San Francisco Bay Tidal Marsh Project Annual Report 2006

SAN FRANCISCO BAY TIDAL MARSH PROJECT ANNUAL REPORT 2006

Distribution, abundance, and reproductive success of tidal marsh birds

January 31, 2007

Prepared by: Leonard Liu, Parvaneh Abbaspour, Mark Herzog, Nadav Nur, and Nils Warnock PRBO Conservation Science 3820 Cypress Drive, #11 Petaluma, CA 94954 http://www.prbo.org

Contribution # 1557 EXECUTIVE SUMMARY Human impacts on the tidal salt marshes of the San Francisco Bay estuary have drastically reduced and degraded this important habitat. Tidal marshes are biologically productive, and are an integral part of the proper functioning of the overall bay ecosystem. They are also home to a number of state and federal listed endangered or threatened species of plants and animals. Recognizing the importance of this habitat, many agencies and organizations have planned or completed wetland restoration projects in the Bay. Restoring wetlands to functioning tidal marsh habitat requires monitoring to assess the health and success of restoration sites relative to natural marshes.

Many bird species depend on tidal marsh habitat to nest and raise their young. Populations of these tidal marsh dependent birds have declined significantly due to the loss of habitat around the Bay. A number of these birds have special conservation status, such as the federally endangered California Clapper Rail ( Rallus longirostris obsoletus ), State of California threatened California Black Rail ( Laterallus jamaicensis coturniculus ), and four State Species of Special Concern: Alameda Song Sparrow (Melospiza melodia pusillula ), San Pablo Song Sparrow ( M. m. samuelis ), Suisun Song Sparrow ( M. m. maxillaris ), and Salt Marsh Common Yellowthroat ( Geothlypis trichas sinuosa ). The subject of studies in the past, the population biology of these species still is not well known, nor have long-term population trends been established due to the lack of long-term monitoring studies.

PRBO Conservation Science (founded as the Point Reyes Bird Observatory) began a long-term monitoring project in 1996 to study the population status and processes of tidal marsh birds of the Bay. Synthesizing data from point count surveys and demographic data from reproductive studies has provided insights into how tidal marsh birds respond to both physical and biological processes. An important topic of recent study has been the response of tidal marsh birds to ongoing restoration projects. This report summarizes results of our 2006 studies in the Bay.

We conducted point count surveys at 32 sites in the 2006 breeding season (March through May). A density index for each focal taxon (Song Sparrow, Common Yellowthroat, Marsh Wren ( Cistothorus palustris ), and Black Rail) was calculated for each point using detections within 50 m of the observer; the mean at each site for each

PRBO Tidal Marsh Annual Report 2006 2 round was then averaged to produce a single density index for each site. Similarly derived data since 1996 are included for comparison with 2006 data. The density index of Song Sparrows in San Pablo and Suisun Bays was the lowest recorded since monitoring began in 1996. The density index of Salt Marsh Common Yellowthroats in San Pablo and Suisun Bays also declined steeply. Marsh Wren density indices were generally stable.

Nests were monitored at three marshes using standardized methodology. Nest monitoring allows measurement of reproductive success and therefore is an indication of population health. Nest survival probability, one component of reproductive success, was calculated both by the overall proportion of successful nests, and by the Mayfield method, which provides an estimate of the daily probability of nest survival. Observers also used behavioral clues to estimate territory boundaries and map breeding territories.

Analysis of 2006 data indicates that nest survival rate was below the long-term average compared with sites previously surveyed. A total of 608 nests of 10 bird species were found in 2006. Of these, 555 were Song Sparrow nests. Since this species is the most abundant breeding species in SF Bay and endemic Song Sparrow subspecies are restricted to tidal marsh habitat, this species is used as an indicator species to reveal patterns of reproductive success. The nest survival rate of Song Sparrows decreased slightly to approximately 16% overall. However, there was significant variation among the three sites. Of particular note, nest survival for Song Sparrows at the young restoration site (Carl’s Marsh) was nearly twice the observed value at the two mature marsh sites (China Camp and Benicia).

In 2006, researchers from several organizations collaborated with PRBO to survey over 90 sites in the San Francisco Estuary for breeding Clapper Rails. Clapper Rails were detected in small numbers in Suisun Bay. The trend between 2005 and 2006 in South San Francisco Bay is generally positive at sites for which we have data to compare the two years.

In an analysis completed this year, we analyzed ten years (1996-2005) of point count and nest data at the two San Francisco Bay National Estuarine Research Reserve (NERR) sites, China Camp State Park and Rush Ranch. We found a significantly higher measured density of Song Sparrows at China Camp than at Rush Ranch. No

PRBO Tidal Marsh Annual Report 2006 3 relationship between population density in one year and nest survival in the previous year was found. Total nest survival at the two sites from 1996-2002 showed a notable correspondence, suggesting the importance of regional influences on nest survival in the long-term. There was no correlation between Song Sparrow density and clutch size or number of attempts per pair (in the same year or in the previous year) at either site. We found that China Camp Song Sparrows nested significantly earlier than Rush Ranch Song Sparrows. These two largely intact tidal marshes represent salt marsh and brackish marsh ecosystems and our long-term datasets can be used as a basis of comparison for recently restored tidal marsh sites. Understanding the demographic parameters of common species in existing tidal marshes is important, as they can serve as easily monitored indicators of ecosystem health. The knowledge gained from their study allows researchers to assess how certain restorations are progressing in relation to an example “final” outcome, as well as assist in the management of these remaining intact ecosystems.

PRBO Tidal Marsh Annual Report 2006 4 INTRODUCTION Throughout the world, tidal salt marshes have faced and continue to endure threats from humans (Adam 2002). The tidal marshes of San Francisco Bay, since their establishment approximately 10,000 years ago (Atwater 1979, Atwater et al. 1979, Josselyn 1983), have played an important role in maintaining proper functioning of the Bay ecosystem. During the last 200 years, however, the system has been altered and broken down through human induced habitat conversion and loss (Nichols et al. 1986). Habitat losses in San Francisco Bay include a 79% reduction of tidal marsh habitat and 42% reduction of tidal flat habitat (Goals Project 1999). Over the past decade, through wetland acquisition and restoration, tidal marsh habitat has increased substantially in San Francisco Bay. About 35 restoration projects are underway or actively being planned, with sizes ranging from a few hectares to much larger efforts (S. Scoggin, pers. comm.). In 1994 the Cargill Salt Company sold nearly 4,000 ha of its salt pond complex in North San Francisco Bay (San Pablo Bay) to the State of California (Siegel and Bachand 2002). The state of California and the federal government purchased over 6,100 additional ha of salt pond operations in South San Francisco Bay from Cargill Salt in March 2003 to further wetland restoration efforts (S. Scoggin, pers. comm.). Together, state and federal agencies and non-governmental organizations are developing strategies to restore much of these lands. A dominant feature of the coastal tidal marsh habitat in San Francisco Bay is its avian community (Josselyn 1983), and it is assumed that the significant amount of habitat lost in the past, reduced the numbers and diversity of birds substantially (Marshall and Dedrick 1994; see also Nichols et al. 1986). However, little quantitative data on birds exist prior to the last half of the 20 th century. For example, California Clapper Rails, formerly a common characteristic resident in the Bay, were anecdotally reported by Grinnell and Wythe (1927) to be rare. The loss of tidal marsh habitat is reflected by the number of San Francisco Bay tidal marsh-dependent birds with special conservation status, such as the California Clapper Rail, California Black Rail, Alameda Song Sparrow, San Pablo Song Sparrow, Suisun Song Sparrow, and Salt Marsh Common Yellowthroat (Nur et al. 1997, Goals Project 2000, Spautz and Nur 2002, Spautz and Nur in press a, Spautz and Nur in press b, Chan and Spautz in press ). More recently, many of the species designated with a special conservation status, have been the focus of various studies (e.g., Clapper Rail - Harvey 1988, Albertson 1995, Garcia 1995; Black Rail - Manolis 1978, Evens et al. 1989, 1991, Evens

PRBO Tidal Marsh Annual Report 2006 5 and Nur 2002; Song Sparrow - Marshall 1948, Johnston 1956, Chan and Arcese 2002; Salt marsh Common Yellowthroat - Marshall and Dedrick 1994), yet little of this work has been long-term. Because of the lack of long-term monitoring, few quantitative data exist on the trends of tidal marsh birds for San Francisco Bay (but see Evens and Nur 2002). PRBO Conservation Science (PRBO) has been studying San Francisco Bay's tidal marsh birds since the early 1980s, and in 1996 initiated a long-term population study designed to examine the long-term demographic patterns of San Francisco Bay's tidal marsh birds. PRBO's research design includes a combination of annual point count data from over 80 sites in the Bay, annual demographic data collected at up to 5 sites in the Bay, as well as associated habitat and landscape level variables at each site (see Figure 1a, b and Table 1). With these data, PRBO is now able to examine how tidal marsh birds respond to the heterogeneity of physical and biological processes found within the diverse landscape throughout the San Francisco Bay estuary (see Nur et al. 1997, Evens and Nur 2002, Stralberg et al. 2003, Spautz et al. in press ). We examine trends for five focal species (California Clapper Rail, California Black Rail, Song Sparrow, Common Yellowthroat, and Marsh Wren) for the entire Estuary—by bay—and we examine population and demographic trends at select study sites. In this report we also summarize the results of a poster we presented at the CALFED conference in 2006 that compared the demography of San Pablo and Suisun Song Sparrow nest success at the San Francisco Bay NERR sites, China Camp State Park and Rush Ranch. We examined factors influencing population density and nest survival, as well as some life history parameters, for San Pablo (China Camp) and Suisun (Rush Ranch) Song Sparrows. The variability in landscape and vegetative characteristics between the two NERR sites provides us with the opportunity to compare and contrast the strategies these two subspecies of Song Sparrows employ within the rigorous and variable tidal marsh environment of the San Francisco Estuary.

PRBO Tidal Marsh Annual Report 2006 6 METHODS Point count surveys Variable radius point count surveys (Reynolds et al. 1980; Ralph et al. 1995; Nur et al. 1999) were conducted twice at each of 32 sites during spring 2006 (Fig. 1a,b; Table 1). Surveys were conducted within 4 hours of sunrise, twice between March 22 and May 31. Successive rounds were conducted at least 3 weeks apart. Survey points (or stations) were placed 150-200 m apart, with five to 13 points per site depending on marsh size. Field biologists, with extensive knowledge of songs and calls of the birds in the area, conducted all surveys. At each station, the observer recorded all birds detected by sight and sound for five minutes. For detections within 100 m from the observer, distance was estimated within 10 m bands; detection type (visual or auditory) was also recorded for each bird (WRMP 2002). A density index (birds detected per hectare of suitable habitat) for each focal taxon (including rails) was estimated at each site. Based on prior analysis of detection rates at various distances (Nur et al. 1997), we restricted the data to detections within 50 m of the observer. If a specific station was surveyed more than once, we averaged across the multiple surveys to obtain a mean and variance estimate for the density index of each station. Stations were not always entirely surrounded by marsh habitat. Therefore final breeding season density estimates for each station were adjusted based on the proportion of tidal marsh habitat present within the 50 m radius of the station. Density estimates for each site were estimated as the average of all point count station estimates within the site. The apparent density index is an underestimate of true density since detection probabilities are considerably less than 100% for many species; for Song Sparrows and Black Rails, detection probabilities are about 30% (Nur et al. 1997). Cumulative species richness for each site was estimated by counting the total number of unique species detected across all surveys within the site.

Reproductive success Nest monitoring allows measurement of a number of parameters associated with reproductive success (clutch size, number of broods, number of nesting attempts) and with our long term study we are able to examine how these parameters vary across space and time as well as providing information on population health and sustainability (Martin and Geupel 1993).

PRBO Tidal Marsh Annual Report 2006 7 Field biologists searched for and monitored nests at China Camp State Park (Marin County), Carl's Marsh (Sonoma County), and Benicia State Recreation Area (Solano County) (Figure 1a; Table 1) in tidal marsh habitat during the breeding season (March 1 to August 14, 2006). Nests have been monitored by PRBO at China Camp and Benicia annually since 1996 and at Carl’s Marsh since 2004. Within 2-4 focal study plots per site, we intensively searched for the nests of Song Sparrow, Common Yellowthroat, Marsh Wren, and Black Rail; nests of other species were also opportunistically found. All known nests were monitored using a standard protocol (Martin and Geupel 1993). Nests were usually visited every 2-4 days (range: 1 to 9 days) and careful attention was given to minimize human disturbance. Frequent visits to nests allowed more accurate estimates for the dates of predation events as well as dates of egg laying, hatching of eggs, and fledging of young, all of which are valuable for the estimation of daily survival rate and nest success. Life history parameters, such as clutch size, initiation date, and nest attempts, are collected at each site as well. Nests were located at all stages (construction, egg-laying, incubation, and nestling periods, as well as after termination of the nesting attempt). Nest contents were recorded at each visit and the ultimate outcome of each nest (success or failure) was decided based on nest condition and behavior of the breeding pair. Song Sparrow nestlings were banded when they were about 7 days old with USGS numbered bands and a unique combination of colored leg bands to allow field identification after fledging. Nests and the vegetation in the immediate vicinity of the nest were measured to provide information about nest location selection. We calculated nesting success of a specific site (defined as the proportion of the total number of nests that fledged at least 1 chick) and also daily survival rate for each site using the Mayfield method (Mayfield 1975). We estimated the daily survival rates of nests at each site separately for each nesting stage (egg laying/incubation, and nestling). We also estimated an overall nest survival for each site by combining the separate nest survival rates for each stage (Johnson 1979, Nur et al. 1999).

Territory mapping For defined plots within each nest-monitoring site, we mapped the breeding territories of all individuals of all species (Verner, 1985). The region mapped included the territories where nests were monitored (where territory boundaries were the most accurately discerned), but also included additional adjacent habitat. We defined the approximate territory boundary by observing the behavior of each bird, particularly

PRBO Tidal Marsh Annual Report 2006 8 singing and territory defense behavior. The entire area being mapped was visited at least four times during the breeding season: twice during the first half of the season to produce mid-season maps (before May 1) and at least twice during the late season, between May 1 and June 30. Although territories boundaries are dynamic, and individuals often appear or disappear during the season (PRBO unpubl. data), the best possible estimates of territory locations and the locations of color-banded birds were made by combining data at mid-season and at late season. Here we only present territorial data from the late season, because by that time highly inconspicuous individuals are usually detected and territory boundaries are probably more accurately mapped than earlier in the season. We counted the number of territories in each study area within each marsh and divided it by the area studied to derive a density of breeding birds for each marsh. This number can be compared with the density index derived from point count surveys to determine the relative accuracy of the survey sampling methods.

Banding Since 1996 PRBO has been banding Song Sparrows and Common Yellowthroats in the San Pablo and Suisun bays; in 1997, we initiated individual, unique color-banding of Song Sparrows. In the future these data will be used to estimate demographic parameters such as survival, dispersal, and ultimately recruitment of new breeders. Presently, the banded individuals allow PRBO to monitor unique pairs throughout the breeding season, and thus determine season-long reproductive success. In the beginning of the season, biologists used mist nests to opportunistically capture and band birds, primarily Song Sparrows. During the breeding season, biologists used more direct methods, targeting specific unbanded pairs with known nest locations. In addition, many nestlings were banded just prior to fledging. Morphometric data (wing- length, fat scores, etc.; Ralph et al. 1993) and sometimes plumage characteristics (e.g., color) are noted at capture (see Nur et al. 1997).

Clapper Rail surveys Surveys were conducted from December 2005 through April 2006, under Federal Fish and Wildlife Permit #TE807078-7. Most marshes were surveyed 3 times in a 2- hour period around sunrise and sunset along an established transect, with 10 minutes per listening station (Albertson et al. 2004). Two to nine listening stations were placed 200-400 m apart, depending on marsh size. All Clapper Rail vocalizations were

PRBO Tidal Marsh Annual Report 2006 9 recorded with the time, direction and distance from the listening station. If no Clapper Rail had been previously detected at a listening station after three surveys, tape playback of California Clapper Rail vocalizations was utilized to stimulate a response. Vocalizations were assumed to represent 1-2 rails, except when known to be a single individual or a pair. A mean based on the minimum and maximum number of Clapper Rails detected (using the survey with the most overall detections) was calculated for each survey site. The mean number of Clapper Rails at each survey point was then used to calculate an approximate density (birds/hectare). Detectability of Clapper Rail vocalizations decreases at 200 m, so densities were calculated using detections out to 200 m. Survey areas were calculated using marsh areas generated by the Invasive Spartina Project and by the San Francisco Estuary Institute’s Bay Area EcoAtlas Version 1.50b4.

PRBO Tidal Marsh Annual Report 2006 10 RESULTS AND DISCUSSION Point count surveys Species richness ranged from 9 to 41 species (mean =19.4 species; s.d. = 7.4) per site across the region (Table 1). Density indices at many sites showed a sharp decline. The intense winter rains the Estuary experienced in the late winter and early spring could have increased pre-breeding season mortality and partially account for the decreases in density indices.

Song Sparrow density indices Within each bay, Song Sparrows are the most abundant of the focal species detected using our point count survey methods. The 2006 mean density indices for Song Sparrows decreased across the entire San Francisco Bay estuary from 2005 (Figure 2). Song Sparrow density indices for Suisun Bay and San Pablo Bay were the lowest ever. Alameda Song Sparrows (Central and South San Francisco Bays) has shown a generally increasing trend from 1996-2003, and a decreasing trend from 2003 to 2006. The density indices of San Pablo Song Sparrows have shown a steady overall decline since 1999, and Suisun Song Sparrows have shown a declining trend from 1996-2006, but particularly in the past three years. Alameda Song Sparrows would show an overall decline from 1996-2006 if not for the high density indices at the Faber-Laumeister tract in East Palo Alto (Figure 3). The Faber-Laumeister tract showed the highest density index of any South San Francisco Bay marsh surveyed in 2006 (Figure 4). However, only one site, Cooley Landing in the Palo Alto marshes, showed an increase in the number of Alameda Song Sparrows detected per hectare, likely due to its recent restoration and increasing vegetation cover (Figure 3). Our surveys at marshes in the Hayward area, detected very low numbers of Alameda Song Sparrows (Figure 5). One major alteration to the marsh habitat in South and Central Bays has been the application of herbicides to control invasive Spartina. San Pablo Song Sparrows have the highest density indices of the three subspecies (Figure 2). Greenpoint Restoration (Toy Marsh) and Petaluma Ancient on the Petaluma River (Figures 6 and 7), and Bull Island and Mare Island A on the Napa River (Figures 8 and 9), were the only marshes to show increases in density indices. Neighboring marshes showed opposite trends, notably in the case of Mare Island B, a plot immediately adjacent to Mare Island A. It is possible that the individual marsh fluctuations are just natural or weather-related, but the negative population trend is cause for concern.

PRBO Tidal Marsh Annual Report 2006 11 The decreasing trend in density indices for Suisun Song Sparrows was offset at just one site, Blacklock Restoration (Table 1). The site was flooded during the first visit of the breeding season, but by the second visit the water had receded substantially, possibly leading to increased habitat access for passerines. For Suisun Song Sparrows at sites with datasets from 1996 to present, Benicia SRA has had density indices between 3-5 birds/ha since 1999, and Pt. Edith marsh and Rush Ranch have had density indices between 4-7 birds/ha since 2000 (Figure 10). We performed our first point counts at Hill Slough East in 4 years, and the density index was almost identical to the last survey in 2002 (Figure 10). The trends in Suisun Bay may be cyclical, but additional years of monitoring will be needed to confirm this.

Common Yellowthroat density indices Across the entire estuary, Common Yellowthroats mean density indices were lower compared to 2005, and also showed sharp declines in San Pablo and Suisun Bays (Figure 11). In Central and South San Francisco Bays and San Pablo Bay, there have been slight upward trends in density indices observed from 1996 to 2006. Suisun Bay has shown a decline in density index the last two years, although density indices are still much higher than in the rest of the San Francisco Bay estuary. The overall trend from 1996-2006 is stable. Tracking changes in Common Yellowthroat densities is difficult using standard point count, as variability in detections among sites is high. While some preliminary analyses have already been performed we hope to implement distance sampling to a greater extent which may provide additional power to examine trends in the population (Buckland et al. 2001).

Marsh Wren density indices The mean density indices of Marsh Wrens declined slightly in every Bay in 2006 (Figure 12). San Pablo Bay continues to have an increasing trend 1996-2006, and to a lesser extent Suisun Bay as well.

Reproductive success Song Sparrows Song sparrows are the most common nesting bird in the tidal marshes of the San Francisco Bay Estuary. Nesting densities observed here are some of the highest reported for any non-colonial bird species (Johnston 1956). Estimated nest survival rate

PRBO Tidal Marsh Annual Report 2006 12 (per nest), from initiation of laying to fledging showed some variation among individual sites (Figure 13 & Table 2). Nest success at Benicia, a Suisun Bay marsh, was extremely poor (Figure 13). Benicia had its 2nd lowest rate of nest success in 10 years of monitoring. For nests of known fate, 66% were depredated and 13% were flooded (Table 3). Predators observed at Benicia included gopher snakes, corvids, raptors, river otters, and rodents. It is unknown if any of these predators is more successful than others in finding Song Sparrow nests. China Camp had the lowest rate of nest success in 2006 (6%) and had one of its poorest breeding seasons ever over 10 seasons of nest monitoring. Over 50% of nest failures at China Camp were due to flooding, significantly higher than in past seasons. There was a significant amount of heavy rain in the early breeding season, which likely compounded the difficulties of nesting at China Camp, as the average vegetation height in that marsh is lower than at the other four marshes, as is the nest height. About 30% of nests at China Camp were depredated. Carl’s Marsh had a fairly high nest survival rate (18%), almost triple the rate in 2005 (6.4%, Table 2). Survival during egg and nestling periods rose among years, but the laying and incubation periods remained a time of higher failure than the nestling period. Forty-five percent of nests at Carl’s Marsh were depredated, and 21% were lost to flooding.

Common Yellowthroats Common Yellowthroat nesting activity was reported at one site, Benicia. Only one active nest was found this year, and the parents fledged young.

Marsh Wrens Within the nest monitoring sites, Marsh Wren nests were the second most common species found. They were primarily found within recently restored Carl’s Marsh. Of the 17 nests found, 8 were built but unoccupied, and only 1 fledged young.

Other marsh birds We found nests of 8 other bird species at nest monitoring sites (Table 3). Only one active Black Rail nest was found at Benicia, and none were found at China Camp for the first time since 1998. Black Rail nest sites at China Camp tend to be near marsh edges and may be more vulnerable to predation. Allen’s Hummingbirds were

PRBO Tidal Marsh Annual Report 2006 13 documented nesting at Benicia and fledged young. An American Bittern nest was discovered at Hill Slough East during a vegetation survey.

Territory density Estimates of density using territory mapping are generally higher than estimates of relative density as much more time is spent within a specific area and, therefore, detection rates are higher. In addition, territory mapping is conducted only on breeding pairs which are much more conspicuous than non-breeding individuals. Only territory mapping and distance-sampling (Nur et al. 1997) can provide estimates of absolute density. There was considerable variation in density among marsh sites and to a lesser degree within marsh sites (Table 4). The density of Song Sparrows at Carl’s Marsh increased in 2006, whereas the density index derived from point counts declined compared to 2005. The decline of Song Sparrow density indices at China Camp and Benicia were reflected in the density derived from territory mapping, though to a lesser degree at China Camp. One hypothesis for the disparity between the two methods of calculating density is that suitable breeding areas are saturated with territorial Song Sparrows and do not reflect a decline in numbers in less suitable breeding habitat, which point counts cover more thoroughly.

Banding data In 2006, a total of 247 Song Sparrows were newly banded between the three nest-monitoring sites (Table 5). An increased effort was made to target-net the adult birds holding territory and breeding on the intensive plots, and a total of 42 adult birds were newly banded. Despite, markedly low nesting success at two of our plots, a total of 205 nestlings survived to be banded by biologists from nests located at our sites. Additionally, we recaptured five birds in mist-nets on our plots. One of these birds was first banded as a nestling by a PRBO biologist on a study plot in 1997! In 2007, we intend to match our target-netting effort and work toward the goal having at least 50% of the birds breeding on our intensive plots marked with a unique set of color bands (currently we average 30% across our plots). Marking individual birds aids spot-mapping and nest-searching, lending precision to our territory estimates and accuracy to assignments of ownership to nesting attempts. In 2006, because of observations of birds marked in our target-netting efforts, we were able to document a polygamous male breeding on our plots. Also we were able to confirm a male who took over a neighbor’s territory and mate halfway through the

PRBO Tidal Marsh Annual Report 2006 14 season, as well as a pair which disappeared altogether mid-season from our intensive plots.

Clapper Rail surveys In Suisun Bay, 14 sites were surveyed in 2006. A total of 6 Clapper Rails were detected in 4 locations, including Pt. Edith marsh and Benicia SRA. All of the detections were in areas where Clapper Rails had been detected in the 1990s. No Clapper Rails were detected at the Martinez marsh. In San Pablo Bay, Clapper Rails were detected in small numbers in Petaluma Marsh. The number of Clapper Rails detected in the White Slough area of Vallejo continues to show a steady decline. No Clapper Rails were detected in the Pt. Pinole marshes. About 20 individuals were detected along Novato Creek. There was a sharp decline in detections in the marshes north of Gallinas Creek. A few birds were detected at Sonoma Creek mouth, and the number of detections along Tolay Creek and Lower Tubbs Island showed an increase over 2005. In South San Francisco Bay, Clapper Rail detections increased overall compared to 2005 surveys. For example, Cogswell Marsh in Hayward had a mean of 69 Clapper Rails detected in 2006, and a mean of 38 in 2005. The Faber tract in East Palo Alto had a mean of 76 Clapper Rails detected in 2006, compared to a mean of 45 in 2005. At Palo Alto Baylands, a mean of 29 birds were detected in 2006 and a mean of 14 birds in 2005. A more thorough discussion of PRBO’s Clapper Rail surveys from 2005-06 will be available under separate cover.

Song Sparrows at SF Bay NERR sites We chose to investigate the demographic trends at the two SF Bay NERR sites (China Camp and Rush Ranch) because they are representative of the saltwater and brackish tidal marsh systems that are present in the Estuary. There are three endemic subspecies of Song Sparrows (San Pablo at China Camp and Suisun at Rush Ranch) that are abundant in these marshes, making them ideal candidates for indicators of marsh health. Both spot mapping and point count methodologies recorded a significantly higher measured density of Song Sparrows at China Camp than at Rush Ranch (Fig. 14. The annual fluctuations in Song Sparrow density indices at a site were not correlated with each other. As discussed earlier, the apparent density index is an underestimate of true

PRBO Tidal Marsh Annual Report 2006 15 density since detection probabilities are considerably less than 100% for many species. Spot mapping density may be a slight overestimate of true density, as most but not all males are paired with a female. However, unpaired birds that are not visibly holding territory are difficult to quantify, possibly leading to a slight underestimate of true density. The avian diversity at Rush Ranch is much higher than at China Camp, where Song Sparrows face almost no competition for nest sites. Rush Ranch supports relatively large populations of Common Yellowthroat, Marsh Wren, and Red-winged Blackbird. It is possible that the competition for resources and territory at Rush Ranch has an impact on the population size of Song Sparrows. No relationship between population density in one year and nest survival in the previous year was found. All else being equal, we would expect that higher nest survival in one year would result in greater adult population in the following year. That this pattern was not borne out, at either site, could be due to one or more of the following: 1) higher nest survival in one year may not have been correlated with higher production of fledged young per pair per breeding season (cf. Chase et al. 2005 for Palomarin Song Sparrows), 2) over-winter mortality of juvenile Song Sparrows may have been greater following years with higher nest survival (perhaps due to competition), or 3) greater number of fledglings may have been produced following years with higher nest survival, but juveniles produced may not have been able to secure a breeding territory at the study site and thus they may have emigrated. The year-specific variation in total nest survival (from egg laying to nestling fledging) at the two sites showed a notable correspondence (Fig. 15), with the sites tracking quite closely from 1996-2002. The annual total nest survival at Rush Ranch did show a significant increase from 1997 to 2006 (Fig. 13). Some control of feral pigs at Rush Ranch took place in 2005, which could account for some of the increase in nest survival that year. Survival during the egg (laying and incubation) stages has shown a positive trend at Rush Ranch (Fig. 7). The concordance in temporal patterns of nest survival across the 2 sites, located 45 km apart, suggests the importance of regional influences on nest survival in the long- term, rather than local factors. One such factor that has been identified is El Nino Southern Oscillation (ENSO events), which has been show to be important for Song Sparrows in British Columbia (Wilson & Arcese 2003) and in the Cosumnes River watershed (Howell et al. 2006). On the Cosumnes River, nest survival was lower during El Niño years and higher in La Niña years.

PRBO Tidal Marsh Annual Report 2006 16 There was no correlation between Song Sparrow density and clutch size (in the same year or in the previous year) at either site. The San Pablo Song Sparrows at China Camp had smaller average clutch sizes than Rush Ranch Suisun Song Sparrows. China Camp’s saltier environment is correlated with smaller clutch sizes (Greenberg et al., in press ). Looking at the average date of each pair’s first known breeding attempt, restricted to nests found before May 1, we found that China Camp Song Sparrows nested significantly (P<.03) earlier (March 27) than Rush Ranch Song Sparrows (April 8) (Table 7). Earlier studies comparing salt marsh sparrows with interior populations showed a similar nest initiation pattern (Greenberg et al., in press ). More study is needed into the reasons for the differences in the two populations of Song Sparrows at China Camp and Rush Ranch with respect to both population density and nest success. Further research into the nest predators at the two sites is warranted, as Rush Ranch nest survival during the egg stages has been increasing over the last 10 years, while remaining steady at China Camp. Since predation is the most common cause of failure (and the more common outcome than nest success), this provides further impetus to investigate predators.

PRBO Tidal Marsh Annual Report 2006 17 GOALS FOR 2007 PRBO is committed to reporting and presenting our data to the public and community annually through peer reviewed literature, progress reports, and this annual report on tidal marsh research. These annual reports will continue to provide an assessment of current conditions, as well as long-terms trends in the population biology of the tidal marsh bird community in the San Francisco Bay estuary. We believe that the collection of long-term data at a variety of locations and of contrasting site types (e.g., ancient vs. restored) is an important strategy towards tracking changes in the health of the San Francisco Estuary. Therefore, we will continue to monitor and collect reproductive data at one of our long-term nest-monitoring study sites, China Camp, as well as one long-term restoration monitoring site, Carl’s Marsh. We will be adding a nest-monitoring study site in Petaluma Marsh, near PRBO’s new headquarters building. In addition, we will continue to monitor marsh bird abundance and diversity at select ancient and restored sites. PRBO will also continue to conduct point count and area surveys at a handful of our long-term sites throughout the San Francisco Estuary. Efforts in 2007 will focus on comparing bird populations and the species assemblage in restored and mature marshes in South San Francisco Bay to complement studies that we have conducted in the North Bay, Suisun, and the Western Delta (through the BREACH 2 Project and the Integrated Regional Wetland Monitoring [IRWM] Project). In 2005 field work was completed for the IRWM Project. Preliminary results of the 2003-2005 field seasons were presented at the State of the Estuary Conference. In conjunction with Diana Stralberg (PRBO), co-PI of the Landscape Ecology Team of IRWM, analyses of nest survival in relation to fine scale variation in vegetation and channel morphology will be completed and presented at scientific meetings. In addition, bird data will be integrated with information on benthic invertebrates and fish, also collected as part of the IRWM project. In 2006 PRBO completed the initial two year project to assess Clapper Rail populations throughout the San Francisco Bay Estuary. PRBO, in conjunction with Avocet Research Associates and other groups, will have surveyed about 90 sites in 2005 and 2006. In addition, 18-20 of these will be sampled in both years. The product will be the first San Francisco Bay Estuary-wide assessment of Clapper Rail populations since 1992-93. In 2007, PRBO is continuing to survey for Clapper Rails. Since 1996, PRBO has maintained a banding and resighting program within the long-term monitoring sites. In 2007, we will again couple this effort with intensive re-

PRBO Tidal Marsh Annual Report 2006 18 sighting of marsh areas outside of those regularly surveyed. We hope that, eventually, these efforts will enable us to establish a benchmark estimate for population recruitment that can be further investigated in future studies, and additionally, will allow us to look at juvenile dispersal within marshes, drawing on our recapture and re-sighting data since 1998.

LIST OF PRBO PRODUCTS RELATED TO TIDAL MARSH WORK IN 2006 In 2006, PRBO produced a number of papers and presentations that have examined much of what is discussed in this annual report, but at greater detail. Below is a list of peer-reviewed articles, internal PRBO reports and talks/posters that have abstracts available. Please feel free to contact PRBO ([email protected] ) to receive a reprint of any of these papers.

PRBO Reports Liu, L., M. Herzog, N. Nur, P. Abbaspour, A. Robinson, and N. Warnock. 2006. San Francisco Bay Tidal Marsh Project Annual Report 2005: Distribution, abundance, and reproductive success of tidal marsh birds. PRBO Conservation Science, Stinson Beach, CA. Stralberg, D., M. Herzog, N. Warnock, N. Nur, and S. Valdez. December 2006. Habitat- based modeling of wetland bird communities: an evaluation of potential restoration alternatives for South San Francisco Bay : Draft final report to California Coastal Conservancy.

Posters Liu, L., N. Nur, M. Herzog. 2006. Demographic comparison of Suisun and San Pablo Song Sparrows at San Francisco Bay NERR sites , CALFED Science Conference, Sacramento, CA.

Presentations Liu, L. 2006. Birds of San Francisco Bay: ecology and conservation . San Francisco Bay Flyway Festival, Vallejo, CA. Nur, N., D. Stralberg, M. Herzog, N. Warnock, L. Liu, and P. Abbaspour, 2006. Predictive Models of the Demographic Response of Tidal-Marsh Birds to Vegetation, Geomorphology and Surrounding Land-use in the San Francisco Estuary: Implications for Monitoring and Restoration . CALFED Science Conference, Sacramento, CA, October 2006.

ACKNOWLEDGMENTS Field work in 2006 was conducted by: biologists April Robinson and Jason Scott; interns Mark Dettling, Mark Jasper, and Braden Ramage; volunteers Louis DeMais, Robin Leong, Stacy Moskal, Wally Neville, and Michael Perrone. D. Stralberg and S.

PRBO Tidal Marsh Annual Report 2006 19 Valdez also provided GIS assistance throughout the year. Clapper Rail collaborators included Avocet Research Associates, HT Harvey and Associates, and Invasive Spartina Project. Lisa Schile helped with the identification of marsh plants.

Funding for work done in 2006 was provided by Bernice Barbour Foundation, Marin Community Foundation, Long Foundation, Richard Grand Foundation, Rintels Charitable Trust, California Dept. of Water Resources, San Francisco State University, California State Coastal Conservancy, Bay-Delta Science Consortium, Marin Audubon Society, U.S. Fish and Wildlife Service’s Coastal Program, and CALFED Bay/Delta Program.

Permission to work with California State Species of Special Concern, and State Threatened and Endangered Species, was given to PRBO by California Dept. Fish and Game Memorandum of Understanding.

We would like to thank the following agencies and private landowners for support and access to study sites: California State Lands Commission, California State Parks and Recreation, California Department of Fish and Game, U. S. Fish and Wildlife Service: San Pablo Bay National Wildlife Refuge and Don Edwards San Francisco Bay NWR, East Bay Regional Park District, Hayward Regional Shoreline, Pacific Gas & Electric, Community o Redwood City, City of Palo Alto, Peninsula Open Space Trust, Port Sonoma Marina, Solano County Farmlands and Open Space, Sonoma Land Trust, the City of Vallejo, Greg Tonnesen, Shell Oil Martinez, and Marin County Parks.

PRBO Tidal Marsh Annual Report 2006 20 LITERATURE CITED Adam, P. 2002. Saltmarshes in a time of change. Environmental Conservation 29:39- 61. Albertson, J. D. 1995. Ecology of the California Clapper Rail in South San Francisco Bay. M.Sc. thesis, San Francisco State University. Albertson, J. D., and G. Downard. 2004. Draft clapper rail protocol for the San Francisco Estuary large-scale population surveys. Atwater, B. F. 1979. Ancient processes at the site of Southern San Francisco Bay: movement of the crust and changes in sea level. Pages 31-45 in T. J. Conomos, editor. San Francisco Bay: the urbanized estuary. American Association for the Advancement of Science, San Francisco. Atwater, B. F., S. G. Conrad, J. N. Dowden, C. W. Hedel, R. L. MacDonald, and W. Savage. 1979. History, landforms, and vegetation of the estuary's tidal marshes. Pages 347-386 in T. J. Conomos, editor. San Francisco Bay: the urbanized estuary. American Association for the Advancement of Science, San Francisco. Buckland, S.T., D.R. Anderson, K.P. Burnham, J.L. Laake, D.L. Borchers, and L. Thomas. 2001. Introduction to Distance Sampling. Oxford University Press, Oxford. Chan, Y., and P. Arcese. 2002. Subspecific differentiation and conservation of Song Sparrows (Melospiza melodia) in the San Francisco Bay region inferred by microsatellite loci analysis. Auk 119:641-657. Chan, Y., and H. Spautz. 2006. Bird Species of Special Concern account: Alameda Song Sparrow. in Western Birds (D. Shuford and T. Gardali, Eds.). Chase, M.K. 2005. Effects of weather and population density on reproductive success and population dynamics in a song sparrow (Melospiza melodia) population: a long-term study. Auk 122:571-592. Evens, J. G., G. W. Page, L. E. Stenzel, R. W. Stallcup, and R. P. Henderson. 1989. Distribution and relative abundance of the California black rail (Laterallus jamaicensis coturniculus) in tidal marshes of the San Francisco estuary. Report to the California Department of Fish and Game from Point Reyes Bird Observatory. Evens, J. G., G. W. Page, S. A. Laymon, and R. W. Stallcup. 1991. Distribution, relative abundance and status of the California Black Rail in western North America. Condor 93:952-966.

PRBO Tidal Marsh Annual Report 2006 21 Evens, J. G., and N. Nur. 2002. California Black Rails in the San Francisco Bay region: spatial and temporal variation in distribution and abundance. Bird Populations 6:1-12. Garcia, E. J. 1995. Conservation of the California Clapper Rail: an analysis of survey methods and habitat use in Marin County, California. M.Sc. Thesis, University of California, Davis. Goals Project. 1999. Baylands ecosystem habitat goals. A report of habitat recommendations prepared by the San Francisco Bay Area Wetlands Ecosystems Goals Project. Joint publication of the U. S. Environmental Protection Agency, San Francisco, California, and San Francisco Bay Regional Water Quality Control Board, Oakland, CA. Goals Project 2000. Baylands ecosystem species and community profiles: Life histories and environmental requirements of key plants, fish, and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project. P.R. Olofson, editor. San Francisco Bay Regional Water Quality Control Board, Oakland, Calif. Greenberg, R., C. Elphick, J.C. Nordby, C. Gjerdrum, H. Spautz, G. Shriver, B. Schmeling, B. Olsen, P. Marra, N. Nur, and M. Winter. In Press . Between the devil and the deep blue sea: Nesting ecology of tidal marsh sparrows in The Vertebrates of Tidal Salt Marshes (S. Droege, R. Greenberg, J. Maldonado, and M.V. McDonald, eds.). Grinnell, J., and M. W. Wythe. 1927. Directory to the bird-life of the San Francisco Bay region. Pac. Coast Avifauna 18. Harvey, T. E. 1988. Breeding biology of the California clapper rail in South San Francisco Bay. Trans. Western Sect. Wildl. Soc. 24:98-104. Howell, C.A., Wood, J.K., Nur, N., and Lindquist, K. 2006. Impacts of flooding and global climate cycle on Song Sparrow reproductive success at Cosumnes River Preserve, California, U.S.A. Report to California Bay Delta Authority by PRBO Conservation Science, Petaluma, CA. Johnson, D.H. 1979. Estimating nest success: the Mayfield method and an alternative. Auk 96:651-661. Johnston, R. F. 1956. Population structure in salt marsh Song Sparrows. Part I- environment and the annual cycle. Condor 58:24-44. Johnston, R.F. 1956. Population structure in salt marsh Song Sparrows. Part II. density, age structure, and maintenance. Condor 58:254-272.

PRBO Tidal Marsh Annual Report 2006 22 Josselyn, M. 1983. The ecology of San Francisco Bay tidal marshes: a community profile. U.S. Fish and Wildlife Service, Division of biological Services, FWS/OBS- 83/23. Washington D.C.:102 pp. Marshall, J. T. 1948. Ecologic races of song sparrows in the San Francisco Bay region. Part I. habitat and abundance. Condor 50:193-215 Marshall, J. T., and K. G. Dedrick. 1994. Endemic Song Sparrows and yellowthroats of San Francisco Bay. Studies in Avian Biology No. 15:316-327. Martin, T.E. and G.R. Geupel. 1993. Nest-monitoring plots: Methods for locating nests and monitoring success. Journal of Field Ornithology 64:507-519. Mayfield, H.F. 1975. Suggestions for calculating nest success. Wilson Bulletin. 87:456- 466. Nichols, F. H., J. E. Cloern, S. N. Luoma, and D. H. Peterson. 1986. The modification of an estuary. Science 231:567-573. Nur, N., S. Zack, J. Evans, and T. Gardali. 1997. Tidal marsh birds of the San Francisco Bay region: status, distribution, and conservation of five Category 2 taxa. Report of the Point Reyes Bird Observatory, 4990 Shoreline Hwy., Stinson Beach, CA 94970 to USGS-Biological Resources Division. Nur, N., S.L. Jones, and G.R. Geupel. 1999. A Statistical Guide to Data Analysis of Avian Monitoring Programs. Biological Technical Publication, US Fish & Wildlife Service, BTP-R6001-1999. Ralph, C. J., G. R. Geupel, P. Pyle, T. E. Martin, and D. F. DeSante. 1993 . Field Methods for Monitoring Landbirds. USDA Forest Service Gen. Tech. Rep. PBSD-GTR-144. Albany, CA. Ralph, C.J., J.R. Sauer, and S. Droege (Eds.). 1995. Monitoring Bird Populations by Point Counts. Gen. Tech. Rep. PSW-GTR-149. Albany, CA: Pacific Southwest Research Station, USDA Forest Service. Reynolds, R. T., J. M. Scott, and R. A. Nussbaum. 1980. A variable circular-plot method for estimating bird numbers. Condor 82:309-313. SFEI. 1998. EcoAtlas beta release, version 1.5b4. San Francisco Estuary Institute, Oakland, CA. Siegel, S. W., and P. A. M. Bachand. 2002. Feasibility analysis of South Bay salt pond restoration, San Francisco Estuary, California. Wetlands and Water Resources, San Rafael, California. Spautz, H., and N. Nur. 2002. Distribution and Abundance in relation to habitat and landscape features and nest site characteristics of California Black Rail

PRBO Tidal Marsh Annual Report 2006 23 (Laterallus jamaicensis coturniculus) in the San Francisco Bay Estuary. A report to the US Fish and Wildlife Service. Available from PRBO, Stinson Beach, CA. Spautz, H., and N. Nur. 2006. Bird Species of Special Concern account: Samuel’s Song Sparrow. in Western Birds (D. Shuford and T. Gardali, Eds.). Spautz, H. and N. Nur. 2006. Bird Species of Special Concern account: Suisun Song Sparrow. in Western Birds (D. Shuford and T. Gardali, Eds.). Spautz, H., N. Nur, D. Stralberg, and Y. Chan. 2006. Multiple-scale habitat relationships of tidal marsh breeding birds in the San Francisco Bay estuary. Environmental threats to tidal marsh vertebrates of the San Francisco Estuary. Studies in Avian Biology. Verner, J. 1985. Assessment of counting techniques. Current Ornithology. 2:247-301. Wilson, S., and P. Arcese. 2003. El Niño drives timing of breeding but not population growth in the Song Sparrow (Melospiza melodia). Proceedings of the National Academy of Sciences USA 100:11139-11142. WRMP (Bird Focus Group). 2002. Wetlands Regional Monitoring Program Plan. Data Collection Protocol: Wetland Bird Monitoring. Available at: http://www.wrmp.org/documents.html

PRBO Tidal Marsh Annual Report 2006 24 Figure 1a. Map of 2006 San Francisco Bay Tidal Marsh study sites, North Bay region.

PRBO Tidal Marsh Annual Report 2006 25 Figure 1b. Map of 2006 San Francisco Bay Tidal Marsh study sites, South Bay region.

PRBO Tidal Marsh Annual Report 2006 26 Figure 2. Density indices by bay of Song Sparrow in the San Francisco Estuary: 1996-2006. Breeding Season Density Indices for Song Sparrow )

8 Central San Francisco Bay Delta San Pablo Bay South San Francisco Bay Suisun Bay

2 Breeding Season Density (birds detected per hectare per detected (birds Density Season Breeding 8 0 2 4 6 0 0 0 99 1996 1 20 200 20 20 Year

PRBO Tidal Marsh Annual Report 2006 27 Figure 3. Population trends of Alameda Song Sparrows at Palo Alto marshes.

PRBO Tidal Marsh Annual Report 2006 28 Figure 4. Breeding season density indices for Alameda Song Sparrow in South San Francisco Bay.

PRBO Tidal Marsh Annual Report 2006 29 Figure 5. Population trends of Alameda Song Sparrows at Hayward area marshes.

PRBO Tidal Marsh Annual Report 2006 30 Figure 6. Population trends of San Pablo Song Sparrows at restored marshes on the Petaluma River.

PRBO Tidal Marsh Annual Report 2006 31 Figure 7. Population trends of San Pablo Song Sparrows at Petaluma River marshes.

PRBO Tidal Marsh Annual Report 2006 32 Figure 8. Population trends of San Pablo Song Sparrows at Napa River marshes.

PRBO Tidal Marsh Annual Report 2006 33 Figure 9. Population trends of San Pablo Song Sparrows at marshes on San Pablo Bay.

PRBO Tidal Marsh Annual Report 2006 34 Figure 10. Population trends of Suisun Song Sparrows at marshes in Suisun Bay.

PRBO Tidal Marsh Annual Report 2006 35 Figure 11. Density indices by bay of Salt Marsh Common Yellowthroat in the San Francisco Estuary: 1996-2006. Breeding Season Density Indices for Common Yellowthroat )

2.5 Central San Francisco Bay Delta San Pablo Bay South San Francisco Bay Suisun Bay 2.0

1.5

1.0

0.5 Breeding Season Density (birds detected per hectare per detected (birds Density Season Breeding 6 2 9 0 9 0 1 1998 2000 2 2004 2006 Year

PRBO Tidal Marsh Annual Report 2006 36 Figure 12. Density indices by bay of Marsh Wren in the San Francisco Estuary: 1996-2006. Breeding Season Density Indices for Marsh Wren )

5 Central San Francisco Bay Delta San Pablo Bay South San Francisco Bay 4 Suisun Bay

1 Breeding Season Density (birds detected per hectare per detected (birds Density Season Breeding

1996 1998 2000 2002 2004 2006 Year

PRBO Tidal Marsh Annual Report 2006 37 Figure 13. San Francisco Bay tidal marsh Song Sparrow nesting success: estimated probability nesting attempt survives to fledging of young (Mayfield) from 1996 to 2006.

PRBO Tidal Marsh Annual Report 2006 38

Figure 14. Song Sparrow densities at China Camp and Rush Ranch, 1996-2006.

PRBO Tidal Marsh Annual Report 2006 39

Figure 15. Song Sparrow nest survival at China Camp and Rush Ranch.

PRBO Tidal Marsh Annual Report 2006 40 Table 1. Mean relative abundance over two breeding season site visits (birds/ha); based on variable circular plots and detections within 50 m. ↑ ↓ indicates trend compared with 2005. Absence of an arrow indicates no data for comparison.

# of point # of stations vegetation Species count assessment Common Red-winged Site name richness stations performed Black Rail Yellowthroat Marsh Wren Blackbird Song Sparrow birds/ha SE birds/ha SE birds/ha SE birds/ha SE birds/ha SE San Pablo Bay Black John Slough A 17 8 6 0.159 0.159 0.600 0.455 2.191 0.362 0.490 0.346 4.756 ↓ 0.678 Bull Island 11 10 8 0.127 0.000 0.321 0.205 7.095 0.975 2.701 2.892 5.101 ↑ 0.837 Carl's Marsh 14 8 7 0.000 0.000 0.000 0.000 6.575 1.157 0.952 0.448 5.311 ↓ 0.982 China Camp State Park 19 10 7 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 5.157 ↓ 0.413 Coon Island 26 10 4 0.318 0.238 0.382 0.255 3.247 0.485 0.318 0.371 4.647 ↓ 0.299 Greenpoint Restoration 18 6 4 0.107 0.152 0.318 0.150 5.993 0.687 0.000 0.000 5.550 ↑ 1.084 Mare Island A 11 10 0 0.064 0.090 0.000 0.000 0.000 0.000 0.000 0.000 2.228 ↑ 1.225 Mare Island B 12 10 0 0.191 0.201 0.000 0.000 0.127 0.180 0.000 0.000 2.558 ↓ 0.795 Napa Centennial Marsh 11 10 10 0.127 0.127 1.401 0.337 3.119 0.432 0.000 0.000 6.112 0.525 Petaluma Ancient Marsh 36 10 5 0.382 0.180 0.318 0.156 1.464 0.517 0.000 0.000 4.456 ↑ 0.459 Petaluma River Mouth 9 10 0 0.064 0.090 0.000 0.000 0.000 0.000 0.000 0.000 8.185 ↓ 0.852 Pond 2A Restoration 14 10 9 0.191 0.156 0.468 0.255 2.868 0.644 0.000 0.000 4.573 ↓ 0.573 White Slough Marsh 30 9 7 0.141 0.141 1.132 0.313 3.442 0.923 0.283 0.200 4.197 ↓ 0.638 South San Francisco Bay Cooley Landing 29 11 11 0.000 0.000 0.058 0.082 0.000 0.000 0.058 0.082 1.447 ↑ 0.537 Dumbarton West 16 13 0 0.000 0.000 0.112 0.112 0.378 0.126 0.000 0.000 3.732 ↓ 0.334 Faber-Laumeister tract, East Palo Alto 21 11 6 0.000 0.000 1.050 0.347 0.120 0.000 0.000 0.000 6.479 ↓ 1.562 Hayward Regional Shoreline 18 11 0 0.000 0.000 0.088 0.124 1.413 0.501 0.251 0.257 0.330 ↓ 0.237 Middle Bair East 10 5 5 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 5.093 ↓ 0.441 Outer Bair East 41 18 7 0.000 0.000 0.077 0.077 0.224 0.183 0.000 0.000 3.204 ↓ 0.557 Palo Alto Baylands 20 7 6 0.000 0.000 0.686 0.325 1.336 0.349 0.000 0.000 4.337 ↓ 0.754 Ravenswood Slough 20 9 8 0.000 0.000 0.000 0.000 1.177 0.500 0.000 0.000 3.277 ↓ 0.750 Whaletail Marsh 20 12 0 0.000 0.000 0.000 0.000 0.637 0.150 0.318 0.000 2.546 ↓ 0.260

PRBO Tidal Marsh Annual Report 2006 41 Table 1 continued. Mean relative abundance over two breeding season site visits (birds/ha); based on variable circular plots and detections within 50 m. ↑ ↓ indicates trend compared with 2005. Absence of an arrow indicates no data for comparison.

PRBO Tidal Marsh Annual Report 2006 42 Table 2. Song Sparrow nest survival probability: Mayfield method and proportion of nests successful. A comparison of San Pablo Bay Song Sparrow ( Melospiza melodia samuelis ) at China Camp State Park and Carl's Marsh, and Suisun Song Sparrow ( M. m. maxillaris ) at Benicia State Park for the 2006 field season. Overall nest survival rate for entire nesting period is also shown in Figure 3. ↑ ↓ indicates trend compared with 2005.

Mayfield nest Mayfield period Raw Sample Daily Mayfield success rate for nest success Proportion Site Nest Phase size nest success 1 period 2 95% confidence interval Successful 3 Rate SE Lower Upper San Pablo Bay Overall 187 0.883 0.009 0.058 ↓ 0.037 0.090 0.107 China Camp Laying / Incubation 126 0.889 0.009 0.200 ↓ 0.042 0.110 Nestling 61 0.858 0.021 0.247 ↓ 0.010 0.089 Overall 104 0.928 0.008 0. 180 ↑ 0.121 0.267 0.279 Carl's Marsh Laying / Incubation 55 0.926 0.010 0.35 1 ↑ 0.108 0.278 Nestling 49 0.931 0.015 0.519 ↑ 0.093 0.400 Suisun Bay Overall 156 0.903 0.008 0.097 ↓ 0.064 0.146 0.167 Benicia Laying / Incubation 89 0.911 0.009 0.278 ↓ 0.074 0.185 Nestling 67 0.880 0.018 0.311 ↑ 0.021 0.133 1 The Mayfield method of calculating nest survival probability or success takes into account the number of days each nest was under observation (see text) 2 The success rate for each phase or period of the nest cycle is calculated as the daily survival for the period to the nth power where n = the number of days in the period: laying = 1.996 days, incubation = 11.661, nestling = 9.145. The arrows represent change in rate from 2005. 3 The proportion successful is the number of nests that fledged at least one young divided by the total number of active nests found. Here the sample size includes only nests used for Mayfield calculations, i.e. nests observed while still active.

PRBO Tidal Marsh Annual Report 2006 43 Table 3. Nests of breeding birds located during the 2006 breeding season at tidal marsh study sites in China Camp State Park, Carl’s Marsh, and Benicia State Park.

Allen's American Anna's Black Common Marsh Northern Red-winged Song Hummingbird 1 Goldfinch 2 Hummingbird 3 Rail Yellowthroat Mallard 4 Wren Mockingbird 5 Blackbird 6 Sparrow Carl’s Marsh Total nests found 0 0 0 0 0 1 17 0 2 126 Total nests of known fate 0 0 0 0 0 1 10 0 1 104 Depredated nests 0 0 0 0 0 1 8 0 1 57 Flooded nests 0 0 0 0 0 0 0 0 0 22 Successful nests 0 0 0 0 0 0 1 0 0 29 Benicia Total nests found 2 4 2 2 2 2 8 1 10 203 Total nests of known fate 1 4 2 1 1 0 6 1 7 156 Depredated nests 0 4 1 0 0 0 2 1 1 103 Flooded nests 0 0 0 0 0 0 0 0 0 20 Successful nests 1 0 1 1 1 0 2 0 6 26 China Camp Total nests found 0 0 0 0 0 1 4 0 0 227 Total nests of known fate 0 0 0 0 0 1 0 0 0 187 Depredated nests 0 0 0 0 0 0 0 0 0 55 Flooded nests 0 0 0 0 0 0 0 0 0 101 Successful nests 0 0 0 0 0 1 0 0 0 20

1 Selasphorus sasin 2 Carduelis tristis 3 Calypte anna 4 Anas platyrhynchos 5 Mimus polyglottos 6 Agelaius phoeniceus

PRBO Tidal Marsh Annual Report 2006 44 Table 4. Song Sparrow breeding densities at nest monitoring sites, 2006. For territory mapping method, please see text.

2006 density index number of 2006 density 2006 density 2005 density point count data marsh territories (2006) area (ha) (pairs/ha) (birds/ha) (birds/ha) (birds/ha) China Camp State Park Plot A 55 7.20 7.64 15.28 13.23 n/a Plot B 34 8.09 4.20 8.40 13.81 n/a Total 89 15.28 5.82 11.65 13.50 4.69±0.38 Carl’s Marsh Plot A 62 14.03 4.42 8.84 6.84 n/a Total 62 14.03 4.42 8.84 7.58 3.82±0.72 Benicia State Park Plot A 36 7.20 5.00 10.00 9.84 n/a Plot B 35 10.63 3.29 6.58 7.20 n/a Total 71 17.83 3.98 7.96 8.53 3.53±0.46

PRBO Tidal Marsh Annual Report 2006 45 Table 5. Summary of banding results in 2006 field season for Song Sparrows ( Mature marshes in italics ).

Total

Newly Site Captured Adults Nestlings Recaptures

China Camp State Park 68 17 51 2

Carl's Marsh 85 13 72 1

Benicia State Park 94 12 82 2

Totals 247 42 205 5

PRBO Tidal Marsh Annual Report 2006 46 Table 6. Select Clapper Rail survey sites for 2005-06. An empty cell indicates that either a survey was not conducted in that year, or that data has not been entered. 2005 2006 Site Name mean mean Central San Francisco Bay Corte Madera Ecological Reserve (Muzzi) 40 40 Creekside Park 7 9 Bothin Marsh 3 Meeker Slough 3 Emeryville Crescent West 2 8 Elsie Roemer 12 15 Bay Farm Island 5 8 Arrowhead Marsh 64 Coliseum Channels 5 Airport Channel 9 9 Doolittle Pond 3 2

South San Francisco Bay Oro Loma West 7 18 Citation Marsh 10 5 East Marsh (Hayward shore) 5 2 North Marsh (Hayward shore) 13 20 Bunker Marsh 9 10 San Lorenzo Creek & Mouth 10 8 Hayward Landing 0 5 Cogswell Marsh 38 69 Whale's Tail Complex 37 Alameda Flood Control Channel 45 Palo Alto Baylands 14 29 Laumeister 67 Faber 45 76 Mowry Slough 14 16 Lower Coyote Creek 0 18 Upper Coyote Creek 0 0 Dumbarton/Audubon Marsh 19 37 Newark Slough 3 8 La Riviere Marsh 16 Calaveras Point 0 43 Triangle Marsh 0 0 Bird Island/Redwood Shores 0 15 Corkscrew Slough 14 Middle Bair E 28 30 Ravenswood Slough & mouth 3 21 Colma Creek/San Bruno Marsh 59 54 Seal Slough Mouth 5 23

PRBO Tidal Marsh Annual Report 2006 47 Table 6 (continued). Select Clapper Rail survey sites for 2005-06. 2005 2006 Site Name mean mean San Pablo Bay Whittel Marsh/Pt.Pinole North 0 0 Southern Marsh 0 Wildcat Marsh north 7 6 Wildcat Marsh south 5 Day Island 12 Novato Creek upstream 0 Novato Creek mouth 8 Hamilton north 2 5 Hamilton south 44 24 Gallinas Ck. mouth north 60 39 China Camp 16 20 Gallinas Ck. upstream 4 10 Gallinas Ck. mid-reach 15 19 Gallinas Ck. north branch 8 7 Green Point 15 12 Toy Marsh 5 Black Point 5 Bahia channel 20 5 Black John Slough mouth north 10 Petaluma Marsh 2 Carl's Marsh 6 6 Petaluma River Mouth 5 6 Tolay Creek 2 4 Tubbs Is. 4 7 Sonoma Creek mouth 3 Skaggs Is. Bridge 0 Pond 2A 2 Napa Centennial 0 White Slough N 10 8 White Slough S 3 2 Coon Island 19 Bull Island/Napa R. upstream 0

Suisun Bay Benicia SRA 2 Martinez Reg. Shoreline 0 Point Edith 0 2 Reserve Fleet/Goodyear Slough 0 0 Roe Is. 0 Suisun Slough mouth 0 0 Cordelia Slough 0 2nd Mallard Slough 0 0 Cutoff Slough 0 1 1st Mallard Slough 0 1 Hill Slough 0 0

PRBO Tidal Marsh Annual Report 2006 48 Table 7. Song Sparrow life history parameters.

Average julian Average # date of 1 st nest eggs/clutch China Camp 87.5 ± 11.9 2.89 ± 0.58 Rush Ranch 99.2 ± 9.4 3.02 ± 0.77

PRBO Tidal Marsh Annual Report 2006 49