Wild Harbor Seal (Phoca Vitulina) Population Dynamics and Survival in Northern California

Home , Bair Island, Castro Rocks, Elkhorn Slough, Harbor seal, Mowry Slough, The Marine Mammal Center

WILD HARBOR SEAL (PHOCA VITULINA) POPULATION DYNAMICS AND SURVIVAL IN NORTHERN CALIFORNIA

A thesis submitted to the faculty of Moss Landing Marine Laboratories San Francisco State University In partial fulfillment of The Requirements for The Degree

Master of Science In Marine Science

Suzanne Camille Manugian

San Francisco, California

December 2013

CERTIFICATION OF APPROVAL

I certify that I have read Wild harbor seal (Phoca vitulina) population dynamics and survival in northern California by Suzanne Camille Manugian, and that in my opinion this work meets the criteria for approving a thesis submitted in partial fulfillment of the requirements for the degree: Master of Science in Marine Science at San Francisco State

University.

______James T. Harvey Director, Moss Landing Marine Laboratories

______Ellen Hines Professor, Department of Geography and Environment

______Benjamin Becker Director and Marine Ecologist, Pacific Coast Science and Learning Center

WILD HARBOR SEAL (PHOCA VITULINA) POPULATION DYNAMICS AND SURVIVAL IN NORTHERN CALIFORNIA

Suzanne Camille Manugian San Francisco, California 2013

Pacific harbor seals (Phoca vitulina) within San Francisco Bay (SFB) have been described as stable compared with those in coastal northern California, like Tomales Bay (TB). Historical data (1970s – early 2000s) indicated an overall increase in adults and pup production. Recent data, however, revealed SFB and TB adult counts decreased while pup production increased. There is a paucity of life history data, such as survival rates, for northern California harbor seals. For 32 radio-tagged adult females, survival was 98.2% over 20 months 2011 through 2013, constant between bays and influenced by an individual’s axillary girth. Movement between bays supported this survival estimate. Lower resight probability in SFB compared with TB was likely due to multiple factors including sampling bias and haulout quality and area. These are the first adult/subadult survival and resight estimates for harbor seals in California, and suggest the stable SFB population is due to some reason other than poor adult female survival (e.g. emigration, poor pup survival).

I certify that the Abstract is a correct representation of the content of this thesis.

______Chair, Thesis Committee Date ACKNOWLEDGEMENTS

I would like to thank my thesis committee, Jim Harvey, Ellen Hines, and Ben Becker for assistance and guidance throughout my MLML career. I’d also like to extend a special thank you to unofficial committee members Denise Greig, Sarah Allen, and Frances Gulland for always being in my corner and selflessly offering advice and support throughout this long journey. Thanks to The Marine Mammal Center (TMMC) for surgical support: Bill Van Bonn and Vanessa Fravel for surgeries, Lauren Campbell and Erin Brodie for veterinary tech support, Matt Hoard for all things USDA pool-related, and a tremendous number of volunteers for care and release of pilot study animals. An army of volunteers helped out with seal captures and sample collection, and the students, faculty, and staff at MLML helped make it all possible. A special thanks goes to Stephanie Hughes, Liz McHuron, Deasy Lontoh, Tenaya Norris, Scott Hansen, Alex Olson, Sean Hayes, Greg Frankfurter, Patrick Flanagan, and my VELers (both past and current). Aerial tracking for this study was graciously donated by K. Harmon, who both flew and looked for seals with me: without you this could not have been a success. Joe Merz (Cramer Fish Sciences) and B. Van Wagenen (Ecoscan Resources) also provided sage tracking advice and several survey flights. Additional funding was provided by The Marine Mammal Center, the Student Packard Fund, and the San Francisco State University travel fund. This project would not have been possible without support from the National Parks Service, Don Edwards National Wildlife Refuge, MLML, Kathy Hieb, and the CDFG San Francisco Bay Study and the Interagency Ecological Program for the San Francisco Estuary. Lastly, I am eternally grateful for the unconditional love, encouragement, and support from my amazing folks and wonderful friends. To those who are always jokingly asking “What’s taking so long?” I now have a response: “I’ve reached the finish line!”

TABLE OF CONTENTS

List of Tables ……..….……..….……..….……..….……..….……..…..….……..... vii

List of Figures ……..…..….……..….……..….……..….……..….….…….….....… viii

List of Appendices ……..…..….……..….……..….……..….………….………..… xii

Introduction ………..….……..….……..………..……..….……..………….……… 1 Hypotheses …..…..….……..…………..….……..…………..….….…….… 11

Methods …..……..….……..….……..….……..….……..….……...….……..…….. 13

Results …………..….……..….……..….……..….……..….…….……..….….…… 22

Discussion ………..….……..….……..….……..….……..….…..….……...…...…. 26 Conclusions …………………………………………………………....….... 39

Literature Cited …………..…..….……..…….……..……..….….……..…….……. 41

Appendix 1 …………..….……..….….……..….….…….…..….……..…………… 90

Appendix 2 …………………………………………………………………………. 92

Appendix 3 …………………………………………………………………………. 93

LIST OF TABLES

Table Page

1. 16 original survival and recapture models in MARK, with description …...……… 57

2. 40 new survival and recapture models in MARK with covariates, built off 16 original models (Table1), with description ………………………………………....… 58 - 60

3. Models built to examine tag effects over August 2011 – March 2013 by varying time frames. Monthly, biology, and seasonal effects examined ……...….……….…..... 61

4. Selection table for survival (Φ) and recapture (p) probability models. Time is recorded in monthly intervals, site is either SFB or TB. No individual covariates are included. No ^c adjustments made …….…………….………………………....…. 62

5. Selection table for survival (Φ) and recapture (p) probability models. Time is recorded in monthly intervals, site is either SFB or TB. Individual covariates are included. No ^c adjustments made ………………………….………………….…………..… 63

6. Real survival (Φ) and recapture (p) parameter estimate values from model 1 (Table 5): Φ (ax girth) p (site). Standard Error (SE) and 95% confidence intervals (LCL and UCL) also reported ……………………………………………………………….. 64

7. 27 resighted harbor seals. Animals with + indicate inclusion in Φ/p estimates. Total time: months to last resight occasion. Animals with * indicate > 15 months until first resight. Minimum total distance: reasonable travel pattern for harbor seals…..…. 65

8. Mean minimum total distance traveled (miles) ± standard error (SE) for subadult and adult harbor seals tagged in SFB and TB. Values pooled and averaged from minimum total travel distance values for each seal (from Table 7) …………………..……... 66

vii

LIST OF FIGURES

Figure Page

1. Northern California study area: tagging haulouts and additional aerial and ground resight locations. Circles denote tagging and surveyed haulout sites, stars denote surveyed haulout sites, triangles denote CDFW trawl stations (station number in parentheses) ……………………………………………………………………..... 67

2. Telonics IMP/300/L implantable radio tag (23mm x 81mm; 40g; Paraplast® wax coating …………………………………………………………………………… 68

3. Maximum counts of adult harbor seals, by month, in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs) during pupping (March through May) and Molt (June and July) from 2008 to 2012. ……………………………………..… 69

4. Maximum counts of adult harbor seals, by month, in TB during pupping (March through May) and molt (June and July) from 2008 to 2012. ………….………… 70

5. Mean maximum counts of adult harbor seals in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs) and TB by year during pupping (March through May) and molt (June and July) from 2008 to 2012. The red rectangle denotes time-frame of the survival implant tagging study. …………………...….……… 71

6. Relationship of LN of maximum count to year (2008 to 2012) for adult harbor seals in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs, P = 0.29) and TB (P = 0.23) from March through July. The red rectangle denotes time-frame of the survival implant tagging study. …………………………………………… 72

7. Relationship of proportion of pups to year (2008 to 2012) in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs, P = 0.15) and TB (P = 0.34). The red rectangle denotes time-frame of the survival implant tagging study…… 73

viii

LIST OF FIGURES

Figure Page

8. Total adult harbor seal counts (lines; black denotes CR, gray denotes YBI) and percentage of adult females (circle denotes CR, triangle denotes YBI) during molt May to August 2013. ……...……………...……………...……...……....…….… 74

9A. Movement pattern for seal 360: resighted 6 times, alive 30 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Elkhorn Slough. …………………………………………………..…….…….… 75

9B. Movement pattern for seal 920: resighted 6 times, alive 19 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Tomales Bay.………………………………………………………...……….… 76

9C. Movement pattern for seal 960: resighted 20 times, alive 21 months. The animal was tagged at Tomales Bay and never resighted at another haulout, remaining there at least 21 months (when surveys were completed)..…………….….....……….… 77

9D. Movement pattern for seal 640: resighted 2 times, alive 16 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Bair Island. ……..………………………………………………………..….… 78

10. Bar chart of movement patterns for SFB (n=20) and TB (n=17) non-pups including both sexes (from Table 7). Each seal was assigned a category. ……………… 79

11. Bar chart of movement patterns for SFB (n=17) and TB (n=15) subadult and adult females (from Table 7). Each seal was assigned a category. …….….… 80

LIST OF FIGURES

Figure Page

12. Histogram of months to first resight; TB females (n=11), SFB males and females (n=13), and SFB females (n=11) (from Table 7). Each seal was assigned to a unique category.………………………………………………………………….. 81

13. Histogram of total number of resights for TB females (n=11), SFB males and females (n=13), and SFB females (n=11) (from Table 7). Each seal was assigned to a unique category.……………………….……………………………………. 82

14. Movement pattern for seal 670: resighted 3 times, alive 8 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Bair Island, 8 months post-release stranded live near Pillar Point Harbor, taken to TMMC and died overnight. …………………………………………………………...… 83

15. Combined Otter and Mid-Water Trawl CPUE from two open water stations from 2007 to 2012 (black denotes South SFB: 101; gray denotes Central SFB: 214), combined for five prey species of known importance to harbor seals (Bay goby, Lepidogobius lepidus; chameleon goby, Tridentiger trigonocephalus; cheekspot goby, Ilypnus gilberti; shiner perch, Cymatogaster aggregata; and yellowfin goby, Acanthogobius flavimanus). ……………………………………………….….. 84

16. Northern Oscillation Index (NOIx) and Multivariate ENSO Index (MEI) oceanographic conditions from 2007 through September 2013. Annotated in gray rectangles: moderately cool conditions (2007-2009), strong El Niño season (2009- 2010), La Niña seasons (2010 - 2012), and moderately warm conditions (2012 – 2013). …………………………………………………………..…………..…. 85

LIST OF FIGURES

Figure Page

17. San Francisco Bay slope and two harbor seal haulouts (Castro Rocks and Bair Island). Circles represent one and five kilometer buffers from each of the haulouts. ……………………………………………………………………... 86

18. San Francisco Bay rugosity and two harbor seal haulouts (Castro Rocks and Bair Island). Circles represent one and five kilometer buffers from each of the haulouts. ……………………………………………………………………... 87

19A. Top three marine habitats from predictive model for two SFB sites: Castro Rocks and Bair Island. Rings represent 1 and 5km from haulout. Habitats are intersection of 5-30m depth, low and medium rugosity, and medium slope. Within 5 km of Castro Rocks: 3.9% Habitat 1, 0.2% Habitat 2, 0% Habitat 3. Within 5 km of Bair Island: 1.8% Habitat 1, 0% Habitats 2 and 3. ………………………….…… 88

19B. Top three marine habitats from predictive model for Tomales Bay. Rings represent 1 and 5km from haulout. Habitats are intersection of 5-30m depth, low and medium rugosity, and medium slope. Within 5 km of Tomales Bay: 4.3% Habitat 1, 0% Habitats 2 and 3. …………………………………………………….... 89

LIST OF APPENDICES

Appendix Page

1. Seal Database (41 tagged individuals). Seal Identification (ID, flipper tag numbers (L/R)); capture location at Castro Rocks (CR), Elkhorn Slough (EHS), Tomales Bay (TB), Corkscrew Slough (CSS), or Bair Island (BI); capture date; radio transmitter frequency; weight (kg); sex; standard length (SL, cm); axillary girth (AG, cm); and age of harbor seals. Animals with “R” indicate resighted at least once. …… 90-91

2. Ground tracking efforts used in survival and recapture estimates and movement patterns between August 2011 and March 2013 by site including frequency of monitoring and methods ……………………………………………………...…. 92

3. Aerial tracking efforts used in survival estimates and movement patterns between March 2010 and March 2013 by date including sites monitored, pilot and tracker(s), and methods. Haulouts were circled at 1,200 to 1,500 feet altitude with a speed of approximately 80 to 90 knots. * denotes effort used solely in movement pattern analysis and not in survival or recapture estimate analysis. ……...……….…. 93-95

xii 1

INTRODUCTION

The Pacific harbor seal (Phoca vitulina richardii) inhabits waters off western

North America from Baja California, Mexico, to the Aleutian Islands, Alaska (Bigg 1969,

Reeves 1992). Harbor seals haul out (e.g. coming ashore) in groups coastally and in estuaries on a variety of substrates including tidal mud flats, rocky and sandy beaches, sand bars, and drifting glacial ice (Bigg 1969, Steward 1984). Hauling out benefits seals by lowering energy costs used to contend with waves and currents, allowing increased body temperature (Hayward et al. 2005). Multiple factors can influence daily seal activity including tidal height, wave dynamics, time of day and year, and disturbances

(Brown and Mate 1983, Stewart 1984, Harvey 1987, Allen-Miller 1988). Generally, harbor seals are year-round, non-migratory residents, exhibiting site fidelity to one, or a few, geographically close sites (Bigg 1969, Divinyi 1971, Brown and Mate 1983, Reeves et al. 1992). However, advances in technology in the form of telemetry studies reveal long distance movements in some individuals (Harvey 1987, Allen-Miller 1988, Oates

2005, Grigg et al. 2012) with differences in movement based on age; pups and juveniles tend to disperse further with unknown outcomes (Thompson et al. 1994, Lander et al.

2002, Oates 2005, Greig 2011).

Harbor seals off the western coast of the United States have been subdivided into three genetically different stocks for management purposes: those found along the

Washington and Oregon coastline, those in inland waters of Puget Sound, and those along coastal California (Lamont et al. 1996). However, greater genetic distinction lies 2

between animals in the Puget Sound region compared with those along the coast. There is a paucity of genetic work has been conducted within the California population.

Harbor seals in Point Reyes National Seashore (PRNS), just north of the San

Francisco Bay (SFB), represent the largest concentration of harbor seals in California, or about 20% of the mainland breeding population (Lowry et al. 2005). Tomales Bay (TB), in northern PRNS, has large numbers of harbor seals and is less impacted by urban influences compared with SFB. In SFB, the largest coastal embayment on the west coast of the United States, harbor seals are the most common marine mammal, and the only year-round pinniped residents in the estuary (Allen-Miller 1988, Grigg et al. 2002).

Unlike in TB, the habitat of seals in SFB is contracting because of urban spreading within the Bay Area (SFAAP report 1999).

Since passage of the 1972 Marine Mammal Protection Act, most marine mammal populations have increased due to decreased hunting, capturing, killing, and harassment.

Consequently, some populations may be close to carrying capacity (Harvey et al. 1990,

Jeffries et al. 2003, Grigg et al. 2004). The National Marine Fisheries Service’s most recent harbor seal population estimates were 10,000 in Oregon (Brown et al. 2005),

19,000 in Washington (Jeffries et al. 2003), and 34,000 in California (Caretta et al. 2009).

However, the estimate of stock size in California is becoming outdated and based on data collected in 2008. Population growth for harbor seals in all three states was projected at

3.5% annually (Caretta 2001). 3

Despite the expected annual growth of 3.5%, there are some populations of harbor seals that are decreasing, like those in Glacier Bay National Park, AK (Mathews and

Pendleton 2006), and others that are stable. From 1975 to 1995, Grigg et al. (2004) hypothesized the SFB harbor seal population to be relatively stable at around 500 individuals. Kopec and Harvey (1995) reported that unlike other populations along the coastal western US, there has been no significant increase in the SFB population since the mid 1970s, and estimated the population was around 600 individuals. Using a northern

California correction factor (1.54 ± 0.38), the most recent estimate is 700-900 individuals

(Harvey and Goley 2011). Increases in populations elsewhere indicate resident seals in

SFB, unlike those living north in PRNS and in other states, may be experiencing unique factors affecting harbor seal health or survival, some negatively. These might include contaminants, human interaction, local- and basin-wide oceanographic processes, prey availability, preferred habitat based on bathymetry and geography, and loss of suitable habitat to human expansion.

Most harbor seal haul-out sites within SFB have been monitored since the 1970s for population estimates. California Department of Fish and Wildlife (CDFW) has conducted statewide aerial surveys since the early 1980s to assess population numbers of harbor seals and SFB was included in this assessment (Fluharty 1999, Grigg et al. 2004).

Monitoring is year-round in some locations but the National Park Service (NPS) has been focusing on counts at sites March through July, during pupping and molt. This is because throughout their northern California range, more seals haul out during the spring and 4

summer reproductive and molt seasons than during the remainder of the year (Allen-

Miller 1988, Grigg et al. 2002). At Castro Rocks in north SFB and Mowry and Newark

Sloughs in south SFB, there has been an increase in overall numbers of adults between

1970 and 2002 (Grigg et al. 2004). Pup production also has been increasing at those sites since 1970 leading to the question of why has the SFB population not been increasing

(Fancher 1979, Kopec and Harvey 1995). Increased long-term studies of individual movement patterns and survival are necessary to answer this question.

Population dynamics of species are driven by multiple factors that can include age at first reproduction, fecundity, life span, and mortality. First-year survival may be the most important factor affecting the growth of a population (Eberhardt and Siniff 1977).

Survival rates in large mammals are decreased early in life, increase and plateau when the animal reaches adulthood, and possibly decrease during senescence. Eberhardt and Siniff

(1977) tested this hypothesis using data from four species of marine mammals: Pribilof fur seal (Callorhinus ursinus, Chapman 1961 and 1973), Weddell seal (Leptonychotes weddellii, Stirling 1971), harp seal (Pagophilus groenlandicus, Seargeant 1971), and ringed seal (Phoca hispida, Smith 1973). Age at first reproduction and fecundity were not as important to pinniped population growth rates as first year survival. It is especially important in marine mammal populations because pinniped females have one pup annually and do not reach sexual maturity until three to five years of age (Reeves et al.

1992). Additionally, individual covariates, such as body condition, are another important 5

factor for individual, and subsequently, a population’s success (Pitcher et al. 1998, Craig and Ragen 1999, Hall and McConnell 2007).

Worldwide estimates of survival rates in pinnipeds are few and variable, and are estimated from mortality and life tables. Among species, neonatal survival is 69% to

93.1% whereas post-weaning survival is 35% to 98% (Bemmel 1956, Bigg 1969,

Reijnders 1978, Reijnders et al. 1981, Steiger et al. 1989). After five years of age, survival in monk seals increases (Baker and Thompson 2007) and adult harbor seal survival is an estimated 85% for females and 71% for males (Bigg 1969). Adult female inter-annual survival estimates in harbor seals range from 81.3% to 97% (Bigg 1969,

Boulva and McLaren 1979, Pitcher and Calkins 1979, Harkonen and Heide-Jorgensen

1990), however, these estimates were not based on assessing live animals. Researchers either used a harvesting sampling regime (Bigg 1969, Boulva and McLaren 1979, Pitcher and Calkins 1979) or carcasses from a epidemic outbreak (Harkonen and Heide-

Jorgensen 1990). There is need for survival estimates based on live captures and resights.

In California, there is a paucity of basic life history data, such as survival rates, for harbor seals. Assessing baseline survival is critical to understanding wild, healthy populations

(Lebreton et al. 1992) and population dynamics within SFB and TB.

In northern California, there are no estimates of adult survival rates for harbor seals in SFB or TB, and few estimates for non-adults. Post weaning pup survival varied by year, and estimates were affected by length of time that pups were monitored (Lander et al. 1998, Lander et al. 2002, Oates 2005, Greig 2011). Lander et al. (1998) reported 6

three-month post weaning survival of 20% in 1995 and 60% in 1996, whereas Oates

(2005) reported 37% post weaning survival of male pups after nine months and 71% survival of female pups from 1999 to 2002. Wild pups had decreased survival compared with rehabilitated pups in the same geographical range (Lander et al. 2002, Greig 2011).

First-year survival was typically less than in subsequent years because smaller, younger animals were more susceptible to factors such as starvation, predation, diseases, and human impact (Gilmartin et al. 1993, Lander et al. 2002, Muelbert et al. 2003). Short- term studies have been conducted on adults in northern California but none that tracked seals long enough to estimate inter-annual survival.

A popular method of conducting a survival study relies on use of marked and unmarked animals. Mark-recapture methods are used to estimate the abundance of a population, survival parameters, and recapture (or resight if the animal is not caught again) parameters. Researchers have used numerous methods of marking animals and subsequently resighting them.

Non-transmitting tags are flipper tags, hat tags, and PIT tags; however, substantial effort is needed to read the numbered code or detect the PIT tag (Wright et al. 1998).

Forcada et al. (2009) modeled predation by transient leopard seals (Hydrurga leptonyx) using photographs of distinct marks and Hernandez-Camacho et al. (2008) assessed survival rates of California sea lions (Zalophus californianus) using branded individuals with unique numbers. There also have been extensive studies to assess survival and capture probability using uniquely coded and colored flipper tags like those on fur seals 7

(Arctocephalus forsteri); (Bradshaw et al. 2003) and the Hawaiian monk seal (Monachus schauinslandi); (Gilmartin et al. 1993).

Transmitting tags compared with non-transmitting tags make information more readily available to researchers. External tags can be glued onto the animal’s head or back and are effective in data transfer. However, they pose a suite of problems including general wear, loss during annual molt, and possible entanglement in marine debris

(Lander et al. 2001). These factors all have potential to increase mortality thus negatively affecting survival rate. These tags, however, are frequently used to study pinniped survival and movement patterns.

VHF telemetry (very high frequency; 30 to 300 MHz) is a relatively inexpensive and reliable method of tracking animals. However, it involves extensive effort to resight the animal with antennae and receiver. The range of this type of tag is about a kilometer depending on tracking method, transmitter’s signal strength, and antennae strength. In addition, radio interference from populated urban areas (airports and shopping malls, for example) can overwhelm a transmitter’s presence. Because VHF signals are attenuated under water, tracking tagged individuals in the aquatic environment is constrained by the amount of time they spend diving (Tremblay et al. 2006). Movement patterns and survival of wild and rehabilitated harbor seals have been assessed using VHF tags off northern California (Lander 1998, Lander et al. 2002, Oates 2005). VHF telemetry has been used to assess habitat selection, movements, dispersal, and survival of harbor seals 8

of all ages in many geographic locations (Allen-Miller 1988, Bjorge et al. 2002, Eguchi and Harvey 2005, Oates 2005, Waring et al. 2006, Blundell et al. 2007).

Recently, internal placement of VHF transmitters has been explored to negate tag loss during the annual molt thus extending monitoring time. These tags are popular because they can be formatted to transmit for long time-periods. However, they still require substantial tracking effort, and the surgical implant procedure has potential for infection. Furthermore, the range and signal strength is decreased because the tag has to transmit through the animal. There are many success stories of implants in terrestrial species including the arctic fox (Alopex lagopus) (Fuglei et al. 2002), European wild boar

(Sus scrofa) (Enqvist et al. 2000), Eurasian beaver (Castor fiber) (Ranheim et al. 2004), lynx (Lynx lynx), European river otters (Lutra lutra) (Arnemo 1991), brown bears (Ursus arctos) and wolverines (Gulo gulo) (Arnemo et al. 1998, Arnemo et al. 1999). Horning et al. (2008 and 2012) implanted rehabilitated California sea lions (Zalophus californianus) and wild Steller sea lions (Eumetopias jubatus) with satellite-linked life history transmitters (LHX tags). Green et al. (2009) implanted rehabilitated California sea lions and northern elephant seals (Mirounga angustirostris) with heart rate data loggers but were only successful in the former. VHF implanted transmitters have been successfully placed subcutaneously in rehabilitated and wild harbor seals (Lander et al.

2005) and intra-abdominally in otters (sea otters, Enhydra lutris (Monnett and Rotterman

2000); marine otters, Lontra felina (Soto-Azat et al. 2008); and Eurasian otters, Lutra lutra (O’Neill et al. 2008)). 9

Use of tag technology has documented seals’ movements in and around SFB.

Seals tagged at Castro Rocks between the years of 2001 and 2005, with either radio

(n=27) or satellite (n=19) tags, used foraging areas that included SFB and outside the bay as far south as Pillar Point (<50 km) and as far north as Point Reyes (<75 km) (Green et al. 2006). Tagged animals largely foraged in SFB and, though they were found on the outer northern coast (Duxbury Reef, Pillar Point, Double Point), they spent the majority of their time within SFB (Torok 1994, Nickel 2003). Nickel (2003) hypothesized prey availability dictated this pattern with seals using fall Chinook salmon and spring anchovy and herring runs. Diet studies revealed predominantly local prey including Pacific herring (Clupea pallasii), northern anchovy (Engraulix mordax), plainfin midshipman

(Porichthys notatus), Pacific staghorn sculpin (Leptocottus armatus), white croaker

(Genyonemus lineatus), yellowfin goby (Acanthogobuis flavimanus), jacksmelt

(Atherinopsis californiensis), and English sole (Pleuronectes vetulus) and few offshore prey species (Torok 1994). Animals radio tagged within SFB and PRNS (n=120) displayed similar movement patterns: PRNS animals foraged around PRNS and SFB animals stayed within or just outside SFB (Harvey and Goley 2005). Grigg et al. (2012) hypothesized harbor seal foraging (n=19, satellite tags) was associated with prey abundance and distance to haulout as seals were closer to primary haul-outs and in areas with greater bathymetric relief associated with more benthic prey. It is important to remember this movement, however, is based on age and although adults tend to display 10

this site fidelity, pups and juveniles exhibit a much greater range. Tagged pups have traveled as far north as Oregon and as far south as Mexico (Greig 2011).

HYPOTHESES

Given the historical increases along the coast and a stable SFB population, this study aims to compare SFB with an outer coast site, TB, and to use individually tagged animals to learn more about life history parameters, such as survival, for a particular sex and age class. The two main objectives for this thesis were 1) to examine abundance of harbor seals in SFB and TB and 2) to assess survival and movement patterns of seals in

SFB and TB.

The abundance objectives were 1) to compare interannual variability in pupping and molting seasons between SFB and TB from 2008 through 2012, 2) to examine overall maximum non-pup counts in SFB and TB and assess trends from 2008 through

2012, 3) to evaluate pup production trends in SFB and TB from 2008 through 2012, and

4) to generate a sex ratio from two SFB sites (one predominantly male, one predominantly female) and apply current population estimates to generate a total number of female harbor seals in SFB.

I hypothesized an increase in adult counts in both areas over the four-year period.

Grigg et al. (2004) found increases for 1970 to 2002 at Castro Rocks and Mowry Slough but not at YBI. This might be a function of a paucity of data at that haulout before the

1990s. It was expected that overall non-pup counts would be stable or slightly decreasing in SFB, but would be stable or increasing in TB. I also hypothesized an increase in pup production within SFB. Pup number increased at all SFB sites between 1970 and 2002 12

(Grigg et al. 2004). Finally, I had no expectation regarding the number of female harbor seals in SFB.

The survival and movement objectives were 1) to tag adult and subadult females immediately post weaning to assess survival, 2) to tag animals in SFB and TB to test differences in survival and recapture rates between bays, 3) to determine whether individual covariates of morphological measurements such as mass, axillary girth, or a combined mass/standard length ratio could better predict survival, and 4) to assess movement patterns for tagged harbor seals in both bays.

Adult survival was hypothesized to be greater than previous estimates of harbor seals of younger age classes in this area. The expected range was 80 - 95 % inter-annual survival based on previous estimates of adult survival (Bigg 1969, Boulva and McLaren

1979, Pitcher and Calkins 1979, Harkonen and Heide-Jorgensen 1990). Survival and recapture rates were hypothesized to be slightly lesser in SFB than in TB because of haulout conditions, available space, and sampling bias. Adult female survival was hypothesized to be predicted better by models including individual covariates such as axillary girth (Pitcher et al. 1998, Craig and Ragen 1999, Hall and McConnell 2007).

Lastly, it was hypothesized that most animals would remain faithful to tagging sites whereas few would travel great distances and disperse from tagging haulouts.

METHODS

To test hypotheses at the population scale I used sites in PRNS and SFB. Seals were counted in Tomales Bay, a site in the northern region of PRNS (Figure 1), and at several SFB areas, which included Castro Rocks, Yerba Buena Island, and Mowry and

Newark Sloughs (Figure 1).

Each site was surveyed as part of the National Park Service’s regional harbor seal monitoring efforts from early March through late July 2008 through 2012. Surveys were conducted between Thursday and Monday every two weeks except at the height of the pupping season when they were conducted weekly. Surveys at CR, YBI, and TB were conducted around low tide whereas Mowry and Newark Slough sites were surveyed during a rising, mid level tide. The greatest number of seals came ashore when the most haul-out area was exposed. Maximum counts of adults and pups were recorded, along with disturbance and tagged individual information.

To determine a sex ratio for SFB, I surveyed Castro Rocks and Yerba Buena

Island a minimum of every two weeks from the end of May through mid August 2013.

Sex ratio was calculated as the number of females divided by total number of animals where sex was determined accurately. Surveys were conducted post pupping to avoid the search image bias of easily determining pregnant females or females with pups.

Maximum counts of adults were determined at sites in two areas: TB in PRNS and SFB. Average monthly counts of non-pups for March through July were calculated for each area and two seasons: pupping (March through May) and molt (June and July). 14

Means for each season and a mean for the entire year (combined pupping and molt seasons) were calculated. To determine trends in maximum adult seal counts, each area was analyzed using a regression on the natural logarithm of maximum count vs. year. An analysis of variance (ANOVA) was used to examine differences in the slopes of the regression lines for the two areas and an analysis of covariance (ANCOVA) used to examine differences with the effect of a covariate (year).

Pup production was calculated using the maximum pup count divided by the maximum number of seals recorded between March and May (after the first pup had been born), multiplied by 100 (Grigg et al. 2004). Pup production, not pup count, is used because it is standardized by the size of a haulout (using total adults) for comparison between areas. To examine differences in pup production between the two areas, an analysis of variance (ANOVA) was used to test for differences in the means.

Percentage of females at each of the two sites was averaged (assuming YBI to be predominantly male and Castro Rocks predominantly female, and both a good representation of SFB), and multiplied by current population estimates to get an estimate of the total number of females in SFB. Using a different method (for example including more sites and monitoring over a longer time period) would produce different results.

YBI was a recently colonized site compared with CR and as late as 1980 only 10 seals were utilizing the space (Fancher 1987). CR had more total haulout area and had been used by females longer. 15

To test survival and movement hypotheses, harbor seals (n=41) were captured using methods of Jeffries et al. (1993) in PRNS (n=17), several SFB sites (n=20), and

Elkhorn Slough (n=4) between February 2010 and July 2011 and implanted with radio transmitters (Figure 1). A subset of these were adult and subadult females, captured during June at PRNS (n=15) and July at several SFB sites (n=17) 2011, to be included in survival and recapture analyses. Animals were sampled under Dr. James T. Harvey’s permit (National Marine Fisheries Services, NMFS, No. 555-1870-00) and approved animal research protocols (SFSU IACUC for Off-Campus Student Research Covered by an Approved Protocol from Another Institution, SJSU IACUC No. 931). Post-weaning, adult females were in poor body condition from fasting; thus this age class was separated for survival and recapture analyses because of expected behavioral differences. Adult females immediately post-weaning are taking foraging trips to increase body condition for the upcoming reproductive season.

SFB sites included Castro Rocks, Bair Island, Corkscrew Slough, and Mowry

Slough and Tomales Bay in PRNS (Figure 1). Animals were captured with a variety of methods, depending on site. Morphometrics were determined for all harbor seals sampled: standard length, curvilinear length, girth, mass, age, and sex. Individuals were photographed, tagged with a blue numbered flipper tag in the hind flipper webbing

(Temple Tags®), and injected with a PIT tag under the skin in the lumbar hip to avoid resampling. 16

Seals were administered a sedative Valium (generic Diazepam) in the epidural vein (0.25-0.5 mg/kg, concentration of 5 mg/mL or 1-2mL / 20 kg body weight). After the seal became sedated, blood samples were collected from the extradural invertebral sinus (35 – 60 mL, mass dependent), and transported to The Marine Mammal Center

(TMMC) in Sausalito, CA.

Surgery protocol for tag implantation was modified from Lander et al. (2005).

The designated site was 10 cm lateral to the spine on the left dorsal thorax and five cm caudal to the scapula. A 2% Lidocaine injection was administered at the implantation site, a patch of hair was shaved, and designated incision site cleaned. A vertical skin incision (six to eight cm wide) was made, underlying blubber incised, and transmitter inserted beneath the blubber layer over the superficial cutaneous trunci muscle positioned parallel to the longitudinal axis of the seal to minimize stresses on the implant from body movement. The incision site was sutured in a four-layer closure using 3-0 PDS II monofilament absorbable sutures within the deep subcutaneous tissue and fascia

(including subdermal fat). 2-0 PDS II monofilament absorbable sutures also were used for the subcuticular tissue and skin. Animals were monitored and released when Valium effects had worn off, approximately 30 to 45 minutes duration.

Radio transmitters were pressure tested by the manufacturer to depths exceeding the physiological diving capabilities of a harbor seal, equipped with temperature mortality sensors, operated at 60 pulses per minute, and duty-cycled (eight hours on, 16 hours off) to achieve life span of at least three years. The eight active hours were set 17

during daylight hours to optimize tracking. Transmitters were gas sterilized and rinsed with sterile saline immediately before implantation. Each seal was implanted with a transmitter (IMP/300/L; Telonics, Mesa, AZ; Figure 2).

Tracking began August 2011 and continued through March 2013. Monthly acquisitions were obtained using an aircraft surveying well-established haul-outs within northern California (Tomales Bay, Drakes Bay, Bolinas, all SFB sites, Figure 1) by

Suzanne Manugian and pilot Kyle Harmon. A Cessna 172 was used and well-established aerial tracking methods employed (Appendix 2). A larger area was surveyed by Ecoscan

Resources (Bob van Wagenen) during January and February 2013 ranging from Elkhorn

Slough in the south to Humboldt Bay in the north. Tomales Bay and Castro Rocks, along with several other sites, were scanned from the ground bimonthly (Appendix 3).

The Cormack-Jolly-Seber (CJS) model was applied to estimate survival (Φ or phi) and recapture probabilities (p) (Cormack 1964, Jolly 1965, Lebreton et al. 1992,

White and Burnham 1999). CJS was used to model open populations within MARK, a non-parametric procedure which outputs maximum-likelihood estimates (MLE) of survival and capture probabilities, the value for each parameter that is most likely relative to other values. It requires resight data on live animals after release. Assumptions of CJS are: [1] every animal must have the same capture and recapture probability, [2] every animal must have the same mortality probability or probability of emigration, [3] marks will be recorded correctly and will not be lost, and [4] all samples are instantaneous

(Cooch and White 2012). 18

Model notation, which includes survival and recapture parameters for each model and notation within each parameter, refers to primary factors of site (SFB or TB; site), time (monthly encounters), mass (mass), standard length (SL), mass / standard length ratio (mass/SL), axillary girth (AG), or constant (.). Combinations of factors are denoted with (*) for multiplicative and (+) for additive interactions.

Goodness of fit (GOF) was used to test assumptions of the models. To adjust for a lack of fit, a measure of variation inflation was assessed. Median ^c , a GOF test, was used to test the GOF of the most parameterized (global) model for survival (Φ) and recapture (p) probabilities with site and time effects (Φ (site * time) p (site * time)). ^c is a test statistic generated from the dataset and a saturated model reports a median ^c of 1.

MARK was unable to conduct a GOF on the dataset because the global model was saturated, thus, ^c was not adjusted because no successful GOF was conducted.

Biologically relevant top models were selected using Aikaike’s Information

Criterion adjusted for small sample size (AICC). Sixteen general models were built to fit the data using site (SFB and TB) and time (equal monthly intervals) as primary factors to test hypotheses (Table 1). Individual covariates were included as additive and interactive effects on models from the original 16 that included a time effect on survival (Table 2).

Only models built using a priori hypotheses (40 out of 112) based on previous studies and understanding of harbor seals’ biology were included. Generally, models with

ΔAICC ≤ 2 were considered different. 19

The time effect also was examined and models were created using broader time frames. Time frames were 1) seasonally relevant with each of the four seasons unique or with season identical between year, and 2) biologically relevant with each reproductive and molting season unique or with those seasons identical between year. Varying time frames interacting with site were included in Φ probability estimates to examine tag effect (Table 3).

Data from aerial and ground surveys were combined for movement analyses.

Geographic positions of tagging sites and resight locations for each seal were plotted using ArcGIS (ver 10.1, ESRI 2013). Distances traveled were calculated using near shore routes with no meandering and classified as one of five categorical movement behaviors used by prior studies (Lander et al. 2002, Oates 2005). Categories were [1] never resighted away from tagging site, displayed site fidelity, [2] traveled < 50km from tagging site, stayed local, [3] traveled > 50km but returned to tagging site during study period, [4] traveled > 50km and did not return to tagging site during study period, and [5] disappeared with unknown outcome. These categories account for assumptions made about a reasonable travel speed and pattern for harbor seals.

Regression analyses were conducted to determine relationships between the following: number of times resighted and minimum distance traveled, number of months from tagging to last resight event (considered “alive” by hearing a tag pulse, only one seal was confirmed dead), and minimum distance traveled. Data for each bay was pooled and an analysis of variance (ANOVA) was conducted to compare mean number of 20

months from tagging to last resight event, mean number of resights, and mean minimum distance traveled between the two bays.

EXTERNAL DATASETS

To explain survival, recapture, and movement patterns, SFB trawl data for five prey species and several oceanographic conditions were examined. Also, a predictive model based on documented seals’ habits was created using bathymetric and distance analyses, though course tracking data did not allow testing of seals within these areas of potential importance to seals.

Fish catch for five species common in harbor seals’ diet (Bay goby, Lepidogobius lepidus; chameleon goby, Tridentiger trigonocephalus; cheekspot goby, Ilypnus gilberti; shiner perch, Cymatogaster aggregata; and yellowfin goby, Acanthogobius flavimanus)

(Torok 1994, Gibble 2011) were obtained through CDFW’s San Francisco Bay Study and the Interagency Ecological Program for the San Francisco Estuary. Otter trawl and mid- water trawl data were standardized by station (using Series 1 stations, or original open water stations), site (south SFB: 101; central SFB: 214), month (February through

October for otter trawl data, August through October for mid-water trawl data), year

(2007 through 2012), and CPUE ((number of fish caught / tow volume (mid-water) or area (otter)) * 10,000).

Several indices were used to examine oceanographic conditions along the western coast of the United States: Northern Oscillation Index (NOI, http://www.pfeg.noaa.gov/) and Multivariate ENSO Index (MEI, http://www.esrl.noaa.gov/). The NOI is created with 21

sea level pressure anomalies in the western tropical Pacific and southeast Asia (Schwing et al. 2002) whereas the MEI is an index of six variables observed in the tropical Pacific

(sea-level pressure, two components of surface wind, sea surface temperature, surface air temperature, and cloudiness fraction of the sky) (Wolter and Timlin 1993). These indices were examined from 2009 through 2013 for trends and relationships to seal survival: El

Niño event years have positive NOI and negative MEI (warm ENSO) values whereas La

Niña event years are the opposite.

A predictive model generated three marine habitats, identified in ArcGIS, to predict where animals might forage within SFB. Habitats were created based on where prey aggregate (based on slope and rugosity), known foraging depths of seals (5-30m), and known foraging locations of seals (1-5km from haulout) using several bathymetric datasets (http://www.dfg.ca.gov/marine/gis/downloads.asp). The three common harbor seal prey from diet studies conducted in SFB (Torok 1994, Gibble 201) were used as representative prey. Slope and rugosity were used to predict where prey would aggregate: areas of steeper slope and increased rugosity were more complex and had greater relief that aggregated more animals.

RESULTS

Maximum monthly counts of non-pups remained consistent during pupping and molting in SFB (Figs. 3 & 5) and TB (Figs. 4 & 5) from 2008 – 2012. There was no significant difference between the two areas in mean maximum count of adults among years (F = 1.71, P = 0.227) and no significant difference between the two areas in mean maximum counts of adults with the year effect controlled (F = 2.425, P = 0.163). A linear regression for each area indicated a decreasing trend but not a strong signal in the numbers of adults counted between 2008 and 2012 (SFB: F = 1.59, P = 0.29, r2 = 0.346, y

= -0.049x + 5.722; TB: F = 2.21, P = 0.23, r2 = 0.424, y = -0.069x + 5.658) (Figure 6).

There was no significant difference between the two areas in pup production from

2008 to 2012 (F = 0.893, P = 0.372) (Figure 7) and no significant difference between the two areas in pup production with the year effect controlled (F=1.234, P = 0.303). A linear regression for each area indicated an increasing trend in numbers of pups born between 2008 and 2012 (SFB: F = 3.79, P = 0.15, r2 = 0.558, y = 3.191x + 13.69; TB: F =

1.22, P = 0.34, r2 = 0.289, y = 3.596x + 17.78) (Figure 7).

Number of seals at Castro Rocks and Yerba Buena Island were variable during molt (May – August) (Figure 8). Counts were greater at Castro than at Yerba Buena and there was a greater percent of females at Castro (Figure 8). During May – August 2013,

51% of animals were female at YBI whereas 65% were female at CR. Using the most recent estimate of harbor seals within SFB combined with an average of 58% females 23

from the two sites, there were between 406 and 522 adult females in SFB during this time period.

The best CJS model had no effect of site or time on survival and recapture probability between bays (Table 4). The second model (36.73% AICC weight) had differences between bays in survival and recapture. The top two models accounted for

96.31% certainty in model selection.

From 56 models tested including additive and multiplicative interactions with individual covariates, those with greatest support included axillary girth or the mass/standard length ratio effect on survival and recapture differences between bays

(Table 5). The top three models accounted for 83.36% certainty in the best model selection and 12 models accounted for 100% AICC weight.

From the top model (Model 1, Table 5), survival estimates were the same between bays and varied by individual’s axillary girth (0.9820, SE = 0.01, 95% CI = 0.9468 –

0.9941) whereas recapture estimates differed by location with recapture more likely in

TB: SFB (0.0618, SE = 0.02, 95% CI = 0.0374 – 0.1006) and TB (0.2685, SE = 0.03,

95% CI = 0.2085 – 0.3383) (Table 6).

All ages and both sexes were used in analyses of movement. Twenty-seven of 41 radio tagged animals were resighted at least once (Table 7). Several seals moved from one bay to the other and returned to the tagging haulout site (Figure 9A and B). One animal was resighted 20 times at one haulout (Figure 9C), whereas others were resighted at several haulouts for extended periods of time (Figure 9D). There was variability in 24

distances traveled, reflected in movement behavior categories, for animals in both bays

(Figures 10 and 11, Table 7). Animals from Tomales Bay tended to display site fidelity

(Movement Category 1) whereas animals from SFB traveled farther and did not return to the tagging site (Movement Category 4). Mean minimum distance traveled was similar between bays (Table 8). Nine animals were resighted within three months of tagging, a few were not located for many months, and eleven were never resighted (Figure 12,

Table 7). Most seals were resighted less than six occasions (Figure 13, Table 7).

A regression analysis indicated no significant relationship between the number of times an animal was resighted and the minimum distance traveled for 27 male and female, yearling subadult and adult seals (r2 = 0.003, P = 0.787) or for 24 subadult and adult females (r2 = 0.000, P = 0.936). There also was no significant relationship between the time the animal was considered alive and the minimum distance traveled for 27 male and female, yearling subadult and adult seals (r2 = 0.075, P = 0.168) or for 24 subadult and adult females (r2 = 0.000, P = 0.952).

Total distance traveled was not significant between the two bays for 24 non-pups

(F1, 22 = 0.03, P = 0.866) or for 22 subadult and adult females (F1, 20 = 0.01, P = 0.928).

There was also no significant relationship in time animals were alive between the two bays for 24 non-pups (F1, 22 = 0.33, P = 0.570) or for 22 subadult and adult females (F1, 20

= 0.67, P = 0.421). The total number of times an animal was resighted was not significant between bays for the 24 non-pups (F1, 22 = 4.01, P = 0.058) and for the 22 subadult and adult females (F1, 20 =3.06, P = 0.096). 25

Of the tagged animals, only one tagged individual from SFB was confirmed dead.

It was resighted three times during eight months post-tagging (Figure 14). It traveled to

TB one month post-tagging and returned to SFB after one month before stranding live on the outer coast at Half Moon Bay three months later. TMMC personnel conducted a rescue and the animal died overnight. Necropsy results indicated a healed radio tag incision site clean of infection and a working radio tag. Serology results revealed the animal had Sarcocystis neurona titers present (1:5120), none for Toxoplasma gondii

(≤1:40), and a severe meningoencephalitis possibly caused by Sarcocystis neurona or a mixed infection. No parasites were cultured.

DISCUSSION

The number of harbor seals in SFB has been characterized as stable, and has not changed significantly since the 1970s (Fancher 1979, Allen et al. 1989, Kopec and

Harvey 1995). Estimating population dynamics can be difficult, and SFB offers an added challenge because of a lack of data before 1970 and incomplete records at certain sites.

While there is variability among sites and seasons, overall, adult counts and pup production have increased in SFB in the past (Grigg et al. 2004). Despite previous reports of an increase in pups and adults (Grigg et al. 2004), data in my study indicated variability among sites and years in adult counts: most years counts decreased later in the season compared with earlier (Figs. 3 – 5). There was a slight overall decrease in adults, both in SFB and TB (Figure 6), although it was not statistically significant most likely due to a short sampling period. I reported an increase in pup production, both in SFB and

TB (Figure 7), which was consistent with a previously reported trend (Grigg et a. 2004), however this too was not statistically significant likely caused by minimal sampling period. Numerous factors likely affect the structure of the harbor seal populations in northern California, including prey availability, oceanographic conditions, differing census techniques (affecting apparent structure), and factors affecting individuals including competition, disturbance, haul-out site usage, and survival.

Examination of fish productivity can be used to assess abundance of harbor seal prey. Harbor seal diet in Scotland was variable and heavily influenced by an individual’s use of different foraging habitats (Tollit et al. 1998), whereas in Sweden, the predominant 27

prey species were similar to the relative abundance and presence of that species

(Harkonen 1987). In the early 1990s, SFB seals were predominantly feeding on yellowfin goby (Acanthogobius flavimanus), staghorn sculpin (Leptocottus armatus), and plainfin midshipman (Porichthys notatus) (Torok 1994) but within two decades Gibble

(2011) found an overall decrease in species diversity (yellowfin goby, shiner surfperch

(Cymatogaster aggregata), and chameleon / cheekspot goby (Tridentiger trigonocephalus / Illypnus gilberti)) and increased consumption of non-native prey species.

Increasing productivity of harbor seal prey and other fish species from 2011 to

2012 indicate more available food for seals, which, in turn, may explain the great adult female survival rates reported in this study. Otter and mid-water trawls sampled different portions of the water column and captured species at varying numbers throughout the year (Figure 15). Harbor seals are benthic foragers and the otter trawl, sampling along the benthos, provided a better representation of their prey (Figure 15). Between 2007 and

2012, prey availability was variable, thus this factor did not explain the overall decrease in adult counts. Though not tested in this study, prey increases in fall and winter should lead to an increase in pup production the following spring, as well-fed moms are more likely to successfully produce a pup. During this study, increased harbor seal prey availability occurred in SFB beginning early 2012, compared with 2011, and lasted through the year (personal communication, Kathy Hieb). Also, increases in spawn escapements of other fish, such as the Pacific herring (Clupea pallasii), within SFB from 28

2011 to 2012 (personal communication, Ryan Bartling) indicate overall ecosystem productivity.

Local- and basin-wide oceanographic processes and environmental conditions influence survival rates and can structure populations. Harding et al. (2005) examined the relationship between metabolic rate of harbor seal pups and factors including mass, blubber thickness, and water temperature. Smaller pups were negatively impacted by lesser water temperatures and also had a lesser chance of survival compared with heavier members of their cohort (Harding et al. 2005, Trillmich and Wood 2008).

Survival often is correlated with upwelling indices in California sea lions

(Zalophus californianus), harbor seals, northern elephant seals (Mirounga angustirostris), and Steller sea lions (Sydeman and Allen 1999). Along the California coast, food web development hinges on the predictable patterns of upwelling. In poor upwelling years there is less primary productivity due to reduced winds reducing upwelling of nutrient- rich deep water. Upper trophic level predators like pinnipeds, therefore, exhibit reductions in productivity, survival rates, and population size as many fish species leave or die because of lessened plankton availability (Trillmich et al. 1991). Sea surface temperature and the upwelling index significantly correlated with annual harbor seal population counts. El Niño Southern Oscillation (ENSO) events also affect pinniped survival rates (McMahon and Burton 2005, Becker et al. 2009). ENSO influences oceans by changing the availability of nutrients, which, in turn, affects primary and secondary productivity, especially in the eastern Pacific. McMahon and Burton (2005) reported that 29

mass of weaners explained 88% of first-year survival in elephant seal pups, and hypothesized mothers were able to find and store more resources in productive years.

Harding et al. (2005) found a similar correlation between survival and pup body mass: smaller pups (< 20kg) had 63% survival probability whereas larger pups (30kg) had 96% survival probability. Studies indicate greater food stores lead to greater pup survival.

The best fitting model to predict harbor seal counts in PRNS included the anthropogenic factor of oyster harvest, used by researchers as a disturbance proxy as harvesting occurs near seals’ haulout sites, and years since a natural disturbance, an ENSO event (Becker et al. 2009). Times of increased oyster harvest influenced the numbers and locations of harbor seals hauling out, with lesser numbers of seals during anthropogenic disturbance.

Greater counts occurred with greater time since the most recent ENSO event, explained by apex foragers forgoing pupping in years of low productivity to increase foraging efforts to build body reserves (Sydeman and Allen 1999).

The ENSO regime has been used as an explanatory variable affecting prey resources and thus, pinniped survival, especially in pups and juveniles (Trillmich et al.

1991). However, caution should be exercised in assuming direct causality associated with harbor seals because productivity changes are more likely occurring in pelagic environments while lesser effects are occurring in benthic habitats where harbor seals often forage. Furthermore, there is often a lag in visible effects on pinnipeds as most immediate effects are caused by oceanographic disturbances and changes in prey species’ distribution (Trillmich 1991). During the tagging study, July 2011 – March 2013, the 30

northeast Pacific Ocean was in a La Niña or neutral state (Figure 16). Moderate conditions occurred during 2007-2008 followed by a relatively weak El Niño event in

2009-2010 brought cold waters to northern California, which set up an increase in plankton and increased fish biomass (Figure 15 and Figure 16). This could be one explanation for the greater numbers of pups born to healthy adult females in 2011 and

2012 (Figure 7). As recently as 2009 – 2010, there was an El Niño event directly and though the event fell outside the study period, I would hypothesize survival to have decreased during this season of lower productivity. The years 2010 through 2012 were

La Niña years where good conditions were available for seals (Benson et al. 2002).

Survival rates were expected to be greater during these years, all other factors held constant. No El Niño occurred during the tagging study, thus the greater survival value I report compared with similar studies examining adult female survival (Bigg 1969, Boulva and McLaren 1979, Pitcher and Calkins 1979, Harkonen and Heide-Jorgensen 1990) might be a different, greater, value if future studies were conducted during times of lesser productivity.

Differences in census techniques, independent of environmental factors, may explain trends and counts. Different observers introduced biases, such as variations in search image and counting abilities, and though biases were consistent over time at a particular site, they might not have been among sites. Area-wide surveys in close temporal proximity would have provided a more accurate count of seals throughout the year. National Park Service counts (2008-2012) reflect a small portion of the year and 31

may capture an influx of seals from the outer coast during breeding months. To accurately assess population dynamics more sites should be documented with regularity throughout the year. This will provide a more accurate annual count and incorporate effects of factors directly affecting individual seals, such as: competition, disturbance, and haul-out site usage.

Other factors besides prey availability and oceanography might have influenced harbor seals. During the months surveyed, an increase in competition for resources due to an influx of outer coast seals might have affected dynamics. An influx of seals from the outer coast was recorded in south SFB in 1976 (Fancher 1979). The influx would have further limited space and food supply in an already strained SFB population. This would not have been a factor for seals in TB, which was within close proximity to the outer coast where space was not limiting. Human disturbance also may have played a role. SFB seals live in proximity to humans, interact with large vessel traffic, and are experiencing loss of habitat. In TB, seals deal with different types of anthropogenic disturbances including: small vessel traffic, clammers on the exposed mudflats at low tide, and the effects of oyster farming.

Haulout use by seals change; shifts can occur both within a single season and during much longer time scales. As recently as the late 1970s, seals abandoned

Strawberry Spit in north SFB and have been using Yerba Buena Island since the early

1980s (Paulbitski 1976). This shift exemplifies the importance of considering all SFB 32

sites as a single area with separate parts that are in flux. Sites not only vary with season, they can also be dominated by a single sex.

Surveys to determine a sex ratio were conducted at several sites within SFB, both accurate representations of SFB haulouts, though one is predominantly male (YBI) and the other is predominantly female (Castro Rocks). Confirmed by personal observation from previous sampling seasons, there were more animals present at Castro Rocks than at

YBI, and there were a greater percentage of females at Castro Rocks than at YBI (Figure

8). During 10 surveys in 11 weeks, counts of adult decreased at both sites (Figure 8). It is possible that an influx of outer coast males, entering SFB to breed, congregated with other males at YBI leading to an increase of adults before the surveys, and that the percentage of males then gradually decreased during molt. Also, there was an influx of females earlier in the season during pupping at Castro Rocks, where upwards of 50 pups were seen during a single survey (personal observation). This number decreased as pupping ended and molt began. Because 58% of the population in SFB is female and it is a stable population with increasing numbers of pups, further research on life history parameters is needed to determine why numbers of seals in SFB have not increased through recent time.

Survival and recapture probabilities were reported for northern California, however, parameter estimates are only accurate if tagged animals are representative of the entire population. The best model indicated similar survival between bays. This model was strongly supported by movement data and a priori hypotheses. Tagged 33

animals typically foraged locally (Torok 1994, Kopec and Harvey 1995, Nickel 2003,

Grigg et al. 2009, Grigg et al. 2012), however, my data was the first example of tagged individuals moving between bays over short time frames, then returning to the tagging site. None of the best models included the factor of time. This indicated time had no role during the 20-month study period, and there was no negative effect of the tag on female survival.

Inclusion of individual covariates (axillary girth and mass/standard length ratio) explained female survival better than factors of time or tagging site alone. Axillary girth in grey seal pups was a good indicator of body condition (Hall and McConnell 2007), and a decreasing population of Hawaiian monk seals was correlated with decreased weaner size and juvenile emaciation, both contributing to decreased survival (Craig and Ragen

1999). Female harbor seals were tagged in June and July, the time of year when they are at their weakest state and worst body condition. Axillary girth, a measure of an animal’s fat stores, has been used as a metric of body condition (Ryg et al. 1990), so it is a better explanatory metric than mass or length. Individual covariates were not included in recapture parameters because there was no biological reason to expect body condition to affect the changes of resighting an individual.

The best models indicated recapture was site dependent, which supported the a priori hypothesis that there were differences between bays. SFB has a greater number of haul-out sites and the total haul-out area is greater. There was an additional effect of sampling bias in recapture efforts between sites with less effort in SFB compared with 34

TB, which in turn, resulted in more occasions for resight events in TB compared with

SFB. These differences in haul-out sites, in addition to the sampling bias, might explain site-dependent recapture results. Furthermore, the total number of times an animal was resighted, though not statistically significant, indicated there might be a potential relationship. This potential relationship might be an artifact of inadequate sampling, therefore, I recommend increased sample size and efforts in SFB.

It was logistically difficult to locate tagged animals in south SFB: airspace restrictions were in place from multiple airports (Palo Alto, San Carlos, and Moffet Air

Force Base), and there was more background interference in SFB compared with TB.

Resights in SFB were a combination of land surveys in central SFB (YBI and Castro

Rocks) and aerial surveys in south SFB (Mowry Slough, Newark Slough, and Bair Island

/ Corkscrew Slough). Access to south SFB via land was not allowed due to restrictions on privately owned Cargill land. This introduced a bias in the dataset because seals tagged in south SFB were only detected once a month and only when the plane was circling over haulouts. The study would have benefited from increased efforts.

There were no airspace restrictions in PRNS so locating tags by flying directly above their haul-out site was a possibility. There was less background interference, most likely a function of being near a national park. Also, efforts tracking in TB were increased and overall less complex: seals used two main haul-outs making resights easier.

Resights in TB were a combination of land surveys (from Tom’s Point) and aerial surveys. Search effort was greater in TB than in SFB, therefore there were more 35

occasions to resight animals which, in turn, would artificially inflate resight rates in TB compared with SFB.

Prey availability and oceanographic conditions also affected survival, recapture, and movement patterns, but additional factors like habitat preferences, tagging hardware, maternal behavior, characteristics of the animal or colony, and contaminants could explain some of the variability.

Harbor seals primarily forage close to local haul-outs (Torok 1994, Nickel 2003,

Grigg et al. 2012). In Sweden, tagged seals in estuaries foraged in shallow waters

(<50m) (Harkonen 1987), and in Scotland, seals living in estuaries fed over soft or sandy sediments (Tollit et al. 1998). Tagged seals dove on the continental shelf to depths of five to 100m in Monterey Bay (Eguchi and Harvey 2005). Harbor seals foraged in SFB between one to five km from the haulout (Torok 1994, Nickel 2003), and animals used areas of increased depth and bottom relief close to their haulouts, which generally had increased prey abundance (Grigg et al. 2012).

Harbor seals are capable of foraging many kilometers away from their main haulout and at depths greater than 500m, but generally forage close to their haulout and at relatively shallow depths. Important prey items and habitat types based on examining slope (Figure 17) and rugosity (Figure 18) within SFB are found in locations close to haulouts. Thus, seals do not range far for prey because haul-out sites occur near good foraging areas (Figure 19A-B). Results of my predictive model agreed with the results of 36

other researchers, which indicate that harbor seals forage on benthic resources and require relatively shallow water near their haulouts.

The effects of tagging may have influenced reported survival rates. Tag range, in ideal conditions, was minimal so unless the receiver was within 1km of the individual, they were not detected thus considered not present. Infection at the incision site could have caused tag migration, causing a decrease in range of detection (Frances Gulland, personal communication). In this case the animal would have appeared dead.

Alternatively, the incision site may have become infected post-surgery resulting in actual death (Frances Gulland, personal communication). Battery failure also would have appeared, incorrectly, as a death. Tags were ordered in several batches and a few were refurbished old tags so it was difficult to determine with any certainty if a tag was still transmitting because not all tags operated in an identical manner. Projected battery life was greater than three years so tag failure was an unlikely issue during the 20 months and no mortality signals were reported. Finally, seal migration out of the survey range would appear incorrectly as a death. A larger survey was conducted at the beginning of 2013 but there is a chance an animal was not in that area or not hauled out during that survey period available to be resighted or heard.

Maternal behavior, along with conditions of the animal, are two other factors that affect survival (Lunn et al. 1993, Bowen et al. 1994), which might explain results. In northern California, females spend a greater proportion of time ashore at the haulout during spring and summer when they give birth, nurse a pup, and molt (Reeves et al. 37

1992). Females spend three to four weeks with the pup, forage little, and wean the pup leaving it to fend for itself (Reeves et al. 1992). It is during this time that females are weakest. After molt, more time is spent at sea, foraging and rebuilding fat stores for the next reproductive season (Allen et al. 1989). Pup growth and survival is influenced heavily by the condition, and thus, the foraging efficiency of the mother. Harbor seal pups born to lighter females were lighter and slower growing than pups born to heavier females (Bowen et al. 2001), and during a period of population decline, pups born to females on Sable Island had a later mean birth date suggesting delayed implantation possibly due to nutritional stress (Bowen et al. 2003). The probability of survival to age one increased with weaning body condition in grey seals (Hall et al. 2001) supporting the hypothesis that body condition was important for survival. Furthermore, heavy harbor seal pups were in better body condition, and had greater total body energy than lighter ones (Muelbert et al. 2003).

Characteristics of the colony also have been hypothesized to be important for survival. These include population density and size, leading to competition for food and space resources (Hastings and Testa 1998, Bradshaw et al. 2003). Factors such as disease can cause a significant difference in survival among years for animals of any age class.

An outbreak of the bacteria Klebsiella pneumoniae impacted pup survival in New

Zealand sea lions on the Auckland Islands (Chilvers et al. 2007). Phocine distemper virus (PDV) spread through colonies of harbor seals in Europe killing thousands of seals in 1988 and 2002 (Harkonen et al. 2006). Differences in mortality rates between the two 38

epidemics indicated animals in the later epidemics had immunity to PDV from the previous outbreak.

Contaminants are important when examining species living in close proximity to major cities and towns. They persist in the marine environment and, because of bioaccumulation, exposure poses a potentially high risk to apex predators like pinnipeds.

Researchers have documented contaminants are present in SFB and TB (Risebrough et al.

1980, Kopec and Harvey 1995, Neale et al. 2005, Greig et al. 2011). Contaminants

(PCBs, DDTs, and PBDEs) occur in blood and blubber of harbor seals in SFB (Kopec and Harvey 1995) and similar levels were found in seals in other northern California sites

(PRNS) (Risebrough et al. 1980). Recent studies, however, indicated a possible link between contaminants and survival, especially survival of pups or individuals with increased contaminant burdens (Neale et al. 2005, Hall et al. 2009, Greig et al. 2011).

Hall et al. (2009) examined concentrations of blubber contaminants that disrupt endocrine and immune functioning in grey seal pups. They estimated 47% male and 63.9% female survival, regardless of condition, using a model that incorporated the presence of tetra-

PBDEs, BDE-47, DDTs, and penta-PCBs. Greig et al. (2011) found blubber contaminant levels were greater and six-month survival less in SFB harbor seal pups than those in

PRNS. Contaminant load in pinnipeds has been linked to deleterious health effects such as cancer in California sea lions and lowered reproductive success in harbor seals

(Reijnders 1986, Ylitalo et al. 2005). Survival could be impacted by contaminants but there is no direct evidence of the link to survival in this study. 39

CONCLUSIONS

Baseline data of healthy wild harbor seal populations (e.g., population dynamics, movement patterns, and survival estimates) are necessary for management and conservation in northern California. Researchers have demonstrated that seals in SFB have stable numbers (Fancher 1979, Risebrough et al. 1980, Kopec and Harvey 1995,

Grigg et al. 2004), however, I provided evidence that indicates a slight decrease in adult counts in SFB and TB between 2008 and 2012. Potential factors affecting seals (prey availability, oceanographic conditions, and habitat) appear to jointly contribute to seal population growth, adult female survival, and movements affecting distribution in northern California. Despite a decrease in estimates, pup production rates have increased and adult female survival estimates remain stable in SFB and TB.

These are the first subadult/adult female estimates of survival and resight for harbor seals in California, and the first documented movement between bays on a short time-scale. The stable population was most likely not a result of poor subadult or adult female survival, but perhaps was caused by emigration, poor pup survival, and effects of environmental factors. The survival rate I report should be interpreted with caution: it is possibly inflated due to productive oceanographic conditions during the study, increased prey availability, and a small sample size.

Non-significant results in movement patterns between bays (total distance traveled by an individual, number of resights per individual, and number of months to first resight) should also be interpreted using caution, in part because of a small sample 40

size. Adult female activity patterns change during pupping and non-pupping seasons

(Thompson et al. 1994), however, this study encapsulated several seasons so differences in seasonal movements were captured. In addition, adult movement data were not the same as other studies on the western coast of the United States. Female harbor seals near

Vancouver Island moved relatively less than males: 8 males moved >100km at least once whereas no females moved >50km (Peterson et al. 2012). Variation in haulout site location, relative to food supply, or intraspecific dynamics possibly explain movement pattern differences.

Further evaluation of demographic data is necessary. Survival studies sampling health indices of individuals (e.g., testing for contaminants from blubber or hair samples) should be conducted in conjunction with measuring indices of haulout behaviors (e.g., measuring some metric of “haulout quality”) to gain a better understanding of factors affecting life history patterns, which will allow for better informed management decisions.

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Table 1. 16 original survival and recapture models in MARK, with description.

Model Title Model Description phi (time) p (site * time) Effect of time on survival, effect of site / time interaction on recapture phi (time) p (time) Effect of time on survival, effect of time on recapture phi(time) p (site) Effect of time on survival, effect of site on recapture phi (time) p (.) Effect of time on survival, constant recapture rate phi (.) p (site * time) Constant survival rate, effect of site / time interaction on recapture phi (.) p (time) Constant survival rate, effect of time on recapture phi (.) p (site) Constant survival rate, effect of site on recapture phi (.) p (.) Constant survival rate, constant recapture rate phi (site * time) p (site * time) Effect of site /time interaction on survival, effect of site / time interaction on recapture phi (site * time) p (site) Effect of site /time interaction on survival, effect of site on recapture phi (site * time) p (time) Effect of site /time interaction on survival, effect of time on recapture phi (site * time) p (.) Effect of site /time interaction on survival, constant recapture rate phi (site) p (site * time) Effect of site on survival, effect of site / time interaction on recapture phi (site) p (site) Effect of site on survival, effect of site on recapture phi (site) p (time) Effect of site on survival, effect of time on recapture phi (site) p (.) Effect of site on survival, constant recapture rate

Table 2. 40 new survival and recapture models in MARK with covariates, built off 16 original models (Table1), with description.

Model Title Model Description phi (mass) p (site) Effect of mass on survival, effect of site on recapture phi (SL) p (site) Effect of standard length on survival, effect of site on recapture phi (AG) p (site) Effect of axillary girth on survival, effect of site on recapture phi (mass/SL) p (site) Effect of mass/SL ratio on survival, effect of site on recapture phi (mass) p (.) Effect of mass on survival, constant recapture rate phi (SL) p (.) Effect of standard length on survival, constant recapture phi (AG) p (.) Effect of axillary girth on survival, constant recapture phi (mass/SL) p (.) Effect of mass/SL ratio on survival, constant recapture phi (mass) p (time) Effect of mass on survival, effect of time on recapture phi (SL) p (time) Effect of standard length on survival, effect of time on recapture phi (AG) p (time) Effect of axillary girth on survival, effect of time on recapture phi (mass/SL) p (time) Effect of mass/SL ratio on survival, effect of time on recapture phi (mass) p (site * time) Effect of mass on survival, effect of site * time interaction on recapture phi (SL) p (site * time) Effect of standard length on survival, effect of site * time interaction on recapture phi (AG) p (site * time) Effect of axillary girth on survival, effect of site * time interaction on recapture phi (mass/SL) p (site * time) Effect of mass/SL ratio on survival, effect of site * time interaction on recapture phi (time + mass) p (site * time) Additive effect of time and mass on survival, effect of site * time interaction on recapture phi (time * mass) p (site * time) Interaction effect of time and mass on survival, effect of site * time interaction on recapture

Table 2. 40 new survival and recapture models in MARK with covariates, built off 16 original models (Table1), with description.

Model Title Model Description phi (time + AG) p (site * time) Additive effect of time and axillary girth on survival, effect of site * time interaction on recapture phi (time * AG) p (site * time) Interaction effect of time and axillary girth on survival, effect of site * time interaction on recapture phi (time + mass/SL) p (site * time) Additive effect of time and mass/SL ratio on survival, effect of site * time interaction on recapture phi (time * mass/SL) p (site * time) Interaction effect of time and mass/SL ratio on survival, effect of site * time interaction on recapt. phi (time + mass) p (site) Additive effect of time and mass on survival, effect of site on recapture phi (time * mass) p (site) Interaction effect of time and mass on survival, effect of site on recapture phi (time + AG) p (site) Additive effect of time and axillary girth on survival, effect of site on recapture phi (time * AG) p (site) Interaction effect of time and axillary girth on survival, effect of site on recapture phi (time + mass/SL) p (site) Additive effect of time and mass/SL ratio on survival, effect of site on recapture phi (time * mass/SL) p (site) Interaction effect of time and mass/SL ratio on survival, effect of site on recapture phi (time + mass) p (time) Additive effect of time and mass on survival, effect of time on recapture

Table 2. 40 new survival and recapture models in MARK with covariates, built off 16 original models (Table1), with description.

Model Title Model Description phi (time * mass) p (time) Interaction effect of time and mass on survival, effect of time on recapture phi (time + AG) p (time) Additive effect of time and axillary girth on survival, effect of time on recapture phi (time * AG) p (time) Interaction effect of time and axillary girth on survival, effect of time on recapture phi (time + mass/SL) p (time) Additive effect of time and mass/SL ratio on survival, effect of time on recapture phi (time * mass/SL) p (time) Interaction effect of time and mass/SL ratio on survival, effect of time on recapture phi (time + mass) p (.) Additive effect of time and mass on survival, constant recapture phi (time * mass) p (.) Interaction effect of time and mass on survival, constant recapture phi (time + AG) p (.) Additive effect of time and axillary girth on survival, constant recapture phi (time * AG) p (.) Interaction effect of time and axillary girth on survival, constant recapture phi (time + mass/SL) p (.) Additive effect of time and mass/SL ratio on survival, constant recapture phi (time * mass/SL) p (.) Interaction effect of time and mass/SL ratio on survival, constant recapture

60 Table 3. Models built to examine tag effects over August 2011 – March 2013 by varying time frames. Monthly, biology, and seasonal effects examined.

Model Survival Parameter (Φ) Description (Constant p) phi (time * site) p (.) Φ varied by site & time, each month unique phi (time_bio_same * site) p (.) Φ varied by site & time, each March-July identical (biology effect) phi (time_bio_diff * site) p (.) Φ varied by site & time, each March-July unique (biology & year) phi (time_season_same * site) p (.) Φ varied by site & time, each season identical between years (seasonal effect) phi (time_season_diff * site) p (.) Φ varied by site & time, each season unique (seasonal & year effect)

61 62

Table 4. Selection table for survival (Φ) and recapture (p) probability models. Time is recorded in monthly intervals, site is either SFB or TB. No individual covariates are included. No ^c adjustments made.

AICc No. Model AICc ∆ AICc Weight Par. Deviance 1 Φ (.) p (site) 372.3076 0.5958 3 245.6062 2 Φ (site) p (site) 373.2748 0.9672 0.3673 4 244.3863 3 Φ (site) p(.) 378.2334 5.9258 0.0308 20 205.9737

Table 5. Selection table for survival (Φ) and recapture (p) probability models. Time is recorded in monthly intervals, site is either SFB or TB. Individual covariates are included. No ^c adjustments made.

AICc No. Model AICc ∆ AICc Weight Par. Deviance 1 Φ (AG) p (site) 412.0617 0.6025 4 404.6362 2 Φ (mass/SL) p (site) 416.0102 2.9485 0.1379 4 407.5846 3 Φ (.) p (site) 416.7956 3.7339 0.0932 3 410.5429

Table 6. Real survival (Φ) and recapture (p) parameter estimate values from model 1 (Table 5): Φ (ax girth) p (site). Standard Error (SE) and 95% confidence intervals (LCL and UCL) are also reported.

Estimate SE UCL LCL SFB Φ 0.9829 0.010 0.9468 0.9941 TB Φ 0.9829 0.010 0.9468 0.9941 SFB p 0.0618 0.016 0.0374 0.1006 TB p 0.2685 0.033 0.2085 0.3383

Table 7. 27 resighted harbor seals. Animals with + indicate inclusion in Φ/p estimates. Total time: months to last resight occasion. Animals with * indicate > 15 months until first resight. Minimum total distance: reasonable travel pattern for harbor seals.

Total Minimum Resighted Total Time Travel Movement Tagging Haulouts ID Sex Age Resights (mos) (mi) Category Site 281 M SA 2 22 75 4 CR FAR, TB 790 F A 11 27 61 2 CR CR, SSFB 730 F Y 1 18 * 58 4 CR TB 930 F SA 1 3 0 1 EHS EHS 740 M Y 1 3 0 1 EHS EHS 360 F Y 6 30 354 3 EHS EHS, Mow, TB 820+ F SA 3 16 155 3 CSS TB, CSS 870 F SA 3 13 0 1 CR CR 810+ F SA 12 19 0 1 TB TB 880+ F A 3 14 0 1 TB TB 830+ F A 4 21 0 1 TB TB 610+ F A 5 21 155 3 TB CSS, TB 630+ F A 3 21 * 0 1 TB TB 690+ F A 1 2 0 1 TB TB 620+ F A 5 19 0 1 TB TB 940+ F A 2 19 * 155 3 TB CSS, TB 920+ F A 6 19 229 3 TB CSS, TB, Bol 480+ F A 4 14 0 1 TB TB 960+ F A 20 21 0 1 TB TB 670+ F A 3 8 228 4 – died CSS TB, Mow, HMB 720+ F A 1 1 77 4 CSS TB 650+ F A 2 8 30 3 CSS BI, CR 900+ F A 1 16 * 0 2 BI CSS 640+ F A 2 16 22 2 BI Mow, CSS 770+ F A 1 20 * 0 1 CSS CSS 860+ F A 1 20 * 0 1 CSS CSS 910+ F A 1 20 * 0 1 CSS CSS

Table 8. Mean minimum total distance traveled (miles) ± standard error (SE) for subadult and adult harbor seals tagged in SFB and TB. Values pooled and

averaged from minimum total travel distance values for each seal (from Table 7).

SFB TB SA + A, Both Sexes SA + A, Females SA + A, Females (n = 13) (n = 12) (n = 10) Mean Minimum Distance 54.01 ± 20.1 52.10 ± 21.9 53.80 ± 28.1 Traveled (mi)

Figure 1. Northern California study area: tagging haulouts and additional aerial and ground resight locations. Circles denote tagging and surveyed haulout sites, stars denote surveyed haulout sites, triangles denote California Department of Fish and Wildlife trawl stations (with station number in parentheses).

Figure 2. Telonics IMP/300/L implantable radio tag (23mm x 81mm; 40g; Paraplast® wax coating.

Figure 3. Maximum counts of adult harbor seals, by month, in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs) during pupping (March through May) and molt (June and July) from 2008 to 2012.

Figure 4. Maximum counts of adult harbor seals, by month, in TB during pupping (March through May) and molt (June and July) from 2008 to 2012.

Figure 5. Mean maximum counts of adult harbor seals in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs) and TB by year during pupping (March through May) and molt (June and July) from 2008 to 2012. The red rectangle denotes time-frame of the survival implant tagging study.

Figure 6. Relationship of LN of maximum count to year (2008 to 2012) for adult harbor seals in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs, P = 0.29) and TB (P = 0.23) from March through July. The red rectangle denotes time-frame of the survival implant tagging study.

Figure 7. Relationship of proportion of pups to year (2008 to 2012) in SFB (Castro Rocks, Yerba Buena Island, and Newark and Mowry Sloughs, P = 0.15) and TB (P = 0.34). The red rectangle denotes time-frame of the survival implant tagging study.

Figure 8. Total adult harbor seal counts (lines; black denotes CR, gray denotes YBI) and percentage of adult females (circle denotes CR, triangle denotes YBI) during molt May to August 2013.

Figure 9A. Movement pattern for seal 360: resighted 6 times, alive 30 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Elkhorn Slough.

_\ N

Tomales Bay

1 (3 MOS)

ID 920: 6 Resoghts Alive 19 Months 811 1r • Island

Figure 9B. Movement pattern for seal 920: resighted 6 times, alive 19 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Tomales Bay.

_\ N

Tomales Bay • ~

10 960: 20 Resights Alive 2 1 Months

0 10 ~0

Figure 9C. Movement pattern for seal 960: resighted 20 times, alive 21 months. The animal was tagged at Tomales Bay and never resighted at another haulout, remaining there at least 21 months (when surveys were completed). 78

~ N

•

Ba ir • ~ (2 mos) Island ~ • (14 mos) Mowry Slough

10 640: 2 Resights Alive 16 Months

0 10 20 "«! MIIIes

Figure 9D. Movement pattern for seal 640: resighted 2 times, alive 16 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Bair Island. 79

Figure 10. Bar chart of movement patterns for SFB (n=20) and TB (n=17) non-pups including both sexes (from Table 7). Each seal was assigned a category.

Figure 11. Bar chart of movement patterns for SFB (n=17) and TB (n=15) subadult and adult females (from Table 7). Each seal was assigned a category.

Figure 12. Histogram of months to first resight; TB females (n=11), SFB males and females (n=13), and SFB females (n=11) (from Table 7). Each seal was assigned to a unique category.

Figure 13. Histogram of total number of resights for TB females (n=11), SFB males and females (n=13), and SFB females (n=11) (from Table 7). Each seal was assigned to a unique category.

Figure 14. Movement pattern for seal 670: resighted 3 times, alive 8 months. Lines represent hypothetical trips between haulouts numbered in chronological order and duration between resights annotated in parentheses (months). The animal was tagged at Bair Island, 8 months post-release stranded live near Pillar Point Harbor, taken to TMMC and died overnight.

Figure 15. Combined Otter and Mid-Water Trawl CPUE from two open water stations from 2007 to 2012 (black denotes South SFB: 101; gray denotes Central SFB: 214), combined for five prey species of known importance to harbor seals (Bay goby, Lepidogobius lepidus; chameleon goby, Tridentiger trigonocephalus; cheekspot goby, Ilypnus gilberti; shiner perch, Cymatogaster aggregata; and yellowfin goby, Acanthogobius flavimanus).

Figure 16. Northern Oscillation Index (NOIx) and Multivariate ENSO Index (MEI) oceanographic conditions from 2007 through September 2013. Annotated in gray rectangles: moderately cool conditions (2007 - 2009), strong El Niño season (2009 - 2010), La Niña seasons (2010 - 2012), and moderately warm conditions (2012 – 2013).

Figure 17. San Francisco Bay slope and two harbor seal haulouts (Castro Rocks and Bair Island). Circles represent one and five kilometer buffers from each of the haulouts.

Figure 18. San Francisco Bay rugosity and two harbor seal haulouts (Castro Rocks and Bair Island). Circles represent one and five kilometer buffers from each of the haulouts.

.... -· \..

Castro Rocks

_\ "~ .... N .• .# • • . .. • ·..J" \·: •.• '· .. - ··~..... : ...... ~v· ... • 1 ·-•

--Marine Habitat 1 Marine Habitat 2 --Marine Habitat 3

. Bair Island

0 2.5 5 10 Miles

Figure 19A. Top three marine habitats from predictive model for two SFB sites: Castro Rocks and Bair Island. Rings represent 1 and 5km from haulout. Habitats are intersection of 5-30m depth, low and medium rugosity, and medium slope. Within 5 km of Castro Rocks: 3.9% Habitat 1, 0.2% Habitat 2, 0% Habitat 3. Within 5 km of Bair Island: 1.8% Habitat 1, 0% Habitats 2 and 3. 89

_\ N

, Tomales ~ Bay ·. (.') Y. --Marine Habitat 1 •... .. Marine Habitat 2 •• --Marine Habitat 3

0 1.5 3 6 Miles

Figure 19B. Top three marine habitats from predictive model for Tomales Bay. Rings represent 1 and 5km from haulout. Habitats are intersection of 5-30m depth, low and medium rugosity, and medium slope. Within 5 km of Tomales Bay: 4.3% Habitat 1, 0% Habitats 2 and 3.

Appendix 1. Seal Database (41 tagged individuals). Seal Identification (ID, flipper tag numbers (L/R)); capture location at Castro Rocks (CR), Elkhorn Slough (EHS), Tomales Bay (TB), Corkscrew Slough (CSS), or Bair Island (BI); capture date; radio transmitter frequency; weight (kg); sex; standard length (SL, cm); axillary girth (AG, cm); and age of harbor seals. Animals with “R” indicate resighted at least once.

Seal Capture Capture Transmitter Age ID Location Date Frequency Weight Sex SL AG Class 1850/1851 CR 2/5/10 162. .730 21 F 97 73 Y R 1868/1869 CR 2/5/10 .281 58 M 138 98 SA R 1930/1931 CR 10/21/10 .790 54 F 125 94 A R 1856/1857 EHS 10/27/10 .980 43 F 130 85 SA 1853/1852 EHS 10/27/10 .740 23 M 101 70 Y R 1864/1865 EHS 10/27/10 .360 27 F 111 73 Y R 1858/1859 EHS 10/27/10 .930 36 F 114 85 SA R 1970/1971 TB 12/2/10 .950 28 M 118 79 1-2Yr 1901/1902 TB 12/3/10 .840 38 M 122 90 1-2Yr 2030/2031 TB 6/6/11 .660 74 F 139 123 A 2046/2047 TB 6/6/11 .460 50 F 118 96 SA 2056/2057 TB 6/6/11 .970 86 F 142 116 A 2044/2045 TB 6/6/11 .920 56 F 133 96 A R 2040/2041 TB 6/7/11 .620 56 F 138 91 A R 2042/2043 TB 6/7/11 .630 69 F 140 101 A R 2067/2068 TB 6/7/11 .880 71 F 140 99 A R 2063/2064 TB 6/7/11 .810 44 F 121 87 SA R 2069/2070 TB 6/7/11 .470 53 F 141 85 A 2079/2080 TB 6/7/11 .940 67 F 144 92 A R 2096/2097 TB 6/7/11 .960 47 F 130 80 A R 2050/2054 TB 6/7/11 .690 51 F 136 85 A R 2052/2053 TB 6/7/11 .830 52 F 138 89 A R -- /2036 TB 6/8/11 .610 58 F 142 97 A R 2034/2035 TB 6/7/11 .990 51 F 126 91 A R 2108/2109 CSS 7/6/11 .650 43 F 118 86 SA R 2128/2129 CSS 7/6/11 .820 57 F 149 90 A R 2118/2119 CSS 7/6/11 .680 40 F 113 85 SA R 2116/2117 CSS 7/6/11 .780 45 F 126 89 A 2114/2115 CSS 7/6/11 .890 50 F 158 88 A

Seal Capture Capture Transmitter Age ID Location Date Frequency Weight Sex SL AG Class 2106/2107 CSS 7/6/11 162. .860 50 F 158 92 A 2104/2105 CSS 7/6/11 .700 48 F 125 85 A R 2102/2103 CSS 7/6/11 .870 54 F 129 92 A 2140/2141 CR 7/7/11 .640 43 F 124 91 SA R 2143/2142 BI 7/8/11 .900 51 F 128 90 A R 2110/2111 BI 7/8/11 .910 54 F 132 91 A R 2100/2101 CSS 7/8/11 .710 65 F 151 95 A R 2146/2147 CSS 7/8/11 .670 56 F 139 96 A 2148/2149 CSS 7/8/11 .770 59 F 136 95 A R 2182/2183 CSS 7/8/11 .720 45 F 123 89 A R 2144/2145 CSS 7/8/11 .930 66 F 146 97 A R 2188/2189 CSS 7/8/11 .850 41 F 121 85 SA

Appendix 2. Ground tracking efforts used in survival and recapture estimates and movement patterns between August 2011 and March 2013 by site including frequency of monitoring and methods.

Site(s) Monitoring Range Frequency Method(s) Castro Rocks & Yerba August 2011 – x1 / month Handheld receiver, Buena Island February 2012 scope + binoculars Castro Rocks & Yerba March 2012 – x2 / month Handheld receiver, Buena Island April 2012 scope + binoculars Castro Rocks & Yerba May 2012 x1 / week Handheld receiver, Buena Island scope + binoculars Castro Rocks & Yerba June 2012 – x2 / month Handheld receiver, Buena Island July 2012 scope + binoculars Castro Rocks & Yerba August 2012 – x1 / month Handheld receiver, Buena Island February 2013 scope + binoculars Castro Rocks & Yerba March 2013 x2 / month Handheld receiver, Buena Island scope + binoculars Tomales Bay: November 2011 – x2-3 / Handheld receiver, kayaking to west bank February 2012 month passive listening (Seal / Clam, Hog station (DCC setup) islands) Tomales Bay: March 2012 – x2-3 / Handheld receiver, car access from east bank March 2013 month passive listening (Seal / Clam islands) station (DCC setup) October 2011 – x1 / month Handheld receiver, Bolinas Lagoon May 2012 scope + binoculars

Appendix 3. Aerial tracking efforts used in survival estimates and movement patterns between March 2010 and March 2013 by date including sites monitored, pilot and tracker(s), and methods. Haulouts were circled at 1,200 to 1,500 feet altitude with a speed of approximately 80 to 90 knots. * denotes effort used solely in movement pattern analysis and not in survival or recapture estimate analysis.

Date Site(s) Pilot Tracker(s) Method * 3/5/2010 Elkhorn Slough, S SFB, Bob Van B.V.W. Dual Yagi PRNS (Drakes, Tomales), Wagnen antennae + Bolinas, Farallon Islands (B.V.W.) receiver box * 3/23/2010 Elkhorn Slough, S SFB, Bob Van B.V.W. Dual Yagi PRNS (Drakes, Tomales), Wagnen antennae + Bolinas (B.V.W.) receiver box * 1/15/2011 Elkhorn Slough Kyle Suzanne Dual Yagi Harmon Manugian antennae + (K.H.) (S.M.), K.H. receiver box 8/15/2011 Elkhorn Slough, S SFB, Bob Van B.V.W. Dual Yagi PRNS (Drakes, Tomales), Wagnen antennae + Bolinas, Bodega Bay, (B.V.W.) receiver box Farallon Islands, outer San Mateo county coastline 9/11/2011 S SFB, Tomales Bay, Drakes K.H. S.M. + K.H. Dual Yagi Bay, Bolinas antennae + receiver box 10/8/2011 S SFB K.H. S.M. + K.H. Dual Yagi antennae + receiver box 10/9/2011 Tomales Bay K.H. S.M. + K.H. Dual Yagi antennae + receiver box 10/13/2011 Elkhorn Slough, Monterey NOAA S.M. Dual Yagi Bay coastline, San Mateo Twin antennae + county coastline Otter receiver box 10/19/2011 Elkhorn Slough, Monterey NOAA S.M. Dual Yagi Bay coastline, San Mateo Twin antennae + county coastline Otter receiver box 11/13/2011 S SFB, Tomales, Bolinas K.H. S.M. + K.H. Dual Yagi antennae + receiver box

Date Site(s) Pilot Tracker(s) Method 11/23/2011 Elkhorn Slough, S SFB, B.V.W. B.V.W Dual Yagi PRNS (Drakes, antennae + Tomales), Bolinas receiver box 12/17/2011 S SFB, Tomales, Bolinas K.H. S.M. + K.H. Dual Yagi antennae + receiver box 1/15/2012 S SFB, Tomales, Bolinas K.H. S.M. + K.H. Dual Yagi antennae + receiver box 2/26/2012 S SFB, Tomales, Bolinas K.H. S.M. + K.H. Dual Yagi antennae + receiver box 4/7/2012 S SFB, Tomales, Bolinas, K.H. S.M. + K.H. Dual Yagi Drakes antennae + receiver box 5/15/2012 Elkhorn Slough, S SFB, Joe Merz S.M. Dual Yagi San Mateo county outer antennae + coast receiver box 6/8/2012 Elkhorn Slough, S SFB, B.V.W. B.V.W Dual Yagi PRNS (Drakes, antennae + Tomales), Bolinas receiver box 6/23/2012 S SFB K.H. S.M. + K.H. Dual Yagi antennae + receiver box 8/21/2012 Elkhorn Slough, S SFB, B.V.W. B.V.W Dual Yagi PRNS (Drakes, antennae + Tomales), Bolinas receiver box

Date Site(s) Pilot Tracker(s) Method 11/3/2012 S SFB, Tomales, Bolinas, K.H. S.M. + K.H. Dual Yagi Drakes antennae + receiver box 1/5/2013 Northern CA coastal + B.V.W. B.V.W. Dual Yagi bay search (1 of 2) antennae + receiver box 1/6/2013 Northern CA coastal + B.V.W. B.V.W. Dual Yagi bay search (2 of 2) antennae + receiver box 3/10/2013 Tomales, Bolinas, B.V.W B.V.W Dual Yagi Bodega, Drakes antennae + receiver box 3/23/2013 S SFB, Elkhorn Slough, B.V.W. B.V.W. Dual Yagi San Mateo county coastal antennae + sites receiver box