2013 Update on Sea Otter Studies to Assess Recovery from the 

1989 Exxon Valdez Oil Spill, Prince William Sound, Alaska

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2014–1030
Cover: Sea otter in kelp. Photograph by Benjamin Weitzman, U.S. Geological Survey. 

 
2013 Update on Sea Otter Studies to Assess Recovery 

from the 1989 Exxon Valdez Oil Spill, Prince William 

Sound, Alaska

By B.E. Ballachey, D.H. Monson, G.G. Esslinger, K. Kloecker, J. Bodkin, L. Bowen, and A.K. Miles

Open-File Report 2014–1030

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2014 

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Suggested citation:

Ballachey, B.E., Monson, D.H., Esslinger, G.G., Kloecker, K., Bodkin, J., Bowen, L., and Miles, A.K., 

2014, 2013 update on sea otter studies to assess recovery from the 1989 Exxon Valdez oil spill, Prince 

William Sound, Alaska: U.S. Geological Survey Open-File Report 2014-1030, 40 p., 

http://dx.doi.org/10.3133/ofr20141030. 

ISSN 2331-1258 (online)

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents 

Executive Summary....................................................................................................................................... 1

Introduction.................................................................................................................................................... 2

Chapter 1. Sea Otter Abundance in Western Prince William Sound through 2013........................................ 5

Introduction ................................................................................................................................................ 5

Methods ..................................................................................................................................................... 6

Results....................................................................................................................................................... 6

Chapter 2. Age Distributions of Sea Otters Found Dead in Western Prince William Sound, Alaska,

through 2013 ............................................................................................................................................... 11

Introduction .............................................................................................................................................. 11

Methods ................................................................................................................................................... 12

Results..................................................................................................................................................... 13

Discussion................................................................................................................................................ 15

Chapter 3. Gene Transcript Profiles in Sea Otters from Prince William Sound, Alaska, 2008 and 2012, and 

Clinically Normal and Wild Reference Sea Otters........................................................................................ 17

Introduction .............................................................................................................................................. 17

Methods ................................................................................................................................................... 17

Free-Ranging Target Sea Otters.......................................................................................................... 17

Captive and Free-Ranging Reference Sea Otters................................................................................ 18

Blood Collection and RNA Extraction ................................................................................................... 18

Statistical Analysis................................................................................................................................ 18

Results..................................................................................................................................................... 19

Discussion................................................................................................................................................ 23

Synthesis and Conclusions.......................................................................................................................... 26

References Cited......................................................................................................................................... 28

Appendix 1. Publications and Reports on Sea Otter Oil Spill Studies, Authored or Co-authored by 

USGS Scientists, 1989–2013 ...................................................................................................................... 34

Figures

Figure 1. Map of Prince William Sound showing sea otter study areas .......................................................3

Chapter 1

Figure 1.1. Prince William Sound (PWS), Alaska.........................................................................................7

Figure 1.2. Trend in sea otter abundance (± standard error) in western Prince William Sound, 

Alaska, 1993–2013........................................................................................................................................9

Figure 1.3. Estimated numbers of sea otters (± standard error) at heavily oiled northern 

Knight Island, Prince William Sound, Alaska, 1993–2013, compared to the pre-spill abundance estimate

(Dean and others, 2000)................................................................................................................................9

Figure 1.4. Estimated numbers of sea otters (± standard error) at the unoiled Montague Island

study area, Prince William Sound, Alaska, 1993–2012 .............................................................................. 10

Chapter 2

Figure 2.1. Relative age distributions of sea otter carcasses collected on western Prince William 

Sound beaches from 1976 to 2013.............................................................................................................. 14
iv

Figure 2.2. Relative proportion of prime-age animals (2–8 yrs-old) in age distributions of sea otter 

carcasses collected on western Prince William Sound beaches from 1976 to 2013.................................... 15

Chapter 3

Figure 3.1. Multivariate, nonparametric, multidimensional scaling of gene transcription profiles (see table 

3.1 for description of genes) of sea otters sampled at three locations in western Prince William Sound, 

Alaska, 2008 and 2012, the Alaska Peninsula, and in captivity at aquaria .................................................. 20

Figure 3.2. Distribution of average cycle threshold (CT) values across genes targeted by the 

panel of 13 primer sets ................................................................................................................................ 21

Tables

Chapter 1

Table 1.1. Estimates of sea otter numbers based on aerial surveys in western Prince William Sound, 

1993–2013, including estimates for the heavily oiled Knight Island and unoiled Montague Island intensive 

study areas....................................................................................................................................................8

Chapter 3

Table 3.1. Function of 13 genes identified in free-ranging sea otters sampled in western Prince William 

Sound, Alaska, in 2008 and 2012, and Alaska Peninsula in 2009, and in clinically normal captive sea otters 

sampled in 2008, 2009, or 2010 .................................................................................................................. 24

Conversion Factors and Datum

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2) 0.3861 square mile (mi2)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound avoirdupois (lb)

Volume

liter (L) 0.2642 gallon (gal)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.

Datum

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
1 

2013 Update on Sea Otter Studies to Assess Recovery 

from the 1989 Exxon Valdez Oil Spill, Prince William 

Sound, Alaska

By B.E. Ballachey, D.H. Monson, G.G. Esslinger, K. Kloecker, J. Bodkin, L. Bowen, and A.K. Miles

Executive Summary

On March 24, 1989, the tanker vessel Exxon Valdez ran aground in Prince William 

Sound, Alaska, spilling an estimated 42 million liters of Prudhoe Bay crude oil. Oil spread in a 

southwesterly direction and was deposited on shores and waters in western Prince William 

Sound (WPWS). The sea otter (Enhydra lutris) was one of more than 20 nearshore species 

considered to have been injured by the spill. Since 1989, the U.S. Geological Survey has led a 

research program to evaluate effects of the spill on sea otters and assess progress toward 

recovery, as defined by demographic and biochemical indicators. Here, we provide an update on 

the status of sea otter populations in WPWS, presenting findings through 2013. To assess 

recovery based on demographic indicators, we used aerial surveys to estimate abundance and 

annual collections of sea otter carcasses to evaluate patterns in ages-at-death. To assess recovery 

based on biochemical indicators, we quantified transcription rates for a suite of genes selected as 

potential indicators of oil exposure in sea otters based on laboratory studies of a related species, 

the mink (Mustela vison). In our most recent assessment of sea otter recovery, which 

incorporated results from a subset of studies through 2009, we concluded that recovery of sea 

otters in WPWS was underway. This conclusion was based on increasing abundance throughout 

WPWS, including increasing numbers at northern Knight Island, an area that was heavily oiled 

in 1989 and where the local sea otter population had previously shown protracted injury and lack 

of recovery. However, we did not conclude that the WPWS sea otter population had fully 

recovered, due to indications of continuing reduced survival and exposure to lingering oil in sea 

otters at Knight Island, at least through 2009. Based on data available through 2013, we now 

conclude that the status of sea otters—at all spatial scales within WPWS—is consistent with the 

designation of recovery from the spill as defined by the Exxon Valdez Oil Spill Trustee Council. 

The support for this conclusion is based primarily on demographic data, including (1) a return to 

estimated pre-spill abundance of sea otters at northern Knight Island, and (2) a return to pre-spill 

mortality patterns. Gene transcription rates in 2012 were similar in sea otters from oiled, 

moderately oiled and unoiled areas, suggesting abatement of exposure effects in 2012. However, 

because 2012 gene transcription rates generally were low for sea otters from all areas relative to 

2008, we cannot fully interpret these observations without data from a wider panel of genes. This 

slight uncertainty with respect to the data from the biochemical indicator is outweighed by the 

strength of the data for the demographic indicators. The return to pre-spill numbers and mortality 

patterns suggests a gradual dissipation of lingering oil over the past two decades, to the point 

where continuing exposure is no longer of biological significance to the WPWS sea otter 

population. 
2 

Introduction

On March 24, 1989, the tanker vessel Exxon Valdez ran aground on Bligh Reef in 

northeastern Prince William Sound (PWS), Alaska (fig. 1), spilling an estimated 42 million L of 

Prudhoe Bay crude oil (Spies and others, 1996). At that time, the Exxon Valdez oil spill (EVOS) 

was the largest recorded accidental release of oil into U.S. waters. Oil spread in a southwesterly 

direction, leaving a heavy layer on many beaches within western Prince William Sound (WPWS) 

before exiting Montague Strait and other passages at the southwestern corner of PWS (Galt and 

Payton, 1990). Islands in the central part of WPWS, particularly the Knight Island complex, were 

in the direct path of the moving oil and relatively close to the source, and thus were heavily 

contaminated. Oil eventually covered more than 26,000 km2 of water in WPWS and the Gulf of 

Alaska and contaminated more than 1,900 km of coastline (Morris and Loughlin, 1994; Spies 

and others, 1996). 

Much of the area affected by the spill was prime sea otter (Enhydra lutris) habitat. Sea 

otters were particularly vulnerable to acute effects of the spilled oil as they rely on their pelage 

rather than blubber for insulation, and oil drastically reduces the insulative value of the fur 

(Costa and Kooyman, 1982; Siniff and others, 1982). Within days of the spill, many live and 

dead oiled sea otters were captured or collected by spill response personnel, and nearly 1,000 sea 

otter deaths were documented over the months following the spill. However, not all carcasses 

were recovered and the total number of sea otters that succumbed to acute injuries has been 

estimated to be as high as several thousand (Ballachey and others, 1994). 

Following initial injury assessment, research to evaluate the process and progress toward 

recovery of injured species and ecosystems identified unexpected delays for several species that 

occupy nearshore habitats (Peterson and others, 2003; Rice and others, 2007), including sea 

otters. Concerns about long-term lack of recovery of sea otters in WPWS led to implementation 

of an extensive and diverse series of post-spill studies that has spanned the 24 years since the 

spill. Recovery of sea otters has been defined by the Exxon Valdez Oil Spill Trustee Council as:

“...when the population in oiled areas returns to conditions that would have existed had the 

spill not occurred and when biochemical indicators of hydrocarbon exposure in otters in the 

oiled areas are similar to those in otters in unoiled areas. An increasing population trend and 

normal reproduction and age structure in western Prince William Sound will indicate that 

recovery is underway” (Exxon Valdez Oil Spill Trustee Council, 2010; 

www.evostc.state.ak.us/Recovery/status.cfm).
3 

Figure 1. Map of Prince William Sound showing sea otter study areas. The dark gray area represents the 

extent of the spilled oil coverage in the Prince William Sound in 1989.
4 

Findings of sea otter studies by the U.S. Geological Survey have been presented in 

multiple publications (appendix 1). Briefly, sea otter abundance in heavily oiled WPWS 

remained depressed, at about one-half the pre-spill estimate, with no evidence of recovery 

through 2005 (Bodkin and others, 2002, 2011). Reduced survival rates appeared to be the 

proximate factor for delayed sea otter recovery (Monson and others, 2000, 2011; Ballachey and 

others, 2003). Food limitation was discounted as contributing to that reduced survival, whereas 

chronic exposure to residual oil was implicated as a concern (Bodkin and others, 2002; Dean and 

others, 2002; Peterson and Holland-Bartels, 2002; Bodkin and others, 2012).

Several lines of evidence demonstrated that oil from the spill persisted in the environment 

longer than anticipated. In 2001, Short and others (2004, 2006) documented unexpected amounts 

(>55,000 kg) of Exxon Valdez oil remaining in intertidal habitats in WPWS, and estimated that 

subsurface oil might persist at some sites for several decades (Short and others, 2007). Studies of 

mussels and clams, both common prey items of sea otters foraging in intertidal habitats, 

indicated that lingering oil was bioavailable as late as 2002 (Fukuyama and others, 2000; 

Thomas and others, 2007). As recently as 2008, sea otters from WPWS showed elevated 

transcription in several genes consistent with potential recent and chronic exposure to organic 

contaminants (Miles and others, 2012). Evidence of exposure to lingering oil through metabolic 

pathways also has been documented in other nearshore species, including harlequin duck 

(Histrionicus histrionicus; Trust and others, 2000; Esler and others, 2010), Barrow’s goldeneye 

(Bucephala islandica; Trust and others, 2000; Esler and others, 2011), pigeon guillemot 

(Cepphus columba; Golet and others, 2002) and two nearshore fishes—the masked greenling 

(Hexagrammos octogrammus) and the crescent gunnel (Pholis laeta) (Jewett and others, 2002). 

Considering all data collected through 2009, we concluded that the body of evidence for 

sea otters suggested recovery in the spill area of PWS was underway but not yet complete 

(Bodkin and others, 2011, 2012; Monson and others, 2011; Miles and others, 2012). The finding 

of progress toward recovery was based on increased abundance of sea otters in the area of 

northern Knight Island in WPWS in 2009, following almost two decades of reduced numbers 

relative to estimated pre-spill numbers (Bodkin and others, 2011). Evidence for continuing 

exposure to lingering oil in the environment remained, based on potential for exposure to oil 

lingering in intertidal habitats (Bodkin and others, 2012), persistent depressed survival of sea 

otters in oiled areas (Monson and others, 2011), and molecular measures suggesting exposure to 

organic contaminants for sea otters in oiled areas (Miles and others, 2012). 

In this report, we update findings on three aspects of long-term sea otter studies:

1. Aerial surveys of abundance in WPWS through 2013 (Chapter 1; update of Bodkin and 

others, 2011); 

2. Ages-at-death, based on annual recovery of sea otter carcasses on shorelines of WPWS

through 2013 (Chapter 2; update of data presented in Monson and others, 2011); 

3. Gene transcription analyses of sea otters in oiled and unoiled areas of WPWS through 

2012 (Chapter 3; update of Miles and others, 2012). 

The report concludes with a synthesis and conclusions section in which we integrate 

findings from the three chapters. 
5 

Chapter 1. Sea Otter Abundance in Western Prince William Sound 

through 2013

By G.G. Esslinger, B.E. Ballachey, and J.L. Bodkin

Introduction

The 1989 Exxon Valdez oil spill (EVOS) caused significant sea otter mortality in western 

Prince William Sound (WPWS), both in the immediate weeks and months post-spill (Ballachey 

and others, 1994) and over longer time frames (years and decades; Monson and others, 2011). To 

assess recovery of sea otters, the Exxon Valdez Oil Spill Trustee Council established both 

demographic and biochemical criteria. As part of our effort to assess recovery based on 

demographic indicators, we used aerial surveys to estimate abundance in WPWS, including at 

the heavily oiled area of northern Knight Island and at Montague Island, an unoiled reference 

area (fig. 1.1). 

At the time of the spill, survey data on the abundance of sea otters in WPWS were 

lacking. Aerial survey methods were developed after the spill (Bodkin and Udevitz, 1999), and 

annual surveys commenced in 1993. Our approach for assessing demographic recovery based on 

abundance was to consider overall trend (increasing, decreasing, or stable), and the time point at 

which the estimated number of new otters in the population was equal to or greater than the 

number of otters estimated to have died in the immediate aftermath of the spill. Acute spillrelated mortality estimates for WPWS ranged from 750 (Garshelis, 1997) to 2,650 sea otters 

(Garrott and others, 1993). For northern Knight Island, Dean and others (2000) estimated prespill abundance to be 165 sea otters, based on the number of carcasses collected, an estimated 

number of unrecovered carcasses, and the number of sea otters removed for rehabilitation. 

A comprehensive analysis of results of aerial surveys from 1993 to 2009 was presented 

by Bodkin and others (2011). They found that numbers of sea otters in WPWS increased through 

2000 at an average annual rate of 4 percent. However, at northern Knight Island, where oiling 

was heaviest and sea otter mortality highest, no increase in abundance was evident by 2000. A 

continued significant increase in abundance was observed in WPWS between 2001 and 2009, 

with an average annual rate of increase from 1993 to 2009 of 2.6 percent. The 2009 estimate of 

numbers of sea otters in WPWS was 3,958 (standard error=653), nearly 2,000 more than the first 

post-spill estimate in 1993. Surveys between 2003 and 2009 also identified a significant 

increasing trend at heavily oiled northern Knight Island, averaging about 25 percent annually and 

resulting in a 2009 estimate of 116 sea otters (standard error=19). This 2009 abundance estimate 

was about 30 percent less than the pre-spill estimate of 165 sea otters, but was interpreted as 

evidence of progress toward recovery of sea otters in the most heavily oiled areas of WPWS.

Here, we update aerial survey results of Bodkin and others (2011) with data from 2011 to 

2013, and evaluate trends in sea otter abundance in WPWS, including northern Knight Island. 
6 

Methods

Consistent with prior sea otter surveys in WPWS, we used an aerial survey method 

developed specifically for estimating sea otter abundance (Bodkin and Udevitz, 1999). As part of 

the survey design, a combination of water depth and distance from shore is used to divide sea 

otter habitat into high and low density strata (fig. 1.1). Transects are spaced systematically within 

strata according to expected sea otter densities and time available to conduct the survey. The 

400-m wide strip transects are surveyed by a pilot and an observer in a fixed-wing aircraft at an 

altitude of 91 m and an airspeed of 65 mph. Because sea otters can be difficult to sight in areas 

with kelp and usually are not visible when they dive underwater to gather prey, intensive 

searches are conducted periodically throughout the survey area to estimate the proportion of sea 

otters being detected on the transects. The detection probability is used to adjust the estimate of 

abundance. 

For the WPWS survey, the same set of transects was surveyed from 1995 to 2013, once 

for each survey year (fig. 1.1) except in 2001, 2006, and 2010. To increase precision in estimates 

for the intensive oiled (northern Knight Island) and unoiled (Montague Island) study areas, up to 

five replicate surveys were conducted each year (except in 1993, 1994, 2006, and 2010 for both 

areas, and in 2013 at Montague Island) using the same techniques described in Bodkin and 

Udevitz (1999). Each replicate survey was randomly selected from 18 possible combinations of 3 

high density and 6 low density sets of spatially unique transects. During each survey, data were 

entered using a custom survey application (Doug Burn, U.S. Fish and Wildlife Service, 

Anchorage, Alaska) in ArcPad® (ESRI®, Inc., Redlands, Calif.) on a Toughbook® laptop 

computer (Panasonic©, Secaucus, N.J.). Survey data were post-processed in ArcMapTM (ESRI®, 

Inc.) and SAS® 9.2 (SAS Institute©, Cary, N.C.) to estimate abundance and associated variance 

at different spatial scales. To estimate population growth rate for WPWS, we used linear 

regression (PROC GLM, SAS Institute©, Cary, N.C.) to fit log-transformed population estimates 

weighted by standard errors. 

Results

Results of aerial surveys conducted from 1993 to 2013 are summarized in table 1.1. Since 

aerial surveys designed specifically to estimate sea otter abundance began in 1993, numbers of 

sea otters in WPWS have increased at an average annual growth rate of 3 percent (fig. 1.2). 

Consistent with the upward trend in WPWS, numbers of sea otters at both the Knight Island

(2011–2013; fig. 1.3) and Montague Island (2011–2012; fig. 1.4) study areas were elevated in 

recent years. The three most recent WPWS abundance estimates (2011–2013) represent an 

increase of about 850–2,200 sea otters since 1993 (table 1.1). Numbers of sea otters at northern 

Knight Island in 2011–2013 are similar to the pre-spill estimate of 165 (fig. 1.3). 
7 

Figure 1.1. Prince William Sound (PWS), Alaska. Blue lines delineate the western PWS survey transects 

and collectively represent the survey area. Red ovals indicate general location of the intensive study areas 

at northern Knight Island (oiled area) and Montague Island (unoiled area) where up to five replicate surveys 

were conducted each survey year. The high density stratum is defined by water depths less than 40 m or 

400 m from shore, whichever is greater. The low density stratum extends from the 40- to 100-m depth 

contour or 2 km from shore, whichever is greater. The high density stratum was sampled at a higher 

intensity (1,200 m between transects) than the low density stratum (4,800 m between transects).
8 

Table 1.1. Estimates of sea otter numbers based on aerial surveys in western Prince William Sound, 

1993–2013, including estimates for the heavily oiled Knight Island and unoiled Montague Island intensive 

study areas.

[–, no estimate]

Western PWS Knight Island Montague Island

Abundance Standard Abundance Standard Abundance Standard

Year estimate error estimate error estimate error

1993 2,054 698 75 – 335 –

1994 2,228 356 78 – 303 –

1995 2,185 225 89 22 297 50

1996 2,180 218 65 13 382 39

1997 2,341 202 76 19 595 31

1998 3,119 494 76 16 623 92

1999 2,475 381 81 15 586 109

2000 2,658 294 79 6 544 95

2001 – – 79 20 659 189

2002 1,840 334 38 11 369 48

2003 2,631 540 26 8 619 46

2004 2,704 315 54 17 561 86

2005 2,751 311 37 14 725 105

2006 – – – – – –

2007 2,380 372 71 14 356 58

2008 3,609 635 98 24 589 162

2009 3,958 653 116 29 310 62

2010 – – – – – –

2011 2,896 392 169 30 662 224

2012 3,459 448 152 28 995 136

2013 4,277 638 139 33 – –
9 

Figure 1.2. Trend in sea otter abundance (± standard error) in western Prince William Sound, Alaska, 

1993–2013.

Figure 1.3. Estimated numbers of sea otters (± standard error) at heavily oiled northern Knight Island, 

Prince William Sound, Alaska, 1993–2013, compared to the pre-spill abundance estimate (Dean and 

others, 2000).
10

Figure 1.4. Estimated numbers of sea otters (± standard error) at the unoiled Montague Island study area, 

Prince William Sound, Alaska, 1993–2012.

Discussion

Following their recovery from the commercial fur harvests and reoccupation of WPWS 

prior to 1970, sea otters were thought to be at or near equilibrium density prior to the spill 

(Bodkin and others, 2000). However, no surveys were conducted in WPWS just prior to the spill, 

and accurate data on abundance of sea otters in the area were not available. Survey methods were 

developed in the first post-spill years (Bodkin and Udevitz, 1999) and implemented in 1993. To 

determine whether WPWS sea otter numbers had recovered from the spill, we used estimates of 

acute mortality from the spill, and considered when the number of otters that died immediately 

after the spill had been replaced. By this measure, the increased abundance of sea otters in 

WPWS was consistent with recovery by 2009, following almost a decade of population growth. 

At the heavily oiled northern Knight Island study area, however, the point at which sea 

otter abundance recovered to the pre-spill abundance apparently was delayed relative to WPWS 

overall. The abundance estimates at northern Knight Island did not exceed the estimated pre-spill 

level until 2011, and the 2012 and 2013 survey results were consistent with the 2011 finding (no 

survey data are available for 2010). Thus by 2011, for both WPWS and northern Knight Island, 

the aerial survey data indicate that sea otter abundance is consistent with the definition of 

population recovery from the spill. 
11

Chapter 2. Age Distributions of Sea Otters Found Dead in Western Prince 

William Sound, Alaska, through 2013

By D.H. Monson

Introduction

In spring 1989, the Exxon Valdez oil spill (EVOS) resulted in acute mortality of 1,000 to 

several thousand sea otters in western Prince William Sound (WPWS) and the central Gulf of 

Alaska (Ballachey and others, 1994). The spill also left crude oil in the intertidal zone in 

unconsolidated sediments of some WPWS beaches (Morris and Loughlin, 1994; Spies and 

others, 1996), some of which remained for more than two decades (Boufadel and others, 2010; 

Li and Boufadel, 2010; Xia and others, 2010). As sea otters forage, they excavate clams and 

other intertidal invertebrates, which can re-suspend buried oil and function as a pathway for 

chronic exposure of sea otters to toxic oil residues remaining in the environment (Bodkin and 

others, 2012). Surveys of sea otters indicated that numerical recovery in the most heavily oiled 

areas did not occur until approximately two decades post-spill (Chapter 1, this report). Extensive 

studies (appendix 1) suggested that delayed sea otter recovery was due to chronic exposure to oil, 

likely through effects on survival (Monson and others, 2000, 2011) rather than food limitation, 

reproductive constraints, or other alternative explanations. 

To assess recovery of sea otters, the Exxon Valdez Oil Spill Trustee Council established 

both demographic and biochemical criteria. As part of our effort to assess recovery based on 

demographic indicators, we estimated abundance using aerial surveys (Chapter 1). We also 

continued collections of sea otter carcasses, a monitoring practice that began in WPWS in the 

1970s. Age distributions of recovered carcasses can be used to describe trends and patterns in 

mortality of wild mammal populations (Caughley, 1966). Generally, mortality patterns of longlived mammals include peaks in young and old age classes, with lower mortality in the primeage class (Caughley, 1966; Emlen, 1970; Siler, 1979; Eberhardt, 1985). Sea otters are relatively 

long-lived, attaining ages of 15–20 years (Riedman and Estes, 1990), and follow this general 

pattern, with most natural mortality occurring in young and old age classes (Kenyon, 1969). 

Based on age distributions of beach-cast sea otter carcasses collected each spring prior to 

the spill, the sea otter population in WPWS fit the previously described pattern with most natural 

mortality occurring in young and old age classes (Monson and others, 2000). Monson and others 

(2000) used the age distribution data to quantify the long-term effects of the oil spill on survival 

of sea otters. They found that from 1989 to 1998, survival of sea otters in WPWS was lower than 

pre-spill estimates, and that the magnitude of the difference was related to both age class of 

animals and time since the spill. Generally, survival of juveniles was low during the first few 

years following the spill while prime-age and old-age survival rates were less affected. Over 

time, juvenile survival increased, while survival of prime-age and old-age animals decreased 

(Monson and others, 2000). Decreases in survival were not limited to animals alive at the time of 

the spill (that is, individuals that potentially survived acute exposure), indicating that chronic 

exposure to residual contaminants in the environment continued to affect animals born in or 
12

migrating into oiled habitats. Low survival of tagged juvenile sea otters following the spill 

(Monnett and Rotterman, 1995; Ballachey and others, 2003) and discovery of elevated activity of 

biomarkers associated with hydrocarbon exposure in other nearshore species (Esler and others, 

2002, 2010, 2011; Golet and others, 2002; Jewett and others, 2002; Bowyer and others, 2003; 

Ricca and others, 2010) provided additional evidence that reduced survival may have been 

caused by lingering oil.

Only a portion of the WPWS sea otter population appeared to be experiencing decreased

survival rates, creating a population sink that continued to limit the rate of recovery of the entire 

WPWS population through at least 2005 (Monson and others, 2011). Source-sink models fit to 

mortality data collected through 2008 found no indication that elevated mortality had ceased by 

2008 (Monson and others, 2011). However, survey data indicated that significant increases in sea 

otter abundance occurred in the heavily oiled areas between 2005 and 2013 (Bodkin and others, 

2011; Chapter 1, this report) suggesting that mortality effects may have modulated during the 

late 2000s (Monson and others, 2011). Here, we present age distributions of carcasses collected 

through 2013, and show that mortality patterns in WPWS have returned to “normal,” defined as 

the pre-spill pattern of mortality. 

Methods

Sea otter carcass collections from 1976 through 2008 have been described previously 

(Monson and others, 2000, 2011), and similar collections continued from 2010 through 2013. 

Green Island (fig. 1), which was oiled in 1989, was the site of pre-spill collections, and carcass 

collections were continued there through 2013. Beginning in 1996, in addition to Green Island 

collections, carcasses were collected from shorelines throughout WPWS that received heavy 

oiling in 1989, including areas where residual oil was found through at least 2008 (Short and 

others, 2004, 2006, 2007; U.S. Geological Survey, unpub. data, 2008). Because the sex of dead 

animals often could not be determined, sexes were combined when examining age-at-death 

distributions. Skulls were collected when present, and a tooth (preferentially a premolar) 

removed for age analysis, although pups (<1 year old) also were identified by open skull sutures 

and deciduous teeth (Schneider, 1973). Longitudinal sections of each tooth were decalcified for 

cementum annuli readings, generally providing age estimates ±1 year (Bodkin and others, 1997). 

Matson’s Laboratory (Milltown, Mont.) sectioned and aged all teeth.

Kolmogorov-Smirnov (K-S) tests (Sokal and Rohlf, 1995) were used to compare the 

2010–2013 age distribution to four other distributions including: (1) pre-spill (1974–1989), (2) 

spill-year (1989), (3) 1990–1993, and (4) 1994–2008. The two post-spill distributions (1990–

1993 and 1994–2008) corresponded to two distinct periods of mortality pattern shifts identified 

by Monson and others (2011). Specifically, 1990–1993 was characterized by very low juvenile 

survival and only slightly reduced survival in the prime-age and old-age classes (Monson and 

others, 2011). In contrast, 1994–2008 was characterized by relatively normal juvenile survival 

but declining survival rates in the older age classes (Monson and others, 2011). For graphical 

presentation, age distributions were lumped into three age classes including—(1) juveniles (0-

age pups and 1-yr-old juveniles), (2) prime-age (2–8-yr-olds), and (3) old-age (>8 yr), and 

variability was calculated as simultaneous confidence intervals for multinomial proportions 

(Quesenberry and Hurst, 1964). The age range for “prime-age” was defined based on pre-spill 

age-at-death data and prior to any post-spill carcass collections. Subsequent statistical models 

(Udevitz and Ballachey, 1998) supported our definition of “old-age” beginning at 9 years of age 

(that is, the first year adult survival began to decrease under normal conditions). For K-S tests, 
13

ages were not lumped although 0-age animals were excluded because small pups are easily 

removed by scavengers and thus are known to be under-represented in carcass collections. As a 

result, yearly variability in proportions of 0-age animals may be influenced as much by 

variability in scavenging rates as actual mortality rates (Bodkin and Jameson, 1991). 

Variability in the proportion of prime-age animals in the carcass collections was 

examined over time by plotting this proportion for each year with equal to or greater than five 

individuals in each age-class. For years with small sample sizes, defined as any age class having 

less than five individuals, that year’s collection was combined with the following year, providing 

the combination did not cross any previously established “boundary” points (that is, 1989, 1993, 

and 2008, based on findings in Monson and others, 2011). If a small sample size distribution 

occurred at the boundary point, it was combined with the previous year’s collection. 

Results

From 2010 to 2013, 166 carcasses were recovered and had ages-at-death determined (fig. 

2.1). In 2010, the proportion prime-age was high (0.56) and appeared similar to collections made 

in the previous 8–9 years (fig. 2.2). However, the 2010 sample was too small (n=18) for valid 

statistical comparisons and could not be combined a priori with the previous (1994–2008) 

grouping, and thus was included with the 2011–2013 data to form the most recent grouping. As a 

whole, the 2010–2013 distribution differed significantly from the spill-year distribution (K-S 

dmax = 0.29, p<0.0001) and the 1994–2008 post-spill distribution (K-S dmax = 0.17, p=0.025) but 

not from the 1990–1993 post-spill distribution (K-S dmax = 0.17, p=0.14; fig. 2.1). The 2010–

2013 distribution also did not differ from the 1976–1989 pre-spill distribution (K-S dmax = 0.12, 

p=0.33; fig. 2.1), which is significant because it is the first post-spill grouping that did not differ 

from the pre-spill distribution. The 1989 spill year distribution was significantly different from 

all other age distributions (K-S dmax> 0.16, p < 0.05) while the 1990–1993 and 1994–2008 postspill distributions both differed from the 1976–1989 pre-spill distribution (K-S dmax> 0.23, 

p < 0.01) and did not differ from each other (K-S dmax = 0.11, p=0.4) (fig. 2.1).

When the proportion of prime-age otters in the annual carcass collections is compared 

across years (fig. 2.2), lower proportions are noted for 2010–2013 relative to the proportions in 

collections from the previous decade. The 2010–2013 proportions are similar to those noted in 

the pre-spill collections. 
14

Year groupings

76-89 89 (spill) 90-93 94-08 10-13

Relative Freq.

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0-1 yrs 

2-8 yrs 

>8 yrs 

(215 a) (419 b) (119 c,d) (411 d) (166 a,c)

Figure 2.1. Relative age distributions of sea otter carcasses collected on western Prince William Sound 

beaches from 1976 to 2013. All non-pup ages were estimated by tooth cementum analysis (Matson’s 

Laboratory, Milltown, Mont.). Total numbers of carcasses collected are in parentheses above each 

grouping and distributions with the same letter do not differ significantly from each other.
15

Year

1975

1980

1985

1990

1995

2000

2005

2010

2015

Relative Freq.

0.0

0.1

0.2

0.3

0.4

0.5

0.6

(34)

26

(40)

58

419

59

(60)

(31)

22

22

51 29

54

(85)

26

57

25

(66)

(60)

57

49

Spill

Figure 2.2. Relative proportion of prime-age animals (2–8 yr-olds) in age distributions of sea otter 

carcasses collected on western Prince William Sound beaches from 1976 to 2013. Open circles denote 

pre-spill collections and filled circles denote post-spill collections. Note: Carcasses recovered the year of 

the spill but deemed to be pre-spill deaths make up the 1989 pre-spill distribution, and carcasses recovered 

in 1989 after the spill and deemed to be spill-related deaths make up the 1989 post-spill distribution. 

Numbers above symbols indicate total N for each distribution, and numbers in parentheses signify multiyear collections combined to ensure equal to or greater than five individuals in each age-class. 

Discussion

Survey data indicated increasing sea otter numbers in WPWS and at heavily oiled Knight 

Island, starting in about 2007 (Chapter 1, this report). However, survival models based on 

carcass collections did not predict improved survival rates through at least 2008 (Monson and 

others, 2011). In general, the proportion of prime-age animals in carcass collections had been 

increasing since the spill (fig. 2.2) while the proportion of older animals had been decreasing. In 

2011, the proportion of prime-age animals decreased to pre-spill levels, and remained similar to 

pre-spill values in 2012 and 2013 (fig. 2.2). Thus, it appears that the elevated mortality described 

by Monson and others (2000, 2011) may have continued to affect at least some portion of the 

population until about 2010, with the combined 2010–2013 distribution representing a transition 

period in sea otter mortality to the pre-spill pattern.
16

The observed increase in sea otter abundance at heavily oiled northern Knight Island 

began between 2005 and 2007 (Chapter 1, this report), and preceded the return of the age-atdeath distribution to the pre-spill pattern by four to six years. The lag between the increase in 

abundance and a return to a “normal” pre-spill age-at-death distribution may be explained by the 

time required for the standing population age-structure (that is, the distribution of ages of the 

living animals) to stabilize. Specifically, under normal conditions, the age-at-death distribution 

developed from a stable standing age-structure typical of a relatively long-lived species. 

However, during the period when survival rates were transitioning from post-spill rates to more 

normal rates, the standing age-structure of the population was shifting, and the age-at-death 

distributions reflected both the changing standing age-structure and the changing survival rates. 

As chronic exposure to lingering oil declined to a level where adverse effects on survival 

diminished, the living population began to increase in size. However, it took several years of 

relatively constant survival rates for the standing age-structure to re-stabilize, and allow the 

return of the age-at-death distribution to the normal pattern, dominated by juvenile and old-age 

classes.

Based on sea otter abundance data through 2013 (Chapter 1, this report) and return of the 

sea otter carcass age distributions to pre-spill proportions by 2013, exposure of pups and 

juveniles likely decreased to biologically insignificant levels by the early to mid-2000s, with the 

last of the affected cohorts dying out by the early 2010s. These findings are supported by the 

gene transcription data (Chapter 3, this report), which suggest that effects of exposure persisted 

through 2008 but declined by 2012. It appears that for all ages, survival consequences of 

exposure have abated over the past few years and the WPWS sea otter population no longer is 

limited to any demographically meaningful degree by oil exposure. 
17

Chapter 3. Gene Transcript Profiles in Sea Otters from Prince William 

Sound, Alaska, 2008 and 2012, and Clinically Normal and Wild Reference 

Sea Otters

By L. Bowen, A.K. Miles, B.E. Ballachey, and J.L. Bodkin

Introduction

To assess recovery of sea otters from the 1989 Exxon Valdez oil spill, the Exxon Valdez

Oil Spill Trustee Council established demographic and biochemical criteria. To examine the 

biochemical status of the sea otters in the oiled area of western Prince William Sound (WPWS), 

we used gene transcription studies. Exposure to petroleum hydrocarbons has the potential to 

cause not only catastrophic short-term effects, but also important but often underappreciated 

long-term damage to individuals, populations, and ecosystems. The question of extent and 

duration of long-term effects is difficult to answer, as the pathophysiological changes within an 

individual may be significant yet subtle, and consequently undetectable using classical diagnostic 

methods. The earliest observable signs of health impairment are altered levels of gene 

transcripts, evident prior to clinical manifestation (McLoughlin and others, 2006). As a result of 

this keystone function, analysis of mRNA can provide information about dynamic changes in the 

functional state of an organism. The utility of the methodology used in our study relies on the 

assumption that oil-induced pathology in sea otters is accompanied by predictable and specific 

changes in gene transcription. 

In 2008, we sampled sea otters in oiled and unoiled areas of WPWS and compared them 

to captive and wild reference otters from the Alaska Peninsula. We concluded that sea otters in 

oiled areas had gene transcription patterns consistent with chronic, low-grade exposure to 

organic compounds (Miles and others, 2012). In 2012, we resampled sea otters in the same areas 

of WPWS to evaluate whether gene transcription patterns observed in 2008 persisted. Here, we 

provide results of gene transcription analyses on sea otters sampled in the summer of 2012, and 

compare these findings to those from 2008. 

Methods

Free-Ranging Target Sea Otters

Forty-five sea otters from three different areas of WPWS were captured in summer 2008 

and 60 sea otters were captured in 2012. Sea otters were captured at Knight Island (heavily oiled; 

n=16, 2008; n=24, 2012), Prince of Wales Passage (moderate level of oil contamination; n=15, 

2008; n=18, 2012), and Montague Island (unoiled, reference area; n=14, 2008; n=18, 2012) (fig.

1, “Introduction”). Lingering oil from the EVOS was more prevalent at Knight Island than at 

Prince of Wales Passage at least through 2002 (Short and others, 2004). Sea otters were captured 

and blood drawn within 1–2 hours. All target as well as captive and free-ranging reference sea 

otters were anesthetized with fentanyl citrate and midazolam hydrochloride (Monson and others, 

2001) prior to blood draw. Capture methods are presented in greater detail in Miles and others 

(2012) and Bodkin and others (2012). 
18

Captive and Free-Ranging Reference Sea Otters

Blood samples from 17 captive reference sea otters were obtained from the Monterey 

Bay Aquarium (Monterey, Calif.), Shedd Aquarium (Chicago, Ill.), Oregon Coast Aquarium 

(Newport, Oreg.), and the Vancouver Aquarium (Vancouver, B.C.) in 2008, 2009, and 2010, and 

included both northern and southern subspecies (Bowen and others, 2011). These animals were 

identified as clinically normal by staff veterinarians at these aquaria at the time of blood 

collection.

Wild reference sea otters were captured along the southwestern Alaska Peninsula in 

summer 2009, and 25 of these sea otters used in our study were deemed clinically normal by the 

attending veterinarian. Alaska Peninsula sea otters were included as reference because they were 

from an area not affected by the EVOS, far removed from any known human perturbations, and 

were at or below equilibrium density. These sea otters were captured and processed the same as 

the WPWS sea otters.

Blood Collection and RNA Extraction

A 2.5 mL sample from each sea otter was drawn directly into a PAXgeneTM blood RNA 

collection tube (PreAnalytiX©, Switzerland) from either the jugular or popliteal vein and then 

frozen at - 20oC until extraction of RNA (Bowen and others, 2011). The PAXgeneTM tube 

contains RNA stabilizing reagents that protect RNA molecules from degradation by RNases and 

prevents further induction of gene transcription. Without stabilization, copy numbers of 

individual mRNA species in whole blood can change more than 1,000-fold during storage and 

transport. The RNA from blood in PAXgeneTM tubes was isolated according to manufacturer’s 

standard protocols (Bowen and others, 2007, 2011; Miles and others, 2012). All RNA was 

checked for quality by running on both an agarose gel and on a nanodrop 2000 and achieved 

A260/A280 ratios of approximately 2.0 and A260/A230 ratios of less than 1.0. A standard cDNA 

synthesis was performed on 2 μg of RNA template from each animal (Bowen and others, 2007, 

2012; Miles and others, 2012). Real-time PCR systems for the individual, sea otter-specific 

reference or housekeeping gene (S9) and genes of interest were run in separate wells (Bowen and 

others, 2007, 2011; Miles and others, 2012; table 1). Amplifications were conducted on a 7300 

Real-time Thermal Cycler (Applied BiosystemsTM, Foster City, Calif.) with reaction conditions 

identical to those in Bowen and others (2007, 2011) and Miles and others (2012). 

Statistical Analysis

We used nonparametric statistical analyses because the cycle threshold (CT) measure of 

gene transcription provided by qPCR may have a lognormal distribution (McLoughlin and 

others, 2006). We used ANOSIM (Primer v6 software, Plymouth, U.K.) nonparametric analysis 

of variance to test for differences in gene transcription among locations, that is, the WPWS 

subpopulations and reference sea otters (Alaska Peninsula and captive), and between years. We 

used conventional nonparametric mean comparison tests (Kruskal-Wallis with Dunns’ Multiple 

Comparison; NCSS© Statistical Software, 2007, Kaysville, Utah) to evaluate transcript values of 

each gene by classification groups (that is, location [including reference] and year). 
19

We conducted multivariate, multidimensional scaling analysis (MDS) in conjunction with 

cluster analysis of individual sea otters clustered by similarity in transcription and not by predefined groups such as location in order to facilitate comparison to Miles and others (2012). 

Statistical comparisons of clusters were made using SIMPROF (Primer v6). Statistical 

significance was based on p values <0.05, and in the case of the ANOSIM tests, relative to the R 

statistic value.

Results

Overall gene transcription (CT) values differed between sea otters from WPWS in 2008 

or 2012 and the Alaska Peninsula or captive sea otters (ANOSIM, p< 0.001, Global R=0.46, with 

0 permuted statistics > Global R) (fig. 3.1). The Alaska Peninsula and captive sea otters did not 

differ (p=0.46) and hereafter “reference” refers to these two groups collectively. Individually, the 

three 2008 WPWS subpopulations differed significantly (p<0.001) from the reference sea otters, 

with indication of less chance of overlap in transcription profiles with Knight Island (R=0.40 

[Alaska Peninsula], 0.53 [captives]) than with Montague Island (R=0.25, 0.28) or Prince of 

Wales Passage (R=0.28, 0.21) sea otters. Transcription profiles did not differ significantly within 

the three 2008 subpopulations (p>0.16). 

The three 2012 WPWS subpopulations differed significantly (p<0.001) from the 

reference sea otters. There was less chance of overlap in transcription profiles with sea otters 

from moderately oiled Prince of Wales Passage (R=0.71, 0.85) than with those from oiled Knight 

Island (R=0.64, 0.75) or unoiled Montague Island (R=0.65, 0.83) (fig. 3.1). Transcription 

profiles did not differ significantly among the three 2012 WPWS subpopulations (p>0.42).All 

2012 WPWS subpopulations differed significantly from all 2008 WPWS subpopulations 

(p<0.001), with an overall pattern of lower levels of gene transcription (“down-regulation” of 

genes) noted in 2012 (fig. 3.2). 

Using Kruskal-Wallis, 11 of 13 genes were identified that had significant differences 

between at least two classification groups (fig. 3.2). Most evident, HDC, THRB, HSP70, IL10, 

MX1, and CaM differed between 2008 and 2012 otters regardless of location, with higher levels 

of gene transcription in 2008 than in 2012. Although not statistically significant, HDC 

(associated with tumor-formation) was more highly transcribed at Knight Island than at 

Montague Island or Prince of Wales Passage in 2008 (fig. 3.1), but this finding did not persist in 

2012. There were minimal differences in transcription levels for COX2, AHR, IL18, DRB, and 

5HTT between 2008 and 2012. Transcription of CYT and CCR3 did not differ among 

classification groups. 

Patterns depicted by the MDS analyses were similar to that reported in Miles and others 

(2012), with differences attributable to the inclusion of the 2012 samples (fig. 3.2). More 2008 

sea otters from Knight Island were found in Clusters 1, 1a, and 1b than those from Prince of 

Wales Passage or Montague Island, and these clusters included no sea otters from 2012. Cluster 

2 included all captive and most (76 percent) Alaska Peninsula sea otters. Cluster 1 was 

characterized in particular by higher levels of transcription of HDC, CYT, and HSP70. 

Importantly, the 2008 and 2012 samples were distinctly separate; Cluster 3 contained mostly 

2012 sea otters (regardless of location), attributed primarily to lower levels of gene transcription. 
20

Figure 3.1. Multivariate, nonparametric, multidimensional scaling of gene transcription profiles (see table 

3.1 for description of genes) of sea otters sampled at three locations in western Prince William Sound, 

Alaska, 2008 and 2012, the Alaska Peninsula, and in captivity at aquaria. Interpretive cluster analysis and 

SIMPROF (similarity profile permutation test; Primer, v6, Plymouth, U.K.) indicated significant (p< 0.001–

0.05) separation among all clusters depicted by circles. The figure is two-dimensional (Stress=0.11), 

however, three-dimensional (Stress=0.08) representation depicted further separation among clusters in 

3–D space.
21

Figure 3.2. Distribution of average cycle threshold (CT) values across genes targeted by the panel of 13 

primer sets. Bars range from the 10th to the 90th percentile of values for each gene, normalized to the S9 

housekeeping gene for each sea otter. Circles represent 5th and 95th percentile outliers. Indicated are 

those genes that differed significantly among sea otters by classification groups (location and year), using 

Kruskal-Wallis and Dunns’ Multiple Comparison Tests. K, Knight Island; M, Montague Island; P, Prince of 

Wales Passage; R, Reference; 08, 2008; 12, 2012. Classification groups with like letters (a, b, or c) do not 

differ significantly; no letter, does not differ from any comparisons.
22

Figure 3.2.—Continued.
23

Discussion

Gene transcription patterns in the 2008 WPWS sea otters, particularly those from Knight 

Island, generally were suggestive of molecular reactions to organic exposure, tumor formation, 

inflammation, and viral infection that may be consistent with chronic, low-grade exposure to an 

organic substance (Miles and others, 2012). This is consistent with findings from Bodkin and 

others (2012), which document a potential pathway of exposure to lingering oil for sea otters 

foraging in the intertidal where lingering oil persisted. In particular, sea otters from the spill area 

demonstrated elevated transcription of several of the genes measured, including HDC and THR, 

and lower transcription, or down-regulation, of DRB. Dong and others (1997) reported downregulation of DRB by a dioxin compound, and both polycyclic aromatic hydrocarbons 

(constituents of crude oil) and dioxin-like compounds have been implicated in similar 

biochemical detoxification responses. 

In contrast, the 2012 WPWS sea otters had an overall pattern of down-regulation of gene 

transcription. In general, the regulation of gene transcription includes mechanisms to increase or 

decrease the production of mRNA, and the occurrence of low gene transcription has been 

observed in other marine mammal studies (Stott and McBain, 2012). However, the prevalence of 

down-regulation among 2012 WPWS sea otters was noteworthy and contributing factors are not 

fully understood. We confirmed that the observed low transcription values were not a result of a 

laboratory artifact. We analyzed all samples in duplicate, and if any duplicate samples were 

greater than 1 CT difference, they were re-analyzed. All samples were run with an internal 

reference standard (the S9 housekeeping gene). If the internal reference was greater than 3 CT

values from the average internal reference value for control populations, the entire panel was rerun in duplicate; this always resulted from insufficient RNA and those samples were omitted 

from analysis (that is, <1 percent of the samples). Finally, samples were run with other samples 

from other Alaska and also California populations and re-run in different combinations to check 

for ‘plate’ or ‘batch’ effects; no such effects were encountered. Of significance, we conducted 

analyses of sea otters from California during the same time period as analyses of the 2012 

WPWS sea otters. About 50 percent of the California otters analyzed aligned with the reference 

group, about 10 percent displayed high transcription, and about 40 percent had low transcription 

of 3–6 of 13 genes. Most of these low transcription animals were from a specific area of the 

California coastline. Causes of down-regulation of gene transcription in WPWS in 2012 are not 

certain, and should be a topic of continued research.

We found no evidence that gene transcription in sea otters captured in WPWS in 2012 

differed by oiling history, including genes that indicated potential responses to organic 

compounds in 2008. We conclude that these findings indicate that conditions specific to effects 

of exposure to oil characterized by our suite of genes improved between 2008 and 2012. We 

caution that the implications of overall low transcription observed in 2012, in terms of 

interpretation of potential exposure to oil, are not certain. We note that the timing of convergence 

of patterns of transcription of potentially exposure-related genes in our suite across different 

oiling histories in 2012 relative to 2008 is consistent with improvements in survival (Chapter 2) 

and increasing population trajectories (Chapter 1) during that same period. 
24

Table 3.1. Function of 13 genes identified in free-ranging sea otters sampled in western Prince William 

Sound, Alaska, in 2008 and 2012, and Alaska Peninsula in 2009, and in clinically normal captive sea otters 

sampled in 2008, 2009, or 2010.

Gene Gene function

HDC The HDCMB21P gene codes for a translationally controlled tumor protein (TCTP) implicated 

in cell growth, cell cycle progression, malignant transformation, tumor progression, and in the 

protection of cells against various stress conditions and apoptosis (Bommer and Thiele, 

2004;Tuynder and others, 2004; Ma and others, 2010). Up-regulation of HDC is indicative of 

the development or existence of cancer. Environmental triggers may be responsible for 

population-based, up-regulation of HDC. HDC transcription is known to increase with 

exposure to carcinogenic compounds such as polycyclic aromatic hydrocarbons (Bowen and 

others, 2007; Raisuddin and others, 2007; Zheng and others, 2008). 

COX2 Cyclooxygenase-2 catalyzes the production of prostaglandins that are responsible for 

promoting inflammation (Goldsby and others, 2003). Cox2 is responsible for the conversion 

of arachidonic acid to prostaglandin H2, a lipoprotein critical to the promotion of 

inflammation (Harris and others, 2002). Up-regulation of Cox2 is indicative of cellular or 

tissue damage and an associated inflammatory response.

CYT The complement cytolysis inhibitor protects against cell death (Jenne and Tschopp, 1989). 

Up-regulation of CYT is indicative of cell or tissue death.

AHR The arylhydrocarbon receptor responds to classes of environmental toxicants including 

polycyclic aromatic hydrocarbons, polyhalogenated hydrocarbons, dibenzofurans, and dioxin 

(Oesch-Bartlomowicz and others, 2005). Depending upon the ligand, AHR signaling can 

modulate T-regulatory (TREG) (immune-suppressive) or T-helper type 17 (TH17) (proinflammatory) immunologic activity (Quintana and others, 2008; Veldhoen and others, 2008).

THR The thyroid hormone receptor beta can be used as a mechanistically based means of 

characterizing the thyroid-toxic potential of complex contaminant mixtures (Tabuchi and 

others, 2006). Thus, increases in THR transcription may indicate exposure to organic 

compounds including PCBs and associated potential health effects, such as developmental 

abnormalities and neurotoxicity (Tabuchi and others, 2006). Hormone-activated transcription 

factors bind DNA in the absence of hormone, usually leading to transcriptional repression 

(Tsai and O’Malley, 1994).

HSP 70 The heat shock protein 70 is produced in response to thermal or other stress (Iwama and 

others, 1999; Tsan and Gao, 2004). In addition to being expressed in response to a wide array 

of stressors (including hyperthermia, oxygen radicals, heavy metals, and ethanol), heat shock 

proteins act as molecular chaperones (De Maio, 1999). For example, heat shock proteins aid 

the transport of the AHR/toxin complex in the initiation of detoxification (Tanabe and others,

1994).

IL-18 Interleukin-18 is a pro-inflammatory cytokine (Goldsby and others, 2003) and plays an 

important role in inflammation and host defense against microbes (Krumm and others, 2008).
25

Table 3.1. Function of 13 genes identified in free-ranging sea otters sampled in western Prince 

William Sound, Alaska, in 2008 and 2012, and Alaska Peninsula in 2009, and in clinically normal 

captive sea otters sampled in 2008, 2009, or 2010.—Continued

Gene Gene function

IL-10 Interleukin-10 is an anti-inflammatory cytokine (Goldsby and others, 2003). Levels of IL-10 

have been correlated with relative health of free-ranging harbor porpoises, for example,

increased amounts of IL-10 correlated with chronic disease whereas the cytokine was 

relatively reduced in apparently fit animals experiencing acute disease (Beineke and others,

2007). Association of IL-10 transcription with chronic disease also has been documented in 

humans (Rigopoulou and others, 2005).

DRB A component of the major histocompatibility complex, the DRB class II gene, is responsible 

for the binding and presentation of processed antigen to TH lymphocytes, thereby facilitating 

the initiation of an immune response (Goldsby and others, 2003; Bowen and others, 2006). 

Up-regulation of MHC genes has been positively correlated with parasite load (Wegner and

others, 2006), whereas down-regulation of MHC has been associated with contaminant 

exposure (Dong and others, 1997).

Mx1 The Mx1 gene responds to viral infection (Tumpey and others, 2007). Vertebrates have an 

early strong innate immune response against viral infection, characterized by the induction 

and secretion of cytokines that mediate an antiviral state, leading to the up-regulation of the 

MX-1gene (Kibenge and others, 2005).

CCR3 The chemokine receptor 3 binds at least seven different chemokines and is expressed on 

eosinophils, mast cells (MC), and a subset of Th cells (Th2) that generate cytokines 

implicated in mucosal immune responses (Gurish and others, 2002; Kringel and others, 2006). 

Up-regulation of CCR3 occurs in the presence of parasites (Gurish and others, 2002; Kringel

and others, 2006).

5HTT The serotonin transport gene codes for an integral membrane protein that transports the 

neurotransmitter serotonin from synaptic spaces into presynaptic neurons. This transport of 

serotonin by the SERT protein terminates the action of serotonin and recycles it in a sodiumdependent manner (Jennings and others, 2006; Squire and others, 2008). Increased 

transcription of 5HTT confers a low anxiety phenotype (Jennings and others, 2006).

CaM Calmodulin (CaM) is a small acidic Ca2+-binding protein, with a structure and function that is 

highly conserved in all eukaryotes. CaM activates various Ca2+-dependent enzyme reactions, 

thereby modulating a wide range of cellular events, including metabolism control, muscle 

contraction, exocytosis of hormones and neurotransmitters, and cell division and 

differentiation (Chen and others, 2012). CaM also has been reported to be a pivotal calcium 

metabolism regulator in shell formation (Li and others, 2004).
26

Synthesis and Conclusions

In this report, we present the latest findings from post-spill studies on sea otters that have 

been ongoing for more than two decades. The Exxon Valdez Oil Spill Trustee Council 

(EVOSTC) defined recovery for sea otters as the point in time when abundance of sea otters in 

oiled areas returns to level that would have existed had the spill not occurred, and there is no 

evidence of continuing exposure to lingering oil in the environment. In our summaries of data 

available through 2009 (Bodkin and others, 2011, 2012; Miles and others, 2012) for sea otters in 

areas of western Prince William Sound (WPWS) that received heavy shoreline oiling in 1989, 

these conditions had not been met, although there were indications that recovery was underway 

based on increasing numbers of sea otters at Knight Island. Further, demographic models based 

on ages-at-death and abundance data through 2008 (Monson and others, 2011) suggested that 

depressed survival of sea otters in heavily oiled areas continued to constrain recovery. Here, we 

integrate the results through 2013 and find our most recent data are consistent with the EVOSTC

definition of recovery for sea otters. 

Aerial surveys of abundance (Chapter 1) are a main component of our studies to evaluate 

status of recovery. By 2013, at the broader scale of WPWS, the estimated number of sea otters 

had more than doubled relative to the 1993 estimate (4,277 versus 2,054, respectively), and the 

increase over that time frame was greater than or similar to estimates of sea otters that died 

within the first year of the spill, indicating that the demographic metric of the recovery definition 

had been met. For the region of northern Knight Island, which received heavy oiling of 

shorelines in 1989 and consequently was anticipated to be an area where recovery would be 

slowest, abundance was depressed for almost two decades relative to the pre-spill estimate. By

2011, the number of sea otters at Knight Island was similar to estimated pre-spill numbers, and 

similar levels of abundance continued through 2012 and 2013. Thus, based solely on abundance 

estimates, the sea otter population in WPWS in 2013 had grown to a number consistent with the 

definition of recovery. 

The most recent data on ages-at-death of sea otters in WPWS (Chapter 2) provide 

additional findings consistent with recovery of the population. Annual carcass collections were 

initiated in WPWS in the 1970s, so the ages-at-death data provide a solid empirical baseline for 

evaluating recovery from the spill. Pre-spill data indicate that mortality of sea otters typically 

was comprised largely of very young and older sea otters, with relatively few prime age (defined 

here as 2–8-year olds) otters dying each year. This pattern was altered after the spill when, for 

about two decades, annual carcass collections showed a relatively high proportion of prime-age 

otters dying each year. Starting in 2011, we observed a distinct change in the age-class 

proportions of dying sea otters, with a return to the pre-spill pattern of predominantly young and 

older sea otters recovered as carcasses. This pattern continued in 2012 and 2013, which we 

interpret as evidence that over the past few years, chronic exposure to lingering oil and/or 

chronic effects due to previous exposure have abated to the point where they are no longer 

factors constraining survival. A higher proportion of sea otters in oiled areas are again surviving 

to older ages, as documented in WPWS prior to the spill. 
27

To assess continuing exposure to lingering oil, we have utilized gene transcription assays, 

monitoring an array of 13 genes selected based on studies of mink exposed to oil (Bowen and 

others, 2007). Results from sea otters sampled in WPWS in 2008 were consistent with ongoing 

exposure to organic compounds (Miles and others, 2012), and in concert with other data, we 

interpreted the gene transcription data to suggest continuing chronic exposure to oil from the 

1989 spill. Sea otters were resampled in 2012 for gene transcription (Chapter 3), and gene 

transcription values from 2012 differed from 2008, as well as from the two reference groups 

(captive and Alaska Peninsula sea otters) used for comparison to the 2008 samples (Miles and 

others, 2012). In contrast to previous data, the 2012 samples indicated low levels of gene 

expression for all otters sampled in WPWS (that is, in both oiled and unoiled areas). This result 

was not expected, and is difficult to interpret without data from a wider panel of genes. However, 

the low transcription levels for genes that previously showed elevated levels, and lack of 

difference in transcription rates between otters from heavily, moderately, and unoiled areas of 

WPWS suggest that sea otters were not exposed to oil in 2012. 

Overall, we conclude that current population level data for sea otters in WPWS are 

consistent with the EVOSTC definition of recovery for sea otters from the long-term injury 

incurred in the wake of the 1989 oil spill. The support for this is based primarily on demographic 

data, including (1) a return to estimated pre-spill abundance of sea otters at northern Knight 

Island, a heavily oiled area within WPWS, and (2) a return to pre-spill mortality patterns based 

on ages-at-death. Gene transcription rates in 2012 were similar in sea otters from oiled, 

moderately oiled and unoiled areas, suggesting abatement of exposure effects in 2012. However, 

because 2012 gene transcription rates generally were low for sea otters from all areas relative to 

2008, we cannot fully interpret these observations without data from a wider panel of genes. This 

slight uncertainty with respect to the data from the biochemical indicator is outweighed by the 

strength of the data for the demographic indicators. The return to pre-spill numbers and mortality 

patterns suggests a gradual dissipation of lingering oil over the past two decades, to the point 

where continuing exposure is no longer of biological significance to the WPWS sea otter 

population. 
28

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Appendix 1. Publications and Reports on Sea Otter Oil Spill Studies, 

Authored or Co-authored by USGS Scientists, 1989–2013

Ballachey, B.E., 1995, Biomarkers of damage to sea otters in Prince William Sound, Alaska, 

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p. 47–59. 

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Ballachey, B.E., Bodkin, J.L., Howlin, S., Kloecker, K.A., Monson, D.H., Rebar, A.H., and 

Snyder, P.W., 2002, Hematology and serum chemistry of sea otters in oiled and unoiled areas 

of Prince William Sound, Alaska, 1996–98—Appendix BIO-01 in Holland-Bartels, L., ed., 

Mechanisms of impact and potential recovery of nearshore vertebrate predators following the 

1989 Exxon Valdez oil spill: U.S. Geological Survey Exxon Valdez Oil Spill Trustee Council 

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Ballachey, B.E., Bodkin, J.L., and Monson, D.H., 2013, Quantifying long-term risks to sea otters 

from the 1989 ‘Exxon Valdez’ oil spill: Reply to Harwell and Gentile, Marine Ecology 

Progress Series, v. 488, p. 297–301. 

Ballachey, B.E., and Kloecker, K.A., 1997, Hydrocarbons in hair, livers and intestines of sea 

otters (Enhydra lutris) found dead along the path of the Exxon Valdez oil spill: Anchorage, 

Alaska, U.S. Fish and Wildlife Service Exxon Valdez Oil Spill State/Federal Natural Resource 

Damage Assessment Final Report, Marine Mammal Study 6-3. 

Ballachey, B.E., and Kloecker, K.A., 1997, Hydrocarbon residues in tissues of sea otters 

(Enhydra lutris) collected following the Exxon Valdez oil spill Anchorage, Alaska, U.S. Fish 

and Wildlife Service Exxon Valdez Oil Spill State/Federal Natural Resource Damage 

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Ballachey, B.E., and Kloecker, K.A., 1997, Hydrocarbon residues in tissues of sea otters 

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Service Exxon Valdez Oil Spill State/Federal Natural Resource Damage Assessment Final 

Report, Marine Mammal Study 6-2. 

Ballachey, B.E., Stegeman, J.J., Snyder, P.W., Blundell, G.M., Bodkin, J.L., Dean, T.A., Duffy, 

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K.A., 2002, Oil exposure and health of nearshore vertebrate predators in Prince William Sound 

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impact and potential recovery of nearshore vertebrate predators following the 1989 Exxon 

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