacy of threats. A 

number three listing priority is the 

highest listing allowed for a DPS under 

the current listing priority guidance. 

One or more of the threats discussed 

above are occurring (or we anticipate 

they will occur in the near future) 

within the range of the Bay-Delta DPS 

of the longfin smelt. These threats are 

ongoing and, in some cases (such as 

nonnative species), are considered 

irreversible. While we conclude that 

listing the Bay-Delta DPS of longfin 

smelt is warranted, an immediate 

proposal to list this species is precluded 

by other higher priority listings, which 

we address below. 

Preclusion and Expeditious Progress 

Preclusion is a function of the listing 

priority of a species in relation to the 

resources that are available and the cost 

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and relative priority of competing 

demands for those resources. Thus, in 

any given fiscal year (FY), multiple 

factors dictate whether it will be 

possible to undertake work on a listing 

proposal regulation or whether 

promulgation of such a proposal is 

precluded by higher priority listing 

actions. 

The resources available for listing 

actions are determined through the 

annual Congressional appropriations 

process. The appropriation for the 

Listing Program is available to support 

work involving the following listing 

actions: Proposed and final listing rules; 

90-day and 12-month findings on 

petitions to add species to the Lists of 

Endangered and Threatened Wildlife 

and Plants (Lists) or to change the status 

of a species from threatened to 

endangered; annual ‘‘resubmitted’’ 

petition findings on prior warrantedbut-precluded petition findings as 

required under section 4(b)(3)(C)(i) of 

the Act; critical habitat petition 

findings; proposed and final rules 

designating critical habitat; and 

litigation-related, administrative, and 

program-management functions 

(including preparing and allocating 

budgets, responding to Congressional 

and public inquiries, and conducting 

public outreach regarding listing and 

critical habitat). The work involved in 

preparing various listing documents can 

be extensive and may include, but is not 

limited to: Gathering and assessing the 

best scientific and commercial data 

available and conducting analyses used 

as the basis for our decisions; writing 

and publishing documents; and 

obtaining, reviewing, and evaluating 

public comments and peer review 

comments on proposed rules and 

incorporating relevant information into 

final rules. The number of listing 

actions that we can undertake in a given 

year also is influenced by the 

complexity of those listing actions; that 

is, more complex actions generally are 

more costly. The median cost for 

preparing and publishing a 90-day 

finding is $39,276; for a 12-month 

finding, $100,690; for a proposed rule 

with critical habitat, $345,000; and for 

a final listing rule with critical habitat, 

$305,000. 

We cannot spend more than is 

appropriated for the Listing Program 

without violating the Anti-Deficiency 

Act (see 31 U.S.C. 1341(a)(1)(A)). In 

addition, in FY 1998 and for each fiscal 

year since then, Congress has placed a 

statutory cap on funds that may be 

expended for the Listing Program, equal 

to the amount expressly appropriated 

for that purpose in that fiscal year. This 

cap was designed to prevent funds 

appropriated for other functions under 

the Act (for example, recovery funds for 

removing species from the Lists), or for 

other Service programs, from being used 

for Listing Program actions (see House 

Report 105–163, 105th Congress, 1st 

Session, July 1, 1997). 

Since FY 2002, the Service’s budget 

has included a critical habitat subcap to 

ensure that some funds are available for 

other work in the Listing Program (‘‘The 

critical habitat designation subcap will 

ensure that some funding is available to 

address other listing activities’’ (House 

Report No. 107–103, 107th Congress, 1st 

Session, June 19, 2001)). In FY 2002 and 

each year until FY 2006, the Service has 

had to use virtually the entire critical 

habitat subcap to address courtmandated designations of critical 

habitat, and consequently none of the 

critical habitat subcap funds have been 

available for other listing activities. In 

some FYs since 2006, we have been able 

to use some of the critical habitat 

subcap funds to fund proposed listing 

determinations for high-priority 

candidate species. In other FYs, while 

we were unable to use any of the critical 

habitat subcap funds to fund proposed 

listing determinations, we did use some 

of this money to fund the critical habitat 

portion of some proposed listing 

determinations so that the proposed 

listing determination and proposed 

critical habitat designation could be 

combined into one rule, thereby being 

more efficient in our work. At this time, 

for FY 2012, we plan to use some of the 

critical habitat subcap funds to fund 

proposed listing determinations. 

We make our determinations of 

preclusion on a nationwide basis to 

ensure that the species most in need of 

listing will be addressed first and also 

because we allocate our listing budget 

on a nationwide basis. Through the 

listing cap, the critical habitat subcap, 

and the amount of funds needed to 

address court-mandated critical habitat 

designations, Congress and the courts 

have in effect determined the amount of 

money available for other listing 

activities nationwide. Therefore, the 

funds in the listing cap, other than those 

needed to address court-mandated 

critical habitat for already listed species, 

set the limits on our determinations of 

preclusion and expeditious progress. 

Congress identified the availability of 

resources as the only basis for deferring 

the initiation of a rulemaking that is 

warranted. The Conference Report 

accompanying Public Law 97–304 

(Endangered Species Act Amendments 

of 1982), which established the current 

statutory deadlines and the warrantedbut-precluded finding, states that the 

amendments were ‘‘not intended to 

allow the Secretary to delay 

commencing the rulemaking process for 

any reason other than that the existence 

of pending or imminent proposals to list 

species subject to a greater degree of 

threat would make allocation of 

resources to such a petition [that is, for 

a lower-ranking species] unwise.’’ 

Although that statement appeared to 

refer specifically to the ‘‘to the 

maximum extent practicable’’ limitation 

on the 90-day deadline for making a 

‘‘substantial information’’ finding, that 

finding is made at the point when the 

Service is deciding whether or not to 

commence a status review that will 

determine the degree of threats facing 

the species, and therefore the analysis 

underlying the statement is more 

relevant to the use of the warranted-butprecluded finding, which is made when 

the Service has already determined the 

degree of threats facing the species and 

is deciding whether or not to commence 

a rulemaking. 

In FY 2011, on April 15, 2011, 

Congress passed the Full-Year 

Continuing Appropriations Act (Pub. L. 

112–10), which provided funding 

through September 30, 2011. The 

Service had $20,902,000 for the listing 

program. Of that, $9,472,000 was used 

for determinations of critical habitat for 

already listed species. Also $500,000 

was appropriated for foreign species 

listings under the Act. The Service thus 

had $10,930,000 available to fund work 

in the following categories: Compliance 

with court orders and court-approved 

settlement agreements requiring that 

petition findings or listing 

determinations be completed by a 

specific date; section 4 (of the Act) 

listing actions with absolute statutory 

deadlines; essential litigation-related, 

administrative, and listing programmanagement functions; and highpriority listing actions for some of our 

candidate species. In FY 2010, the 

Service received many new petitions 

and a single petition to list 404 species. 

The receipt of petitions for a large 

number of species is consuming the 

Service’s listing funding that is not 

dedicated to meeting court-ordered 

commitments. Absent some ability to 

balance effort among listing duties 

under existing funding levels, the 

Service was only able to initiate a few 

new listing determinations for candidate 

species in FY 2011. For FY 2012, on 

December 17, 2011, Congress passed a 

continuing resolution which provides 

funding at the FY 2011 enacted level 

with a 1.5 percent rescission through 

December 23, 2011 (Pub. L. 112–68). 

Until Congress appropriates funds for 

FY 2012, we will fund listing work 

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based on the FY 2011 amount minus the 

1.5 percent. 

In 2009, the responsibility for listing 

foreign species under the Act was 

transferred from the Division of 

Scientific Authority, International 

Affairs Program, to the Endangered 

Species Program. Therefore, starting in 

FY 2010, we used a portion of our 

funding to work on the actions 

described above for listing actions 

related to foreign species. In FY 2011, 

we anticipated using $1,500,000 for 

work on listing actions for foreign 

species, which reduces funding 

available for domestic listing actions; 

however, only $500,000 was allocated 

for this function. Although there are no 

foreign species issues included in our 

high-priority listing actions at this time, 

many actions have statutory or courtapproved settlement deadlines, thus 

increasing their priority. The budget 

allocations for each specific listing 

action are identified in the Service’s FY 

2011 and FY 2012 Allocation Tables 

(part of our record). 

For the above reasons, funding a 

proposed listing determination for the 

Bay-Delta DPS of longfin smelt is 

precluded by court-ordered and courtapproved settlement agreements, listing 

actions with absolute statutory 

deadlines, and work on proposed listing 

determinations for those candidate 

species with a higher listing priority 

(i.e., candidate species with LPNs of 1 

or 2). 

Based on our September 21, 1983, 

guidelines for assigning an LPN for each 

candidate species (48 FR 43098), we 

have a significant number of species 

with a LPN of 2. Using these guidelines, 

we assign each candidate an LPN of 1 

to 12, depending on the magnitude of 

threats (high or moderate to low), 

immediacy of threats (imminent or 

nonimminent), and taxonomic status of 

the species (in order of priority: 

Monotypic genus (a species that is the 

sole member of a genus); species; or part 

of a species (subspecies, or distinct 

population segment)). The lower the 

listing priority number, the higher the 

listing priority (that is, a species with an 

LPN of 1 would have the highest listing 

priority). 

Because of the large number of highpriority species, we have further ranked 

the candidate species with an LPN of 2 

by using the following extinction-risk 

type criteria: International Union for the 

Conservation of Nature and Natural 

Resources (IUCN) Red list status/rank, 

Heritage rank (provided by 

NatureServe), Heritage threat rank 

(provided by NatureServe), and species 

currently with fewer than 50 

individuals, or 4 or fewer populations. 

Those species with the highest IUCN 

rank (critically endangered), the highest 

Heritage rank (G1), the highest Heritage 

threat rank (substantial, imminent 

threats), and currently with fewer than 

50 individuals, or fewer than 4 

populations, originally comprised a 

group of approximately 40 candidate 

species (‘‘Top 40’’). These 40 candidate 

species have had the highest priority to 

receive funding to work on a proposed 

listing determination. As we work on 

proposed and final listing rules for those 

40 candidates, we apply the ranking 

criteria to the next group of candidates 

with LPNs of 2 and 3 to determine the 

next set of highest priority candidate 

species. Finally, proposed rules for 

reclassification of threatened species to 

endangered species are lower priority, 

because as listed species, they are 

already afforded the protections of the 

Act and implementing regulations. 

However, for efficiency reasons, we may 

choose to work on a proposed rule to 

reclassify a species to endangered if we 

can combine this with work that is 

subject to a court-determined deadline. 

With our workload so much bigger 

than the amount of funds we have to 

accomplish it, it is important that we be 

as efficient as possible in our listing 

process. Therefore, as we work on 

proposed rules for the highest priority 

species in the next several years, we are 

preparing multi-species proposals when 

appropriate, and these may include 

species with lower priority if they 

overlap geographically or have the same 

threats as a species with an LPN of 2. 

In addition, we take into consideration 

the availability of staff resources when 

we determine which high-priority 

species will receive funding to 

minimize the amount of time and 

resources required to complete each 

listing action. 

As explained above, a determination 

that listing is warranted but precluded 

must also demonstrate that expeditious 

progress is being made to add and 

remove qualified species to and from 

the Lists of Endangered and Threatened 

Wildlife and Plants. As with our 

‘‘precluded’’ finding, the evaluation of 

whether progress in adding qualified 

species to the Lists has been expeditious 

is a function of the resources available 

for listing and the competing demands 

for those funds. (Although we do not 

discuss it in detail here, we are also 

making expeditious progress in 

removing species from the list under the 

Recovery program in light of the 

resource available for delisting, which is 

funded by a separate line item in the 

budget of the Endangered Species 

Program. During FY 2011, we completed 

delisting rules for three species.) Given 

the limited resources available for 

listing, we find that we made 

expeditious progress in FY 2011 and are 

making expeditious progress in FY 2012 

in the Listing Program. This progress 

included preparing and publishing the 

following determinations: 

FY 2011 AND FY 2012 COMPLETED LISTING ACTIONS

Publication date Title Actions FR Pages 

10/6/2010 ........................ Endangered Status for the Altamaha Spinymussel 

and Designation of Critical Habitat.

Proposed Listing Endangered ............. 75 FR 61664–61690 

10/7/2010 ........................ 12-month Finding on a Petition to list the Sacramento Splittail as Endangered or Threatened.Notice of 12-month petition finding, 

Not warranted.

75 FR 62070–62095 

10/28/2010 ...................... Endangered Status and Designation of Critical 

Habitat for Spikedace and Loach Minnow.

Proposed Listing Endangered 

(uplisting).

75 FR 66481–66552 

11/2/2010 ........................ 90-Day Finding on a Petition to List the Bay 

Springs Salamander as Endangered.

Notice of 90-day Petition Finding, Not 

substantial.

75 FR 67341–67343 

11/2/2010 ........................ Determination of Endangered Status for the Georgia Pigtoe Mussel, Interrupted Rocksnail, and 

Rough Hornsnail and Designation of Critical 

Habitat.

Final Listing Endangered .................... 75 FR 67511–67550 

11/2/2010 ........................ Listing the Rayed Bean and Snuffbox as Endangered.Proposed Listing Endangered ............. 75 FR 67551–67583 

11/4/2010 ........................ 12-Month Finding on a Petition to List Cirsium 

wrightii (Wright’s Marsh Thistle) as Endangered 

or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

75 FR 67925–67944 

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FY 2011 AND FY 2012 COMPLETED LISTING ACTIONS—Continued 

Publication date Title Actions FR Pages 

12/14/2010 ...................... Endangered Status for Dunes Sagebrush Lizard .... Proposed Listing Endangered ............. 75 FR 77801–77817 

12/14/2010 ...................... 12-month Finding on a Petition to List the North 

American Wolverine as Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

75 FR 78029–78061 

12/14/2010 ...................... 12-Month Finding on a Petition to List the Sonoran 

Population of the Desert Tortoise as Endangered 

or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

75 FR 78093–78146 

12/15/2010 ...................... 12-Month Finding on a Petition to List Astragalus 

microcymbus and Astragalus schmolliae as Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

75 FR 78513–78556 

12/28/2010 ...................... Listing Seven Brazilian Bird Species as Endangered Throughout Their Range.Final Listing Endangered .................... 75 FR 81793–81815 

1/4/2011 .......................... 90-Day Finding on a Petition to List the Red Knot 

subspecies Calidris canutus roselaari as Endangered.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 304–311 

1/19/2011 ........................ Endangered Status for the Sheepnose and 

Spectaclecase Mussels.

Proposed Listing Endangered ............. 76 FR 3392–3420 

2/10/2011 ........................ 12-Month Finding on a Petition to List the Pacific 

Walrus as Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 7634–7679 

2/17/2011 ........................ 90-Day Finding on a Petition To List the Sand Verbena Moth as Endangered or Threatened.Notice of 90-day Petition Finding, 

Substantial.

76 FR 9309–9318 

2/22/2011 ........................ Determination of Threatened Status for the New 

Zealand-Australia Distinct Population Segment of 

the Southern Rockhopper Penguin.

Final Listing Threatened ...................... 76 FR 9681–9692 

2/22/2011 ........................ 12-Month Finding on a Petition to List Solanum 

conocarpum (marron bacora) as Endangered.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 9722–9733 

2/23/2011 ........................ 12-Month Finding on a Petition to List Thorne’s 

Hairstreak Butterfly as Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 9991–10003 

2/23/2011 ........................ 12-Month Finding on a Petition to List Astragalus 

hamiltonii, Penstemon flowersii, Eriogonum 

soredium, Lepidium ostleri, and Trifolium 

friscanum as Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded & Not 

Warranted.

76 FR 10166–10203 

2/24/2011 ........................ 90-Day Finding on a Petition to List the Wild Plains 

Bison or Each of Four Distinct Population Segments as Threatened.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 10299–10310 

2/24/2011 ........................ 90-Day Finding on a Petition to List the Unsilvered 

Fritillary Butterfly as Threatened or Endangered.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 10310–10319 

3/8/2011 .......................... 12-Month Finding on a Petition to List the Mt. 

Charleston Blue Butterfly as Endangered or 

Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 12667–12683 

3/8/2011 .......................... 90-Day Finding on a Petition to List the Texas 

Kangaroo Rat as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 12683–12690 

3/10/2011 ........................ Initiation of Status Review for Longfin Smelt .......... Notice of Status Review ...................... 76 FR 13121–13122 

3/15/2011 ........................ Withdrawal of Proposed Rule to List the Flat-tailed 

Horned Lizard as Threatened.

Proposed rule withdrawal .................... 76 FR 14210–14268 

3/15/2011 ........................ Proposed Threatened Status for the Chiricahua 

Leopard Frog and Proposed Designation of Critical Habitat.

Proposed Listing Threatened; Proposed Designation of Critical Habitat.76 FR 14126–14207 

3/22/2011 ........................ 12-Month Finding on a Petition to List the Berry 

Cave Salamander as Endangered.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 15919–15932 

4/1/2011 .......................... 90-Day Finding on a Petition to List the Spring 

Pygmy Sunfish as Endangered.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 18138–18143 

4/5/2011 .......................... 12-Month Finding on a Petition to List the 

Bearmouth Mountainsnail, Byrne Resort 

Mountainsnail, and Meltwater Lednian Stonefly 

as Endangered or Threatened.

Notice of 12-month petition finding, 

Not Warranted and Warranted but 

precluded.

76 FR 18684–18701 

4/5/2011 .......................... 90-Day Finding on a Petition To List the Peary 

Caribou and Dolphin and Union population of the 

Barren-ground Caribou as Endangered or 

Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 18701–18706 

4/12/2011 ........................ Proposed Endangered Status for the Three Forks 

Springsnail and San Bernardino Springsnail, and 

Proposed Designation of Critical Habitat.

Proposed Listing Endangered; Proposed Designation of Critical Habitat.76 FR 20464–20488 

4/13/2011 ........................ 90-Day Finding on a Petition To List Spring Mountains Acastus Checkerspot Butterfly as Endangered.Notice of 90-day Petition Finding, 

Substantial.

76 FR 20613–20622 

4/14/2011 ........................ 90-Day Finding on a Petition to List the Prairie 

Chub as Threatened or Endangered.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 20911–20918 

4/14/2011 ........................ 12-Month Finding on a Petition to List Hermes 

Copper Butterfly as Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 20918–20939 

4/26/2011 ........................ 90-Day Finding on a Petition to List the Arapahoe 

Snowfly as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 23256–23265 

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FY 2011 AND FY 2012 COMPLETED LISTING ACTIONS—Continued 

Publication date Title Actions FR Pages 

4/26/2011 ........................ 90-Day Finding on a Petition to List the SmoothBilled Ani as Threatened or Endangered.Notice of 90-day Petition Finding, Not 

substantial.

76 FR 23265–23271 

5/12/2011 ........................ Withdrawal of the Proposed Rule to List the Mountain Plover as Threatened.Proposed Rule, Withdrawal ................. 76 FR 27756–27799 

5/25/2011 ........................ 90-Day Finding on a Petition To List the Spot-tailed 

Earless Lizard as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 30082–30087 

5/26/2011 ........................ Listing the Salmon-Crested Cockatoo as Threatened Throughout its Range with Special Rule.Final Listing Threatened ...................... 76 FR 30758–30780 

5/31/2011 ........................ 12-Month Finding on a Petition to List Puerto Rican 

Harlequin Butterfly as Endangered.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 31282–31294 

6/2/2011 .......................... 90-Day Finding on a Petition to Reclassify the 

Straight-Horned Markhor (Capra falconeri 

jerdoni) of Torghar Hills as Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 31903–31906 

6/2/2011 .......................... 90-Day Finding on a Petition to List the Goldenwinged Warbler as Endangered or Threatened.Notice of 90-day Petition Finding, 

Substantial.

76 FR 31920–31926 

6/7/2011 .......................... 12-Month Finding on a Petition to List the Striped 

Newt as Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 32911–32929 

6/9/2011 .......................... 12-Month Finding on a Petition to List Abronia 

ammophila, Agrostis rossiae, Astragalus 

proimanthus, Boechera (Arabis) pusilla, and 

Penstemon gibbensii as Threatened or Endangered.

Notice of 12-month petition finding, 

Not Warranted and Warranted but 

precluded.

76 FR 33924–33965 

6/21/2011 ........................ 90-Day Finding on a Petition to List the Utah Population of the Gila Monster as an Endangered or a 

Threatened Distinct Population Segment.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 36049–36053 

6/21/2011 ........................ Revised 90-Day Finding on a Petition To Reclassify the Utah Prairie Dog From Threatened to 

Endangered.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 36053–36068 

6/28/2011 ........................ 12-Month Finding on a Petition to List Castanea 

pumila var. ozarkensis as Threatened or Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 37706–37716 

6/29/2011 ........................ 90-Day Finding on a Petition to List the Eastern 

Small-Footed Bat and the Northern Long-Eared 

Bat as Threatened or Endangered.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 38095–38106 

6/30/2011 ........................ 12-Month Finding on a Petition to List a Distinct 

Population Segment of the Fisher in Its United 

States Northern Rocky Mountain Range as Endangered or Threatened with Critical Habitat.

Notice of 12-month petition finding, 

Not warranted.

76 FR 38504–38532 

7/12/2011 ........................ 90-Day Finding on a Petition to List the Bay Skipper as Threatened or Endangered.Notice of 90-day Petition Finding, 

Substantial.

76 FR 40868–40871 

7/19/2011 ........................ 12-Month Finding on a Petition to List Pinus 

albicaulis as Endangered or Threatened with 

Critical Habitat.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 42631–42654 

7/19/2011 ........................ Petition To List Grand Canyon Cave 

Pseudoscorpion.

Notice of 12-month petition finding, 

Not warranted.

76 FR 42654–42658 

7/26/2011 ........................ 12-Month Finding on a Petition to List the Giant 

Palouse Earthworm (Drilolerius americanus) as 

Threatened or Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 44547–44564 

7/26/2011 ........................ 12-month Finding on a Petition to List the Frigid 

Ambersnail as Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 44566–44569 

7/27/2011 ........................ Determination of Endangered Status for Ipomopsis 

polyantha (Pagosa Skyrocket) and Threatened 

Status for Penstemon debilis (Parachute 

Beardtongue) and Phacelia submutica (DeBeque 

Phacelia).

Final Listing Endangered, Threatened 76 FR 45054–45075 

7/27/2011 ........................ 12-Month Finding on a Petition to List the Gopher 

Tortoise as Threatened in the Eastern Portion of 

its Range.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 45130–45162 

8/2/2011 .......................... Proposed Endangered Status for the Chupadera 

Springsnail (Pyrgulopsis chupaderae) and Proposed Designation of Critical Habitat.

Proposed Listing Endangered ............. 76 FR 46218–46234 

8/2/2011 .......................... 90-Day Finding on a Petition to List the Straight 

Snowfly and Idaho Snowfly as Endangered.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 46238–46251 

8/2/2011 .......................... 12-Month Finding on a Petition to List the Redrock 

Stonefly as Endangered or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 46251–46266 

8/2/2011 .......................... Listing 23 Species on Oahu as Endangered and 

Designating Critical Habitat for 124 Species.

Proposed Listing Endangered ............. 76 FR 46362–46594 

8/4/2011 .......................... 90-Day Finding on a Petition To List Six Sand 

Dune Beetles as Endangered or Threatened.

Notice of 90-day Petition Finding, Not 

substantial and substantial.

76 FR 47123–47133 

8/9/2011 .......................... Endangered Status for the Cumberland Darter, 

Rush Darter, Yellowcheek Darter, Chucky 

Madtom, and Laurel Dace.

Final Listing Endangered .................... 76 FR 48722–48741 

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FY 2011 AND FY 2012 COMPLETED LISTING ACTIONS—Continued 

Publication date Title Actions FR Pages 

8/9/2011 .......................... 12-Month Finding on a Petition to List the Nueces 

River and Plateau Shiners as Threatened or Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 48777–48788 

8/9/2011 .......................... Four Foreign Parrot Species [crimson shining parrot, white cockatoo, Philippine cockatoo, yellowcrested cockatoo].Proposed Listing Endangered and 

Threatened; Notice of 12-month petition finding, Not warranted.

76 FR 49202–49236 

8/10/2011 ........................ Proposed Listing of the Miami Blue Butterfly as Endangered, and Proposed Listing of the Cassius 

Blue, Ceraunus Blue, and Nickerbean Blue Butterflies as Threatened Due to Similarity of Appearance to the Miami Blue Butterfly.

Proposed Listing Endangered Similarity of Appearance.76 FR 49408–49412 

8/10/2011 ........................ 90-Day Finding on a Petition To List the Saltmarsh 

Topminnow as Threatened or Endangered Under 

the Endangered Species Act.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 49412–49417 

8/10/2011 ........................ Emergency Listing of the Miami Blue Butterfly as 

Endangered, and Emergency Listing of the 

Cassius Blue, Ceraunus Blue, and Nickerbean 

Blue Butterflies as Threatened Due to Similarity 

of Appearance to the Miami Blue Butterfly.

Emergency Listing Endangered and 

Similarity of Appearance.

76 FR 49542–49567 

8/11/2011 ........................ Listing Six Foreign Birds as Endangered Throughout Their Range.Final Listing Endangered .................... 76 FR 50052–50080 

8/17/2011 ........................ 90-Day Finding on a Petition to List the Leona’s 

Little Blue Butterfly as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 50971–50979 

9/01/2011 ........................ 90-Day Finding on a Petition to List All Chimpanzees (Pan troglodytes) as Endangered.Notice of 90-day Petition Finding, 

Substantial.

76 FR 54423–54425 

9/6/2011 .......................... 12-Month Finding on Five Petitions to List Seven 

Species of Hawaiian Yellow-faced Bees as Endangered.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 55170–55203 

9/8/2011 .......................... 12-Month Petition Finding and Proposed Listing of 

Arctostaphylos franciscana as Endangered.

Notice of 12-month petition finding, 

Warranted; Proposed Listing Endangered.

76 FR 55623–55638 

9/8/2011 .......................... 90-Day Finding on a Petition To List the Snowy 

Plover and Reclassify the Wintering Population 

of Piping Plover.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 55638–55641 

9/13/2011 ........................ 90-Day Finding on a Petition To List the Franklin’s 

Bumble Bee as Endangered.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 56381–56391 

9/13/2011 ........................ 90-Day Finding on a Petition to List 42 Great Basin 

and Mojave Desert Springsnails as Threatened 

or Endangered with Critical Habitat.

Notice of 90-day Petition Finding, 

Substantial and Not substantial.

76 FR 56608–56630 

9/21/2011 ........................ 12-Month Finding on a Petition to List Van 

Rossem’s Gull-billed Tern as Endangered or 

Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 58650–58680 

9/22/2011 ........................ Determination of Endangered Status for Casey’s 

June Beetle and Designation of Critical Habitat.

Final Listing Endangered .................... 76 FR 58954–58998 

9/27/2011 ........................ 12-Month Finding on a Petition to List the 

Tamaulipan Agapema, Sphingicampa blanchardi 

(no common name), and Ursia furtiva (no common name) as Endangered or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 59623–59634 

9/27/2011 ........................ Partial 90-Day Finding on a Petition to List 404 

Species in the Southeastern United States as 

Endangered or Threatened With Critical Habitat.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 59836–59862 

9/29/2011 ........................ 90-Day Finding on a Petition to List the American 

Eel as Threatened.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 60431–60444 

10/4/2011 ........................ 12-Month Finding on a Petition to List the Lake 

Sammamish Kokanee Population of 

Oncorhynchus nerka as an Endangered or 

Threatened Distinct Population Segment.

Notice of 12-month petition finding, 

Not warranted.

76 FR 61298–61307 

10/4/2011 ........................ 12-Month Finding on a Petition to List Calopogon 

oklahomensis as Threatened or Endangered.

Notice of 12-month petition finding, 

Not warranted.

76 FR 61307–61321 

10/4/2011 ........................ 12-Month Finding on a Petition To List the 

Amargosa River Population of the Mojave 

Fringe-toed Lizard as an Endangered or Threatened Distinct Population Segment.

Notice of 12-month petition finding, 

Not warranted.

76 FR 61321–61330 

10/4/2011 ........................ Endangered Status for the Alabama Pearlshell, 

Round Ebonyshell, Southern Sandshell, Southern Kidneyshell, and Choctaw Bean, and Threatened Status for the Tapered Pigtoe, Narrow 

Pigtoe, and Fuzzy Pigtoe; with Critical Habitat.

Proposed Listing Endangered ............. 76 FR 61482–61529 

10/4/2011 ........................ 90-Day Finding on a Petition To List 10 Subspecies of Great Basin Butterflies as Threatened 

or Endangered with Critical Habitat.

Notice of 90-day Petition Finding, 

Substantial and Not substantial.

76 FR 61532–61554 

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FY 2011 AND FY 2012 COMPLETED LISTING ACTIONS—Continued 

Publication date Title Actions FR Pages 

10/5/2011 ........................ 90-Day Finding on a Petition to List 29 Mollusk 

Species as Threatened or Endangered With Critical Habitat.

Notice of 90-day Petition Finding, 

Substantial and Not substantial.

76 FR 61826–61853 

10/5/2011 ........................ 12-Month Finding on a Petition to List the Cactus 

Ferruginous Pygmy-Owl as Threatened or Endangered with Critical Habitat.

Notice of 12-month petition finding, 

Not warranted.

76 FR 61856–61894 

10/5/2011 ........................ 12-Month Finding on a Petition to List the Northern 

Leopard Frog in the Western United States as 

Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 61896–61931 

10/6/2011 ........................ Endangered Status for the Ozark Hellbender Salamander.Final Listing Endangered .................... 76 FR 61956–61978 

10/6/2011 ........................ Red-Crowned Parrot ................................................ Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 62016–62034 

10/6/2011 ........................ 12-Month Finding on a Petition to List Texas 

Fatmucket, Golden Orb, Smooth Pimpleback, 

Texas Pimpleback, and Texas Fawnsfoot as 

Threatened or Endangered.

Notice of 12-month petition finding, 

Warranted but precluded.

76FR 62166–62212 

10/6/2011 ........................ 12-Month Finding on a Petition to List the Mohave 

Ground Squirrel as Endangered or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 62214–62258 

10/6/2011 ........................ Partial 90-Day Finding on a Petition to List 404 

Species in the Southeastern United States as 

Threatened or Endangered With Critical Habitat.

Notice of 90-day Petition Finding, Not 

substantial.

76 FR 62260–62280 

10/7/2011 ........................ 12-Month Finding on a Petition to List the Blackfooted Albatross as Endangered or Threatened.Notice of 12-month petition finding, 

Not warranted.

76 FR 62504–62565 

10/11/2011 ...................... 12-Month Finding on a Petition to List Amoreuxia 

gonzalezii, Astragalus hypoxylus, and Erigeron 

piscaticus as Endangered or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 62722–62740 

10/11/2011 ...................... 12-Month Finding on a Petition and Proposed Rule 

to List the Yellow-Billed Parrot.

Notice of 12-month petition finding, 

Warranted Propose Listing, threatened.

76 FR 62740–62754 

10/11/2011 ...................... 12-Month Finding on a Petition to List the 

Tehachapi Slender Salamander as Endangered 

or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 62900–62926 

10/11/2011 ...................... Endangered Status for the Altamaha Spinymussel 

and Designation of Critical Habitat.

Final Listing Endangered .................... 76 FR 62928–62960 

10/11/2011 ...................... 12-Month Finding for a Petition to List the California Golden Trout as Endangered.Notice of 12-month petition finding, 

Not warranted.

76 FR 63094–63115 

10/12/2011 ...................... 12-Month Petition Finding, Proposed Listing of 

Coquı ́ Llanero as Endangered, and Designation 

of Critical Habitat for Coquı ́ Llanero.

Notice of 12-month petition finding, 

Warranted; Proposed Listing Endangered.

76 FR 63420–63442 

10/12/2011 ...................... 12-Month Finding on a Petition to List Northern 

Leatherside Chub as Endangered or Threatened.

Notice of 12-month petition finding, 

Not warranted.

76 FR 63444–63478 

10/12/2011 ...................... 12-Month Finding on a Petition to List Two South 

American Parrot Species.

Notice of 12-month petition finding, 

Not warranted.

76 FR 63480–63508 

10/13/2011 ...................... 12-Month Finding on a Petition to List a Distinct 

Population Segment of the Red Tree Vole as 

Endangered or Threatened.

Notice of 12-month petition finding, 

Warranted but precluded.

76 FR 63720–63762 

12/19/2011 ...................... 90-Day Finding on a Petition To List the Western 

Glacier Stonefly as Endangered With Critical 

Habitat.

Notice of 90-day Petition Finding, 

Substantial.

76 FR 78601–78609 

1/3/2012 .......................... 90-Day Finding on a Petition to List Sierra Nevada 

Red Fox as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

77 FR 45–52 

1/5/2012 .......................... Listing Two Distinct Population Segments of 

Broad-Snouted Caiman as Endangered or 

Threatened and a Special Rule.

Proposed Reclassification ................... 77 FR 666–697 

1/12/2012 ........................ 90-Day Finding on a Petition To List the Humboldt 

Marten as Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

77 FR 1900–1908 

1/24/2012 ........................ 90-Day Finding on a Petition to List the ‘I’iwi as 

Endangered or Threatened.

Notice of 90-day Petition Finding, 

Substantial.

77 FR 3423–3432 

2/1/2012 .......................... 90-Day Finding on a Petition to List the San 

Bernardino Flying Squirrel as Endangered or 

Threatened With Critical Habitat.

Notice of 90-day Petition Finding, 

Substantial.

77 FR 4973–4980 

2/14/2012 ........................ Determination of Endangered Status for the Rayed 

Bean and Snuffbox Mussels Throughout Their 

Ranges.

Final Listing Endangered .................... 77 FR 8632–8665 

Our expeditious progress also 

includes work on listing actions that we 

funded in previous fiscal years and in 

FY 2012 but have not yet been 

completed to date. These actions are 

listed below. Actions in the top section 

of the table are being conducted under 

a deadline set by a court. We are 

implementing a work plan that 

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19796 Federal Register / Vol. 77, No. 63 / Monday, April 2, 2012 / Proposed Rules 

establishes a framework and schedule 

for resolving by September 30, 2016, the 

status of all of the species that the 

Service had determined to be qualified 

as of the 2010 Candidate Notice of 

Review. The Service submitted such a 

work plan to the U.S. District Court for 

the District of Columbia in In re 

Endangered Species Act Section 4 

Deadline Litigation, No. 10–377 (EGS), 

MDL Docket No. 2165 (D. D.C. May 10, 

2011), and obtained the court’s 

approval. The Service had already 

begun to implement that work plan last 

FY and many of these initial actions in 

our work plan include work on 

proposed rules for candidate species 

with an LPN of 2 or 3. As discussed 

above, selection of these species is 

partially based on available staff 

resources, and when appropriate, 

include species with a lower priority if 

they overlap geographically or have the 

same threats as the species with the 

high priority. Including these species 

together in the same proposed rule 

results in considerable savings in time 

and funding, when compared to 

preparing separate proposed rules for 

each of them in the future. Actions in 

the lower section of the table are being 

conducted to meet statutory timelines, 

that is, timelines required under the 

Act. 

ACTIONS FUNDED IN PREVIOUS FYS AND IN FY 2012 BUT NOT YET COMPLETED

Species Action 

Actions Subject to Court Order/Settlement Agreement 

4 parrot species (military macaw, yellow-billed parrot, scarlet macaw).5 12-month petition finding. 

Longfin smelt .................................................................................................................................................................. 12-month petition finding. 

20 Maui-Nui candidate species 2 (17 plants, 3 tree snails) (14 with LPN = 2, 2 with LPN = 3, 3 with LPN = 8) ......... Proposed listing. 

Umtanum buckwheat (LPN = 2) and white bluffs bladderpod (LPN = 9).4 Proposed listing. 

Grotto sculpin (LPN = 2) 4 .............................................................................................................................................. Proposed listing. 

2 Arkansas mussels (Neosho mucket (LPN = 2) & Rabbitsfoot (LPN = 9)).4 Proposed listing. 

Diamond darter (LPN = 2) 4 ............................................................................................................................................ Proposed listing. 

Gunnison sage-grouse (LPN = 2) 4 ................................................................................................................................ Proposed listing. 

Coral Pink Sand Dunes Tiger Beetle (LPN = 2) 5 .......................................................................................................... Proposed listing. 

Lesser prairie chicken (LPN = 2) ................................................................................................................................... Proposed listing. 

4 Texas salamanders (Austin blind salamander (LPN = 2), Salado salamander (LPN = 2), Georgetown salamander 

(LPN = 8), Jollyville Plateau (LPN = 8)).3

Proposed listing. 

West Texas aquatics (Gonzales Spring Snail (LPN = 2), Diamond Y springsnail (LPN = 2), Phantom springsnail 

(LPN = 2), Phantom Cave snail (LPN = 2), Diminutive amphipod (LPN = 2)).3

Proposed listing. 

2 Texas plants (Texas golden gladecress (Leavenworthia texana) (LPN = 2), Neches River rose-mallow (Hibiscus 

dasycalyx) (LPN = 2)).3

Proposed listing. 

4 AZ plants (Acuna cactus (Echinomastus erectocentrus var. acunensis) (LPN = 3), Fickeisen plains cactus 

(Pediocactus peeblesianus fickeiseniae) (LPN = 3), Lemmon fleabane (Erigeron lemmonii) (LPN = 8), Gierisch 

mallow (Sphaeralcea gierischii) (LPN = 2)).5

Proposed listing. 

FL bonneted bat (LPN = 2).3 Proposed listing. 

3 Southern FL plants (Florida semaphore cactus (Consolea corallicola) (LPN = 2), shellmound applecactus 

(Harrisia (= Cereus) aboriginum (=gracilis)) (LPN = 2), Cape Sable thoroughwort (Chromolaena frustrata) (LPN = 

2)).5

Proposed listing. 

21 Big Island (HI) species 5 (includes 8 candidate species—6 plants & 2 animals; 4 with LPN = 2, 1 with LPN = 3, 

1 with LPN = 4, 2 with LPN = 8) 

Proposed listing. 

12 Puget Sound prairie species (9 subspecies of pocket gopher (Thomomys mazama ssp.) (LPN = 3), streaked 

horned lark (LPN = 3), Taylor’s checkerspot (LPN = 3), Mardon skipper (LPN = 8)).3

Proposed listing. 

2 TN River mussels (fluted kidneyshell (LPN = 2), slabside pearlymussel (LPN = 2)).5 Proposed listing. 

Jemez Mountain salamander (LPN = 2) 5 ...................................................................................................................... Proposed listing. 

Actions with Statutory Deadlines 

5 Bird species from Colombia and Ecuador .................................................................................................................. Final listing determination. 

Queen Charlotte goshawk .............................................................................................................................................. Final listing determination. 

6 Birds from Peru & Bolivia ............................................................................................................................................ Final listing determination. 

Loggerhead sea turtle (assist National Marine Fisheries Service) 5 .............................................................................. Final listing determination. 

Platte River caddisfly (from 206 species petition) 5 ........................................................................................................ 12-month petition finding. 

Ashy storm-petrel 5 ......................................................................................................................................................... 12-month petition finding. 

Honduran emerald .......................................................................................................................................................... 12-month petition finding. 

Eagle Lake trout 1 ........................................................................................................................................................... 90-day petition finding. 

Spring Mountains checkerspot butterfly ......................................................................................................................... 90-day petition finding. 

Aztec gilia 5 ..................................................................................................................................................................... 90-day petition finding. 

White-tailed ptarmigan 5 .................................................................................................................................................. 90-day petition finding. 

Bicknell’s thrush 5 ............................................................................................................................................................ 90-day petition finding. 

Sonoran talussnail 5 ........................................................................................................................................................ 90-day petition finding. 

2 AZ Sky Island plants (Graptopetalum bartrami & Pectis imberbis) 5 .......................................................................... 90-day petition finding. 

Desert massasauga ........................................................................................................................................................ 90-day petition finding. 

Boreal toad (eastern or southern Rocky Mtn population) 5 ............................................................................................ 90-day petition finding. 

Alexander Archipelago wolf 5 .......................................................................................................................................... 90-day petition finding. 

Eastern diamondback rattlesnake .................................................................................................................................. 90-day petition finding. 

1Funds for listing actions for these species were provided in previous FYs. 

2Although funds for these high-priority listing actions were provided in FY 2008 or 2009, due to the complexity of these actions and competing 

priorities, these actions are still being developed. 3Partially funded with FY 2010 funds and FY 2011 funds. 

4Funded with FY 2010 funds. 

5Funded with FY 2011 funds. 

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Federal Register / Vol. 77, No. 63 / Monday, April 2, 2012 / Proposed Rules 19797 

We have endeavored to make our 

listing actions as efficient and timely as 

possible, given the requirements of the 

relevant law and regulations, and 

constraints relating to workload and 

personnel. We are continually 

considering ways to streamline 

processes or achieve economies of scale, 

such as by batching related actions 

together. Given our limited budget for 

implementing section 4 of the Act, these 

actions described above collectively 

constitute expeditious progress. 

The Bay-Delta DPS of longfin smelt 

will be added to the list of candidate 

species upon publication of this 12- 

month finding. We will continue to 

evaluate this DPS as new information 

becomes available. Continuing review 

will determine if a change in status is 

warranted, including the need to make 

prompt use of emergency listing 

procedures. 

We intend that any proposed listing 

determination for the Bay-Delta DPS of 

longfin smelt will be as accurate as 

possible. Therefore, we will continue to 

accept additional information and 

comments from all concerned 

governmental agencies, the scientific 

community, industry, or any other 

interested party concerning this finding. 

References Cited 

A complete list of references cited is 

available on the Internet at http:// 

www.regulations.gov and upon request 

from the San Francisco Bay-Delta Fish 

and Wildlife Office (see ADDRESSES

section). 

Authors 

The primary authors of this notice are 

the staff members of the San Francisco 

Bay-Delta Fish and Wildlife Office. 

Authority 

The authority for this section is 

section 4 of the Endangered Species Act 

of 1973, as amended (16 U.S.C. 1531 et 

seq.). 

Dated: March 13, 2012. 

Gary D. Frazer, 

Acting Director, Fish and Wildlife Service. 

[FR Doc. 2012–7198 Filed 3–30–12; 8:45 am] 

BILLING CODE 4310–55–P 

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