Least Tern Dropped Prey Analyses at Alameda Point, San Francisco Bay, California.

Least Tern Dropped Prey Analyses at Alameda Point, San Francisco Bay, California. by Meredith L. Elliott Marine Ecology Division PRBO Conservation Science 3820 Cypress Drive, #11 Petaluma, CA 94954 January 11, 2008 Submitted to: Richard Morat U. S. Fish and Wildlife Service 2800 Cottage Way, Room W-2605 Sacramento, CA 95825-1846 and Joelle Buffa U. S. Fish and Wildlife Service San Francisco Bay National Wildlife Refuge Complex 9500 Thornton Ave. Newark, CA 94560 Analyses and reporting funded by FWS Coastal Program at San Francisco Bay

EXECUTIVE SUMMARY Prey dropped on seabird colonies may be used as an indicator of foraging and diet. Dropped fish have been collected from the Alameda Point Least Tern colony in most years since 1981, and findings were compared to California Department of Fish and Game (CDFG) fish trawl data of Central and South San Francisco Bay; sizes of dropped fish have been collected since 2000, and these results were compared to sizes of fish found in the Bay. Most of the dropped prey were jacksmelt (Atherinopsis californiensis), topsmelt (Atherinops affinis), and northern anchovy (Engraulis mordax). Surfperch species (family Embiotocidae) were also present in the dropped fish and likely represent fish too large to fit through the gape of a tern chick. Northern anchovy and jacksmelt were the most common prey species sampled in San Francisco Bay. Fish dropped at the colony were generally smaller than Bay fish, although terns chose larger fish than expected during the early part of the breeding season (during courtship and incubation). The largest dropped prey were found in 2006; this was also found in the Bay fish results and was probably driven by significantly larger jacksmelt and northern anchovy in the Bay in that same year. Dropped prey appeared to get smaller as the season progressed, indicating that adult terns switch from feeding larger fish to their mates to feeding smaller fish to chicks. Intraannual Bay fish size results were the opposite, reflecting the growth of the age-0 class fish that had spawned in the winter and spring months. Selectivity analyses illustrate the importance of small, pelagic, schooling fishes to Least Terns, particularly northern anchovy, Pacific herring (Clupea pallasii), and Pacific sardine (Sardinops sagax). Terns also forage on benthic fishes found in the nearshore environment, such as arrow goby (Clevelandia ios) and cheekspot goby (Ilypnus gilberti). Despite the large numbers of jacksmelt and topsmelt collected from the Least Tern colony, results suggest that terns are not selecting these species over northern anchovy. Northern anchovy, Pacific herring, and Pacific sardine are all relatively high in fat and may be the preferred prey to terns. However, if these species are not locally available, terns may switch to catching jacksmelt and topsmelt, as these species may be more abundant near the colony during the breeding season. 2

TABLE OF CONTENTS EXECUTIVE SUMMARY...2 TABLE OF CONTENTS...3 TABLES...4 FIGURES...5 INTRODUCTION...6 METHODS...7 Least Tern data...7 Dropped prey collection...7 CDFG San Francisco Bay prey data...8 Size comparisons...10 Species compositions...10 RESULTS... 11 Dropped prey...11 San Francisco Bay fish...12 Colony and Bay comparisons...13 DISCUSSION... 14 ACKNOWLEDGMENTS... 17 LITERATURE CITED... 19 3

TABLES Table 1. Definitions of breeding stages, 2000-2006... 21 Table 2. San Francisco Bay Monitoring Program sampling months, 1980-2006... 22 Table 3. Minimum lengths of fish sampled in San Francisco Bay... 23 Table 4. Families and species of fish identified in dropped prey, 1981-2006.... 24 Table 5. Standard lengths and body depths of dropped prey, 2000-2006... 26 Table 6. Standard lengths and body depths of dropped prey by breeding stage, 2000-2006... 27 Table 7. Two-factor ANOVA results for dropped fish sizes, 2000-2006... 28 Table 8. Fish sampled in San Francisco Bay during the Least Tern breeding season (April August), 1980-2006.... 29 Table 9. Lengths of fish sampled with different gear types in San Francisco Bay, April-August, 2000-2006... 33 Table 10. Lengths of suitably-sized fish sampled with different gear types in San Francisco Bay, April-August, 2000-2006... 34 Table 11. Lengths of suitably-sized fish sampled with different gear types in San Francisco Bay and in different breeding periods, April-August, 2000-2006... 35 Table 12. Two-factor ANOVA results for Bay fish sizes, 2000-2006... 36 Table 13. Three-factor ANOVA results comparing dropped fish and Bay fish sizes, 2000-2006.... 37 Table 14. Spearman correlations by species between species compositions from dropped fish at the colony to fish sampled in San Francisco Bay.... 38 Table 15. Spearman correlations by year between species compositions from dropped fish at the colony to fish sampled in San Francisco Bay.... 39 Table 16. Rank preference indices for fish species.... 40 Table 17. Sizes of northern anchovy and jacksmelt sampled in San Francisco Bay, April-August, 2000-2006... 41 4

FIGURES Figure 1. Fish sampling stations of CDFG s San Francisco Study... 42 Figure 2. Dropped prey composition by familiy, 1981-2006... 43 Figures 3. Mean midwater trawl CPUE values of suitably-sized fish, April-August, 1980-2006... 44 Figure 4. Mean otter trawl CPUE values of suitably-sized fish, April-August, 1980-2006... 45 5

INTRODUCTION The Least Tern (Sterna antillarum browni) is a federal and state endangered species (Thompson et al. 1997). The Alameda Point Least Tern colony is the largest colony in California north of San Luis Obsipo County, and data on population size and breeding success have been collected since the colony s inception in 1976 (Elliott et al. 2007). A four-year study on diet and foraging habits was conducted (2002-2005), which gave some insight into the important prey species of this colony (Elliott 2005, Ehrler et al. 2006). While diet data have been collected and analyzed, comparisons of diet to available prey in San Francisco Bay have not been investigated. San Francisco Bay is the main foraging area for the Alameda Point colony (Bailey 1992, Ehrler et al. 2006). Data on available prey in San Francisco Bay was obtained from the California Department of Fish and Game s (CDFG) San Francisco Bay Study. CDFG has conducted monthly surveys of fish populations at 35 predetermined locations in San Francisco Bay since 1980, and these data provide insight as to the species composition and sizes of fish available to the terns over most of the years the colony has presided in Alameda. The information on Least Tern diet is not as long-standing. While it would be ideal to compare consumed fish to what fish were available in the Bay, there are only three years of diet data determined from fecal sample analysis (2002-2004; Elliott 2005). Therefore, data on dropped prey was chosen for this analysis, as this is the largest diet-related dataset available. Least Terns drop prey items on the ground of the breeding colony mainly as a result of prey being too large for mates or chicks, a lack of hunger by the recipient, or the tern dropping the fish in-transit. There is debate over what dropped prey truly represent. Some argue that many of these fish are suitable and represent a surplus of food (Palmer 1941), while others point out that dropped prey are typically larger than consumed prey, especially with regard to the deep-bodied surfperches (Atwood and Kelly 1984, Robinette et al. 2001). Atwood and Kelly (1984) concluded that the species composition of dropped prey reflected what Least Terns consumed, making these fish decent indicators of diet. Dropped fish are whole prey items that can be identified and measured with relative ease. In addition, collecting dropped prey causes 6

relatively less disturbance to the colony than other methods of diet collection, an important factor to consider in investigating diet in an endangered species. METHODS Least Tern data Data on tern arrivals to the colony, departures from the colony, and breeding activity were used to determine the three different phases of breeding in each year: courtship/incubation, chick-rearing, and fledging (Table 1). Dropped prey collection Dropped prey were collected from the ground of the Alameda Least Tern colony by Golden Gate Audubon Society (GGAS) personnel (1981-1995), and PRBO Conservation Science and U.S. Fish and Wildlife (USFWS) personnel (2000-2006). GGAS collected prey on an opportunistic basis, and only numbers of prey species collected in each year are provided (Collins 1995). PRBO and USFWS collected prey during standardized type I nest surveys (i.e., surveys conducted in the breeding area). Type I surveys were generally conducted twice a week throughout most of the breeding season and once a week towards the end of the breeding season. We stored specimens in plastic bags labeled with the collection date. The specimens were later soaked in water, cleaned with a fine artist s paintbrush, and set out to dry. We sequentially numbered the dry fish using a fine tip permanent marker. We measured the total length (from the tip of the snout to the end of the caudal fin), standard length (from the tip of the snout to the end of the hypural bone), and body depth (the widest part of the fish) of each specimen to the nearest millimeter. We recorded the dry weight of each fish to the nearest 0.1 gram. Many specimens in each year of this study had only partial caudal fins, showed signs of tissue loss (due to scavenging or evaporation), or dried in a twisted or bent position. 7

Therefore, average weights are likely underestimates, and length measurements are not exact. In addition, while many fish and fish parts were collected and saved, we only analyzed whole fish specimens (i.e., specimens containing a head, body, and caudal peduncle). For the purposes of comparing these fish to the CDFG San Francisco Bay fish data, the standard lengths from dropped fish were used (as this measurement is more accurate than total length), and invertebrates (e.g. Crangon spp.) were dropped from analysis (as these comprised a very small proportion of dropped prey collections). Dropped prey composition has been summarized since collections began in 1981. In addition, analysis of variance (ANOVA) with Bonferroni-adjusted t-tests was used to test for inter- and intra-annual differences in size of dropped prey from 2000 to 2006. CDFG San Francisco Bay prey data Data on fish in San Francisco Bay have been collected since 1980 by the CDFG s San Francisco Bay Study. For the purposes of this study, we obtained the midwater trawl and otter trawl data for Central and South Bay stations, as these are closest to the Alameda tern colony and likely sample the areas used most frequently by foraging terns (Figure 1). Midwater and otter trawls were conducted most months, particularly during the months Least Terns are present in the Bay (April August); the only exception were the midwater trawls for 1994 (Table 2). Midwater and otter trawls do not sample areas <3-4 m in depth, or rocky areas or areas containing eelgrass, so some species (e.g. topsmelt (Atherinops affinis), jacksmelt (Atherinopsis californiensis), surfperch species (family Embiotocidae), and arrow goby (Clevelandia ios)) are likely underrepresented in the dataset (Kathy Hieb, CDFG, personal communication). However, this trawl data provide the best indices of fish abundances for the time period of interest. The midwater trawls sample the water column, while the otter trawls sample the bottom. The midwater trawl net mouth was 3.7 m x 3.7 m (with a 10.7 m 2 effective mouth opening), with mesh graduated in nine sections from 20.3 cm stretch mesh at the mouth to 1.3 cm (0.5 inch) stretch mesh at the codend. It was towed for 12 minutes obliquely to sample all parts of the 8

water column equally. Flow meter counts were recorded and used to calculate the volume of water sampled. The otter trawl had a 4.9 m head rope, a 2.5 cm stretch mesh body, and a 0.6 cm (0.25 inch) delta knotless mesh codend. It was towed on the bottom for five minutes. Distance towed was recorded using a Loran-C or GPS, and was used to calculate the area sampled, assuming a 70% door spread of 3.4 m. For each midwater and otter trawl completed, up to 50 individuals of each species were measured (fork length) and the remainder counted; this subset of length frequency data were used in size comparisons (see Size Comparisons). The length frequency data recorded were expanded by the total catch to estimate the total number of fish for each length; this is called the adjusted frequency. Adjusted frequency numbers for each species were used to calculate the catch per unit effort (CPUE) values for the size range of interest (see Species Compositions). In addition, minimum lengths were established for some species in 1984 (Table 3). Specimens below the designated minimum length were either not counted or recorded, or they were dropped from analyses to be consistent with other years. For more detailed descriptions of the methods for this study may be found at http://www.iep.ca.gov/sf_bay_monitor/. Bay fish data were standardized to a CPUE of fish per 10,000 m 3 for the midwater trawl and fish per 10,000 m 2 for the otter trawl. Each species was evaluated according to its general biology to determine if the midwater or otter trawl was the most appropriate at sampling that species; more specifically, fish that were generally pelagic were evaluated using the midwater trawl data, while demersal fish were evaluated using the otter trawl data. Since Least Terns are small birds and are known to consume small fish (Elliott 2005, Thompson et al. 1997, Atwood and Minsky 1983), CPUE values were calculated by determining the numbers of suitably-sized fish caught in each tow. Based on Elliott (2005), fish less than or equal to 100 mm in length were deemed of suitable size for the terns. This maximum length was applied to all fish except surfperches (family Embiotocidae); these fish are deep-bodied and their body depth cannot exceed the gape width of the tern (Hulsman 1981, Atwood and Kelly 1984, Zuria and Mellink 2005, Thompson et al. 1997). Based on surfperch length and body depth data recorded on dropped fish, we 9

determined the maximum length of surfperches to be 50 mm. Inter- and intra-annual sizes in fish were analyzed with ANOVA (and Bonferroni-adjusted t-tests). Least Terns are present in the San Francisco Bay area from April through August (Collins 2000, Elliott and Sydeman 2001, Elliott and Sydeman 2002, Hurt 2003, Hurt 2006); therefore, only tows conducted in these months were used in the analyses. Size comparisons The standard lengths of dropped fish at the colony and the fork lengths of fish sampled in the Bay were compared for 2000-2006. While standard length is shorter than fork length, there is typically only a few millimeters difference in these two measurements. Length frequency data for all fish sampled in the Bay were summarized; however, analyses were performed on only the suitably-sized fish. Species compositions I investigated species compositions by comparing proportions of fish species collected from the colony in each year and mean CPUE values for species sampled in the Bay. For Bay fish sampled just prior to the arrival of terns or just after their departure, these data were assigned to the nearest breeding period within that year. Spearman correlations were calculated for species and years to see if colony and Bay fish varied similarly. In addition, rank preference indices were calculated for species found in both the dropped prey and the Bay. In this procedure, ranks for both usage and availability of a resource are calculated, and the difference (i.e., usage-availability) is used in determining whether a resource is preferred (positive value), avoided (negative value), or neutral (zero value; Johnson 1980). 10

RESULTS Dropped prey There were 19 families and 34 species of fish identified in dropped prey samples since 1981 (Table 4). Most of the fish collected were jacksmelt, northern anchovy (Engraulis mordax), and topsmelt (Table 4). When condensing the dropped prey to the family level, there were variations in composition and diversity of prey through the years; families Atherinopsidae, Engraulidae, and Embiotocidae dominated most collections, representing 57.5%, 19.7%, and 11.0%, respectively, of all dropped prey samples (Figure 2). The largest mean length and body depth of dropped fish were observed in 2006 (Table 5). A summary of fish sizes by breeding stage showed that the largest fish were collected in the courtship/incubation period, followed by the chick-rearing period, and the smallest fish collected during the fledging period (Table 6). However, this pattern was not similar in each individual year. The size of fish collected in the courtship/incubation period in 2006 were similar to the sizes of fish collected during chick-rearing (Table 6). Also, fish collected in the fledging stage were larger than the chick-rearing fish in 2000, 2001, and 2003 (Table 6). Significant differences in the lengths of dropped prey were found when considering both year and breeding stage (Table 7). The significant interaction term (year*breeding stage) indicated that sizes of dropped prey did not vary similarly in each breeding stage in each year. An examination of each year revealed that fish collected in the courtship/incubation stage were significantly larger than chick-rearing fish in 2001 (ANOVA: F 2,1768 =19.66, p<0.001; Bonferroniadjusted t-test: p<0.001), 2002 (ANOVA: F 2,1120 =40.32, p<0.001; Bonferroni-adjusted t-test: p<0.001), 2003 (ANOVA: F 2,1727 =26.32, p<0.001; Bonferroni-adjusted t-test: p<0.001), 2004 (ANOVA: F 2,1847 =39.80, p<0.001; Bonferroni-adjusted t-test: p<0.001), and 2005 (ANOVA:F 2,2280 =53.93, p<0.001; Bonferroni-adjusted t-test: p<0.001). Courtship fish were significantly larger than fledging fish in 2002 (Bonferroni-adjusted t-test: p<0.001), 2003 (Bonferroni-adjusted t-test: p<0.001), 2004 (Bonferroni-adjusted t-test: p<0.001), 2005 11

(Bonferroni-adjusted t-test: p<0.001), and 2006 (ANOVA: F 2,846 =23.69, p<0.001; Bonferroniadjusted t-test: p<0.001). Chick-rearing fish were significantly larger than fledging fish in 2002 (Bonferroni-adjusted t-test: p<0.001), 2005 (Bonferroni-adjusted t-test: p<0.001), and 2006 (Bonferroni-adjusted t-test: p<0.001). Fish recovered in the fledging period were significantly larger than chick-rearing fish in 2001 (Bonferroni-adjusted t-test: p<0.001) and 2003 (Bonferroni-adjusted t-test: p=0.039). San Francisco Bay fish Out of the 46 families and 107 species of fish identified in the midwater and otter trawl tows since 1980, there were 40 families and 93 species of fish captured during the Least Tern breeding season (April August; Table 8). Of these, 26 families and 68 species were found to be of suitable-size to Least Terns (Table 8). Trends in species composition differed by species (Figures 3 and 4). Some species displayed an apparent decline (e.g. Pacific herring (Clupea pallasii); Figure 3b), strong abundance peaks (e.g. white croaker (Genyonemus lineatus), Figure 4b; Pacific sand lance (Ammodytes hexapterus), Figure 4d), relatively high abundances compared to the other species (e.g. northern anchovy, Figure 3a; bay goby (Lepidogobius lepidus), Figure 4a), relatively low abundances (e.g. threespine stickleback (Gasterosteus aculeatus), Figure 3d), and some only appeared in recent years (e.g. California grunion (Leuresthes tenuis); Figure 3c). The length of prey varied among years (Table 9). The range in the sizes of fish caught goes well beyond what Least Terns are capable of capturing and eating. When restricting the Bay fish data to only the fish suitably-sized for Least Terns, size differed between years, with the largest fish sampled in 2006 (Table 10). Intra-annual fish sizes showed a general trend of increasing size as each season progressed (Table 11). Statistical results showed significant differences in sizes of fish sampled when considering year and breeding stage (Table 12). Similar to the dropped fish results, the significant interaction term (year*breeding stage) signified varying results, which prompted analyses by year. Fish sampled during the courtship/incubation stage were significantly smaller than chick-rearing fish in 2000 (ANOVA: F 2,8351 =217.06, p<0.001; Bonferroni-adjusted t-test: p=0.040), 2001 (ANOVA: 12

F 2,8114 =250.00, p<0.001; Bonferroni-adjusted t-test: p<0.001), 2002 (ANOVA: F 2,11877 =532.17, p<0.001; Bonferroni-adjusted t-test: p<0.001), 2003 (ANOVA: F 2,10158 =371.90, p<0.001; Bonferroni-adjusted t-test: p<0.001), 2004 (ANOVA: F 2,8211 =113.44, p<0.001; Bonferroniadjusted t-test: p<0.001), and 2005 (ANOVA: F 2,6372 =82.75, p<0.001; Bonferroni-adjusted t-test: p<0.001). Bay fish sampled during the chick-rearing period were significantly smaller than fish sampled in the fledging period in all years (ANOVA (2006): F 2,5435 =103.19, p<0.001; Bonferroniadjusted t-test: p<0.001; Bonferroni-adjusted t-tests for 2000-2004: p<0.001; Bonferroniadjusted t-test for 2005: p=0.048). Colony and Bay comparisons The size of suitably-sized fish from the Bay varied significantly from the colony fish when factoring in year and breeding stage (Table 13). Again, the significant interaction terms led to investigating each year individually. Bay fish were significantly larger than colony fish in 2001 (ANOVA: F 1,9886 =17.03, p<0.001), 2003 (ANOVA: F 1,11889 =504.81, p<0.001), 2004 (ANOVA: F 1,10062 =401.66, p<0.001), 2005 (ANOVA: F 1,8656 =631.44, p<0.001), and 2006 (ANOVA: F 1,6285 =75.75, p<0.001). When examining the courtship/incubation period in each year, dropped fish at the colony were significantly larger than Bay fish in 2002 (ANOVA: F 1,5040 =59.16, p<0.001), 2003 (ANOVA: F 1,1540 =23.15, p<0.001), and 2004 (ANOVA: F 1,2603 =7.94, p=0.0049). During the chick-rearing period, fish sampled in the Bay were significantly larger than colony fish in 2001 (ANOVA: F 1,2163 =16.48, p=0.0001), 2003 (ANOVA: F 1,4207 =313.29, p<0.001), 2004 (ANOVA: F 1,2778 =175.14, p<0.001), 2005 (ANOVA: F 1,1548 =83.95, p<0.001), and 2006 (ANOVA: F 1,1643 =5.19, p=0.0228). Similar to the chick-rearing stage, Bay fish were significantly larger than colony fish in the fledging stage of every year (ANOVA results: 2000: F 1,3786 =36.68, p<0.001; 2001: F 1,4827 =217.90, p<0.001; 2002: F 1,5215 =199.17, p<0.001; 2003: F 1,6138 =502.76, p<0.001; 2004: F 1,4677 =628.39, p<0.001; 2005: F 1,4650 =966.90, p<0.001; 2006: F 1,2275 =159.07, p<0.001). When comparing species compositions between the colony and the Bay, 8 species had positive significant correlations and 2 species had near-significant correlations (Table 14). Comparisons by year showed 12 positive significant years and 2 near-significant years of the midwater trawl data, and one positive and one negative near-significant correlations in otter trawls (Table 15). 13

Rank preference indices showed terns preferred 12 species, avoided 13 species, and neutral towards 2 species (Table 16). DISCUSSION Most of the fish collected from the Least Tern breeding area were Atherinopsids (mainly jacksmelt and topsmelt), northern anchovy, and surfperch species (family Embiotocidae). Jacksmelt, topsmelt and northern anchovy are all pelagic, schooling fishes that can presumably be spotted by Least Terns from the air; these species are also the main fish consumed by Least Terns (Elliott 2005). Northern anchovy is the most abundant fish species in San Francisco Bay (Baxter et al. 1999), and while their abundance in the Bay has varied from year to year (Figure 3a), it is more abundant than the other pelagic, schooling, slender-bodied species. While less abundant than northern anchovy, jacksmelt is a fairly common fish of suitable-size sampled in the Bay, even given that it is likely underrepresented. The Embiotocids are likely overrepresented in the dropped fish samples; they are deep-bodied fish that are often unable to fit through the gape of a tern chick (Hulsman 1981, Atwood and Kelly 1984). For the purposes of this report, a tern gape width was defined as 15 mm (Atwood and Kelly 1984), but Zuria and Mellink (2005) reported mean gape widths of 11.2 mm (adults), 7.2 mm (smaller chicks), and 9.1 mm (larger chicks). The mean body depth of 18 ± 3.6 mm (range=7-27, n=701) in surfperches dropped at the colony is larger than the most conservative gape estimate, and it is more than twice the gape width of small chicks. Therefore, the dropped surfperches are too large for chicks (as well as most adults). The mean length of 63 mm in dropped prey (Table 5) is larger than the mean length of consumed prey (60 mm; Elliott 2005), suggesting that dropped fish represent fish that may be too large to eat. The largest dropped prey were found in 2006, and the largest fish were also sampled in the Bay in 2006. This may be driven by the presence of relatively large northern anchovy and jacksmelt sampled during the Least Tern breeding season in that year (Table 17). Dropped prey were significantly smaller than suitably-sized Bay fish in five of the seven years 14

analyzed. Some dropped fish (e.g. northern anchovy) are smaller than the minimum lengths used by CDFG, so this may have affected results. Intra-annual patterns in dropped prey size were somewhat unexpected. The literature on different tern species shows that adults switch from bringing larger prey (for courtship and incubating females) to smaller fish (for chicks; Atwood and Kelly 1984, Shealer 1998). While we saw smaller fish in the chick-rearing period compared to the courtship stage in five of the seven years studied, the fledging stage revealed even smaller fish in three of the years studied. I might have expected to see slightly larger fish during the fledging period, as chicks are larger at this time and capable of handling larger fish, and the fish in the Bay are larger at this time as well; yet only two years showed larger fish in the fledging period, and observations of feedings at the Alameda colony confirm that fledglings receive larger fish than smaller chicks (PRBO, unpublished data). However, the breeding stage designations are rough estimates of breeding phenology at the colony and do not necessarily reflect what may be occurring at the colony. For instance, there may be many smaller chicks in the colony during the fledging period (due to re-nesting or late nesting), which may explain why smaller fish are being collected. In addition, fledglings may be receiving more feedings from parents on the surrounding tarmac areas or by the shores of the Bay, so many of the dropped feedings of fledglings may not be collected during the nest surveys in the colony. It is interesting to note that while dropped fish sizes decrease as the season progresses, the opposite is true of Bay fish and the sizes of fish consumed by Least Terns (Elliott 2005). I would expect Bay fish sizes to increase, as this reflects the growth of the age-0 class fish that were spawned in the winter and spring months (Baxter et al. 1999). The intra-annual colony and Bay fish size comparisons illustrate the switch to foraging for appropriately-sized fish: dropped fish were larger than Bay fish during courtship/incubation, and then Bay fish were larger than dropped fish for the remainder of the season (when chicks and fledglings were present). Correlations between species compositions of dropped prey and Bay fish give more insight into the relationship between tern foraging and prey abundance and availability. The slender-bodied, pelagic schooling fish (northern anchovy, Pacific herring, and Pacific sardine (Sardinops sagax)), as well as fish inhabiting the nearshore environment (California grunion, arrow goby, cheekspot 15

goby (Ilypnus gilberti), and yellowfin goby (Acanthogobius flavimanus)), appear to be the significant positive findings, indicating that terns may be choosing these species in accordance with their availability. White croaker, bay goby, and brown rockfish (Sebastes auriculatus) are generally demersal or benthopelagic species that are not necessarily found in nearshore habitats; these species may have been made locally available in nearshore environments (e.g., during ebb tide). Not surprisingly, other demersal fish (e.g. English sole (Parophrys vetulus), Pacific staghorn sculpin (Leptocottus armatus)) and surfperch species showed no significant results with colony fish. However, jacksmelt the most abundant species collected at the colony had a nonsignificant negative relationship, as well as topsmelt (another important dropped fish); this may be due to underrepresentation in the Bay fish trawls due to sampling methods. The correlations by year also illustrate how midwater trawls sample the fish utilized by terns. Also, when examining only the midwater trawls, Bay fish species compositions and dropped fish compositions varied in similar ways in most years. This lends more evidence that the dropped fish indicate changes in availability and abundance of species in San Francisco Bay. The rank preference indices tell a somewhat different story. There appear to be preferences toward the same slender-bodied pelagic species (northern anchovy, Pacific herring, and Pacific sardine) and some benthic, nearshore species (cheekspot goby, bay goby, white croaker). However, these values indicate that terns avoid jacksmelt and topsmelt, meaning their relative abundance in the environment is large compared to their relative importance in the diet (or in this case, in the dropped prey collections). If jacksmelt and topsmelt are truly underrepresented in Bay trawl surveys, then their true availability in the environment would be even larger than what is reflected here, and their true rank preference indices would show an even stronger avoidance. It is possible that jacksmelt and topsmelt are underrepresented in the dropped fish samples; they may be eaten more often and/or be less likely to be too large for consumption. In addition, our classification of suitably-sized prey may actually include fish that are too large for terns, making the CPUE calculations erroneously high and creating significant findings where there may not be any (or vice versa). This may be the case for fish other than surfperches that may have body depth limitations to consider (e.g., flatfishes), but data to calculate minimum sizes were not available for this investigation. Therefore, these correlation and rank preference indices should be viewed with caution, as they may not reflect selectivity accurately. 16

Despite the shortcomings of the selectivity analyses, northern anchovy, Pacific herring, and, to a lesser extent, Pacific sardine are consistently shown to be important prey items to the Least Terns. These are high-caloric species, making good meals for growing tern chicks, and positive relationships between anchovy abundance in the dropped prey and reproductive success of the Alameda Least Tern colony have already been shown (Elliott et al. 2007). Elegant Tern (Sterna elegans) chicks fed anchovies (the high energy content food) showed a faster gain of body mass and wing length, and had higher lipid reserves than chicks fed topsmelt (the low energy content food; Dahdul and Horn 2003). The authors deduced that a tern colony that had to switch from a high-energy food item (e.g. anchovy) to a low-energy food item (i.e. topsmelt) may produce underweight fledglings with less fat reserves, and parents may have to increase provisioning to chicks, thereby leading to decreased survival and reproductive success. Terns are opportunistic foragers and generally stay within just a few miles of the breeding colony to catch their prey (Atwood and Minsky 1983), so terns may be taking jacksmelt in large numbers as they are more readily available and found closer to the colony than the preferred northern anchovy or Pacific herring. It is difficult to say what we can or cannot conclude about the dropped fish. Northern anchovy are important, yet they are the second most common fish in the dropped fish collections. The results on jacksmelt are less clear; this is the most abundant fish dropped at the colony and their abundances at the colony do not match the trawl abundances. This could be due to underrpresentation in the trawl data, or it could be a less desirable fish that is more abundant near the colony and makes an easy fish to catch and bring back to the chick. ACKNOWLEDGMENTS I would like to thank Kathy Hieb (CDFG) for providing the San Francisco Bay fish data and giving suggestions on the analyses; these data were collected by the Interagency Program for the San Francisco Estuary and the CDFG s San Francisco Bay study. Rachel Hurt, Susan Euing and Joelle Buffa (USFWS) provided breeding data on the Alameda Point Least Tern colony; Rachel, Susan, other Refuge staff and interns collected dropped fish during in-colony reproductive surveys in 2002-2006. I also thank Richard Morat and the FWS Coastal Program 17

at San Francisco Bay for contributing funding to conduct these analyses. Jennifer Roth (PRBO) provided additional input into this report. In 2002-2005, dropped fish were collected during the Least Tern foraging study for the Oakland Harbor deepening project (Ehrler et al. 2006) under contract/subcontract with Tetra Tech, Inc.; data were collected under prime contract DACW07-02-F-0028 (2002-2003), subcontract 2004-03/GS-10F-0268K (2004), and subcontract 2005-21/GS-10F-0268K (2005). This is PRBO Contribution Number 1613. 18

LITERATURE CITED Atwood, J. L. and P. R. Kelly. 1984. Fish dropped on breeding colonies as indicators of Least Tern food habits. Wilson Bulletin 96: 34-47. Atwood, J. L. and D. E. Minsky. 1983. Least Tern foraging ecology at three major California breeding colonies. Western Birds 14: 57-71. Bailey, S. F. 1992. California Least Tern foraging and other off-colony activities around Alameda Naval Air Station during 1991. Unpublished Report, Dept. of Ornithology and Mammalogy, California Academy of Sciences. Baxter, R., K. Hieb, S. DeLeón, K. Fleming and J. Orsi. 1999. Report on the 1980-1995 fish, shrimp, and crab sampling in the San Francisco estuary, California. Prepared for the Interagency Ecological Program for the Sacramento-San Joaquin Estuary, California Department of Fish and Game, Technical Report 63. Collins, L. D. 1995. California Least Tern nesting season at the Alameda Naval Air Station, 1995. Unpublished report prepared for Western Division, Naval Facilities Engineering Command. Collins, L. D. 2000. California Least Tern monitoring report for 1999 at the Naval Air Station, Alameda. Unpublished report prepared for Engineering Field Activity West, Naval Facilities Engineering Command. Dahdul, W. M. and M. H. Horn. 2003. Energy allocation and postnatal growth in captive Elegant Tern (Sterna elegans) chicks: responses to high- versus low-energy diets. Auk 120(4): 1069-1081. Ehrler, C. P., M. L. Elliott, J. E. Roth, J. R. Steinbeck, A. K. Miller, W. J. Sydeman, and A. M. Zoidis. 2006. Oakland Harbor Deepening Project (-50 ): Least Tern, Fish, and Plume Monitoring. Project Year 2005 and Four-Year Final Monitoring Report. Tetra Tech, Inc., San Francisco, California. July 2006. Elliott, M.L. and W.J. Sydeman, 2001. Breeding Status of the California Least Tern at Alameda Point (former Naval Air Station, Alameda), Alameda, California, 2000. Unpublished Report, Point Reyes Bird Observatory, Stinson Beach, California. Elliott, M.L. and W.J. Sydeman, 2002. Breeding Status of the California Least Tern at Alameda Point (former Naval Air Station, Alameda), Alameda, California, 2001. Unpublished Report, Point Reyes Bird Observatory, Stinson Beach, California. Elliott, M. L. 2005. Diet, prey, and foraging habits of the California Least Tern (Sterna antillarum browni). Unpublished Master s thesis, San Francisco State University. 19

Elliott, M. L., R. Hurt, and W. J. Sydeman. 2007. Breeding biology and status of the California Least Tern Sterna antillarum browni at Alameda Point, San Francisco Bay, California. Waterbirds 30(3): 317-325. Hulsman, K. 1981. Width of gape as a determinant of size of prey eaten by terns. Emu 81: 29-32. Hurt, Rachel. 2003. Breeding Status of the California Least Tern at Alameda Point, Alameda, California, 2002. Unpublished Report, U.S. Fish and Wildlife Service, Fremont, California. Hurt, Rachel. 2006. Breeding Status of the California Least Tern at Alameda Point, Alameda, California, 2005. Unpublished Report Prepared for the U.S. Navy, U.S. Fish and Wildlife Service, Fremont, California. Johnson, D. H. 1980. The comparison of usage and availability measurements for evaluating resource preference. Ecology 61(1): 65-71. Palmer, R. S. 1941. A behavior study of the Common Tern (Sterna hirundo hirundo L.). Proceedings of the Boston Society of Natural History 42: 1-119. Robinette, D., N. Collier, A. Brown, and W. J. Sydeman. 2001. Monitoring and management of the California Least Tern colony at Purisma Point, Vandenberg Air Force Base, 1995-2001. Unpublished Report, Point Reyes Bird Observatory, Stinson Beach, CA. Shealer, D. A. 1998. Size-selective predation by a specialist forager, the Roseate Tern. Auk 115(2): 519-525. Thompson, B. C., J. A. Jackson, J. Burger, L. A. Hill, E. M. Kirsch and J. A. Atwood. 1997. Least Tern (Sterna antillarum) in Birds of North America, No. 290 (A. Poole and F. Gill, Eds.). The Academy of Natural Sciences, Philadelphia, PA, and The American Ornithologists Union, Washington, D.C. Zuria, I. and E. Mellink. 2005. Fish abundance and the 1995 nesting season of the Least Tern at Bahía de San Jorge, Northern Gulf of California, México. Waterbirds 28(2): 172-180. 20

Table 1. Definitions of breeding stages, 2000-2006. Breeding stage Year Courtship / Incubation Chick-rearing Fledging 2000 April 28 - June 3 June 4 - July 1 July 2 - Aug 16 2001 April 24 - June 1 June 2 - June 30 July 1 - August 4 2002 April 22 - June 1 June 2 - June 30 July 1 - July 21 2003 April 19 - May 30 May 31 - June 28 June 29 - August 25 2004 April 20 - May 28 May 29 - June 26 June 27 - August 11 2005 April 18 - May 29 May 30 - June 27 June 28 - August 1 2006 April 13 - May 30 June 1 - June 28 June 29 - August 14 21

Table 2. San Francisco Bay Monitoring Program sampling months, 1980-2006. Year Midwater trawl Otter trawl 1980 January-November January-November 1981 January-December January-December 1982 January-December January-December 1983 January-December January-December 1984 January-December January-December 1985 January-December January-December 1986 January-December January-December 1987 January-December January-December 1988 January-December January-December 1989 January-August January-August 1990 February-October February-October 1991 February-October February-October 1992 February-October February-October 1993 February-October February-October 1994 February-April February-October 1995 April-December 1 January-December 1 1996 April-December January-December 1997 January-December 2 January-December 1998 January-December January-December 1999 January-October January-October 2000 January-December January-December 2001 January-December 3 January-December 3 2002 February-December February-December 2003 January-December 4 January-December 4 2004 January-December January-December 2005 January-December January-December 2006 January-December 5 January-December 5 1 Did not sample August 1995 due to mechanical problems. 2 MWT: In 1997 sampled only San Pablo Bay January to March, all stations April to December. 3 Both nets, did not sample March 2001. 4 MWT and OT: survey 5 was conducted in early June (6/2/03-6/4/03); last survey in survey 6 conducted in early July (7/1/03). 5 MWT and OT: part of survey 4 conducted in early May (5/1/06 and 5/3/06). 22

Table 3. Minimum lengths of fish sampled in San Francisco Bay. Species Minimum length (mm) American shad 20 bay goby 20 California grunion 20 California halibut 20 California tonguefish 20 chameleon goby 20 cheekspot goby 20 Chinook salmon 20 delta smelt 30 diamond turbot 20 English sole 20 longfin smelt 40 northern anchovy 40 Pacific herring 30 Pacific staghorn sculpin 20 plainfin midshipman 20 shimofuri goby 20 Shokihaze goby 20 speckled sanddab 20 starry flounder 20 striped bass 25 white croaker 20 yellowfin goby 20 23

Table 4. Families and species of fish identified in dropped prey, 1981-2006. Family Species Scientific name Number Percentage of total collection Clupeidae Pacific herring Clupea pallasii 997 6.59% Pacific sardine Sardinops sagax 50 0.33% Clupeidae spp. 1 0.01% Engraulidae northern anchovy Engraulis mordax 2084 13.78% Salmonidae Osmeridae Chinook salmon Oncorhynchus tshawytscha 582 3.85% coho salmon Oncorhynchus kisutch 31 0.20% Salmonidae spp. 45 0.01% delta smelt Hypomesus pretiosus 9 0.06% longfin smelt Spirinchus thaleichthys 1 0.01% surf smelt Hypomesus pretiosus 94 0.62% Osmeridae spp. 6 0.04% Batrachoididae plainfin midshipman Porichthys notatus 2 0.01% Scomberesocidae Pacific saury Cololabis saira 1 0.01% Fundulidae rainwater killifish Lucania parva 2 0.01% Cyprinidae Cyprinidae spp. 1 0.01% Atherinopsidae California grunion Leuresthes tenuis 269 1.78% jacksmelt Atherinopsis californiensis 6582 43.52% topsmelt Atherinops affinis 1949 12.89% Mississippi silverside Menidia beryllina 11 0.07% Atherinopsidae spp. 1020 6.74% Gasterosteidae threespine stickleback Gasterosteus aculeatus 1 0.01% Scorpaenidae brown rockfish Sebastes auriculatus 2 0.01% rockfish spp. Sebastes spp. 10 0.07% Hexagrammidae unidentified greenling Hexagrammos spp. 13 0.09% Cottidae Pacific staghorn sculpin Leptocottus armatus 5 0.03% Cottidae spp. 1 0.01% Moronidae striped bass Morone saxatilis 9 0.06% Sciaenidae white croaker Genyonemus lineatus 18 0.12% Sciaenidae spp. 5 0.03% Embiotocidae black perch Embiotoca jacksoni 4 0.03% walleye surfperch Hyperprosopon argenteum 276 1.82% silver surfperch Hyperprosopon ellipticum 7 0.05% 24

Table 4 (continued). Family Species Scientific name Number Percentage of total collection Embiotocidae shiner perch Cymatogaster aggregata 56 8 3. 76 % striped seaperch Embiotoca lateralis 1 0. 01 % dwarf perch Micrometrus minimus 05 pile perch Rhacochilus vacca 03 white seaperch Phanerodon furcatus 36 Embiotocidae spp. 11 78 Ammodytidae Pacific sand lance Ammodytes hexapterus 03 Gobiidae 7 0. % 4 0. % 55 0. % 8 0. % 5 0. % 23 0. % 90 0. % 19 0. % 36 0. % 10 7 0. 71 % bay goby Lepidogobius lepidus 15 yellowfin goby Acanthogobius flavimanus 60 cheekspot goby Ilypnus gilberti 13 arrow goby Clevelandia ios 24 Gobiidae spp. sole Pleuronectidae Eng lish Parophrys vetulus 1 0. 01 % unidentifiab le 1 0. 01 % TOTAL 151 23 10 0.00 % 25

Table 5. Standard lengths and body depths of dropped prey, 2000-2006. Standard length (mm) Body depth (mm) Year mean ± s.d. range n mean ± s.d. range n 2000 66 ± 12.8 26-93 785 12 ± 3.4 2-24 792 2001 65 ± 11.2 25-94 1771 12 ± 3.2 2-27 1798 2002 63 ± 15.2 26-106 1123 13 ± 3.9 3-25 1131 2003 59 ± 13.2 28-94 1730 12 ± 3.5 2-23 1939 2004 61 ± 13.7 25-100 1850 12 ± 3.6 2-25 1852 2005 62 ± 11.5 14-102 2283 12 ± 2.9 2-25 2285 2006 71 ± 12.5 25-105 849 11 ± 3.0 3-23 849 TOTAL 63 ± 13.1 14-106 10391 12 ± 3.5 2-27 10646 26

Table 6. Standard lengths and body depths of dropped prey by breeding stage, 2000-2006. a) Courtship/incubation Standard length (mm) Body depth (mm) Year mean ± s.d. range n mean ± s.d. range n 2000 69 ± 8.4 48-78 16 14 ± 2.2 11-17 16 2001 70 ± 10.7 47-88 16 15 ± 2.5 11-21 16 2002 72 ± 10.8 35-98 104 14 ± 2.4 5-20 105 2003 73 ± 14.4 42-92 39 14 ± 2.6 3-21 197 2004 74 ± 12.0 36-95 86 15 ± 2.6 4-22 86 2005 70 ± 12.2 30-91 143 14 ± 2.3 8-20 143 2006 72 ± 10.8 37-97 249 14 ± 2.5 8-21 249 TOTAL 71 ± 11.5 30-98 653 14 ± 2.5 3-22 812 b) Chick-rearing Standard length (mm) Body depth (mm) Year mean ± s.d. range n mean ± s.d. range n 2000 63 ± 14.4 29-88 93 13 ± 4.4 2-24 93 2001 61 ± 12.6 31-93 235 12 ± 4.1 3-27 236 2002 65 ± 15.6 31-103 420 14 ± 3.8 3-25 424 2003 58 ± 12.9 29-91 777 11 ± 3.3 2-23 793 2004 61 ± 14.2 25-100 787 12 ± 3.6 2-24 787 2005 64 ± 13.1 19-102 419 13 ± 3.4 3-25 418 2006 72 ± 12.8 25-105 470 15 ± 2.7 4-24 470 TOTAL 63 ± 14.4 19-105 3201 13 ± 3.7 2-27 3221 c) Fledging Standard length (mm) Body depth (mm) Year mean ± s.d. range n mean ± s.d. range n 2000 66 ± 12.6 26-93 676 12 ± 3.2 2-24 683 2001 66 ± 10.9 25-94 1520 12 ± 3.1 2-26 1546 2002 60 ± 14.6 26-106 599 12 ± 3.9 3-25 602 2003 59 ± 13.0 28-94 914 11 ± 3.6 2-23 949 2004 60 ± 12.8 28-100 977 12 ± 3.6 2-25 979 2005 60 ± 10.7 14-94 1721 11 ± 2.7 2-24 1724 2006 64 ± 12.2 34-92 130 13 ± 3.7 6-24 130 TOTAL 62 ± 12.3 14-106 6537 12 ± 3.3 2-26 6613 27

Table 7. Two-factor ANOVA results for dropped fish sizes, 2000-2006. Source Partial SS df MS F Prob>F Model 171740.5 20 8587.024 54.85 0.0000 year 11844.87 6 1974.145 12.61 0.0000 breeding stage 20959.64 2 10479.82 66.94 0.0000 year * breeding stage 35834.79 12 2986.233 19.08 0.0000 Residual 1623442 10370 156.5517 Total 1795182 10390 172.7798 Number of observations = 10391 Root MSE = 12.5121 R 2 = 0.0957 Adjusted R 2 = 0.0939 28

Table 8. Fish sampled in San Francisco Bay during the Least Tern breeding season (April August), 1980-2006. Family Species Scientific Name Gear type used in analysis Number of suitablysized specimens Percentage of all suitablysized specimens Petromyzontidae Pacific lamprey Lampetra tridentata otter trawl 0 0.00 river lamprey Lampetra ayresii otter trawl 0 0.00 Hexanchidae broadnose sevengill shark Notorynchus cepedianus otter trawl 0 0.00 Squalidae spiny dogfish Squalus acanthias otter trawl 0 0.00 Alopiidae thresher shark Alopias vulpinus midwater trawl 0 0.00 Triakidae leopard shark Triakis semifasciata otter trawl 0 0.00 brown smoothhound Mustelus henlei otter trawl 0 0.00 Torpedinidae Pacific electric ray Torpedo californica otter trawl 0 0.00 Platyrhynidae thornback Platyrhinoidis triseriata otter trawl 0 0.00 Rhinobatidae shovelnose guitarfish Rhinobatos productus otter trawl 0 0.00 Rajidae big skate Raja binoculata otter trawl 0 0.00 Myliobatidae bat ray Myliobatis californica otter trawl 9 0.00 Acipenseridae green sturgeon Acipenser medirostris otter trawl 0 0.00 white sturgeon Acipenser transmontanus otter trawl 0 0.00 Clupeidae threadfin shad Dorosoma petenense midwater trawl 1 0.00 Pacific herring Clupea pallasii midwater trawl 79669 5.40 Pacific sardine Sardinops sagax midwater trawl 3319 0.22 American shad Alosa sapidissima midwater trawl 1 0.00 Engraulidae northern anchovy Engraulis mordax midwater trawl 1228462 83.22 Salmonidae steelhead trout Oncorhynchus mykiss midwater trawl 0 0.00 chinook salmon Oncorhynchus tshawytscha midwater trawl 521 0.04 Osmeridae surf smelt Hypomesus pretiosus otter trawl 6 0.00 eulachon Thaleichthys pacificus midwater trawl 0 0.00 whitebait smelt Allosmerus elongatus otter trawl 6 0.00 night smelt Spirinchus starksi otter trawl 8 0.00 longfin smelt Spirinchus thaleichthys otter trawl 9420 0.64 Synodontidae California lizardfish Synodus lucioceps otter trawl 16 0.00 Batrachoididae plainfin midshipman Porichthys notatus otter trawl 6444 0.44 Ophidiidae spotted cusk-eel Chilara taylori otter trawl 3 0.00 Gadidae Pacific tomcod Microgadus proximus otter trawl 154 0.01 Fundulidae rainwater killifish Lucania parva midwater trawl 2 0.00 29

Table 8 (continued). Family Species Scientific Name Gear type used in analysis Number of suitablysized specimens Percentage of all suitablysized specimens Atherinopsidae California grunion Leuresthes tenuis midwater trawl 130 0.01 jacksmelt Atherinopsis californiensis midwater trawl 4016 0.27 topsmelt Atherinops affinis midwater trawl 501 0.03 Gasterosteidae threespine stickleback Gasterosteus aculeatus midwater trawl 8 0.00 Syngnathidae bay pipefish Syngnathus leptorhynchus otter trawl 29 0.00 Scorpaenidae brown rockfish Sebastes auriculatus otter trawl 571 0.04 black rockfish Sebastes melanops midwater trawl 7 0.00 blue rockfish Sebastes mystinus otter trawl 1 0.00 yellowtail rockfish Sebastes flavidus otter trawl 13 0.00 vermilion rockfish Sebastes miniatus otter trawl 1 0.00 unidentified rockfish Sebastes spp. otter trawl 11 0.00 Hexagrammidae lingcod Ophiodon elongatus otter trawl 82 0.01 kelp greenling Hexagrammos decagrammus otter trawl 43 0.00 Cottidae cabezon Scorpaenichthys marmoratus otter trawl 6 0.00 brown Irish lord Hemilepidotus spinosus otter trawl 2 0.00 Pacific staghorn sculpin Leptocottus armatus otter trawl 3343 0.23 buffalo sculpin Enophrys bison otter trawl 42 0.00 padded sculpin Artedius fenestralis otter trawl 1 0.00 bonyhead sculpin Artedius notospilotus otter trawl 203 0.01 scalyhead sculpin Artedius harringtoni otter trawl 1 0.00 prickly sculpin Cottus asper otter trawl 1 0.00 Agonidae pygmy poacher Odontopyxis trispinosa otter trawl 14 0.00 Liparidae showy snailfish Liparis pulchellus otter trawl 216 0.01 slipskin snailfish Liparis fucensis otter trawl 1 0.00 Moronidae striped bass Morone saxatilis midwater trawl 5 0.00 Carangidae jack mackerel Trachurus symmetricus midwater trawl 0 0.00 Sciaenidae queenfish Seriphus politus midwater trawl 0 0.00 white croaker Genyonemus lineatus otter trawl 15493 1.05 30

Table 8 (continued). Family Species Scientific Name Gear type used in analysis Number of suitablysized specimens Percentage of all suitablysized specimens Embiotocidae rubberlip seaperch Rhacochilus toxotes otter trawl 0 0.00 black perch Embiotoca jacksoni otter trawl 1 0.00 barred surfperch Amphistichus argenteus otter trawl 2 0.00 calico surfperch Amphistichus koelzi otter trawl 0 0.00 redtail surfperch Amphistichus rhodoterus otter trawl 0 0.00 spotfin surfperch Hyperprosopon anale otter trawl 0 0.00 walleye surfperch Hyperprosopon argenteum midwater trawl 10 0.00 silver surfperch Hyperprosopon ellipticum otter trawl 0 0.00 shiner perch Cymatogaster aggregata otter trawl 2432 0.16 striped seaperch Embiotoca lateralis otter trawl 0 0.00 dwarf perch Micrometrus minimus otter trawl 7 0.00 pile perch Rhacochilus vacca otter trawl 0 0.00 white seaperch Phanerodon furcatus otter trawl 5 0.00 unidentified surfperch Embiotocidae spp. otter trawl 0 0.00 Chaenopsidae onespot fringehead Neoclinus uninotatus otter trawl 4 0.00 Pholidae saddleback gunnel Pholis ornata otter trawl 66 0.00 Ammodytidae Pacific sand lance Ammodytes hexapterus otter trawl 28 0.00 Gobiidae chameleon goby Tridentiger trigonocephalus otter trawl 853 0.06 bay goby Lepidogobius lepidus otter trawl 57299 3.88 yellowfin goby Acanthogobius flavimanus otter trawl 595 0.04 cheekspot goby Ilypnus gilberti otter trawl 3576 0.24 arrow goby Clevelandia ios otter trawl 41 0.00 shimofuri goby Tridentiger bifasciatus otter trawl 2 0.00 Shokihaze goby Tridentiger barbatus otter trawl 1 0.00 Stromateidae Pacific pompano Peprilus simillimus midwater trawl 260 0.02 Cynoglossidae California tonguefish Symphurus atricaudus otter trawl 2215 0.15 Paralichthyidae California halibut Paralichthys californicus otter trawl 14 0.00 Pacific sanddab Citharichthys sordidus otter trawl 0 0.00 speckled sanddab Citharichthys stigmaeus otter trawl 33685 2.28 31

Table 8 (continued). Family Species Scientific Name Gear type used in analysis Number of suitablysized specimens Percentage of all suitablysized specimens Pleuronectidae curlfin sole Pleuronichthys decurrens otter trawl 126 0.01 hornyhead turbot Pleuronichthys verticalis otter trawl 3 0.00 sand sole Psettichthys melanostictus otter trawl 38 0.00 diamond turbot Pleuronichthys guttulatus otter trawl 1 0.00 English sole Parophrys vetulus otter trawl 22093 1.50 starry flounder Platichthys stellatus otter trawl 38 0.00 Dover sole Microstomus pacificus otter trawl 2 0.00 TOTAL 1476179 100.00 32

Table 9. Lengths of fish sampled with different gear types in San Francisco Bay, April-August, 2000-2006. midwater trawl otter trawl both nets Year mean ± s.d. range n mean ± s.d. range n mean ± s.d. range n 2000 80 ± 26.6 32-610 4629 78 ± 72.9 20-1300 5292 79 ± 56.2 20-1300 9921 2001 80 ± 29.1 31-632 4427 83 ± 54.7 20-856 6229 82 ± 45.8 20-856 10656 2002 76 ± 35.5 35-627 4867 77 ± 51.0 20-855 9675 77 ± 46.4 20-855 14542 2003 75 ± 25.8 30-582 5164 81 ± 45.2 20-754 7058 79 ± 38.3 20-754 12222 2004 86 ± 26.7 31-324 4690 83 ± 54.3 20-1020 6148 84 ± 44.5 20-1020 10838 2005 77 ± 21.7 30-314 4340 92 ± 81.1 20-900 3250 83 ± 56.0 20-1010 7590 2006 88 ± 23.0 38-530 3927 90 ± 72.6 20-947 2768 89 ± 50.0 20-947 6695 Total 80 ± 27.8 30-632 32044 82 ± 59.1 20-1300 40420 81 ± 47.8 20-1300 72464 33

Table 10. Lengths of suitably-sized fish sampled with different gear types in San Francisco Bay, April-August, 2000-2006. midwater trawl otter trawl both nets Year mean ± s.d. range n mean ± s.d. range n mean ± s.d. range n 2000 73 ± 12.4 32-100 3983 57 ± 20.4 20-100 4371 65 ± 18.8 20-100 8354 2001 71 ± 16.1 31-100 3492 64 ± 20.8 20-100 4625 67 ± 19.2 20-100 8117 2002 67 ± 13.0 35-100 4259 61 ± 20.4 20-100 7621 63 ± 18.3 20-100 11880 2003 71 ± 13.1 30-100 4800 66 ± 18.4 20-100 5361 68 ± 16.3 20-100 10161 2004 78 ± 15.2 31-100 3778 64 ± 19.8 20-100 4436 70 ± 19.1 20-100 8214 2005 73 ± 12.7 30-100 4068 66 ± 19.7 20-100 2307 71 ± 15.9 20-100 6375 2006 82 ± 13.0 38-100 3324 67 ± 17.9 20-100 2114 76 ± 16.8 20-100 5438 Total 73 ± 14.3 30-100 27704 63 ± 20.1 20-100 30835 68 ± 18.3 20-100 58539 34

Table 11. Lengths of suitably-sized fish sampled with different gear types in San Francisco Bay and in different breeding periods, April- August, 2000-2006. a) Courtship/incubation midwater trawl otter trawl both nets Year mean ± s.d. range n mean ± s.d. range n mean ± s.d. range n 2000 69 ± 12.8 32-100 1635 52 ± 20.7 20-100 1520 61 ± 19.1 20-100 3155 2001 60 ± 16.2 31-100 1244 63 ± 24.8 20-100 1634 62 ± 21.6 20-100 2878 2002 61 ± 15.2 35-100 1342 56 ± 20.8 20-100 3596 57 ± 19.6 20-100 4938 2003 53 ± 11.4 30-96 509 61 ± 21.4 20-100 994 58 ± 19.0 20-100 1503 2004 81 ± 19.0 31-100 1025 56 ± 21.8 21-100 1494 66 ± 23.8 21-100 2519 2005 70 ± 14.7 30-100 1568 61 ± 19.8 20-100 745 67 ± 17.1 20-100 2313 2006 81 ± 14.4 38-100 1315 60 ± 17.0 20-100 801 73 ± 18.6 20-100 2116 TOTAL 69 ± 17.3 30-100 8638 58 ± 21.6 20-100 10784 63 ± 20.6 20-100 19422 b) Chick-rearing midwater trawl otter trawl both nets Year mean ± s.d. range n mean ± s.d. range n mean ± s.d. range n 2000 72 ± 13.8 40-100 867 55 ± 19.5 21-100 1220 62 ± 19.3 21-100 2087 2001 74 ± 15.1 43-100 784 61 ± 18.8 20-100 1146 66 ± 18.5 20-100 1930 2002 68 ± 13.8 42-100 692 63 ± 19.0 20-100 1632 64 ± 17.8 20-100 2324 2003 72 ± 13.7 41-100 1312 66 ± 17.1 20-100 2120 69 ± 16.1 20-100 3432 2004 77 ± 14.3 41-100 840 65 ± 17.6 22-100 1153 70 ± 17.3 22-100 1993 2005 74 ± 12.1 41-99 733 67 ± 19.8 20-100 398 72 ± 15.6 20-100 1131 2006 80 ± 13.9 43-100 736 65 ± 17.1 22-100 439 74 ± 16.8 22-100 1175 TOTAL 74 ± 14.3 40-100 5964 63 ± 18.7 20-100 8108 68 ± 17.8 20-100 14072 c) Fledging midwater trawl otter trawl both nets Year mean ± s.d. range n mean ± s.d. range n mean ± s.d. range n 2000 78 ± 9.0 46-100 1481 63 ± 19.2 20-100 1631 70 ± 16.9 20-100 3112 2001 79 ± 9.7 36-100 1464 67 ± 17.5 21-100 1845 72 ± 15.8 21-100 3309 2002 70 ± 9.6 37-100 2225 67 ± 18.5 21-100 2393 69 ± 15.0 21-100 4618 2003 73 ± 10.4 45-100 2979 67 ± 17.9 21-100 2247 71 ± 14.4 21-100 5226 2004 77 ± 13.0 36-100 1913 70 ± 17.1 20-100 1789 74 ± 15.5 20-100 3702 2005 75 ± 10.3 35-100 1767 69 ± 18.9 21-100 1164 73 ± 14.7 21-100 2931 2006 84 ± 10.5 55-100 1273 74 ± 16.1 26-100 874 80 ± 14.0 26-100 2147 TOTAL 76 ± 11.2 35-100 13102 68 ± 18.2 20-100 11943 72 ± 15.5 20-100 25045 35

Table 12. Two-factor ANOVA results for Bay fish sizes, 2000-2006. Source Partial SS df MS F Prob>F Model 1866023 20 93301.13 306.62 0.0000 year 741175.8 6 123529.3 405.96 0.0000 breeding stage 824975.2 2 412487.6 1355.58 0.0000 year*breeding stage 109520.8 12 9126.737 29.99 0.0000 Residual 17806323 58518 304.8796 Total 19672347 58538 336.0611 Number of observations = 58539 Root MSE = 17.4439 R 2 = 0.0949 Adjusted R 2 = 0.0945 36

Table 13. Three-factor ANOVA results comparing dropped fish and Bay fish sizes, 2000-2006. Source Partiall SS df MS F Prob>F Model 2107745 17 123985 436.48 0.0000 collection (Bay or colony) 24422.28 1 24422.28 85.98 0.0000 year 207340.5 6 34556.75 121.65 0.0000 breeding 13873.04 2 6936.518 24.42 0.0000 collection*year 124285.1 6 20714.18 72.92 0.0000 collection*breeding 157781.6 2 78890.81 277.73 0.0000 Residual 19575120 68912 284.0597 Total 21682866 68929 314.5681 Number of observations = 68930 Root MSE = 16.8541 R 2 = 0.0972 Adjusted R 2 = 0.0970 37

Table 14. Spearman correlations by species between species compositions from dropped fish at the colony to fish sampled in San Francisco Bay. Gear type Species ρ n p Midwater trawl Chinook salmon - 0.1655 21 0.4734 northern anchovy 0.6039 21 0.0037 Pacific herring 0.4416 21 0.0451 Pacific sardine 0.8189 21 <0.001 topsmelt - 0.0261 21 0.9104 jacksmelt - 0.1000 21 0.6663 California grunion 0.8408 21 <0.001 striped bass - 0.0910 21 0.6949 threespine stickleback - 0.0910 21 0.6949 walleye surfperch - 0.1664 21 0.4709 Otter trawl surf smelt - 0.1389 21 0.5483 longfin smelt - 0.0739 21 0.7504 white croaker 0.4641 21 0.0341 yellowfin goby 0.526 21 0.0143 arrow goby 0.4343 21 0.0491 bay goby 0.3983 21 0.0737 cheekspot goby 0.5814 21 0.0057 Pacific sand lance 0.3515 21 0.1181 Pacific staghorn sculpin 0.3542 21 0.1152 brown rockfish 0.3798 21 0.0895 unidentified rockfish - 0.2320 21 0.3115 plainfin midshipman 0.1733 21 0.4526 dwarf perch - 0.0038 21 0.987 shiner perch 0.0461 21 0.8426 white seaperch 0.3076 21 0.1749 black perch - 0.0500 21 0.8296 English sole - 0.0739 21 0.7504 Note: Yellow highlights designate significant results (p<0.05), and pink highlights indicate near-significant results (0.1>p>0.05). 38

Table 15. Spearman correlations by year between species compositions from dropped fish at the colony to fish sampled in San Francisco Bay. Gear type Year ρ n p Midwater trawl 1981 0.8833 10 0.0007 1982 0.4606 10 0.1803 1984 0.7889 10 0.0067 1985 0.5448 10 0.1034 1986 0.6828 10 0.0296 1987 0.4614 10 0.1795 1988 0.7343 10 0.0156 1989 0.5003 10 0.1409 1990 0.7115 10 0.0210 1991 0.6083 10 0.0621 1992 0.7949 10 0.0060 1993 0.4684 10 0.1721 1994 0.5107 10 0.1314 1995 0.6097 10 0.0613 2000 0.7198 10 0.0189 2001 0.7723 10 0.0088 2002 0.6773 10 0.0314 2003 0.9179 10 0.0002 2004 0.6462 10 0.0435 2005 0.6911 10 0.0269 2006 0.4985 10 0.1425 Otter trawl 1981-0.0056 17 0.9830 1982 -- -- -- 1984 -- -- -- 1985 0.1105 17 0.6729 1986 0.3131 17 0.2211 1987-0.0839 17 0.7489 1988 0.1565 17 0.5487 1989 0.0085 17 0.9740 1990-0.0746 17 0.7761 1991 0.0778 17 0.7666 1992 0.1121 17 0.6684 1993 0.3861 17 0.1259 1994 0.4129 17 0.0995 1995 0.0816 17 0.7555 2000-0.0160 17 0.9514 2001 0.0632 17 0.8097 2002-0.1090 17 0.6772 2003-0.4220 17 0.0916 2004-0.1412 17 0.5889 2005-0.0647 17 0.8052 2006 0.033 17 0.8998 Note: Yellow highlights designate significant results (p<0.05), and pink highlights indicate near-significant results (0.1>p>0.05). 39

Table 16. Rank preference indices for fish species. Gear type Species (Rank colony) (Rank Bay) Selectivity Midwater trawl Pacific herring 2 preferred Pacific sardine 4 strongly preferred northern anchovy 1 mildly preferred Chinook salmon 0 neutral California grunion 0 neutral jacksmelt -2 avoided topsmelt -3 strongly avoided threespine stickleback 1 mildly preferred striped bass -1 mildly avoided walleye surfperch -2 avoided Otter trawl longfin smelt 10 strongly preferred surf smelt -13 strongly avoided plainfin midshipman 8 preferred brown rockfish 4 preferred unidentified rockfish spp. -3 avoided Pacific staghorn sculpin 4 preferred white croaker 5 preferred black perch -5 avoided shiner perch -7 avoided dwarf surfperch -4 avoided white seaperch -12 strongly avoided Pacific sand lance -2 avoided bay goby 5 preferred yellowfin goby -7 avoided cheekspot goby 1 mildly preferred arrow goby -6 avoided English sole 12 strongly preferred 40

Table 17. Sizes of northern anchovy and jacksmelt sampled in San Francisco Bay, April- August, 2000-2006. northern anchovy jacksmelt Year mean ± s.d. range n 2000 77 ± 9.4 40-100 2989 2001 80 ± 12.0 41-100 1879 2002 73 ± 9.6 41-100 2326 2003 77 ± 9.9 47-100 3161 2004 83 ± 10.3 46-100 2721 2005 75 ± 10.8 40-100 3384 2006 86 ± 9.2 53-100 2740 Total 79 ± 10.9 40-100 19200 2000 71 ± 18.6 44-99 52 2001 79 ± 9.5 36-100 299 2002 77 ± 10.9 50-98 313 2003 78 ± 8.9 48-98 75 2004 66 ± 14.9 36-100 174 2005 67 ± 14.1 40-96 92 2006 81 ± 7.4 59-98 111 Total 75 ± 12.8 36-100 1116 41

Figure 1. Fish sampling stations of CDFG s San Francisco Study. Note: Data from stations in the South Bay (101-142) and Central Bay (211-244) were used in this report. Map obtained from the IEP/CDFG website: http://www.iep.ca.gov/sf_bay_monitor/ 42

Figure 2. Dropped prey composition by familiy, 1981-2006. (Note: No prey were collected in years 1983 and 1996-1999). 43