U. S. DEPARTMENT OF THE INTERIOR 

FISH AND WILDLIFE SERVICE 

 

Species at Risk from Selenium Exposure in the 

San Francisco Estuary 

Final Report to the 

U. S. Environmental Protection Agency 

Inter-Agency Agreement No. DW14922048-01-0 

Prepared by 

William N. Beckon and Thomas C. Maurer 

Sacramento, California 

March 2008
ACKNOWLEDGEMENTS 

We would like to gratefully acknowledge the assistance and support of the following people in 

the preparation of this document: Jenny Peterson for help in obtaining references; Andy 

Hamilton for access to his collection of literature on salmon; Dan Russell for help with bald 

eagle information; Bart Prose for supplying useful documents on endangered aquatic species; 

and Jodi Holm for providing data from her studies of trout. Eugenia McNaughton and Romona 

Haebler, both with the U.S. Environmental Protection Agency, provided kind and patient support 

throughout the preparation of this report. 

This document was prepared for the U.S. Environmental Protection Agency under Inter-Agency 

Agreement No. DW14922048-01-0. 

Literature citation should read as follows:

U. S. Fish and Wildlife Service. 2008. Species at Risk from Selenium Exposure in the San 

Francisco Estuary. U.S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office, 

Environmental Contaminants Division. Sacramento, California. March 2008. 81 pp.
Species at Risk from Selenium Exposure in the San Francisco Estuary 

Table of Contents 

Introduction 1 

Species Considered 1 

Species Most At Risk Summary Table 6 

Species Most At Risk 

 Bald Eagle 8 

 California Clapper Rail 12 

 Greater Scaup 14 

 Lesser Scaup 16 

 White-winged Scoter 18 

 Surf Scoter 19 

 Black Scoter 21 

 Chinook Salmon 23 

 Steelhead 38 

 Green Sturgeon 51 

 White Sturgeon 53 

 Delta Smelt 59 

 Sacramento Splittail 62 

Literature Cited 66 
BLANK PAGE
U. S. DEPARTMENT OF THE INTERIOR 

FISH AND WILDLIFE SERVICE 

Sacramento Fish and Wildlife Office 

2800 Cottage Way, Rm W-2605 

Sacramento, California 95825 

Species at Risk from Selenium Exposure in the San Francisco Estuary 

Prepared by 

WILLIAM N. BECKON 

Environmental Contaminants Division 

william_beckon@fws.gov 

and 

THOMAS C. MAURER 

Branch Chief, Investigations and Prevention 

Environmental Contaminants Division 

INTRODUCTION 

Discharges of selenium from Bay Area oil refineries and in the subsurface drainwater from 

Central Valley farms eventually reach the San Francisco Bay/Delta estuary, where uptake by food 

chains is particularly efficient (Presser and Luoma 2006). Selenium concentrated through food 

chains may have a variety of adverse effects including reduced growth and embryonic deformities 

in wildlife species at risk (Eisler 1985). As part of an effort to revise water quality criteria to be 

protective of federally listed species in California, the U. S. Environmental Protection Agency 

(USEPA) is engaged in an interagency project to determine selenium dietary exposure 

benchmarks that would be protective of wildlife, including aquatic-dependent wildlife, in the San 

Francisco Bay/Delta estuary. This document is the initial contribution of the U. S. Fish and 

Wildlife Service (USFWS) to this interagency project. The role of the USFWS in this initial task 

is to review and compile existing pertinent data (diet, body weight, food ingestion rate, natural 

history) on the species that are most likely to be at risk due to dietary selenium exposure in the 

San Francisco Bay/Delta. 

SPECIES CONSIDERED 

Species considered for evaluation of selenium exposure risk in the San Francisco Bay/Delta are 

listed in Table 1. To keep this list reasonably manageable but representative, it was subject to a 

preliminary screening process that eliminated plants, most invertebrates, and most vertebrates that 

are members of strictly or mainly terrestrial food chains. In compiling this list, species protected 

by federal legislation were given priority. 

1
Table 1. List of species considered for evaluation of selenium exposure risk in the San Francisco Bay/Delt

Common Name 

Scientific Name Federal 

Status 

California State Status 

Potential to be adversely affected by 

Mammalssalt marsh harvest mouse 

Reithrodontomys raviventris 

endangered protected As a terrestrial herbivorous mammal, unlikely 

exposed and sensitive of wildlife species; there“species most at risk.” 

BirdsAmerican white pelican 

Pelecanus erythrorhynchos

MBTA concern SF Bay is North end of West Coast distributio

some bottom-feeding fish as well as schooling “species most at risk.”. 

California brown pelican 

Pelecanus occidentalis californicus 

endangered protected, 

endangered 

SF Bay is North end of W Coast distribution. schooling fish; therefore, not part of benthic-bato be a “species most at risk.” 

white-faced ibis Plegadis chihi concern concern Breeds and winters in San Joaquin Valley. Inh

wetlands, but also estuarine wetlands. Eats aquinvertebrates. At some risk but not likely to be 

double-crested cormorant 

Phalacrocorax auritus MBTA concern Winters in Central Valley and SF Bay/Delta. F

and invertebrates as well as schooling fish. At a “species most at risk.” 

American bittern 

Botaurus lentiginosus concern none Feeds mainly in freshwater marshes, eating ma

vertebrates; therefore not likely to be a “specie

western least bittern 

Ixobrychus exilis hesperis concern concern Breeds in SF Delta. Feeds in fresh and brackis

mainly small fish and insects; therefore not likerisk.”. 

Aleutian Canada goose 

Branta canadensis leucopareia

delisted, MBTA none Winters in California, feeding primarily in upla

Sensitive to selenium but unlikely to be exposelikely to be a “species most at risk.” 

greater scaup Aythya marila MBTA none SF Bay is one of 2 major wintering areas on W 

on benthic mollusks that efficiently bioaccumuBay/estuary, therefore likely to be a “species m

lesser scaup Aythya affinis MBTA none SF Bay is an important wintering area; feeds on 

a “species most at risk.” 

black scoter Melanitta nigra MBTA none Winters along California coast, diving mainly f

to be a “species most at risk.” 

white-winged scoter 

Melanitta fusca MBTA none Winters along California coast and estuaries, d

therefore likely to be a “species most at risk.” 
Common 

Name 

Scientific Name Federal 

Status 

California State Status 

Potential to be adversely affected by 

surf scoter Melanitta perspicillata MBTA none Winters along California coast, diving mainly f

to be a “species most at risk.” 

osprey Pandion haliaetus MBTA concern High trophic level piscivore; not at risk overall 

represented by bald eagle. Therefore not treaterisk.” 

bald eagle Haliaeetus leucocephalus delisted, 

MBTA,BGEPA 

protected, endangered 

High trophic level piscivore; at risk overall and chain in the SF Bay/Delta; therefore likely to b

northern harrier Circus cyaneus MBTA concern High trophic level but less exposed to aquatic f

therefore not likely to be a “species most at risk

white-tailed kite Elanus leucurus concern protected Feeds mainly on terrestrial mammals; minimal 

selenium; therefore not likely to be a “species m

American peregrine falcon 

Falco peregrinus anatum delisted, MBTA protected, 

concern 

Delisted but monitored for population status anselenium in aquatic food chain as predator on pexposure generally diluted by terrestrial compolikely to be a “species most at risk.” 

prairie falcon Falco mexicanus MBTA concern Winters along California coast; high trophic lev

food chain; therefore not likely to be a “species 

California black rail 

Laterallus jamaicensis coturniculus 

MBTA protected, 

concern 

Inhabits tidal marsh in SF Bay estuary. Feeds snails, but also seeds; therefore not likely to be 

California clapper rail 

Rallus longirostris obsoletus 

endangered protected, 

endangered 

Subspecies endangered and endemic to SF estuinvertebrates, including filter-feeders that bioactherefore likely to be a “species most at risk.” 

marbled murrelet 

Brachyramphus marmoratus

threatened endangered Forages in bays along Pacific coast in summer, 

Bay/Delta. Dives for pelagic food: schooling Therefore not likely to be a “species most at ris

California least tern 

Sterna antillarum browni endangered protected, 

endangered 

Breeds primarily in Central San Francisco Bay estuary. Feeds throughout estuary, mainly on sbenthic mollusk-based food chain; therefore noat risk.” 

black tern Chlidonias niger concern concern Breeds in C Valley including SF Delta. Feeds 

surface fish and insects; therefore not likely to 

Caspian tern Sterna caspia MBTA none Preys heavily on juvenile salmonids, but not en

not likely to be a “species most at risk.” 

western snowy plover 

Charadrius alexandrinus threatened concern Terrestrial component of diet likely provides d

system selenium exposures; have been shown tselenium exposure; therefore not likely to be a 
Common 

Name 

Scientific Name Federal 

Status 

California State Status 

Potential to be adversely affected by 

mountain plover Charadrius montanus concern concern Winters in agricultural fields of Sacramento/Sa

mainly terrestrial; therefore not likely to be a “

tricolored blackbird 

Agelaius tricolor concern concern Nests colonially, mainly in freshwater marshes

as freshwater insects; therefore not likely to be 

Reptilesgiant garter snake 

Thamnophis gigas threatened threatened Aquatic predator, but not known to inhabit the 

to be a “species most at risk” in the estuary. 

FishChinook salmon Oncorhynchus 

tshawytscha

endangered/ threatened 

endangered/ threatened 

Sensitive to selenium; most sensitive life stagetherefore likely to be a “species most at risk.” 

steelhead Oncorhynchus mykiss threatened none (in Central 

Valley) 

Sensitive to selenium; most sensitive life stagetherefore likely to be a “species most at risk.” 

delta smelt Hypomesus transpacificus threatened threatened Endemic to the Bay/Delta estuary. Feeds on zo

greatest exposure, but threatened overall, so incrisk.” 

longfin smelt Spirinchus thaleichthys concern endangered SF Bay/estuary is S end of distribution. Prefer

smelt. Overall less threatened and probably lesadequately represented by that species. Theref“species most at risk.” 

green sturgeon Acipenser medirostris threatened concern; fishing 

prohibited 

Threatened overall, and vulnerable to selenium feeder in the SF estuary; therefore likely to be 

Emergency regulations issued by CDFG March green sturgeon year-round in all areas. 

white sturgeon Acipenser transmontanus none limited fishing Population in the SF estuary not federally listed

as a clam-eating bottom feeder. Therefore, treaat risk.” The daily bag and possession limit estthat must be between 46 inches and 72 inches tis three. 

river lamprey Lampetra ayresi none watch list Anadromous; feeds on young salmon. Recorde

and San Joaquin Rivers. Not federally listed; ta “species most at risk.” 

Sacramento perch 

Archoplites interruptus concern concern Fry feed primarily on bottom-dwelling crustace

fish. One captured in the Delta in 1992, not likestablished population there. Therefore not conmost at risk” in the Delta. 

Sacramento splittail 

Pogonichthys macrolepidotus

concern threatened Vulnerable to selenium as clam-eating bottom 

therefore likely to be a “species most at risk.” 
Common 

Name 

Scientific Name Federal 

Status 

California State Status 

Potential to be adversely affected by 

striped bass Morone saxatilis none none Introduced sport fish in California. Population 

early 2000s, but species overall not threatened. be a “species most at risk.” 

threadfin shad Dorosoma pretenense none none Introduced in California as food for game fish. 

sharply in early 2000s, but species overall not tconsidered to be a “species most at risk.” 

tidewater goby Eucyclogobius newberryi endangered endangered Bottom-dwelling carnivore. Prefers semi-close

exposed, but not found recently (since 1984) in 

considered to be a “species most at risk” in the 

California halibut 

Paralichthys californicus none none Bottom dweller inhabiting the SF Bay, but ove

not likely to be a “species most at risk.” 

leopard shark Triakis semifasciata none none Bottom dweller inhabiting the SF Bay, but ove

not likely to be a “species most at risk.” 

starry flounder Platichthys stellatus none none Bottom dweller inhabiting the SF Bay. Popula

since 1980, but overall not threatened; thereformost at risk.” 

InvertebratesDungeness crab Cancer magister none none Estuary is nursery for this ocean-breeding botto

threatened; therefore not likely to be a “species 

Federal Status: Endangered: listed as endangered under the Federal Endangered Species Act; Threatened: listed as threatened under t

Species Act; Proposed threatened: proposed as threatened under the Federal Endangered Species Act; Concern: designated a species o

removed from the list of endangered and threatened species under the Federal ESA; MBTA: protected under Migratory Bird Treaty Acthe Bald and Golden Eagle Protection Act. 

California State Status: Endangered: listed as endangered under the California Endangered Species Act; Threatened: listed as threate

Endangered Species Act; Concern: designated by the California Department of Fish and Game as a species of concern; Protected: Fulland Game Code of California predating the California Endangered Species Act 

* Assessment based upon population status, dependence upon benthic food web, and sensitivity to selenium. Aquatic dependent specie

benthic food web of the San Francisco Estuary were considered to be at greater risk to selenium exposure than those species feeding in web. This assumption is based upon the work of Stewart et al. (2004).
Table 2. Species most at risk from selenium exposure in the San Francisco Estuary: summary data. 

Common Name 

Scientific Name 

Probable critical life stage for selenium effects1

Food ingestion rate at critical life stage (g wet weight per day)2

Food ingestion rate at critical life stage (g dry weight per kg body weight per day)3

Body weight at critical life stage (g)4

Diet 

bald eagle Haliaeetus 

leucocephalus 

Adult female (egg laying) 

644 249 5275 

(female) 

fish, birds, mammals 

California clapper rail 

Rallus longirostris obsoletus 

Adult female (egg laying) 

172 46.8 346 mussels, spiders, 

clams, crabs, snails, marsh cordgrass seeds 

greater scaup 

Aythya marila Adult male and 

female (migration) 

313 85.8 1054 

(male) 

clams, snails, other mollusks, crustaceans, algae 

lesser scaup 

Aythya affinis Adult male and 

female (migration) 

246 67.5 734 

(male) 

clams, other mollusks, aquatic insects, crustaceans, plants 

whitewinged scoter 

Melanitta fusca Adult male and 

female (migration) 

465 127.3 1917 

(male) 

clams, other mollusks, crustaceans, aquatic insects 

surf scoter Melanitta 

perspicillata 

Adult male and female (migration) 

314 86.0 1059 

(male) 

mussels, other mollusks, plants, crustaceans 

black scoter 

Melanitta nigra Adult male and 

female (migration) 

325 89.1 1117 

(male) 

mussels, clams, snails, barnacles 
Chinook salmon 

Oncorhynchus tshawytscha

Migrating/rearing juvenile 

23.3 0.5-18 insects, crustacea, 

juvenile fish 

steelhead Oncorhynchus 

mykiss

Migrating/rearing juvenile 

19.9 31-105 insects, annelids, 

Daphnia

green sturgeon 

Acipenser medirostris 

Juvenile or adult female 

20 1300 

(average caught) 

benthic crustacea, mollusks and fish 

white sturgeon 

Acipenser transmontanus 

Juvenile or adult female 

15-20 6280 

(mode) 

benthic mollusks and crustacea 

delta smelt Hypomesus 

transpacificus

Juvenile or adult female 

114 0.32 

(average JunAug) 

copepods, cladocerans, amphipods, insect larvae 

Sacramento splittail 

Pogonichthys macrolepidotus

Juvenile or adult female 

33.7 121 

(mode) 

benthic detritus, clams, other mollusks, mysids 

1 For most species it is premature and speculative to designate a critical life stage at this time. Such designation prejudges the outcome of a thorough search of the toxic2 Food ingestion rates based on wet weight can be calculated from available parameters (Nagy 2001) for birds, mammals, reptiles and amphibians, but not, in general fo3 For birds, the food ingestion rate as dry weight is calculated from the regression parameters for dry matter intake per day from Table 3 in Nagy (2001), using categorie

ingestion rate in terms of wet weight as described in the text below. 

4 See note 1 above. For anadromous species, a range of body weights is given corresponding to the period spent rearing in the estuary. 5 We interpret “clam-based” broadly to mean filter-feeding benthic mollusk-based. 6 For the worst case, we assume that all birds consumed are those waterfowl (scaups and scoters) that primarily feed on benthic mollusks (clams, etc.). 7 Percent of mollusks in gizzards of 819 adults and 4 juveniles collected in coastal Maine and Washington (Cottam C. U.S. Dep. Agric. Tech. Bull. 643) . 8 Wet weight percents of summer and winter gizzard contents, British Columbia salt water (Vermeer K. 1981 Wildfowl 32:107-116; Vermeer and Bourne 1984 as summ

et al. 1998). 

9 Percent mussels, winter, coastal New England (reviewed in Bordage and Savard 1995). 10 Although the diets of salmon, steelhead and delta smelt are not known to be clam-based, these species may still be at risk from selenium because of greater sensitivity 

salmon and steelhead is documented below. The sensitivity of delta smelt to selenium is unknown; population numbers are alarmingly low, so this species is particula

effect. 

11 Percentage clams by volume, fall, Suisun Bay and Carquinez Strait (Table 10 below). 
SPECIES MOST AT RISK 

Species were selected from among the species considered (Table 1) representing those species 

that are both (1) generally endangered, threatened or of concern, and (2) most at risk specifically 

for selenium toxic effects in the San Francisco Bay/Delta estuary. Information on the diet, body 

weight, and ingestion rate of each of the species most at risk is summarized in Table 2 and 

outlined in greater detail below. 

Bald Eagle (Haliaeetus leucocephalus) 

Status: The bald eagle was federally listed as endangered on February 14, 1978 (43 FR 6233) in 

all of the coterminous United States except Minnesota, Wisconsin, Michigan, Oregon, and 

Washington, where it was classified as threatened. On August 15, 1995 (60 FR 36010), the bald 

eagle was down-listed to threatened throughout its range. On July 6, 1999, the USFWS 

published a proposed rule to remove the bald eagle from the federal list of threatened and 

endangered species (64 FR 36454). On July 9, 2007 the species was removed (delisting effective 

August 8, 2007) from the Federal List of Endangered and Threatened Wildlife (72 FR 37346). 

The protections provided to the bald eagle under the Bald and Golden Eagle Protection Act 

(BGEPA) and the Migratory Bird Treaty Act (MBTA) will continue to remain in place after the 

species is delisted. To help provide more clarity on the management of bald eagles after delisting 

the USFWS published a regulatory definition of ‘‘disturb’’, the final National Bald Eagle 

Management Guidelines and a proposed rule for a new permit that would authorize limited take 

under the BGEPA. 

Size: The bald eagle was a representative species used for the derivation of wildlife criteria in 

the Great Lakes Initiative (GLI) (USEPA 1995). For that effort, the bald eagle body weight used 

in criteria calculations (4.6 kg) was based on the mean of average male and female eagle body 

weights; although it was noted that female eagles are approximately 20 percent heavier than 

males. Because a bald eagle reference dose for selenium should be based on the most sensitive 

endpoint, which most likely is adverse reproductive effects manifested by laying females, it is 

more appropriate to use average female body weights in the calculation of wildlife values. 

In the GLI, the USEPA presented an average body weight of 5.2 kg for female bald eagles. This 

value was based on the weights of 37 birds, taken from Snyder and Wiley (1976). Dunning 

(1993) presented an average female body weight of 5.35 kg, also based on the weights of 37 

birds, taken from Palmer (1988). The average of these two (equally weighted) averages is 5.275 

kg. 

Diet: The bald eagle diet has been extensively studied throughout North America. Although 

generally known as a piscivorous species, bald eagles are opportunistic predators and carrion 

scavengers (Buehler 2000). Various birds, mammals, reptiles, amphibians, and crustaceans may 

serve as additional bald eagle prey (Buehler 2000). In Northern California bald eagle diets 

commonly consist of (but are not limited to) Sacramento sucker (Catostomus occidentalis), 

hardhead (Mylopharodon conocephalus), Sacramento pikeminnow (Ptychocheilus grandis), 

brown bullhead (Ameiurus nebulosus), common carp (Cyprinus carpio), tui chub (Gila bicolor), 

8
rainbow trout (Onchorhyncus mykiss), largemouth bass (Micropterus salmoides), Sacramento 

perch (Archoplites interruptus), American coot (Fulica americana), mallard (Anas 

platyrhynchos), western grebe (Aechmophorus occidentalis), gulls (Larus spp.), pied-billed grebe 

(Podilymbus podiceps), common merganser (Mergus merganser), and other diving ducks (Hunt 

et al. 1992; Jackman et al. 1999). 

Food ingestion rate: California supports both wintering and resident bald eagles, with a broad 

array of suitable foraging habitats. Because of this variety, eagle diets in California span a wide 

range of possible food types and trophic level combinations. Attempting to quantify a specific 

dietary composition for bald eagles is more difficult than for other species with a narrower range 

of prey types, and is further confounded by the fact that food preferences may vary both 

geographically and temporally. It is not possible in the scope of this analysis to determine all the 

potential bald eagle diets in California and evaluate them with regard to the selenium criterion, 

however, a review of several approaches is provided and an average FIR for bald eagles in 

northern California is considered. 

Since bald eagles are well described as “carnivorous birds”, it is possible to calculate the bald 

eagle food ingestion rate (FIR) using the generic allometric equation for carnivorous birds from 

Nagy (2001). This equation is based on body mass and for the reasons stated above we use the 

average body mass of females: 5275 g. 

FIR (wet weight) = 3.048 × (body weight in g)0.665

FIR = 3.048 × 52750.665

FIR = 911 g/day wet weight 

Alternatively, when information is available on the dietary composition and free-living metabolic 

rate (FMR) of a species, USEPA (1993) recommends that this information be used to calculate 

an estimate of the food ingestion rate. Several alternative bald eagle diets are considered below 

using this method. 

The dietary composition of bald eagles was investigated as part of the GLI (USEPA 1995). 

Using information on bald eagles nesting on islands and along the shore of Lake Superior in 

Wisconsin (from Kozie and Anderson 1991), and adjustment factors to estimate the relative 

number of birds and fish delivered to a nest based on the prey remains found under the nest, the 

USEPA determined that 92 percent of the dietary biomass comprised fish and 8 percent 

comprised birds or mammals. The adjustment factor was developed to account for the inherent 

error in estimating a dietary composition based solely on the analysis of prey remains. Using 

this dietary composition of 92 percent fish and 8 percent birds and mammals, along with 

information about the energetic needs of adult eagles and their ability to assimilate the caloric 

content of these food types, the GLI presented estimates of the amount of each food type 

ingested daily: 464 g fish and 40 g birds/mammals for a total of 504 g/day (USEPA 1995). This 

analysis depends upon diets of bald eagles in the Great Lakes area; however, there is sufficient 

dietary data available on bald eagles in California to calculate a FIR representative of local diets. 

The Service’s evaluation of the threatened and endangered wildlife protectiveness of USEPA’s 

human health criterion for methylmercury in California (USFWS 2003) includes a detailed 

9
discussion of the trophic composition of the diet of Northern California bald eagles. This 

assessment utilized detailed bald eagle dietary data from Jackman et al. (1999) who studied 56 

nests across Northern California. Although the FIR calculated in the Service document (600 

g/day) was based upon a diet representative of Northern California bald eagles (83 % fish, 17% 

birds), the assessment was based upon risks and assumptions associated with various trophic 

level diets relevant to mercury biomagnification. This diet represented the highest combined 

percentage of trophic level 4 fish and aquatic-dependent birds from within the Jackman et al. 

(1999) dataset and may not be appropriate for assessing selenium exposure in the Bay area. 

Based on the dietary analysis presented by Jackman et al. (1999) a generic composition for 

Northern California bald eagle diet can be estimated as 71.2 percent fish, 22.8 percent birds, and 

6 percent mammals. These figures represent an average dietary composition for all bald eagles 

in the study area and may be the most appropriate estimate to use for this analysis in lieu of Bay 

area specific bald eagle dietary information. 

When information is available on the dietary composition and free-living metabolic rate 

(FMR) of a species, USEPA (1993) recommends that this information be used to calculate 

an estimate of the food ingestion rate (FIR) of the species using the equation: 

FIR = FMR/ ME avg 

Where ME avg is the weighted average metabolizable energy of the items in the diet. 

FMR can be calculated using the allometric relationship between weight and FMR 

developed by Nagy (1987) for non-passerine birds: 

FMR (kcal/day) = 1.146 Wt 0.749 (g) 

 = 1.146 x 52750.749 

= 703.3 kcal/day 

The generic bald eagle diet proportions (71.2 % fish, 22.8 % birds, and 6 % mammals) 

from Jackman et al. (1999) are then used to calculate average metabolizable energy 

following the method outlined in USEPA (1993): 

Dietary 

item 

Proportion 

of diet 

P 

Gross Energy 

(kcal/g wet wt) 

GE* 

Assimilation 

efficiency 

AE† 

Metabolizable energy 

(kcal/g wet wt) 

ME=GE x AE 

P x ME 

(kcal/g 

wet wt) 

Fish 0.712 1.2 0.79 0.948 0.675

Birds 0.228 1.9 0.78 1.482 0.338

Mammals 0.06 1.7 0.78 1.326 0.080

* from Table 4-1 in USEPA (1993) 

† from Table 4-3 in USEPA (1993) 

The sum of the right-most column in the table above provides the weighted average 

metabolizable energy: 

10
ME avg = Σ (P x ME) 

 = 0.675 + 0.338 + 0.080 

 = 1.09 kcal/g wet weight (following procedure on p. 4-17 EPA 1993) 

The food ingestion rate is then calculated from the above estimates of free-living metabolic rate 

and average metabolizable energy in the diet: 

FIR = FMR/ ME avg

= 703.3/1.09 

= 644 g/day wet weight 

General life history: Breeds in coastal and aquatic habitat with forested shorelines or cliffs in 

North America, including the Pacific Northwest and the northern Sierra Nevada Mountains in 

California (Buehler 2000). More recently breeding pairs occur along reservoirs in the Coast 

Ranges of central and southern California including the Channel Islands (CDFG 2005). 

Wintering areas include coastal estuaries and river systems of northern California (Buehler 

2000). 

Risk of selenium exposure: Lillebo et al. (1988) derived levels of selenium to protect various 

species of waterbirds. Based on an analysis of bioaccumulation dynamics and an estimated 

critical dietary threshold for toxicity of 3 μg/g, they concluded that piscivorous birds would be at 

substantially greater risk of toxic exposure than mallards (Anas platyrhynchos). The calculated 

water criterion to protect piscivorous birds was 1.4 μg/L as opposed to 6.5 μg/L for mallards. It 

should also be noted that the 6.5 μg/L calculated criterion for mallards exceeds the actual 

threshold point for ducks in the wild which is somewhere below 4 μg/L (Skorupa 1998). Thus, 

the 1.4 μg/L calculated criterion for piscivorous birds may be biased high compared to the wild 

as well. 

Applying an energetics modeling approach, modified from the Wisconsin Department of Natural 

Resources, Peterson and Nebeker (1992) calculated a chronic criterion specifically for bald 

eagles. Peterson and Nebeker’s estimate of a protective criterion is 1.9 μg/L. Peterson and 

Nebeker calculated a mallard criterion (2.1 μg/L) that was much closer to their bald eagle 

criterion than Lillebo et al.’s (1988) results would suggest. Peterson and Nebeker’s mallard 

criterion is consistent with real-world data (cf. Skorupa 1998) and therefore their bald eagle 

criterion may also be reliable. 

As potential prey for the bald eagles wintering or breeding in the Bay area, diving ducks such as 

surf scoter and scaup would provide a significant source of selenium (see discussion on these 

species in this document). Surf scoter and scaup are abundant in San Pablo and Suisun Bays in 

the winter (Goals Project 2000). A pair of bald eagles has begun nesting at San Pablo Reservoir 

(ESA 2006, The Quail 2006) about 5-6 miles from North and Central San Francisco Bay. 

11
California Clapper Rail (Rallus longirostris obsoletus)

Status: The California clapper rail was federally listed as endangered on October 13, 1970 (35 

FR 16047-16048). 

Size: In the only literature found for this particular subspecies that provided body weights, 

nineteen female California clapper rails from South San Francisco Bay were examined as part of 

a Master’s Degree thesis (Albertson 1995). Weights ranged from 300 to 400 g, with a mean 

weight of 346 g. 

Diet: The most comprehensive assessment of the California clapper rail diet is presented by 

Moffitt (1941). Stomach contents from 18 birds were examined and the food items identified 

and measured as a volumetric percentage. On average, animal matter accounted for 

approximately 85 percent of the diet, with the remainder composed of seed and hull fragments of 

marsh cordgrass. Over half (56.5%) of the overall diet comprised plaited horse mussels 

(Modiolus demissus). Spiders of the family Lycosidae (wolf spiders) accounted for 15 percent of 

the diet, while the remaining important dietary items were little macoma clams (Macoma 

balthica) (7.6%), yellow shore crabs (Hemigrapsis oregonensis) (3.2%), and worn-out nassa 

snails (Ilyanassa obsoletus) (2.0%). Worms, insects, and carrion combined accounted for a total 

of 1.1 percent of the remaining diet found by Moffitt (1941) in the 18 clapper rail stomachs. The 

importance of crabs in the clapper rail diet was confirmed by Varoujean (1972), who observed 

rails eating striped shore crabs (Pachygrapsus crassipes). 

Although Moffitt (1941) reported that plant matter accounted for approximately 15 percent on 

average of the clapper rail diets, the author stated that this percentage probably represented the 

maximum of a vegetable diet. This conclusion was based on the fact that the birds were 

collected in early February, a time when animal food items would typically be at lowest 

abundance. However, it is important to note that this reported average for plant food (~15%) 

was calculated from a wide range of percentages in the 18 birds examined (0% - 58% plant 

food). As with other omnivorous species, the amount of any particular food item consumed at 

any given time may vary substantially depending on a number of factors. While clapper rails 

most likely do not eat a set amount of plant matter daily, it is clear from Moffitt (1941) that 

vegetation generally constitutes a substantial dietary item over time. 

Based on Moffitt’s (1941) assumption that his mid-winter gut analyses represented a maximum 

for vegetation in the clapper rail diet, and the knowledge that clapper rails nest during a time 

when animal foods would be in greater abundance (mid-March - July) (USFWS 1984), the 

overall rail diet for is assumed to be 10 percent vegetation and 90 percent animal matter. 

Food ingestion rate (FIR): Clapper rails may consume a wide variety of foods. Values for the 

gross energy content for some of these foods (e.g., shell-less bivalves, shelled crabs) and the 

efficiency at which rails assimilate them can be found in the Wildlife Exposure Factors 

Handbook (USEPA 1993). However, because rails do not consume set amounts of these food 

types, FIR must be estimated using one of the generic allometric equations from Nagy (2001). 

Out of the 17 avian categories for predicting FIRs presented by Nagy (2001), Charadriiformes is 

the taxonomic order most closely related to rails (Gill 1995). In addition, the rail’s feeding 

12
ecology most closely resembles that of birds in the Charadriiformes category (i.e., shore birds, 

gulls, auks). Therefore, the FIR for California clapper rails was calculated using the following 

equation: 

FIR (wet weight) = 1.914 × (body weight in g)0.769

FIR = 1.914 × 3460.769

FIR = 172 g/day wet weight

General life history: The California clapper rail inhabits salt marshes surrounding the San 

Francisco Bay, California. Principal habitats are low portions of coastal wetlands dominated by 

cordgrass and pickleweed. Nesting habitat in San Francisco Bay is characterized by tidal 

sloughs, abundant invertebrate populations, pickleweed, gum plant, and wrack in upper zone. 

Individuals do not migrate far from the breeding grounds (Eddleman and Conway 1998). 

Risk of selenium exposure: California clapper rails feed largely on benthic invertebrates, 

including filter-feeding mussels and clams, a well-documented pathway for bioaccumulation of 

selenium (Pease et al. 1992, Stewart et al. 2004). Lonzarich et al. (1992) reported that eggs of 

California clapper rails collected from the north bay in 1987 contained up to 7.4 μg/g selenium. 

Water data from this time and location are not available. The in ovo threshold for selenium 

exposure that causes toxic effects on embryos of California clapper rails is unknown. For 

another benthic-foraging marsh bird, the black-necked stilt, the in ovo threshold for 

embryotoxicity is 6 μg/g selenium (Skorupa 1998). The most widely-used hormetic model 

(Brain and Cousens 1989) applied to Heinz et al. (1989) data from laboratory experiments with 

mallard reproduction indicates that in mallards, a selenium concentration of 7.4 μg/g (dry 

weight) in the eggs would be associated with a 32 percent reduction in hatchability of the eggs 

(Figure 1). 

13
1 10

Selenium concentration in eggs (μg/g dry weight)

0

0.2

0.4

0.6

0.8

1

Egg hatchability

 SlopeLin=1.42 

 ED=1.03

 SlopeHi=-1.49

Residual sum of squares: 0.054

Residual standard error: 0.134264 on 3 degrees of freedom

y=SlopeLin*x/(1+(ED/x)^SlopeHi)

Heinz et al. 1989

Figure 1. The percent hatching success of mallard eggs as a function of selenium 

concentration in the eggs, with the Brain-Cousens (1989) hormetic model fitted by least 

squares regression. Confidence intervals of 95% and 99% are shown. 

In mallard ducks, interactive effects of selenium and mercury can be super-toxic with regard to 

embryotoxic effects (Heinz and Hoffman 1998). Lonzarich et al. (1992) also reported 

potentially embryotoxic concentrations of mercury in eggs of California clapper rails. 

Abnormally high numbers of nonviable eggs, 13.7-22.9 percent, potentially a result of mercury 

contamination, have also been reported for the California clapper rail (Schwarzbach 1994, 

Schwarzbach et al. 2006). Based, in part, on the data for California clapper rails, staff technical 

reports prepared for the San Francisco Bay Regional Water Quality Control Board recommend 

decreasing selenium loading to the estuary by 50 percent or more (Taylor et al. 1992; 1993). 

The California clapper rail is particularly vulnerable to any locally elevated effluent 

concentrations of selenium as the rail generally occupies small home ranges of only a few acres. 

Greater Scaup (Aythya marila) 

Status: The greater scaup is a relatively little-known duck with a circumpolar distribution 

(Kessel et al. 2002). The San Francisco Bay is one of the two main wintering grounds of this 

14
species along the west coast of North America. Regulated hunting of these birds is permitted 

under provisions of the Migratory Bird Treaty Act. 

Size: The mean body mass of 345 adult male greater scaup on Long Island Sound, Connecticut, 

measured between October 1991 and January 1994, was 1,054 g (range: 850-1,350; standard 

deviation: 105); the mean body mass of 104 adult females at the same location was 959 g (range: 

688-1,210; standard deviation: 108) (Kessel et al. 2002). 

Diet: Greater scaup dive in waters from one to ten meters deep to feed mainly on benthic 

invertebrates, especially bivalves in winter (Bellrose 1980). The stomach contents of 119 greater 

scaup in Long Island Sound in the winter of 1952-1953 consisted of 93.5% (by volume) animal 

material, including 56.4% bivalves, 6.1% snails, 24.3% unidentified mollusks, 4.4% crustaceans 

(Cronan 1957). The remaining diet was plant material (6.6%) consisting mainly of algae (3.6%). 

More recent studies suggest that diets vary substantially among different locations, and the 

dietary proportion of animal material has declined in Long Island Sound (review in Kessel et al. 

2002). During the winters of 1998-1999 and 1999-2000, the introduced Asian clam, 

Potamocorbula amurensis, was the most important food of greater scaup in San Pablo Bay 

(Poulton et al. 2002). The Asian clam is an extraordinarily efficient bioaccumulator of selenium 

(Stewart et al. 2004). 

Food ingestion rate: The most likely limiting effect of selenium on wintering greater scaup in 

the San Francisco Bay area is reduction in body mass, or reduction of the rate of increase in body 

mass, as the birds build up reserves in preparation for their migration to breeding grounds in 

Alaska and northern Canada. Because wintering males bioaccumulate selenium to higher 

concentrations than females (see below), their migration is more likely to be adversely affected. 

Therefore, for this study, we use the body mass and estimate the food ingestion rate (FIR) of 

males. Due to the variability of the diets of wintering greater scaup, we use a generic equation to 

estimate FIR based on body mass (Nagy 2001). No such equation is available specifically for 

clam-eating birds, but because greater scaup are largely carnivorous and mainly marine or 

estuarine, we use equations for carnivorous and marine birds (Nagy 2001): 

For carnivorous birds: 

FIR (wet weight) = 3.048 × (body weight in g)0.665 

FIR = 3.048 × 10540.665

FIR = 312 g/day wet weight 

For marine birds: 

FIR (wet weight) = 3.221 × (body weight in g)0.658

FIR = 3.221 × 10540.658

FIR = 314 g/day wet weight 

These estimates are in close agreement; we average them to yield an estimated food ingestion 

rate of 313 g/day wet weight 

General life history: Greater scaup breed mainly on the tundra of Alaska and northern Quebec, 

with some breeding sites scattered across Canada. They winter mainly along the northeast coast 

15
of North America. Along the west coast of North America they winter as far south as northern 

Baja California, but mainly around Vancouver Island and in the San Francisco Bay (Kessel et al. 

2002). 

Risk of selenium exposure: In San Pablo Bay, greater scaup feed primarily on bivalves, which 

are efficient selenium bioaccumulators (Stewart et al. 2004). Consequently, greater scaup can 

bioaccumulate selenium to high concentrations. Bioaccumulation evidently increases through 

the winter, and is greater in males than in females. Two adult males collected along the coast of 

California in early winter had liver selenium concentrations of 7.6 and 23.7 μg/g dry weight 

(geometric mean: 13.4 μg/g). In late winter five males had a geometric mean liver concentration 

of 47.9 μg/g and two females had liver concentrations of 8.9 and 31 μg/g (geometric mean: 16.61 

μg/g) (Takekawa et al. 2002). Eighteen greater scaup collected from San Francisco Bay in 

March and April 1982 had liver selenium concentrations ranging from 6.7 to 31 μg/g dry weight 

(mean: 19.3 μg/g) (Ohlendorf et al. 1986). Males collected in San Francisco Bay in early winter 

of 1986-87 had a geometric mean liver selenium concentration of 20.7 μg/g; in late winter 

geometric means at two sites in San Francisco Bay were 32.7 and 27.4 μg/g (Hothem et al. 

1998). Adult males collected from a reference site and a polluted site in San Francisco Bay in 

March, 1989 had liver selenium concentrations ranging from 7 to 23 μg/g (geometric mean: 13 

μg/g) at the reference site, and ranging from 21 to 140 μg/g (geometric mean: 67 μg/g) at the 

polluted site (Hoffman et al. 1998). Reproductive impairment is associated with a liver 

concentration of 10 μg/g (dry weight), and concentrations above 33 μg/g (dry weight) are 

considered harmful to the health of mallards, Anas platyrhynchos (Heinz et al. 1989). 

Lesser Scaup (Aythya affinis) 

Status: The lesser scaup is the most abundant North American diving duck, but declining 

populations in recent decades (Austin et al. 1998) have raised concerns. Regulated hunting of 

these birds is permitted under provisions of the Migratory Bird Treaty Act. 

Size: On average, male lesser scaup are heavier than females. The mean mass of six adult and 

hatch-year males migrating through the Klamath Basin in northern California in spring was 734 

g (standard deviation: 24); the mean mass of five females was 663 g (standard deviation: 109) 

(Gammonley and Heitmeyer 1990). 

Diet: Wintering lesser scaup feed primarily by diving for clams, other mollusks, aquatic insects 

and crustaceans, but in some places, up to 99 percent of the diet consists of plant material 

(review in Austin et al. 1998). During the winters of 1998-1999 and 1999-2000, 96 percent of 

the dry mass of the esophagus contents of 13 lesser scaup in San Pablo Bay consisted of the 

introduced Asian clam, Potamocorbula amurensis, (Richman and Lovvorn 2004) which is an 

extraordinarily efficient bioaccumulator of selenium (Stewart et al. 2004). 

Food ingestion rate: The most likely limiting effect of selenium on wintering lesser scaup in 

the San Francisco Bay area is reduction in body mass, or reduction of the rate of increase in body 

mass, as the birds build up reserves in preparation for their migration to breeding grounds in 

Alaska and northern Canada. It is likely that wintering males bioaccumulate selenium to higher 

16
concentrations than females because this been clearly shown for the closely related Greater 

Scaup (see above) and the more meager data for lesser scaup are in agreement (Takekawa et al. 

2002). Therefore, the migration of males is more likely to be adversely affected by selenium. 

So, for this study, we use the body mass and estimate the food ingestion rate (FIR) of males. 

Due to the variability of the diets of wintering lesser scaup, we use a generic equation to estimate 

FIR based on body mass (Nagy 2001). No such equation is available specifically for clam-eating 

birds, but because wintering lesser scaup are largely carnivorous and mainly marine or estuarine, 

we use equations for carnivorous and marine birds (Nagy 2001): 

For carnivorous birds: 

FIR (wet weight) = 3.048 × (body weight in g)0.665

FIR = 3.048 × 7340.665

FIR = 245.3 g/day wet weight 

For marine birds: 

FIR (wet weight) = 3.221 × (body weight in g)0.658

FIR = 3.221 × 7340.658

FIR = 247.5 g/day wet weight 

These estimates are in close agreement; we average them to yield an estimated food ingestion 

rate of 246 g/day wet weight. 

General life history: Lesser scaup breed mainly in Alaska and Canada. In the U.S. Pacific 

Northwest they breed as far south as the Klamath basin in northern California. They winter 

mainly along the Gulf coast and the Pacific coast of North and Central America on freshwater 

bays and wetlands as well as estuarine and marine habitats (Austin et al. 1998). 

Risk of selenium exposure: In San Francisco Bay ducks, contaminants, including selenium, are 

associated with reduced body size. This suggests that ducks wintering in the more contaminated 

areas in the bay might be in poor condition when they reach their breeding grounds in the boreal 

forest, which may reduce nesting success (John Takekawa, USGS, quoted in Martin 2002). In 

addition, migration success may be reduced by lowered body condition associated with high 

body burdens of selenium. 

In December 1986 one adult male Lesser Scaup in Lake Earl, northern California, had a 

selenium liver concentration of 11 μg/g dry weight; four juvenile males had a liver 

concentrations ranging from 2.8 to 12.2 μg/g (geometric mean: 6.3 μg/g); the liver concentration 

of one juvenile female was 3.5 μg/g (Takekawa et al. 2002). In March 1987 six adult males in 

Morro Bay, central California, had liver selenium concentrations ranging from 7.1 to 19 μg/g 

(geometric mean: 11.13 μg/g); two juvenile males had liver concentration ranging from 8.9 to 16 

μg/g (geometric mean: 11.92 μg/g) (Takekawa et al. 2002). In these relatively uncontaminated 

sites, Takekawa et al. (2002) found a positive correlation between selenium and carcass mass, as 

would be expected for a biphasic (beneficial at low concentrations; toxic at high concentrations) 

contaminant such as selenium at the lower range of selenium concentrations. 

17
White-winged Scoter (Melanitta fusca) 

Status: The white-winged scoter is the best known of the world’s three species of scoter. It is 

the sea duck most commonly taken by hunters, constituting 30 percent of all sea ducks hunted 

from 1961 to 1986 (USFWS 1988). Despite increasing hunting pressure (Brown and 

Fredrickson 1997), success in hunting white-winged scoters has declined since 1976 (USFWS 

1988), an indication of declining populations. 

Size: Twenty-one male white-winged scoters along the coast of British Columbia throughout the 

year had a mean mass of 1,722 g (standard deviation: 51); nineteen females had a mean mass of 

1,437 g (standard deviation: 46) (Vermeer and Bourne 1984). White-winged scoters exhibit 

seasonal variation in weight, reaching maximum weights before breeding (Brown and 

Fredrickson 1997). Therefore, weight measurements taken in the non-breeding period are most 

relevant to white-winged scoters wintering in the San Francisco Bay area. The averages of 

weights of non-breeding white-winged scoters collected from November to April in Kachemak 

Bay, Alaska, were 1,917 g (28 males) and 1,732 g (10 females). 

Diet: In wintering areas, white-winged scoters usually dive in water depths of less than five 

meters to feed on benthic mollusks (especially clams), crustaceans, and insects (review in Brown 

and Fredrickson 1997). 

Food ingestion rate: The most likely limiting effect of selenium on wintering white-winged 

scoter in the San Francisco Bay area is reduction in body mass, or reduction of the rate of 

increase in body mass, as the birds build up reserves in preparation for their migration to 

breeding grounds in Alaska and northern Canada. It is likely that wintering males bioaccumulate 

selenium to higher concentrations that females, as this has been documented in related and 

ecologically similar diving ducks (see above). Therefore, the migration of males is more likely 

to be adversely affected by selenium, so, for this study, we use the body mass and estimate the 

food ingestion rate (FIR) of males. Due to the variability of the diets of wintering white-winged 

scoter, we use a generic equation to estimate FIR based on body mass (Nagy 2001). No such 

equation is available specifically for clam-eating birds, but because wintering white-winged 

scoters are largely carnivorous and mainly marine or estuarine, we use equations for carnivorous 

and marine birds (Nagy 2001): 

For carnivorous birds: 

FIR (wet weight) = 3.048 × (body weight in g)0.665

FIR = 3.048 × 19170.665

FIR = 464.5 g/day wet weight 

For marine birds: 

FIR (wet weight) = 3.221 × (body weight in g)0.658

FIR = 3.221 × 19170.658

FIR = 465.5 g/day wet weight 

18
These estimates are in close agreement; we average them to yield an estimated food ingestion 

rate of 465 g/day wet weight. 

General life history: North American white-winged scoters breed in Alaska and western 

Canada and winter along the east, west, and gulf coasts of the United States (Brown and 

Fredrickson 1997). 

Risk of selenium exposure: The risk to the migration of white-winged scoters due to selenium 

exposure in their wintering areas is similar to the risks for scaups (see above). In addition, some 

white-winged scoter females arrive in their northern breeding areas with sufficiently high body 

burdens of selenium to be a concern for survival and reproductive success. Reproductive 

impairment is associated with a liver concentration of 10 μg/g (dry weight), and concentrations 

above 33 μg/g (dry weight) are considered harmful to the health of mallards, Anas platyrhynchos 

(Heinz et al. 1989). The liver of a female white-winged scoter found dead at Cape Yakataga, 

Alaska, in August 1992, had a selenium concentration of 53 μg/g dry weight (Henny et al. 1995). 

A pooled sample of livers of 7 female white-winged scoters collected in the Old Crow/Porcupine 

River area in the northern Yukon Territory 1988-1994 had a selenium concentration of 20 μg/g 

wet weight. This is equivalent to 66.7 μg/g dry weight (average 70% moisture in the livers 

analyzed in this study) (Braune and Malone 2006). 

Surf Scoter (Melanitta perspicillata) 

Status: Until recently, the surf scoter has been the least known of North American ducks 

(Belrose 1980), although it is common in winter along the coast of California (Johnsgard 1975; 

Cogswell 1977). 

Size: As with other scoters and scaup (see above) males are heavier than females. In May 1996, 

21 males collected in the St. Lawrence estuary had a mean mass of 1059.3 g (standard deviation: 

133.7); 16 females had a mean mass of 985.3 g (standard deviation: 118.6) (Savard et al. 1998). 

Diet: Surf scoters feed primarily on mussels and other mollusks during all seasons of the year; 

plants and crustaceans are additional minor components of their diets (review in Savard et al. 

1998). 

Food ingestion rate: The most likely limiting effect of selenium on wintering surf scoter in the 

San Francisco Bay area is reduction in body mass, or reduction of the rate of increase in body 

mass, as the birds build up reserves in preparation for their migration to breeding grounds in 

Alaska and northern Canada. It is likely that wintering males bioaccumulate selenium to higher 

concentrations that females, as this has been documented in related and ecologically similar 

diving ducks (see above). Therefore, the migration of males is more likely to be adversely 

affected by selenium. So, for this study, we use the body mass and estimate the food ingestion 

rate (FIR) of males. Due to the variability of the diets of wintering surf scoter, we use a generic 

equation to estimate FIR based on body mass (Nagy 2001). No such equation is available 

19
specifically for clam-eating birds, but because wintering surf scoters are largely carnivorous and 

mainly marine or estuarine, we use equations for carnivorous and marine birds (Nagy 2001): 

For carnivorous birds: 

FIR (wet weight) = 3.048 × (body weight in g) 0.665

FIR = 3.048 × 10590.665

FIR = 313.0 g/day wet weight 

For marine birds: 

FIR (wet weight) = 3.221 × (body weight in g)0.658

FIR = 3.221 × 10590.658

FIR = 315.0 g/day wet weight 

These estimates are in close agreement; we average them to yield an estimated food ingestion 

rate of 314 g/day wet weight. 

General life history: North American surf scoters breed in northern Canada and Alaska and 

winter along the east, west, and gulf coasts of North America (Savard et al. 1998)(Figure 2). 

The San Francisco Bay estuary supports the southernmost large population of wintering surf 

scoters; this species constitutes more than 99 percent of the scoters in the estuary (Takekawa et 

al. 2002). 

Risk of selenium exposure: The risk to the migration of surf scoters due to selenium exposure 

in their wintering areas is similar to the risks for scaups (see above). Livers from 22 surf scoters 

collected in March and April 1982 in south San Francisco Bay had a mean selenium 

concentration of 34.4 μg/g dry weight (Ohlendorf et al. 1986). The average selenium 

concentration in the livers of 79 adult male surf scoters collected in north and south San 

Francisco Bay in January and March 1985 was about 60 μg/g dry weight (Ohlendorf et al. 1991). 

Livers from ten adult male surf scoter collected in Suisun Bay in March 1989 had a mean 

concentration of 119 μg/g dry weight (Hoffman et al. 1998). 

Selenium is depurated fairly rapidly, with a half life of about 19 days in mallards (Heinz et al. 

1990). Therefore, depuration during migration would be expected to mitigate the risk to 

reproduction caused by elevated loads of selenium carried from wintering areas to nesting areas. 

However, surf scoters bioaccumulate selenium to such high levels in the San Francisco Bay area, 

and their migration is so rapid (Savard et al. 1998) that some surf scoter females arrive in their 

northern breeding areas with sufficiently high body burdens of selenium to be a concern for 

hatching success and embryo toxicity. A pooled sample of livers of two female surf scoters 

collected at Old Crow in the northern Yukon Territory 1988-1994 had a selenium concentration 

of 13 μg/g wet weight. This is equivalent to 43.3 μg/g dry weight (average 70% moisture in the 

livers analyzed in this study). A pooled sample of four male surf scoter livers collected at Fort 

Good Hope in northern Northwest Territories, Canada, had a selenium concentration of 17 μg/g 

wet weight, equivalent to 56.7 μg/g dry weight (Braune and Malone 2006). Reproductive 

impairment is associated with a liver concentration of 10 μg/g (dry weight), and concentrations 

above 33 μg/g (dry weight) are considered harmful to the health of mallards, Anas platyrhynchos 

(Heinz et al. 1989). 

20
Figure 2. Tracking of individual surf scoters from their wintering grounds in the San 

Francisco Bay area and coastal North America to their breeding grounds in the north, by 

the US Geological Survey (http://www.werc.usgs.gov/scoter/2005/maps.html) 

Black Scoter (Melanitta nigra) 

Status: The Black Scoter is one of the least-known North American ducks (Bordage and Savard 

1995). Declining populations of sea-ducks (USFWS 1993; Goudie et al. 1994) and of scoters in 

particular (Kehoe et al. 1994) have been a matter of concern. A lower ratio of immature to adult 

birds has been observed in black scoters relative to other scoters (Padding et al. 1992; 1993), 

suggesting that black scoters have been experiencing lower reproductive success. 

Size: As with other scoters and scaup (see above) males are heavier than females. In 1990 in 

Quebec, 34 males had a mean mass of 1117.0 g (standard deviation: 101.6); 21 females had a 

mean mass of 987.4 g (standard deviation: 110.1) (Consortium Gauthier & Guillemette—

GREBE 1993). 

21
Diet: Wintering and migrant black scoters feed primarily on mussels and clams; snails and 

barnacles are additional minor components of their diets (review in Bordage and Savard 1995). 

Food ingestion rate: The most likely limiting effect of selenium on wintering black scoter in 

the San Francisco Bay area is reduction in body mass, or reduction of the rate of increase in body 

mass, as the birds build up reserves in preparation for their migration to breeding grounds in 

Alaska and northern Canada. It is likely that wintering males bioaccumulate selenium to higher 

concentrations that females, as this has been documented in related and ecologically similar 

diving ducks (see above). Therefore, the migration of males is more likely to be adversely 

affected by selenium, so, for this study, we use the body mass and estimate the food ingestion 

rate (FIR) of males. Due to the variability of the diets of wintering black scoter, we use a generic 

equation to estimate FIR based on body mass (Nagy 2001). No such equation is available 

specifically for bivalve-eating birds, but because wintering black scoters are largely carnivorous 

and mainly marine or estuarine, we use equations for carnivorous and marine birds (Nagy 2001): 

For carnivorous birds: 

FIR (wet weight) = 3.048 × (body weight in g)0.665

FIR = 3.048 × 11170.665

FIR = 324.3 g/day wet weight 

For marine birds: 

FIR (wet weight) = 3.221 × (body weight in g)0.658

FIR = 3.221 × 11170.658

FIR = 326.3 g/day wet weight 

These estimates are in close agreement; we average them to yield an estimated food ingestion 

rate of 325 g/day wet weight. 

General life history: North American black scoters breed mainly in northern Quebec and 

Alaska and winter along the east, west, and gulf coasts of North America (Bordage and Savard 

1995). Less than one percent of the scoters wintering in the San Francisco Bay estuary are black 

scoters (Takekawa et al. 2002). 

Risk of selenium exposure: The risk to the migration of black scoters due to selenium exposure 

in their wintering areas is similar to the risks for scaups (see above). In addition, some black 

scoter females may arrive in their northern breeding areas with sufficiently high body burdens of 

selenium to be a concern for hatching success and embryo toxicity. Reproductive impairment is 

associated with a liver concentration of 10 μg/g (dry weight), and concentrations above 33 μg/g 

(dry weight) are considered harmful to the health of mallards, Anas platyrhynchos (Heinz et al. 

1989). The livers of two weakened black scoter live-captured with a net at Cape Yakataga, 

Alaska, in August 1991, had selenium concentrations of 24 and 32 μg/g dry weight (Henny et al. 

1995). An adult black scoter from Quebec had the highest selenium concentration in pectoral 

muscle (10.1 μg/g wet weight) among all 3,957 waterfowl and game birds collected and analyzed 

across Canada between 1987 and 1995 (Braune et al. 1999). 

22
Chinook Salmon (Oncorhynchus tshawytscha ) 

Status: The National Marine Fisheries Service (NMFS) has identified 17 Evolutionarily 

Significant Units (ESUs) of Chinook salmon from Washington, Oregon, Idaho, and California 

(Myers et al. 1998; 63 FR 11482). Three of these use the San Francisco Estuary: the Sacramento 

River winter-run ESU, the Central Valley spring-run ESU, and the Central Valley fall/late fallrun ESU. The Sacramento River winter-run ESU was listed as endangered on January 4, 1994 

(59 FR 440). On September 16, 1999, NMFS listed the Central Valley spring-run ESU as 

threatened (64 FR 50394). In the same rulemaking, NMFS also determined that the Central 

Valley fall/late fall ESU is not warranted for listing at this time. 

Size: Chinook salmon fry remain in the estuarine nursery areas as they grow from about 0.5 g to 

about 18 g (Figure 3). They migrate seaward from the estuary when they reach about 70 mm 

fork length (Healy 1991). 

Diet: Young Chinook salmon in the Sacramento-San Joaquin River delta feed primarily on 

insects (especially chironomid larvae and dipterans) and crustacea (especially Neomysids 

(opossum “shrimp”), amphipods (mud “shrimp”), copepods, and cladocerans (water fleas)) 

(Sasaki 1966, Kjelson et al. 1982). Chinook salmon fry appear to be opportunistic feeders; 

hence their diet varies with locale, season, and available prey (Figure 4, Figure 5, Figure 6, 

Figure 7, and Figure 8). As they grow larger and move to deeper water within the estuary, they 

evidently shift dietary preference to larval and young fishes (Healey 1991). 

Food ingestion rate: The food ingestion rates of wild Chinook salmon are entirely unknown. 

However, ingestion rates in the wild may be estimated from ingestion rates in captivity or from 

growth rates in the wild combined with food conversion efficiency (FCE = wet weight gain of 

fish / dry weight of food) in captivity. Fall-run Chinook salmon from the Cowlitz River had 

conversion rates of 1.32, 1.5, 1.3 and 1.36 in 1991, 1992, 1993 and 1994 respectively (WDFG 

2001). The growth rates of marked fry in the wild (Vancouver Island estuaries) range from 

about 3% to 5% of body weight per day (Healey 1991, Figure 3). Based on the average FCE 

(1.37) from the Cowlitz, a medium growth rate (4% per day), and weights from Vancouver 

Island, Chinook salmon entering the estuary at about 1 g body weight consume about 0.055 g 

(dry weight) of food per day, and when they leave the estuary at about 18 g body weight they 

consume about 1.0 g (dry weight) of food per day. 

MacFarlane and Norton (2002) estimated the growth rate of Chinook salmon in the San 

Francisco estuary to be about 0.02 g per day for young averaging about 7 g in weight (about 

0.3% body weight per day). However, this estimate is not based on recaptures of tagged 

individuals but by comparing averages of all fish captured at different locations along the 

migration route. This method is known to underestimate growth rate because it does not account 

for mortality. However, if the fork length growth rate (0.47 mm/day for fish of about 60 mm 

fork length) of tagged Delta juveniles (Figure 9) is combined with seemingly good data from 

MacFarlane and Norton (2002) relating weight to fork length (best fit equation of Figure 10(A) 

differentiated and evaluated at 60 mm fork length yields 0.10 g/mm growth at 2.74 g), the 

calculated weight growth rate is 0.47 mm/day X 0.10 g/mm = 0.047 g/day. This growth rate 

23
(1.7% of body weight per day for the 60 mm 2.74 g individual) is well below the growth rate of 

tagged individuals in Vancouver Island estuaries, but much higher and probably much more 

realistic than the MacFarlane and Norton (2002) estimate above. This growth rate combined 

with the Cowlitz food conversion efficiency of 1.37 yields a food (dry weight) ingestion rate of 

2.33% of live body weight per day. 

Figure 3. Growth of Chinook salmon fry in the Namaimo and Nitinat River estuaries, 

Vancouver Island, British Columbia. Closed and open circles designate different tagged 

groups of fry (Healey 1991). 

24
Figure 4. Seasonal variation in the diet of juvenile Chinook salmon in Nitinat Lake, 

Vancouver Island, British Columbia. At the top of the figure, O denotes other diet items 

(Healey 1982). 

25
Figure 5. Mean numbers of prey organisms per juvenile Chinook salmon stomach in the 

Mattole River estuary and lagoon, California, 1986 and 1987 (Fig. 6 in Busby and Barnhart 

1995. Salmon fork lengths ranged from 64 to 103 mm. 

Figure 6. Stomach contents of young Chinook salmon (322 stomachs containing food out of 

469 stomachs examined) caught in the Sacramento-San Joaquin Delta from September 

1963 to August 1964 (Table 3 in Sasaki 1966). 

26
Figure 7. Stomach contents of juvenile Chinook salmon in the San Francisco estuary and 

the Gulf of the Farallones (Table 2 in MacFarlane and Norton 2002). %N is the numerical 

percentage; %V is the percent relative volume; %FO is the frequency of occurrence 

percentage; and IRI is the index of relative importance, (%N + %V)%FO. 

27
Figure 8. Stomach contents of juvenile Chinook salmon in the San Francisco estuary and 

the Gulf of the Farallones (Table 2 in MacFarlane and Norton 2002). %N is the numerical 

percentage; %V is the percent relative volume; %FO is the frequency of occurrence 

percentage; and IRI is the index of relative importance, (%N + %V)%FO. 

Figure 9. Growth of tagged Chinook salmon fry from the Coleman Fish Hatchery released 

and recaptured in the Delta (circles) and upper Sacramento River (diamonds) between 

February 7 and April 28, 1982 (Brandes and McLain 2001). 

28
Figure 10. Fork lengths, weights, and ages of all juvenile Chinook salmon collected from 

the San Francisco Estuary and Gulf of the Farallones in 1997 (Figure 2 in MacFarlane and 

Norton 2002). 

29
General Life History 

Summary: Chinook salmon are anadromous and semelparous. That is, as adults they migrate 

from a marine environment into the fresh water streams and rivers of their birth (anadromous) 

where they spawn only once and die (semelparous). Juvenile Chinook may spend from 3 months 

to 2 years in freshwater after emergence before migrating to estuarine areas as smolts, and then 

into the ocean to feed and mature. The timing and duration of the migratory movements of 

Chinook salmon are important in assessing their exposure to selenium and estimating consequent 

risks. Natal streams and estuary rearing habitat vary seasonally in selenium concentration and 

the salmon evidently vary in sensitivity to selenium across stages in their life histories. 

Freshwater migration: Once their downstream migration begins, Chinook salmon fry may stop 

migrating and take up residence in the stream for a period of two weeks to a year or more 

(Healey 1991).

Use of estuarine habitat: On their migration downstream, many Chinook salmon fry take up 

residence in the river estuary where they rear to smolt size (about 70 mm fork length) before 

resuming their migration to the ocean. The proportion of fry that rear in the estuary is not 

known. On Vancouver Island, BC, about 30% of the estimated downstream migrants could be 

accounted for in the estuary; the fate of the remaining 70% is unknown, but they probably 

suffered mortality due to unknown agents (Healey 1991). The maximum residence time of 

Chinook salmon fry in the Sacramento-San Joaquin River delta was estimated to be 64 days in 

1980 and 52 days in 1981 (Kjelson et al. 1981) 

Life history types: Chinook salmon exhibit two generalized freshwater life history types 

(Healey 1991). “Stream-type” Chinook salmon, enter freshwater months before spawning and 

reside in freshwater for a year or more following emergence, whereas “ocean-type” Chinook 

salmon spawn soon after entering freshwater and migrate to the ocean as fry or parr within their 

first year. Spring-run Chinook salmon exhibit a stream-type life history. Adults enter freshwater 

in the spring, hold over summer, spawn in fall, and the juveniles typically spend a year or more 

in freshwater before emigrating. Winter-run Chinook salmon are somewhat anomalous in that 

they have characteristics of both stream- and ocean-type races (Healey 1991). Adults enter 

freshwater in winter or early spring, and delay spawning until spring or early summer (streamtype). However, juvenile winter-run Chinook salmon migrate to sea after only four to seven 

months of river life (ocean-type). Adequate instream flows and cool water temperatures are 

more critical for the survival of Chinook salmon exhibiting a stream-type life history due to over 

summering by adults and/or juveniles. 

Runs: Salmon runs (separate ESUs) are designated on the basis of adult migration timing; 

however, distinct runs also differ in the degree of maturation at the time of river entry, thermal 

regime and flow characteristics of their spawning site, and the actual time of spawning (Myers et 

al. 1998). Both spring-run and winter-run Chinook salmon tend to enter freshwater as immature 

fish, migrate far upriver, and delay spawning for weeks or months. For comparison, fall-run 

Chinook salmon enter freshwater at an advanced stage of maturity, move rapidly to their 

spawning areas on the mainstem or lower tributaries of the rivers, and spawn within a few days 

or weeks of freshwater entry (Healey 1991). 

30
Run-specific downstream migration: Winter-run Chinook salmon fry begin to emerge from 

the gravel in late June to early July and continue through October (Fisher 1994). Spring-run 

Chinook salmon fry emerge from the gravel from November to March and spend about 3 to 15 

months in freshwater habitats prior to emigrating to the ocean (Kjelson et al. 1981). Postemergent fry disperse to the margins of their natal stream, seeking out shallow waters with 

slower currents, finer sediments, and bank cover such as overhanging and submerged vegetation, 

root wads, and fallen woody debris, and begin feeding on small insects and crustaceans. 

When juvenile Chinook salmon reach a length of 50 to 57 mm, they move into deeper water with 

higher current velocities, but still seek shelter and velocity refugia to minimize energy 

expenditures. In the mainstems of larger rivers, juveniles tend to migrate along the margins and 

avoid the elevated water velocities found in the thalweg of the channel. When the channel of the 

river is greater than 9 to 10 feet in depth, juvenile salmon tend to inhabit the surface waters 

(Healey 1982). Emigration of juvenile winter-run Chinook salmon past RBDD may begin as 

early as mid-July, typically peaks in September, and can continue through March in dry years 

(Vogel and Marine 1991; NMFS 1997). From 1995 to 1999, all winter-run Chinook salmon 

outmigrating as fry passed RBDD by October, and all outmigrating pre-smolts and smolts passed 

RBDD by March (Martin et al. 2001). The emigration timing of Central Valley spring-run 

Chinook salmon is highly variable (CDFG 1998). Some fish may begin emigrating soon after 

emergence from the gravel, whereas others over summer and emigrate as yearlings with the 

onset of intense fall storms (CDFG 1998). The emigration period for spring-run Chinook salmon 

extends from November to early May, with up to 69 percent of the young-of-the-year fish 

outmigrating through the lower Sacramento River and Delta during this period (CDFG 1998). 

As Chinook salmon fry and fingerlings mature, they prefer to rear further downstream where 

ambient salinity is up to 1.5 to 2.5 parts per thousand (Healy 1980, 1982; Levings et al. 1986). 

Juvenile winter-run Chinook salmon occur in the Delta from October through early May based 

on data collected from trawls, beach seines, and salvage records at the Central Valley Project 

(CVP) and State Water Project (SWP) pumping facilities (CDFG 1998). The peak of listed 

juvenile salmon arrivals in the Delta generally occurs from January to April, but may extend into 

June. Upon arrival in the Delta, winter-run Chinook salmon spend the first two months rearing 

in the more upstream, freshwater portions of the Delta (Kjelson et al. 1981, 1982). Data from 

the CVP and SWP salvage records indicate that most spring-run Chinook salmon smolts are 

present in the Delta from mid-March through mid-May depending on flow conditions (CDFG 

2000). 

Winter-run Chinook salmon fry remain in the estuary (Delta/Bay) until they reach a fork length 

of about 118 mm (i.e., 5 to 10 months of age) and then begin emigrating to the ocean perhaps as 

early as November and continuing through May (Fisher 1994; Myers et al. 1998). Little is 

known about estuarine residence time of spring-run Chinook salmon. Juvenile Chinook salmon 

were found to spend about 40 days migrating through the Delta to the mouth of San Francisco 

Bay and grew little in length or weight until they reached the Gulf of the Farallones (MacFarlane 

and Norton 2002). Based on the mainly ocean-type life history observed (i.e., fall-run Chinook 

salmon) MacFarlane and Norton (2002) concluded that unlike other salmonid populations in the 

31
Pacific Northwest, Central Valley Chinook salmon show little estuarine dependence and may 

benefit from expedited ocean entry. Spring-run yearlings are larger in size than fall-run 

yearlings and are ready to smolt upon entering the Delta; therefore, they are believed to spend 

little time rearing in the Delta. 

Risk of selenium exposure: California Central Valley Chinook salmon evidently are among the 

most sensitive of fish and wildlife to selenium. They are especially vulnerable during juvenile 

life stages when they migrate and rear in selenium-contaminated Central Valley rivers and the 

San Francisco Bay/Delta estuary. 

In a laboratory experiment, measurements were made of the selenium bioaccumulation, weight 

and survival of juvenile (initially swim-up larvae) San Joaquin River fall run Chinook salmon 

that were exposed for 90 days in fresh water to two parallel graded series of dietary selenium 

treatments (Hamilton et al. 1990). In one series, the food was spiked with seleno-DL-methionine 

(SeMet); in the other series, the source of selenium was mosquitofish collected from the San Luis 

Drain (SLD), which carried seleniferous agricultural drainwater from a subsurface tile drainage 

system in the Westlands Water District in the San Joaquin Valley of California. Although the 

SLD mosquitofish diets may have included other contaminants, such as pesticides, the results of 

this experiment indicate that, once selenium is incorporated into fish tissue, there is no difference 

in the tissue concentration-response relationship due to the different sources of selenium (SLD or 

SeMet). Therefore, all data from both diet series were combined in the analysis presented here. 

The effects of selenium on animals (including fish) are well known to be biphasic (beneficial at 

low doses; toxic at high doses; see for example Hilton et al. 1980), and in the Hamilton et al. 

(1990) experiment, the 90-day survival data appear to confirm a biphasic dose-response 

relationship with respect to the survival endpoint (Figure 11). Therefore, we fitted a biphasic 

model (Brain and Cousens 1989) to the data by least squares regression. This regression 

provides a weight-of-evidence estimate of the maximum survival rate (0.7, or 70 percent) of 

young salmon under these experimental conditions at the estimated optimal selenium 

concentration in the fish (about 1 μg/g whole body dry weight). It also provides an estimate of 

the survival rate at any given selenium concentration above the optimum. Any such survival rate 

estimate can be compared to the maximum survival rate to yield an estimate of the mortality 

(inverse of survival) specifically attributable to selenium. For example, at a fish tissue 

concentration of 7.9 μg/g (whole body dry weight) the regression curve predicts a survival of 

0.29 (29 percent). As a proportion of the maximum survival this is 0.29/0.7 = 0.41, or 41 

percent. Therefore our best weight-of-evidence estimate of the mortality due to selenium 

toxicity at a tissue concentration of 7.9 μg/g is the inverse of 0.41, which is 0.59, or 59 percent. 

Similarly, the model predicts that fish with a selenium concentration of 2.5 μg/g (whole body dry 

weight) after 90 days of exposure would experience 20 percent mortality due to selenium (Figure 

11). 

32
1 1 2 3 4 5 6 7 8 20 30 0

Selenium concentration in fish (μg/g whole body dry wt)

0

0.2

0.4

0.6

0.8

1

Survival

Regression: 

y=1.71*x/(1+(x/0.80)1.67)

n=11

R2=0.946

59% mortality

⎫

⎬

⎭

⎭

⎬

⎫

20% mortality

2.5 μg/g

⎬

7.9 μg/g

Figure 11. Survival as a function of selenium concentration in tissue of juvenile Chinook 

salmon after 90 days of exposure to dietary selenium. A biphasic model (Brain and 

Cousens 1989) was fitted to the data by least squares regression (see text). Dashed lines 

indicate 95% confidence bands around the regressions in this and following figures. 

33
1 1 2 3 4 5 6 7 8 20 30 0

Selenium concentration in fish (μg/g whole body dry wt)

0

1

2

3

4

5

Weight of fish (g)

7.9 μg/g

Regression: y=5.24/(1+(17.5/x)-1.78)

Max

 

Figure 12. Juvenile fall run Chinook salmon weight 90 days after swim up, in fresh water 

with dietary exposure to selenium. 

In the Hamilton et al. (1990) experiment, the weight measurements after 90 days of exposure do 

not exhibit clear evidence of a biphasic dose-response relationship (Figure 12). This suggests 

that none of the dietary treatments in this experiment was low enough in selenium to be 

substantially deficient with respect to weight gain. This is consistent with the results of an 

experiment in which rainbow trout juveniles where exposed to diets spiked with sodium selenate 

for 20 weeks (Hilton et al. 1980). In that experiment, rainbow trout exhibited measurable 

impairment of growth due to selenium deficiency at tissue selenium concentrations of less than 

0.65 μg/g (carcass dry weight). In the Hamilton et al. (1990) experiment, the average selenium 

concentration in fish after 90 days in the lowest selenium treatment was 0.8 μg/g, above the 0.65 

μg/g rainbow trout threshold for the effect of selenium deficiency on growth. 

The considerations outlined above suggest that a biphasic model is not necessary for adequately 

describing the Hamilton et al. (1990) weight data. Therefore, the weight data were modeled with 

a log-logistic function, which is commonly used to model monotonic dose-response data. The 

log-logistic model provides an estimate of the most likely maximum weight (5.24 g), which can 

be used as the basis of comparison for the predicted weight corresponding to any given elevated 

selenium concentration. For example, the model projects that a juvenile Chinook salmon tissue 

34
concentration of 7.9 μg/g (whole body dry weight after 90 days of exposure to dietary selenium) 

would most likely be associated with a weight of 4.21 g. This is about a 20 percent reduction 

from the maximum weight of 5.24 g (Figure 12). 

We conclude that, 90 days after swimup, Chinook salmon juveniles that bioaccumulate selenium 

to a concentration of 7.9 μg/g will most likely suffer 59 percent mortality due to selenium 

(Figure 11), and the survivors will most likely be reduced in weight by 20 percent due to 

selenium (Figure 12). 

Hamilton et al. (1990) also reared San Joaquin River fall run Chinook salmon fingerlings in 

reconstituted brackish water with dietary exposure to selenium for 120 days, simulating the 

rearing of young salmon in the San Francisco estuary. The results of this portion of the 

experiment indicate that salmon fingerlings with a concentration of 7.9 μg/g selenium after 

rearing in brackish water for120 days are likely to experience a 2.3 percent reduction in growth 

due to selenium (Figure 13). 

After rearing the young salmon in brackish water, Hamilton et al. (1990) simulated the passage 

of the salmon from the estuary into the ocean by challenging them with 10 days of emersion in 

reconstituted seawater. The results of this final phase of the experiment suggest that upon 

entering the ocean, young salmon with a tissue concentration of 7.9 μg/g are likely to experience 

15 percent mortality within 10 days, due to selenium (Figure 14). 

35
1 1 2 3 4 5 6 7 8 20 30 0

Selenium concentration in fish (μg/g whole body dry wt)

0

5

10

15

20

25

30

Weight (g)

7.9 μg/g

Regression: y=20.9/(1+(32.3/x)-2.66)

} 2.3% reduction from Max Max

Figure 13. Juvenile fall run Chinook salmon weight after 120 days of rearing in brackish 

water with dietary exposure to selenium. 

36
1 1 2 3 4 5 6 7 8 20 30 0

Selenium concentration in fish (μg/g whole body dry wt)

0

0.2

0.4

0.6

0.8

1

Survival after 10 day seawater challenge

7.9 μg/g

Regression: y=0.852/(1+(21.2/x)-1.74)

15% reduction from Max } Max

Figure 14. Survival of juvenile fall run Chinook salmon after 10 day seawater challenge 

following rearing for 120 days in brackish water with dietary exposure to selenium. 

37
 Steelhead Trout (Oncorhynchus mykiss)

Status: Steelhead trout are the anadromous form of the rainbow trout species. Central 

California Coast steelhead were listed as threatened under the ESA on August 18, 1997 (62 FR 

43937). This Evolutionarily Significant Unit (ESU) includes steelhead in San Francisco and San 

Pablo Bays and their tributaries (Figure 15). Central Valley steelhead were listed as threatened 

under the ESA on March 19, 1998 (63 FR 13347). This ESU consists of steelhead populations in 

the Sacramento and San Joaquin River (inclusive of and downstream of the Merced River) basins 

in California’s Central Valley (Figure 15). 

Figure 15. Status of west coast steelhead (http://swr.nmfs.noaa.gov/psd/stlesu.htm). 

The breeding of wild steelhead in the Central Valley is mostly confined to the upper Sacramento 

River and its tributaries, including Antelope, Deer, and Mill Creeks and the Yuba River. 

Populations may exist in Big Chico and Butte Creeks and a few wild steelhead are produced in 

the American and Feather Rivers (McEwan and Jackson 1996). 

Until recently, steelhead were thought to be extirpated from the San Joaquin River system. 

Recent monitoring has detected small self sustaining populations of steelhead in the Stanislaus, 

38
Mokelumne, Calaveras, and other streams previously thought to be devoid of steelhead 

(McEwan 2001). 

Historically, steelhead were abundant in San Francisco Bay area streams, such as the Napa River 

and its tributaries; however, populations have declined. The South-Central California Coast 

steelhead ESU critical habitat includes all river reaches and estuarine areas accessible to listed 

steelhead in coastal river basins from the Russian River to Aptos Creek, California (inclusive), 

and the drainages of San Francisco and San Pablo Bays. Also included are all waters of San 

Pablo Bay westward of the Carquinez Bridge and all waters of San Francisco Bay from San 

Pablo Bay to the Golden Gate Bridge (65 FR 7764). 

Size: Barnhart (1986) reported that steelhead smolts in California range in size from 140 to 210 

mm (fork length). This corresponds to a weight range of 31-105 g according to the fork lengthweight regression equation shown in Figure 16 for central California coastal steelhead. 

Diet: Juvenile steelhead feed on a wide variety of aquatic and terrestrial insects (Figure 17 and 

Table 3), and emerging fry are sometimes preyed upon by older juveniles. 

Figure 16. Fork length – weight relationships for Central Valley Chinook salmon and 

central California coastal steelhead. Chinook were collected in San Francisco Estuary (Fig. 

6 in Klimley 2004). Data from MacFarlane (unpublished) 

39
Figure 17. Diet composition, shown as % mass of invertebrate food categories, of juvenile 

steelhead and coho salmon from November 24, 1990 to April 14, 1991 in two sites along 

Pudding Creek, California (Fig. 13 in Pert 1987). Aq. Adults = Aquatic Adults, Ephem = 

Ephemeroptera, Plec = Plecoptera, Trich = Trichoptera, Chir = Chironomidae, Dip/Col = 

Diptera (other than Chironomidae) and Coleoptera, Misc. Aq. = Miscellaneous Aquatics, 

Terr. Ad. = Terrestrial Adults, Misc. Terr. = Miscellaneous Terrestrials, and Annelids. 

40
Table 3. Number (No.), percent abundance (Abund.), percent weight (Wt.), and percent 

occurrence frequency (Occur.) of prey items from stomachs of three steelhead, lower 

Willamette River, 2002-2003 (Appendix Table 2 from Vile et al. 2004). L = larvae; P = 

pupae. 

Food ingestion rate: The food ingestion rates of wild steelhead trout are unknown. However, 

ingestion rates in the wild may be estimated from ingestion rates in captivity or from growth 

rates in the wild combined with food conversion efficiencies in captivity. 

The growth rates of wild steelhead can be estimated from measurements of steelhead (Table 4) 

that were marked and recaptured in the Feather River in 2002 (CDWR 2003). Assuming a 

constant specific growth rate (growth rate as a percentage of body weight), growth is modeled by 

bta

ew + =

Where w is fish “weight” (mass) in grams, t is time in days, and a and b are fitted parameters 

representing respectively the intercept and slope of the straight line relationship when weight is 

log-transformed: 

+= btawln

Given two data points, (w1, t1) when a fish was marked, and (w2, t2) when the fish was 

recaptured, then 

21

1 2

tt

wlnwln

b −

−

=

and specific growth rate is given by 

b SpecificGrowthRate 1−= e

41
Table 4. Measurements of all steelhead marked and recaptured in the Feather River in 

2002 (CDWR 2003). Specific locations are BP=Bedrock Park, HD=Hatchery Ditch, 

SR=Steep Riffle.

42
Applying this procedure to the wild steelhead weight data in Table 4 yields the specific growth 

rates listed in Table 5, with an average specific growth rate of 2.29%. 

Table 5. Specific growth rates calculated from the data in Table 4. 

b exp(b) Specific 

growth rate 

g/day/g body 

wt 

0.0384 1.0392 3.92%

0.0252 1.0255 2.55%

0.0266 1.027 2.70%

0.0077 1.0077 0.77%

0.0304 1.0308 3.08%

-0.0056 0.9944 -0.56%

0.0767 1.0797 7.97%

0.0239 1.0242 2.42%

0.0147 1.0148 1.48%

0.02 1.0202 2.02%

0.0203 1.0206 2.06%

0.0173 1.0175 1.75%

0.0124 1.0125 1.25%

0.0271 1.0275 2.75%

0.0211 1.0213 2.13%

0.0288 1.0293 2.93%

0.0078 1.0078 0.78%

0.0257 1.026 2.60%

0.0332 1.0337 3.37%

0.0183 1.0185 1.85%

0.0156 1.0157 1.57%

0.0096 1.0097 0.97%

Average: 2.29%

43
Figure 18. Effects of waterborne and dietary copper exposure on food conversion 

efficiency in juvenile rainbow trout obtained from Humber Spring Trout Hatchery, Mono 

Mills, Ontario, Canada (Fig. 1(B) in Kamunde et al. 2002). Values are means ± S.E.M. on a 

per tank basis, N=3 per data point. LL, low waterborne Cu and low dietary Cu; LN, low 

waterborne Cu and normal dietary Cu; NL, normal waterborne Cu and low dietary Cu; 

NN, normal waterborne Cu and normal dietary Cu; NH, normal waterborne Cu and high 

dietary Cu level. *Significant difference relative to group NN on normal water Cu and 

normal dietary Cu. 

Food conversion efficiencies of about 0.8 were reported for captive juvenile rainbow trout raised 

with exposure to low concentrations of copper in ambient water and food (Kamunde et al. 2002, 

Figure 18). This agrees with the food conversion efficiency of 0.80 recorded by Bear (2005) for 

rainbow trout raised for 60 days in 75 liter aluminum test tanks at 20 ̊ C (Table 6), a water 

temperature commonly encountered in the shallow waters of the Delta. 

44
Table 6. Feed consumption (±SE), and feed conversion efficiency (±SE) for westslope cutthroat (WCT) and 

rainbow trout (RBT). Rainbow trout were raised from eggs obtained from the Ennis National Fish Hatchery 

in Montana (Bear 2005). 

If we use the food conversion efficiency (FCE) of 0.80 and the average specific growth rate 

(SGR) of 2.29% (Table 5) to calculate the food ingestion rate (FIR) for steelhead trout: 

FIR = SGR/FCE 

FIR = 2.29%/0.80 

FIR = 2.86% (dry weight percent of live body weight per day) 

This ingestion rate is substantially higher than the rate of consumption (0.93% of body weight 

per day at 20 ̊ C) of rainbow trout fed to satiation in the experiment reported by Bear (2005). It 

is also substantially higher than the rate at which Coos River Winter Steelhead smolts are 

reported to be fed (1% of body weight per day) at the Bandon Hatchery in Oregon (ODFW 

2005), and the rate at which rainbow trout are fed (0.8% of body weight per day) at the Lake 

Roosevelt Net Pen Program in Washington (LRDA 2000). 

If rearing steelhead actively seek out cooler waters that are closer to the temperature of optimal 

rainbow trout growth (about 13-14 ̊ C, Figure 19, see Natural History below), then the Bear 

(2005) experiment indicates that food conversion efficiency would be about 1.15 (Table 6). This 

is close to the FCE (1.0) reported to be typical for rainbow trout at the Lake Roosevelt Net Pen 

Program (LRDA 2000). Using an FCE of 1.15: 

FIR = SGR/FCE 

FIR = 2.29%/1.15 

FIR = 1.99% (dry weight percent of live body weight per day) 

This is closer to the FIR actually recorded in the Bear (2005) experiment (1.08 at 14 ̊ C, Table 6) 

and closer to hatchery feeding rates, and it may be more likely to represent typical food ingestion 

rates of steelhead rearing in the range of water temperatures experienced in the Delta. 

45
Figure 19. Growth of age-1 rainbow trout over 60 days in relation to temperature (Figure 

8 bottom in Bear 2005). Each circle represents the relative growth rate (%) per tank with 

three tanks tested at each temperature. Dotted lines indicate the 95% confidence interval 

of the regression line and dashed lines indicate the 95% confidence interval of the data. 

General Life History: Steelhead can be divided into two life history types, stream-maturing 

and ocean-maturing, based on their state of sexual maturity at the time of river entry and the 

duration of their spawning migration. Stream-maturing steelhead enter freshwater in a sexually 

immature condition and require several months to mature and spawn, whereas ocean-maturing 

steelhead enter freshwater with well-developed gonads and spawn shortly after river entry. 

These two life history types are more commonly referred to by their season of freshwater entry 

(i.e. summer [stream-maturing] and winter [ocean-maturing] steelhead). Only winter steelhead 

currently are found in the rivers and streams of Central Valley and San Francisco Bay area 

(McEwan and Jackson 1996). 

Winter steelhead generally leave the ocean from August through April, and spawn between 

December and May (Busby et al. 1996). Timing of upstream migration is correlated with higher 

flow events, such as freshets or sand bar breaches, and associated lower water temperatures. In 

general, the preferred water temperature for adult steelhead migration is 46 o

F to 52 oF (McEwan 

and Jackson 1996; Myrick 1998; and Myrick and Cech 2000). 

Unlike Pacific salmon, steelhead are iteroparous, or capable of spawning more than once before 

death (Busby et al. 1996). However, it is rare for steelhead to spawn more than twice before 

dying; most that do so are females (Nickleson et al. 1992; Busby et al. 1996). Iteroparity is more 

common among southern steelhead populations than northern populations (Busby et al. 1996). 

46
Although one-time spawners are the great majority, Shapovalov and Taft (1954) reported that 

repeat spawners are relatively numerous (17.2 percent) in California streams. Most steelhead 

spawning takes place from late December through April, with peaks from January though March 

(Hallock et al. 1961). Steelhead spawn in cool, clear streams featuring suitable gravel size, 

depth, and current velocity, and may spawn in intermittent streams as well (Everest 1973; 

Barnhart 1986). 

The length of the incubation period for steelhead eggs is dependent on water temperature, 

dissolved oxygen concentration, and substrate composition. In late spring and following yolk 

sac absorption, fry emerge from the gravel and actively begin feeding in shallow water along 

stream banks (Nickelson et al. 1992). 

Steelhead rearing during the summer takes place primarily in higher velocity areas in pools, 

although young-of-the-year also are abundant in glides and riffles. Winter rearing occurs more 

uniformly at lower densities across a wide range of fast and slow habitat types. Productive 

steelhead habitat is characterized by complexity, primarily in the form of large and small woody 

debris. Cover is an important habitat component for juvenile steelhead both as velocity refugia 

and as a means of avoiding predation (Shirvell 1990; Meehan and Bjornn 1991). Some older 

juveniles move downstream to rear in large tributaries and mainstem rivers (Nickelson et al.

1992). Juveniles feed on a wide variety of aquatic and terrestrial insects (Chapman and Bjornn 

1969), and older juveniles sometimes prey upon emerging fry. 

Steelhead generally spend two years in freshwater before emigrating downstream (Hallock et al.

1961; Hallock 1989). Rearing steelhead juveniles prefer water temperatures of 45 ̊ F to 58 ̊ F 

and have an upper lethal limit of 75 ̊ F. They can survive up to 81 ̊ F with saturated dissolved 

oxygen conditions and a plentiful food supply. 

Juvenile steelhead emigrate episodically from natal streams during fall, winter, and spring high 

flows. Emigrating Central Valley steelhead use the lower reaches of the Sacramento River and 

the Delta for rearing and as a migration corridor to the ocean. Some may utilize tidal marsh 

areas, non-tidal freshwater marshes, and other shallow water areas in the Delta as rearing areas 

for short periods prior to their final emigration to the sea. Barnhart (1986) reported that 

steelhead smolts in California range in size from 140 to 210 mm (fork length). Hallock et al. 

(1961) found that juvenile steelhead in the Sacramento River Basin migrate downstream during 

most months of the year, but the peak period of emigration occurred in the spring, with a much 

smaller peak in the fall. 

Risk of selenium exposure: Because steelhead are regarded as a life-history variant or “form” 

of the rainbow trout species, studies of the non-anadromous form of rainbow trout may provide a 

good indication of the risks of the exposure of steelhead to selenium. Such studies indicate that 

rainbow trout are among the more sensitive of fish to selenium. One of these studies examined 

the effects of selenium on fry of rainbow and brook trout exposed in streams in Alberta, Canada 

(Holm 2002, Holm et al. 2003). In summary, this study indicates that maternal selenium would 

result in 20 percent mortality of fry if female rainbow trout have a tissue selenium concentration 

of 2.93 μg/g wholebody dry weight (Figure 20). Among the swimup survivors, various 

deformities were also associated with elevated selenium in the eggs from which the fry hatched. 

47
For example, both edema (Figure 21) craniofacial deformities (Figure 22) increase sharply above 

an egg selenium concentration of about 10 μg/g (wet weight), corresponding to a maternal tissue 

concentration of about 6.6 μg/g (whole body dry weight; for details, see USFWS 2005). 

igure 20. Relationship between selenium in rainbow trout eggs and mortality of eggs and 

981). 

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

1 10 100

[Se] in eggs (μg/g wet weight)

Mortality

pre-swimup (arcsine transformation)

 3.51 μg/g egg ww

~ 2.93 μg/g wholebody dw

Regression: 

asin(sqrt(Mortality))=0.2024+0.479*log10(EggSe)

R2

 = 0.167

20% mortality

F

fry by swimup stage. The arcsine transformation is applied to mortality data, as 

appropriate for linear regressions with percents or proportions (Sokol and Rohlf 1

Data are from the years 2000-2002. 

 

48
0

20

40

60

80

100

1 10 100

Selenium concentration in eggs 

(μg/g wet weight)

Edema 

(percent incidence in swimup fry)

Regression:

y = Min + (100-Min)/(1+(ED50/x)Slope)

 Min=9.5

 ED50=10.67

 Slope=19.8 

Figure 21. Relationship between selenium in rainbow trout eggs and edema in surviving 

swimup fry. The eggs were from rainbow trout collected in the McLeod River drainage, 

Alberta, Canada, 2000-2002 (Jodi Holm pers. com.). 

49
0

20

40

60

80

100

1 10

Selenium concentration in eggs 

(μg/g wet weight)

Edema 

(percent incidence in swimup fry

100

)

Regression:

y = Min + (100-Min)/(1+(ED50/x)Slope)

 Min=9.5

 ED50=10.67

 Slope=19.8 

Figure 22. Relationship between selenium in rainbow trout eggs and craniofacial 

deformities in surviving swimup fry. The eggs were from rainbow trout collected in the 

McLeod River drainage, Alberta, Canada, 2000-2002 (Jodi Holm pers. com.). 

Another laboratory experiment monitored the growth of juvenile rainbow trout exposed for 20 

weeks to a diet spiked with selenium in the form of sodium selenite (Hilton et al. 1980). This 

experiment indicates that, relative to optimal selenium exposure, a weight reduction of 20 

percent would be associated with a tissue selenium concentration of 2.15 μg/g (carcass dry 

weight) (Figure 23). 

50
51

0

10

20

30

40

0.1 1 10

[Se] in fish tissue (μg/g carcass dry wt.)

Weight of fish (g)

}20% reduction 

in growth

2.15

y=1.28+62.9/(1+(0.299/x)0.742)/(1+(2.71/x)-2.32 Regression: )

Figure 23. Average weights of juvenile rainbow trout after 20 weeks of exposure to diets 

spiked with sodium selenite (Hilton et al. 1980). The data were fitted with a biphasic model 

(Beckon et al. in prep.). In the model it was assumed that at extremely high and extremely 

low selenium concentrations, the fish would have failed to grow at all, i.e. they would have 

remained at the initial average weight of 1.28 g. Carcass concentrations are from Fig. 2 of 

Hilton et al. 1980. 

Green Sturgeon (Acipenser medirostris) 

Status: The southern distinct population segment, or DPS, of north American green sturgeon 

was federally listed as threatened under the Endangered Species Act on Apr. 7, 2006 (71 FR 

17757). The range of the southern DPS extends southward from the Eel River, in northern 

alifornia, and includes the green sturgeon inhabiting the San Francisco Bay/Delta estuary. 

Size: Green sturgeon caught in the commercial fishery has declined in size over the years. In 

the 1960s, mean size of green sturgeon landed ranged between 17 and 19 kg (37-42 pounds), 

while since 1980, mean weight has usually been between 12 and 14 kg (26-31 pounds) (USFWS 

1996). Here we use the midpoint (13 kg) of this more recent range of means. 

Diet: Sturgeon feed primarily on benthic (bottom) organisms such as worms, mollusks, and 

crustaceans. Juveniles in the Sacramento-San Joaquin Delta feed on opossum shrimp 
(Neomysis inercedis) and amphipods (Corophium sp.) (Table 7, Radtke 1966). 

Table 7. Stomach contents of 74 green sturgeon caught in the Sacramento-San Joaquin Delta with gill nets 

and otter trawl from September 1963 through August 1964 (Radtke 1966). 

Food ingestion rate: The food ingestion rate of green sturgeon in the wild is unknown, but 24 

green sturgeon (average weight: 150 g) that were reared in captivity at 19 ̊C and fed to satiation 

on a diet of commercial Silvercup trout pellets ingested food at a rate of 2% of live fish body 

weight per day (Mayfield and Cech 2004) 

General life history: The ecology and life history of green sturgeon have received 

comparatively little study, evidently because of their generally low abundance and their low 

commercial and sport-fishing value in the past. The adults are more marine than white sturgeon, 

spending limited time in estuaries or fresh water. 

Green sturgeon migrate up the Klamath River between late February and late July. The spawning 

period is March-July, with a peak from mid-April to mid-June (Emmett et al. 1991). Spawning 

times in the Sacramento River are probably similar, based on times when adult sturgeon have 

been caught there. Spawning takes place in deep, fast water. Female green sturgeon produce 

60,000-140,000 eggs (Moyle 1976). Based on their presumed similarity to white sturgeon, green 

sturgeon eggs probably hatch around 196 hours (at 12.7 degrees Celsius [54.9 degrees 

Fahrenheit]) after spawning, and larvae should be 8-19 millimeters (0.3-0.7 inch) long. Juveniles 

likely range in size from 2.0-150 centimeters (1-59 inches) (Emmett et al. 1991). Juveniles 

migrate out to sea before 2 years of age, primarily during summer-fall (Emmett et al. 1991). 

Length-frequency analyses of sturgeon caught in the Klamath Estuary by beach seine indicate 

that most green sturgeon leave the system at lengths of 30-70 centimeters (12-28 inches), when 

they are to 4 years old, although a majority leave as yearlings (USFWS 1996). They remain near 

estuaries at first, but can migrate considerable distances as they grow larger (Emmett et al.

1991). Individuals tagged by DFG in San Pablo Bay (part of the San Francisco Bay system) have 

been recaptured off Santa Cruz, California, in Winchester Bay on the southern Oregon coast, at 

the mouth of the Columbia River and in Gray’s Harbor, Washington (Chadwick 1959; Miller 

1972). Most tags for green sturgeon in the San Francisco Bay system have been returned from 

outside that estuary (D. Kohlhorst, DEG, personal communication, cited in USFWS 1996). 

Risk of selenium exposure: Little is known of the risk of selenium to green sturgeon, but white 

sturgeon (Acipenser transmontanus), a representative surrogate species for the green sturgeon, 

have been the subject of detailed studies within the San Francisco Bay estuary (e.g., Kohlhorst et 

52
al. 1991, Linares et al. 2004, Linville 2006). See the “Risk to selenium exposure” section for 

white sturgeon below. 

White Sturgeon (Acipenser transmontanus) 

Status: According to the World Conservation Union (Duke et al. 2004), in general the white 

sturgeon species is not threatened, but some subpopulations are endangered (Kootenai River and 

Upper Fraiser River) or critically endangered (Nechako River, Upper Columbia River). The 

Kootenai River population of the white sturgeon in Montana and Idaho was federally listed as 

endangered under the Endangered Species Act on September 6, 1994 (59 FR 45989). The 

California Department of Fish and Game (CDFG) established a daily bag and possession limit of 

one fish, which must be between 46 and 72 inches total length (CDFG 2007). Temporary (120 

days) emergency regulations issued by the CDFG in March 2006 restricted fishing in California 

to individuals between 46 and 56 inches total length. 

Size: The white sturgeon is the largest North American fish. A white sturgeon weighing 

approximately 682 kg was taken from the Snake River, Idaho in 1898. Individuals from 

landlocked subpopulations tend to be smaller (Duke et al. 2004). The average length of 390 

white sturgeon captured in the Snake River in 2001 was 107 cm (range 42 to 307 cm; Everett and 

Tuell 2003). This corresponds to an average weight of 5.9 kg according to a weight-length 

regression equation (W=6.5x10-7 L3.43 where W is weight in kg and L is total length in cm) for 

278 white sturgeon from the Middle Snake River 1982-1984 (Lukens 1985 as reported in 

Beamesderfer 1993). The modal length of 2203 white sturgeon collected in the Sacramento-San 

Joaquin Estuary in 1965-1970 and 1973-1976 was 102 cm (Figure 24; Kohlhorst et al. 1980). 

This corresponds to a weight of 6.28 kg according to a weight-length regression equation for 209 

white sturgeon collected in the Sacramento-San Joaquin Estuary in 1965-1970 (Figure 25; 

Kohlhorst et al. 1980) 

53
Figure 24. Age (A) and length frequency (B) distributions of white sturgeon collected in the 

Sacramento-San Joaquin Estuary in 1965-1970 and 1973-1976 (Kohlhorst et al. 1980). 

54
Figure 25. Length-weight relationship of white sturgeon collected in the Sacramento-San 

Joaquin Estuary from 1965 to 1970 (Kohlhorst et al. 1980). 

Diet: Sturgeon feed primarily on benthic (bottom) organisms such as worms, mollusks, and 

crustaceans. Larger individuals are said to eat a greater proportion of fish (Scott and Crossman 

1973). Mysid shrimp (Neomysis awatschensis) and amphipods (Corophium sp.) predominated in 

the stomach contents of 105 white sturgeon (ranging from 19 to 102 cm in total length) collected 

in the Sacramento-San Joaquin Delta in 1963-1964 (Table 8; Radtke 1966). 

Table 8. Stomach contents of 105 white sturgeon caught in the Sacramento-San Joaquin Delta with gill nets 

and otter trawl from September 1963 through August 1964 (Radtke 1966). 

55
Clams predominated in the esophageal and stomach contents of white sturgeon caught by anglers 

in San Pablo Bay (213 fish) and Suisun Bay/Carquinez Strait (142 fish) in 1965-1967 (Table 9

and Table 1; McKechnie and Fenner 1971). More recently with the change in the benthic food 

structure of the estuary (Feyrer et al. 2003) white sturgeon may depend more on the introduced 

Asian clam, Potamocorbula amurensis, which is an extraordinarily efficient bioaccumulator of 

selenium (Stewart et al. 2004). 

Table 9. Esophageal and stomach contents of white sturgeon caught by anglers in San Pablo Bay from April 

1965 to November 1967 (McKechnie and Fenner 1971). 

56
Table 10. Esophageal and stomach contents of white sturgeon caught by anglers in Suisun Bay and 

Carquinez Strait from April 1965 to November 1967 (McKechnie and Fenner 1971). 

Food ingestion rate: The food ingestion rate of white sturgeon in the wild is unknown, but 

feeding experiments in captivity may provide some indication of food ingestion rates. A feeding 

experiment with 240 sub-yearling white sturgeon (initial average weight: 250.5 g) that were 

reared in captivity at 18 ̊C suggested that the optimal feeding rate for growth is between 1.5 and 

2 % (dry weight) of live fish body weight per day (Hung et al. 1989). In another experiment, 

30-g-size white sturgeon maintained at 20 ̊C also showed maximum growth when fed between 

1.5 and 2 % (dry weight) of live fish body weight per day (Hung and Lutes 1987). Hung et al. 

(1993) found that 30-g-size white sturgeon maintained at 23 ̊C and 26 ̊C grew optimally when 

fed 2.0-2.5% and 2.5-3.0%, respectively, of wet weight of fish per day, but temperatures of 18 ̊C 

and 20 ̊C are probably closer to temperatures generally experienced by white sturgeon in their 

natural habitats. 

57
General life history: Like green sturgeon, white sturgeon are anadromous, but the adults are 

less marine than green sturgeon, spending more time in estuaries or fresh water. At sea, white 

sturgeon have been found from Ensenada, Baja California (Mexico) to the Gulf of Alaska (Fry 

1973). The majority of white sturgeon rear in the Columbia-Snake River and Sacramento-San 

Joaquin basins (Duke et al. 2004). White sturgeon have been the subject of detailed studies 

within the San Francisco Bay estuary (e.g., Kohlhorst et al. 1991, Linares et al. 2004, Linville 

2006). White sturgeon are long-lived, large-bodied, and demersal (bottom-dwelling) fish. For 

most species of sturgeon, females require several years for eggs to mature between spawnings 

(Conte et al. 1988). White sturgeon in the San Francisco Bay estuary congregate in Suisun and 

San Pablo Bays where they remain year-round except for a small fraction of the population that 

moves up the Sacramento River, and to a lesser extent the San Joaquin River, to spawn in late 

winter and early spring (Kohlhorst et al. 1991). 

Risk of selenium exposure: Many individuals of this species remain year-round in San Pablo 

Bay, the part of the San Francisco Bay estuary with the highest selenium concentrations (up to 

2.7 μg/L). Stewart et al. (2004) found the median concentration of selenium in Asian clams 

(Potamocorbula amurensis) from San Pablo Bay to be above 10 μg Se/g. Based on 

histopathological alterations in the kidney, Tashjian et al. (2006) estimated that for juvenile 

white sturgeon a threshold dietary selenium toxicity concentration lies between 10 and 

20 μg Se/g. It is uncertain at what point in their life white sturgeon begin feeding on Asian 

clams. Linares et al. (2004) found concentrations of selenium as high as 46.7 μg/g in gonads of 

39 white sturgeon captured in the San Francisco Bay. Kroll and Doroshov (1991) reported that 

developing ovaries of white sturgeon from San Francisco Bay contained as much as 71.8 μg/g 

selenium or 7-times the threshold for reproductive toxicity in fish (Lemly 1996a, 1996b) of 10 

μg/g. The threshold specifically in white sturgeon has been confirmed to be between 9 μg/g and 

about 16 μg/g in experiments in which seleno-L-methionine was injected into yolk sac larvae of 

white sturgeon (Linares et al. 2004). Linville (2006) showed that significant developmental 

defects and mortality occurred in white sturgeon eggs at a threshold of around 11–15 μg/g 

selenium. A hazard threshold of around 3–8 μg/g in developing white sturgeon was suggested 

by Linville (2006). Sampling of pallid sturgeon (Scaphirhynchus albus) in the Missouri River 

system suggests that normal selenium levels in sturgeon eggs are 2-3 μg/g (Ruelle and Keenlyne 

1993) as has been found for many other fish species (see review in Skorupa et al. 1996 and in 

USDI-BOR/FWS/GS/BIA 1998). Thus, white sturgeon in the San Francisco Bay estuary are 

producing eggs with as much as 35-times normal selenium content. Based on studies regarding 

toxicity response functions for avian and fish eggs (e.g., Lemly 1996a, 1996b; Skorupa et al. 

1996; USDI-BOR/FWS/GS/BIA 1998) and assuming that sturgeon are as sensitive to selenium 

as birds and other fish, it is highly probable that these fish are reproductively impaired due to 

selenium exposure. For example, bluegill embryos resulting from ovaries containing 38.6 μg/g 

selenium exhibited 65 percent mortality (Gillespie and Bauman 1986). 

58
Delta Smelt (Hypomesus transpacificus)

Status: Delta smelt were federally listed as a threatened species on March 5, 1993, (58 FR 

12854). In recent years the population of delta smelt has declined dramatically, dropping to the 

lowest levels on record, and placing the species at increased risk of extinction. 

Size: Delta smelt are slender-bodied fish that typically reach 60-70 mm standard length 

(measured from tip of the snout to origin of the caudal fin), although a few may reach 120 mm 

standard length. The median fork length of 113 delta smelt was about 62 mm (Kimmerer et al. 

2005). This corresponds to a weight of 2.1 g, using the regression in Kimmerer et al. (2005): W 

= 0.0000018 L3.38 where W is weight in grams and L is fork length in mm. In tow-net surveys in 

June-August 2000 (Figure 26) 785 Delta smelt young-of-the-year had an average length of 35.7 

mm (Gartz 2001) corresponding to an average weight of 0.32 g, using the above regression. 

Young-of-the-year were defined as less than 69 mm fork length; only six Delta smelt larger than 

this were caught. 

Figure 26. Length-frequency plots for young-of-the-year delta smelt for townet surveys in 

2000 in the Sacramento and San Joaquin Rivers and Bay/Delta system (Figure 2 in Gartz 

2001). 

Diet: Delta smelt feed primarily on planktonic copepods, cladocerans, and amphipods. To a 

lesser extent, they feed on insect larvae. Larger fish may also feed on the opossum shrimp, 

Neomysis mercedis. The most important food organism for all sizes seems to be the euryhaline 

59
copepod, Eurytemora affinis, although by 1992 the exotic species, Pseudodiaptomus forbesi, had 

become a major part of the diet (Moyle et al. 1992). 

Food ingestion rate: Food ingestion rate for wild delta smelt in the estuary may be estimated 

using measured growth rates in the estuary combined with an estimate of food conversion 

efficiency. By tracking the length-frequency distributions of delta smelt in the Sacramento and 

San Joaquin Rivers and Bay/Delta system, Gartz (2001) calculated growth rates to be 0.11 

mm/day from late June to early July, 0.56 mm/day from early to late June, and 0.07 mm/day 

from late June to early August. The average of these growth rates is 0.247 mm/day, which 

corresponds to mass growth rate of 0.0075 g/day, calculated by differentiating the regression W 

= 0.0000018 L3.38 where W is weight in grams and L is fork length in mm (Kimmerer et al. 

2005). The closest (in size and taxonomic relationship) available food conversion efficiency 

(growth in weight / weight of food ingested) is 0.202 for 3 g sea trout (Salmo trutta trutta) in 

Norway (Neveu 1980, as seen in Worldfish Center 2000). Dividing mass growth rate by this 

food conversion efficiency yields an estimated food ingestion rate of 0.037 g /day (dry weight) or 

11.4 % of body wet weight per day for Delta smelt with a fork length of 36 mm weighing 0.32 g. 

Distribution: Delta smelt are endemic to the upper Sacramento-San Joaquin estuary. They 

occur in the Delta primarily below Isleton on the Sacramento River, below Mossdale on the San 

Joaquin River, and in Suisun Bay. They move into freshwater when spawning (ranging from 

January to July) and can occur in: (1) the Sacramento River as high as Sacramento, (2) the 

Mokelumne River system, (3) the Cache Slough region, (4) the Delta, and, (5) Montezuma 

Slough, (6) Suisun Bay, (7) Suisun Marsh, (8) Carquinez Strait, (9) Napa River, and (10) San 

Pablo Bay. It is not known if delta smelt in San Pablo Bay are a permanent population or if they 

are washed into the Bay during high outflow periods. Since 1982, the center of delta smelt 

abundance has been the northwestern Delta in the channel of the Sacramento River. In any 

month, two or more life stages (adult, larvae, and juveniles) of delta smelt have the potential to 

be present in Suisun Bay (DWR and USDI 1994; Moyle 1976; and Wang 1991). 

Life History: Delta smelt of all sizes are found in the main channels of the Delta and Suisun 

Marsh and the open waters of Suisun Bay where the waters are well oxygenated and 

temperatures relatively cool, usually less than 20 ̊-22 ̊ C in summer. When not spawning, they 

tend to be concentrated near the zone where incoming salt water mixes with out flowing 

freshwater (mixing zone). This area has the highest primary productivity and is where 

zooplankton populations (on which delta smelt feed) are usually most dense (Knutson and Orsi 

1983; Orsi and Mecum 1986). At all life stages delta smelt are found in greatest abundance in 

the top two meters of the water column and usually not in close association with the shoreline. 

Delta smelt inhabit open, surface waters of the Delta and Suisun Bay. In most years, spawning 

occurs in shallow water habitats in the Delta. Shortly before spawning, adult smelt migrate 

upstream from the brackish-water habitat associated with the mixing zone to disperse widely into 

river channels and tidally-influenced backwater sloughs (Radtke 1966; Moyle 1976, 2002; Wang 

1991). Some spawning probably occurs in shallow water habitats in Suisun Bay and Suisun 

Marsh during wetter years (Sweetnam 1999 and Wang 1991). Spawning has also been recorded 

in Montezuma Slough near Suisun Bay (Wang 1986) and also may occur in Suisun Slough in 

Suisun Marsh (P. Moyle, UCD, unpublished data). 

60
The spawning season varies from year to year, and may occur from late winter (December) to 

early summer (July). Pre-spawning adults are found in Suisun Bay and the western delta as early 

as September (DWR and USDI 1994). Moyle (1976, 2002) collected gravid adults from 

December to April, although ripe delta smelt were common in February and March. In 1989 and 

1990, Wang (1991) estimated that spawning had taken place from mid-February to late June or 

early July, with peak spawning occurring in late April and early May. 

Delta smelt spawn in shallow, fresh, or slightly brackish water upstream of the mixing zone 

(Wang 1991). Most spawning occurs in tidally-influenced backwater sloughs and channel 

edgewaters (Moyle 1976, 2002; Wang 1986, 1991; Moyle et al. 1992). Laboratory observations 

have indicated that delta smelt are broadcast spawners (DWR and USDI 1994) and eggs are 

demersal (sink to the bottom) and adhesive, sticking to hard substrates such as: rock, gravel, tree 

roots or submerged branches, and submerged vegetation (Moyle 1976, 2002; Wang 1986). 

Growth of newly-hatched delta smelt is rapid and juvenile fish are 40-50 mm long by early 

August (Erkkila et al. 1950; Ganssle 1966; Radtke 1966). By this time, young-of-year fish 

dominate trawl catches of delta smelt, and adults become rare. Delta smelt reach 55-70 mm 

standard length in 7-9 months (Moyle 1976, 2002). Growth during the next 3 months slows 

down considerably (only 3-9 mm total), presumably because most of the energy ingested is being 

directed towards gonadal development (Erkkila et al. 1950; Radtke 1966). There is no 

correlation between size and fecundity, and females between 59-70 mm standard lengths lay 

1,200 to 2,600 eggs (Moyle et al. 1992). The abrupt change from a single-age, adult cohort 

during spawning in spring to a population dominated by juveniles in summer suggests strongly 

that most adults die after they spawn (Radtke 1966 and Moyle 1976, 2002). However, in El 

Nino years when temperatures rise above 18 ̊ C before all adults have spawned, some fraction of 

the unspawned population may also hold over as two-year-old fish and spawn in the subsequent 

year. These two-year-old adults may enhance reproductive success in years following El Nino 

events. 

In a near-annual fish like delta smelt, a strong relationship would be expected between number of 

spawners present in one year and number of recruits to the population the following year. 

Instead, the stock-recruit relationship for delta smelt is weak, accounting for about a quarter of 

the variability in recruitment (Sweetnam and Stevens 1993). This relationship does indicate, 

however, that factors affecting numbers of spawning adults (e.g., entrainment, toxics, and 

predation) can have an effect on delta smelt numbers the following year. 

Risk of selenium exposure: The Recovery Plan for the Sacramento/San Joaquin Delta Native 

Fishes (USFWS 1996) states that delta smelt are ecologically similar to larval and juvenile 

striped bass (Morone saxitilis). Saiki and Palawski (1990) sampled juvenile striped bass in the 

San Joaquin River system including three sites in the San Francisco Bay estuary. Striped bass 

from the estuary contained up to 3.3 μg/g whole-body selenium, a value just below Lemly’s 4 

μg/g toxicity threshold, even though waterborne selenium typically averages <1 μg/L (ppb) and 

has been measured no higher than 2.7 μg/L (ppb) within the estuary (Pease et al. 1992). Striped 

bass collected from Mud Slough in 1986, when the annual median selenium concentration in 

water was 8 μg/L (ppb) (Steensen et al. 1997), contained up to 7.9 μg/g whole-body selenium 

and averaged 6.9 μg/g whole-body selenium. 

61
Delta smelt spawning sites are almost entirely restricted to the north-Delta channels associated 

with the selenium-normal Sacramento River and are nearly absent from the south-delta channels 

associated with the selenium-contaminated San Joaquin River (USFWS 1996). Delta smelt 

(n=41) salvaged from CDFG annual abundance surveys primarily around Chipps Island in 1993 

and 1994 had a mean of 1.5 μg/g whole-body selenium dry weight (range, 0.7-2.3 μg/g) (Bennet 

et al. 2001). Three composite samples of delta smelt eggs also had less than 2 μg/g selenium dry 

weight (USFWS unpublished data). 

Sacramento splittail (Pogonichthys macrolepidotus) 

Status: The Sacramento splittail was listed as threatened on February 8, 1999 (FR 64:5963). 

The listing was challenged in Federal District Court, and rescinded on September 22, 2003 (FR 

68:55139); however, they remain a species of concern. 

Sacramento splittail are endemic to certain waterways in California's Central Valley, where they 

were once widely distributed (Moyle 1976, Moyle 2002). Sacramento splittail currently occur in 

Suisun Bay, Suisun Marsh, the San Francisco Bay-Sacramento-San Joaquin River Estuary 

(Estuary), the Estuary's tributaries (primarily the Sacramento and San Joaquin rivers), the 

Cosumnes River, the Napa River and Marsh, and the Petaluma River and Marsh. 

Size: The average fork length of 14 adult Sacramento splittail captured in a fyke trap on their 

upstream migration in the Yolo Bypass Toe Drain in February 2001 was 320 mm with a standard 

deviation of 31 mm (Sommer et al. 2002). Fork lengths of 83 juvenile and adult splittail 

collected in newly-restored tidal and flood plain habitats in the Napa River/Napa Creek Flood 

Control Project area in 2001-2002 ranged from about 25 to 250 mm with a modal fork length of 

200-224 mm (Dietl et al. 2003) (Figure 27). The center of this modal range is 212 mm. Using 

the length-weight regression of W = 0.000003 L3.27, where W is weight in grams and L is fork 

length in mm (Kimmerer et al. 2005), a modal Sacramento splittail with a fork length of 212 mm 

would be expected to have a weight of 0.000003 x 2123.27 = 121 g. 

62
Figure 27. Lengths of captured Sacramento splittail in newly-restored tidal and flood plain 

habitats in the Napa River/Napa Creek Flood Control Project area in 2001-2002 (Dietl et 

al. 2003). 

Diet: Splittail are benthic (bottom) feeders. Stomach contents from 70 splittail collected in 

Suisun Marsh between March 1998 and January 1999 indicate that their diet consisted mainly 

(43%) of unidentified material, probably detritus. The overbite clam (Asian clam), 

Potamocorbula amurensis, and other mollusks constituted 34% of the diet (Feyrer and Matern 

2000, Feyrer et al. 2003). 

Food ingestion rate: Food ingestion rate for wild splittail in the estuary may be estimated using 

measured growth rates in the estuary combined with an estimate of food conversion efficiency. 

A cohort of 2100 splittail with a median standard length of about 134 mm grew at an average 

rate of about 0.281 mm/day (standard length) from February to September 1980 (Figure 28) 

(Moyle et al. 2004). These data correspond to a median fork length of 154 mm, weight of 42.6 g 

and mass growth rate of 0.292 g/day using the relationship L = (SL+ 0.2657)/ 0.8722 where L is 

fork length in mm and SL is standard length in mm (Randall Baxter pers. com.), and the lengthweight regression of W = 0.000003 L3.27, where W is weight in grams and L is fork length in mm 

(Kimmerer et al. 2005). The closest (in size and taxonomic relationship) available food 

conversion efficiency (growth in weight / weight of food ingested) is 0.202 for 3 g sea trout 

(Salmo trutta trutta) in Norway (Neveu 1980, as seen in Worldfish Center 2000). Dividing mass 

growth rate by this food conversion efficiency yields an estimated food ingestion rate of 1.45 

g/day (dry weight) or 3.37 % of body wet weight per day for splittail with a fork length of 154 

mm weighing 42.6 g. 

63
Figure 28. Mean lengths of monthly samples of three splittail cohorts in Suisun Marsh 

(Figure 11 in Moyle et al. 2004). 

General life history: Splittail are relatively long-lived (about 5-7 years) and are highly 

fecund (up to 100,000 eggs per female). Their populations fluctuate on an annual basis 

depending on spawning success and strength of the year class (Daniels and Moyle 1983). Both 

male and female splittail mature by the end of their second year (Daniels and Moyle 1983), 

although occasionally males may mature by the end of their first year and females by the end of 

their third year (Caywood 1974). Fish are about 180-200 millimeters (7-8 inches) standard 

length when they attain sexual maturity (Daniels and Moyle 1983), and the sex ratio among 

mature individuals is 1:1 (Caywood 1974). 

There is some variability in the reproductive period, with older fish reproducing first, followed 

by younger fish that tend to reproduce later in the season (Caywood 1974). Generally, gonadal 

development is initiated by fall, with a concomitant decrease in somatic growth (Daniels and 

Moyle 1983). By April, ovaries reach peak maturity and account for approximately 18 percent of 

the body weight. The onset of spawning seems to be associated with increasing water 

temperature and day length and occurs between early March and May in the upper Delta 

(Caywood 1974). However, Wang (1986) found that in the tidal freshwater and euryhaline 

habitats of the Sacramento-San Joaquin estuary, spawning occurs by late January and early 

February and continues through July. Spawning times are also indicated by the salvage records 

from the State Water Project pumps. Adults are captured most frequently in January through 

April, when they are presumably engaged in spawning movements, while young-of-year are 

captured most abundantly in May through July (Meng 1993). These records indicate most 

spawning takes place from February through April. 

64
Splittail spawn on submerged vegetation in flooded areas. Spawning occurs in the lower reaches 

of rivers (Caywood 1974), dead-end sloughs (Moyle 1976) and in the larger sloughs such as 

Montezuma Slough (Wang 1986). Larvae remain in the shallow, weedy areas inshore in close 

proximity to the spawning sites and move into the deeper offshore habitat as they mature (Wang 

1986). 

Strong year classes have been produced even when adult numbers are low, if outflow is high in 

early spring (e.g., 1982, 1986). Since 1988, recruitment has been consistently lower than 

expected, suggesting this relationship may be breaking down (Meng 1993). For example, both 

1978 and 1993 were wet years following drought years, yet the young-of-year abundance in 

1993 was only 2 percent of the abundance in 1978. 

Risk of selenium exposure: Splittail are likely to be relatively vulnerable to selenium 

contamination because of their estuarine habitat and bottom-feeding habits. Splittail feed 

primarily on bivalves including the overbite clam, Potamocorbula amurensis, which are efficient 

selenium bioaccumulators (Stewart et al. 2004). Teh et al. (2004) found that juvenile splittail are 

adversely affected (liver lesions) by chronic exposure (nine months) to a diet of 6.6 μg/g 

selenium. Deformities typical of Se exposure have been seen in splittail collected from Suisun 

Bay (Stewart et al. 2004). 

65
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