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Distribution, Abundance, and Breeding Activities of the Southwestern Willow Flycatcher at Marine Corps Base Camp Pendleton, California—2020 Annual Report

Open-File Report 2024-1005
Ecosystems Mission Area—Species Management Research
Prepared in cooperation with Assistant Chief of Staff, Environmental Security, U.S. Marine Corps Base Camp Pendleton
By:  and 
https://doi.org/10.3133/ofr20241005

Links

Acknowledgments

This work was funded by the Environmental Security Department, Resources Management Division, Marine Corps Base Camp Pendleton, California. Data either are not available or have limited availability owing to restrictions of the funding entity (U.S. Marine Corps). Contact Ryan Besser (ryan.besser@usmc.mil) for more information. The authors thank the biologists who assisted in the data collection for this project: Armand Amico, Alessandro Bartolo, Trevin Braun, Jilma Rachel Guinea, Rachelle McLaughlin, Molly Morrissey, and Michelle Treadwell (U.S. Geological Survey).

Executive Summary

Surveys for the endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) were done at Marine Corps Base Camp Pendleton (MCBCP or “Base”), California, between May 4 and July 31, 2020. All of MCBCP’s historically occupied riparian habitat (core survey area) was surveyed for flycatchers in 2020. Additionally, one-fifth of the unoccupied riparian habitat (non-core survey area) was surveyed for flycatchers. Thirteen transient Willow Flycatchers of unknown subspecies were observed on four of the seven drainages surveyed in 2020. No Willow Flycatchers were detected at Fallbrook Creek, Pilgrim Creek, or San Mateo Creek. Transients occurred in a range of habitat types, including mixed willow (Salix spp.) riparian, riparian scrub, willow-sycamore (Platanus racemosa) or willow-cottonwood (Populus fremontii) dominated riparian vegetation, and upland scrub. Exotic vegetation, primarily poison hemlock (Conium maculatum), was present in most flycatcher locations.

The resident population of Southwestern Willow Flycatchers on MCBCP declined 33 percent from three individuals in 2019 to two individuals in 2020. In 2020, the resident Southwestern Willow Flycatcher population on Base consisted of one male and one female. No single males or non-territorial floaters were observed in 2020. Overall, one territory was established consisting of one monogamous pair. Resident flycatchers were restricted to the Santa Margarita River, and distribution was limited to the Pueblitos breeding area. All resident flycatchers were located in mixed willow riparian habitat.

Nesting was initiated in late May and continued into early August. Three nesting attempts were documented, of which 33 percent (1/3) were successful. Predation and substrate failure accounted for the two nest failures. Two fledglings were produced, yielding a seasonal productivity of two young/pair. No instances of Brown-headed Cowbird (Molothrus ater) parasitism were observed. Flycatchers placed nests in two plant species: native sandbar willow (Salix exigua) and exotic poison hemlock.

One hundred percent of resident birds that were present at MCBCP in 2020 were banded in previous years; no unbanded birds were detected. Of the three uniquely banded adult flycatchers present during the 2019 breeding season, 100 percent (1/1) of males and 50 percent (1/2) of females returned to MCBCP in 2020, and both banded flycatchers returned to the same breeding area they occupied in 2019. None of the seven nestlings banded in 2019 returned to MCBCP in 2020, and none were detected off Base. Six nestlings from two nests were banded in 2020; only two survived to fledging.

From 2000 to 2020, overall adult survival of Southwestern Willow Flycatchers on MCBCP was 60 percent, while first-year survival was 20 percent.

A conspecific attraction study initiated on Base in 2018 and repeated annually through 2020 found that 100 percent of breeding flycatchers detected in 2020 settled close to automated playback units.

Introduction

The Southwestern Willow Flycatcher (Empidonax traillii extimus) is one of four subspecies of Willow Flycatcher in the United States, with a breeding range including southern California, Arizona, New Mexico, extreme southern parts of Nevada and Utah, southwestern Colorado, and western Texas (Hubbard, 1987; Unitt, 1987; Browning, 1993). Restricted to riparian habitat for breeding, the Southwestern Willow Flycatcher has declined in recent decades primarily in response to widespread habitat loss throughout its range and, possibly, Brown-headed Cowbird (Molothrus ater; hereafter “cowbird”) parasitism (Wheelock, 1912; Willett, 1912, 1933; Grinnell and Miller, 1944; Remsen, 1978; Garrett and Dunn, 1981; Unitt, 1984, 1987; Gaines, 1988; Schlorff, 1990; Whitfield and Sogge, 1999). By 1993, the species was believed to number approximately 70 pairs in California (U.S. Fish and Wildlife Service, 1993) in small, disjunct populations. The Southwestern Willow Flycatcher was listed as endangered by the State of California in 1992 and by the U.S. Fish and Wildlife Service in 1995.

Southwestern Willow Flycatchers in southern California co-occur with the Least Bell’s Vireo (Vireo bellii pusillus; hereafter “vireo”), another riparian obligate endangered by habitat loss and cowbird parasitism. However, unlike the vireo, which has increased ten-fold since the mid-1980s in response to management alleviating these threats (U.S. Fish and Wildlife Service, 2006), Willow Flycatcher numbers have remained low. As of 2016, most Southwestern Willow Flycatchers in southern California are concentrated at two known sites: (1) the Owens River valley in Inyo County (Greene and others, 2021), and (2) the Upper San Luis Rey River at Lake Henshaw in San Diego County (Howell and others, 2022). Outside of these sites, Southwestern Willow Flycatchers occur as small, isolated populations of one to a half-dozen pairs. Many of these sites in San Diego County have been occupied intermittently, including Whelan Lake, Guajome Lake, Bonsall, and Couser Canyon on the San Luis Rey River, and San Dieguito, San Diego, and Sweetwater Rivers (Unitt, 1987; Kus and others, 2003).

Male Southwestern Willow Flycatchers typically begin arriving in southern California early to mid-May, whereas females arrive approximately 1 week later. Males sing repeatedly from exposed perches while on the breeding grounds. Once the pair bond is established, the female builds an open-cup nest, usually placed in a branch fork of a willow (Salix spp.) or plant with a similar branching structure approximately 1–3 meters (m) above the ground. The typical clutch of three to four eggs is laid in May–June. Females incubate for approximately 12 days, and nestlings fledge within 12–15 days in early July. Adults usually depart from their breeding territory in mid-August/early September to their wintering grounds in central Mexico and northern South America.

The population of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton (MCBCP or “Base”) was at one time one of the largest in southern California (Unitt, 1987). Flycatcher numbers peaked in 2004 at 42 individuals, followed by declines that began in 2005. In response to declining flycatcher numbers on Base, a conspecific playback study was initiated in 2018 to explore if this method could be used to attract breeding flycatchers to recolonize MCBCP. Conspecific attraction, the tendency for individuals of a species to settle near one another, has been successfully used as a tool for recolonizing restored Sierra Nevada meadows by Willow Flycatchers of the adastus and brewsteri subspecies (Schofield and others, 2018), but it has not been applied to any populations of the extimus subspecies. This report presents preliminary evaluation of Southwestern Willow Flycatcher response to conspecific playback.

The purpose of this study, which began in 2000, was to document the status of Southwestern Willow Flycatchers at MCBCP in San Diego County, California. Specifically, our goals were to (1) determine the size and composition of the Willow Flycatcher population on Base, (2) document survivorship and movement of resident flycatchers, (3) document nesting activities, (4) characterize habitat used by flycatchers, and (5) evaluate the use of conspecific playback to attract breeding Willow Flycatchers to historically occupied habitat to facilitate recolonization. These data, combined with data from 2000 to 2019, will inform natural resource managers about the status of this endangered species at MCBCP and guide modification of land use and management practices as appropriate to ensure the species’ continued existence.

This work was funded by and performed in cooperation with the Assistant Chief of Staff (AC/S), Environmental Security, Resources Management Division, Marine Corps Base Camp Pendleton, California. All activities were authorized by 10(a)1(A) Recovery Permit #TE-829554-17.6.

Study Areas and Methods

Protocol Surveys

In 2019, a reduced monitoring plan was implemented in which annual surveys for flycatchers occurred only in “core” survey areas where breeding had historically been documented on Base. The remaining unoccupied riparian habitat was divided into five “non-core” survey groups with each group surveyed on a rotational schedule every 5 years beginning in 2020. In 2020, all MCBCP’s historically occupied riparian habitat (core survey area; fig. 1) was surveyed for Willow Flycatchers. Additionally, one-fifth of the non-historically occupied riparian habitat (non-core survey area Group A; fig. 1) was surveyed for flycatchers. Protocol surveys were done four times between May 14 and July 31 (fig. 1; appendix 1, figs. 1.1–1.5). Field work was carried out by U.S. Geological Survey (USGS) personnel Armand Amico, Alessandro Bartolo, Trevin Braun, Jilma Rachel Guinea, Scarlett Howell, Rachelle McLaughlin, Molly Morrissey, and Michelle Treadwell. The specific areas surveyed were as follows:

Core Areas

  1. 1. Santa Margarita River:

    1. a. Above Hospital, Below Hospital West: from the confluence with De Luz Creek to Basilone Road (appendix 1, fig. 1.1).

    2. b. Air Station East, Effluent Seep, Bell North, Bell South: from Basilone Road to a point approximately 8.5 kilometers (km) downstream on the east side of the Santa Margarita River (appendix 1, fig. 1.2).

    3. c. Rifle Range, Pump Road North: from the Rifle Range along Stagecoach Road to a point approximately 2.5 km downstream (appendix 1, fig. 1.2).

  2. 2. Fallbrook Creek, Lake O’Neill: at the inflow to Lake O’Neill as well as around the lake (appendix 1, fig. 1.1).

  3. 3. Las Flores Creek, Upper Las Flores North: between a point 1.6 km downstream of Basilone Road to the Zulu Impact Area boundary approximately 0.8 km upstream of Basilone Road, including the side drainage adjacent to the 43 area (appendix 1, fig. 1.3).

  4. 4. San Mateo Creek, Lower San Mateo Bottom: between the Pacific Ocean and a point approximately 3.6 km upstream, including habitat south from the creek and south from the agricultural fields (appendix 1, fig. 1.4).

  5. 5. Pilgrim Creek, South of Vandegrift: between the southern Base boundary and Vandegrift Boulevard, including two side drainages east of Pilgrim Creek (appendix 1, fig. 1.5).

1. Overview of the study area with colored polygons indicating core and non-core survey areas, and historic breeding areas.
Figure 1.

Willow Flycatcher survey and historic breeding areas at Marine Corps Base Camp Pendleton, 2020. White labels describe drainages; blue labels describe historic breeding areas (Core and Non-core A surveyed in 2020).

Rotating Non-Core Areas—Group A

  1. 1. Aliso Creek, between the Pacific Ocean and 0.5 km upstream from the electrical transmission lines (appendix 1, fig. 1.2).

  2. 2. Cockleburr Canyon, between the Pacific Ocean and a point 0.25 km east of Interstate 5 (appendix 1, fig.1.2).

  3. 3. Santa Margarita River:

    1. a. Air Station West: from the Rifle Range along Stagecoach Road to a point approximately 1.9 km upstream from the west side of the Santa Margarita River (appendix 1, fig. 1.2).

    2. b. Powerlines: from a point 1.4 km upstream of Stuart Mesa Road to a point 3.5 km upstream from Stuart Mesa Road on the west side of the Santa Margarita River (appendix 1, fig. 1.2).

    3. c. Ysidora Basin: all riparian habitat within Ysidora Basin east of Vandegrift Road (appendix 1, fig. 1.2).

Investigators followed standard survey protocol (Sogge and others, 2010), moving slowly (approximately 2 kilometers per hour [km/hr]) through the riparian habitat while searching and listening for Willow Flycatchers. Observers walked along the edge(s) of the riparian corridor on the upland or river side where habitat was narrow enough to detect a bird on the opposite edge. In wider stands, observers traversed the habitat, choosing routes that permitted detection of all birds throughout its extent. Surveys typically began at sunrise and were completed by early afternoon, avoiding conditions of high winds and extreme heat that can reduce bird activity and detectability.

Upon initiation of the survey, investigators stood quietly for 1–2 minutes (min), listening for spontaneously singing Willow Flycatchers and acclimating to surrounding conditions, such as road noise, air traffic, and other bird songs. If no flycatchers were detected during the initial listening period, investigators broadcasted the Willow Flycatcher song (fitz-bew) using an MP3 player and an amplified speaker at the volume of normal bird songs for approximately 10–15 seconds (s), then looked and listened for approximately 1 min for a response. Song playback was ceased immediately upon detection of a Willow Flycatcher. Willow Flycatchers typically responded by moving silently toward the song, singing in response to the song, or emitting some other call or vocalization. This procedure was repeated (including a 10-s quiet pre-broadcast listening period) every 20–30 m throughout the survey site, more often if background noise was loud. If a Willow Flycatcher was detected, the investigator moved approximately 80–100 m beyond the detection before implementing additional playback to avoid double counting birds. Because Empidonax flycatchers look very similar and species other than Willow Flycatcher may be present in the habitat, identification of Willow Flycatchers was not made by sight alone; the primary fitz-bew song was required for detection purposes (Sogge and others, 2010). If a potential Willow Flycatcher responded silently, approached, or responded with another vocalization (for example, whitts) but did not sing, observers carefully backed away and waited quietly. In most cases, if the bird was a Willow Flycatcher, it sang within a short time (5–10 minutes). Flycatchers that did not sing by the end of the encounter but were suspected to be breeding were re-visited within 3 days (see the “Breeding Productivity” section). Flycatchers that did not sing and were not suspected to be breeding individuals were not counted in survey results unless the flycatcher was detected again in a subsequent survey period (Sogge and others, 2010).

For each bird encountered, investigators recorded age (adult or juvenile), breeding status (paired, undetermined, or transient), and if possible, if the bird was banded. Flycatcher locations were mapped using ESRI Collector (Environmental Systems Research Institute, 2020) on Samsung Galaxy S7 and S8 and LG G5 mobile phones with Android operating systems and built in Global Positioning System to determine geographic coordinates using the World Geodetic System of 1984.

Habitat Characteristics

Habitat was characterized by visual inspection at each flycatcher location. Habitat type was recorded according to the following categories, based on dominant vegetation:

  • Mixed willow riparian: Habitat dominated by one or more willow species, including black willow (S. gooddingii), arroyo willow (S. lasiolepis), and red willow (S. laevigata), with mule fat (Baccharis salicifolia) as a frequent co-dominant.

  • Willow-cottonwood: Willow riparian habitat in which Fremont cottonwood (Populus fremontii) is a co-dominant.

  • Willow-sycamore: Willow riparian habitat in which California sycamore (Platanus racemosa) is a co-dominant.

  • Sycamore-oak: Woodlands in which California sycamore and coast live oak (Quercus agrifolia) occur as co-dominants.

  • Riparian scrub: Dry or sandy habitat dominated by sandbar willow (S. exigua) or mule fat, with few other woody species.

  • Upland scrub: Coastal sage scrub adjacent to riparian habitat.

  • Non-native: Areas vegetated exclusively with non-native species, such as giant reed (Arundo donax) and saltcedar (Tamarix ramosissima).

Percent cover of exotic vegetation at each location was estimated using cover categories of less than 5 percent, 5–50 percent, 51–95 percent, and greater than 95 percent, and the dominant exotic species was recorded.

Conspecific Playback Surveys

Historic breeding territories at MCBCP were grouped into 14 plots; 7 of the plots received conspecific vocalization broadcasts designed to attract Willow Flycatchers, and the remaining 7 plots served as a control group, receiving no vocalization broadcasts (fig. 2; Schofield and others, 2018). Of the seven conspecific playback plots, five were located on the Santa Margarita River, one at Lake O’Neill, and one at Pilgrim Creek. Six of the control plots were located on the Santa Margarita River and the remaining plot was on Pilgrim Creek. In the conspecific playback plots, an automated unit broadcasted a combination of Willow Flycatcher vocalizations (primary fitz-bew song and various calls, interspersed with silence) from 0100 to 0600, 0700 to 0900, and 2000 to 2100 Pacific Standard Time. Vocalizations were broadcast at a volume level mimicking the typical level of spontaneously singing Willow Flycatchers and could be heard by observers a maximum of 80 m away from the broadcast unit. Automated broadcast units consisted of a FOXPRO NX4 wildlife caller (FOXPRO, Lewiston, Pennsylvania) connected to a Favolcano CN101A digital programmable timer (Favolcano, Fujian, China) and an external power source (12-volt, 9 amp-hours, AH, battery). The automated broadcast units were operated from April 30 to August 21, 2020, spanning the time when northbound flycatchers would be searching for locations to settle and potentially encompassing southbound flycatchers that might settle in future breeding seasons. Control plots not receiving broadcast vocalizations were located a minimum of 200 m from the broadcast unit to eliminate influence from the broadcast.

2. Overview of the study area with colored circles for survey plots, symbols for automatic playback units, and colored symbols for historic breeding territories.
Figure 2.

Southwestern Willow Flycatcher conspecific playback survey plots, automated playback unit locations, artificial seep locations, and historic breeding territories at Marine Corps Base Camp Pendleton, 2020.

Once per week in May and June and every other week in July, surveys were done in the conspecific playback and control plots to determine if any Southwestern Willow Flycatchers had established a territory in response to the conspecific playback. Surveys in 2020 began on May 4 and concluded on July 29. Investigators surveyed within 50 m of all historic breeding territories that fell within the playback or control plot, following a slightly modified survey protocol developed to attract Willow Flycatchers to restored Sierra Nevada meadows (Schofield and others, 2018). Upon initiation of the survey, investigators stood quietly for 3–5 min, listening for spontaneously singing or calling Willow Flycatchers. If no flycatchers were detected during the initial listening period, investigators broadcasted the Willow Flycatcher song for approximately 30 s, then looked and listened for approximately 2 min for a response. If no response was detected, investigators repeated the 30-s broadcast and 2-min listening period. If no flycatchers were detected after the second round of broadcasting/listening, the investigator moved to the next historic location within the survey plot and repeated the sequence with a 1-min, pre-broadcast listening period before beginning the 30-s playback. In plots with automated broadcast units, the units were turned off before beginning the survey.

Artificial Seep Monitoring

An artificial seep was installed by MCBCP in 2019 and continued to operate in 2020. The seep was located within one of the conspecific playback plots (fig. 2) along the Santa Margarita River and was designed to increase the amount of surface water present to enhance Southwestern Willow Flycatcher breeding habitat. During the course of conspecific playback surveys, we observed the habitat immediately surrounding the seep and recorded if any Willow Flycatchers were using the area.

Breeding Productivity

Flycatchers observed during protocol surveys that were suspected to be resident birds (for example, observed in more than one survey period, pair vocalizations heard, evidence of nesting seen) were revisited within 3 days of detection date. Resident birds were observed for evidence of nesting, and nests were located and monitored following standard protocol (Rourke and others, 1999). Nests were visited as infrequently as possible to minimize disturbance and reduce the chances of leading predators or cowbirds to nest sites. Typically, there were three to four visits per nest, spaced approximately 5–10 days apart, depending on the stage of the nest when initially detected. The first visit was timed to determine the number of eggs laid, the next to confirm hatching and age of young, and the last to band nestlings. After a nest became inactive, six possible nest fates were assigned based on the parameters listed below:

  • Successful (SUC): Nest fledged at least one young. Fledging was confirmed by detection of young outside the nest.

  • Nest failed as a result of predation (PRE): This category included (1) nests seen in the process of ant or other predation; (2) nests found with evidence, such as eggshell fragments, feathers, or partially consumed nestlings in or below the nest; (3) nests with eggs or nestlings later found empty and torn from supporting branch, either partially or completely, typically indicative of mammal predation (Peterson and others, 2004); and (4) nests that had eggs or nestlings but were later found intact and empty before the expected fledge date with no evidence of eggs or nestlings on the ground, consistent with snake and bird predation, which typically leaves no sign (Peterson and others, 2004).

  • Nest failed as a result of parasitism (PAR): This category included (1) nests that were abandoned with one or more cowbird eggs in the nest, and (2) nests that were tended by the host but contained only cowbird eggs.

  • Incomplete (INC): Nests that were seen under construction but were never completed.

  • Nest failed for other reasons that are known (OTH): This category included (1) nests that failed for reasons such as host plant failure, surrounding vegetation falling and crushing a nest; (2) nests with inviable eggs that did not hatch after more than 2 weeks; and (3) human disturbance, such as mowing or weed-whacking. This category also included nests that appeared to have failed as a result of cowbird “predation,” such as (1) abandoned nests containing punctured eggs in or below the nest, (2) nests where nestlings were killed by a puncture wound to the skull, or (3) nests where nestlings were ejected from the nest and found on the ground.

  • Nest failed for unknown reasons (UNK): This designation was used when no other reason could be confirmed. In many instances, the fate UNK was assigned to nests that were likely depredated but, because we could not confirm egg-laying, did not fit the criteria of the PRE fate; these failures are explained more fully in the “Results” section.

Nest site characteristics were recorded after the abandonment or fledging of nests. Measurements included nest height, host species, host height, distance from the nest to the edge of the host species, and distance from the nest to the edge of the clump of riparian vegetation (Rourke and others, 1999). Distance to edge of clump was expressed as a negative number if the nest was not located in a clump of riparian vegetation. For example, if the nest was in a field of poison hemlock (Conium maculatum) without any other non-hemlock vegetation present, the distance to the nearest clump of riparian vegetation was measured and the value expressed as a negative number.

Survivorship, Fidelity, and Movement

To facilitate analyses of survival, fidelity, and movement, we attempted to capture and color band all resident flycatchers detected on MCBCP starting in 2000. Attempts were made each year to capture any unbanded adults within their territories using mist nets and band them with a numbered federal band on one leg and a solid or bi-colored metal band on the other. Returning adults previously banded as nestlings with a single numbered federal band were target netted to determine their identity, and their original band was supplemented with other bands to generate unique color combinations. Nestlings were banded at 7–10 days of age. Each bird received a silver aluminum federal numbered band on the left leg.

Annual Survivorship

During surveys and nest monitoring activities, we attempted to resight all Willow Flycatchers to determine if they were banded, and if so, to confirm their identity by reading their unique color band combination or by recapturing birds with single federal bands. We used resighting and recapture data to calculate annual survival, or the probability of surviving from one year to the next. Annual survival was calculated for adults and first-year flycatchers that were banded as nestlings or juveniles (first-year survival). Imperfect detectability of banded individuals is typical of mark-recapture studies and occurs for various reasons (for example, females are more cryptic and may be missed on surveys, birds are detected as banded but their full color combinations [and thus identities] are not obtained, or birds with single federal bands are not recaptured and thus their identities not determined). We analyzed annual survival of banded flycatchers from 2000 to 2020 at MCBCP in Program MARK (White and Burnham, 1999) using the RMark package (Laake, 2013) in R (R Core Team, 2020). Survival analysis in Program MARK accounts for individuals that were present but not detected or captured by modeling both survival and recapture probabilities.

Annual survival models were built by creating an encounter history matrix of all individual Southwestern Willow Flycatchers ever detected on MCBCP and if they were observed in each year from 2000 to 2020. Flycatchers were grouped by age (first-year [birds first encountered and banded as nestlings or juveniles] versus adult [birds first encountered and banded as adults and any first-year bird that survived to adulthood]) and sex (female versus male). We created two sets of models: (1) a set including only adults (birds banded as adults or first-year birds that survived beyond their first year and returned to breed), and thus of known sex (“Adults Only”), and (2) a set including adults and nestlings (“Adults and First-year Birds”). We used the “Adults Only” models to test the effects of sex, year, and winter precipitation on adult survival and used the “Adults and First-year Birds” models to evaluate the effects of age, year, and winter precipitation on flycatcher survival. This model set did not include sex because we were unable to determine sex of flycatchers banded as nestlings unless they returned and were recaptured and identified as adults. Therefore, only the nestlings that survived their first winter could be classified retroactively as “male” or “female”, which would severely bias the estimate of sex-related survival of first-year flycatchers. To evaluate the influence of age, sex, year, and winter precipitation on detection probability, we built and compared models holding survival constant. For the Adults Only models, we constrained detection probability to be influenced by sex to account for sex-related behaviors (for example, males sing frequently from exposed perches and are more easily detected than females, females may not respond to playback). For the models that included adults and first-year birds, we determined that detection probability was influenced by age, so it was included in all models of age-dependent flycatcher survival.

Winter precipitation was grouped into two periods of each bio-year (from July 1 to June 30; Office of Water Resources, 2020): early winter (from October to December of the calendar year preceding the breeding season [PrecipEW]) and late winter (January to March of the calendar year of the breeding season [PrecipLW]). We created a set of models using total winter precipitation ([PrecipTW]; the sum of EW and LW precipitation), early winter precipitation, and late winter precipitation as independent variables and an additive model that evaluated early and late winter precipitation together (PrecipEW + PrecipLW) to estimate the coefficients for one variable while controlling for the other.

We used an information-theoretic approach (Akaike’s Information Criterion for small sample size [AICc]) to evaluate support for models that tested the effects of age, sex, year, and winter precipitation on survival (Burnham and Anderson, 2002). We used logistic regression with a logit link to build and rank models by AICc and identified the top model. First, we generated a constant survival model to serve as a reference for the effects of age, sex, year, and winter precipitation on survival. We then modeled the covariates and evaluated support for the models in relation to the constant survival model. We considered models well-supported if they were within two AICc units of the top model (ΔAICc) and had an Akaike Information Criterion (AIC) weight (the weight of evidence for the given model relative to the other models in the set) greater than 0.05. We present real estimates of annual survival from the top model. If there were multiple well-supported models (ΔAICc less than or equal to 2), we averaged over them using AIC weights to obtain real estimates of annual survival for adult females, adult males, all adults, and all first-year flycatchers. We evaluated the contributions of covariates within our top models by calculating the odds ratio for each covariate (the odds that the covariate had an effect on survival, where “no effect” is equal to 1, negative effect is less than 1, and positive effect is greater than 1). We then examined the 95-percent confidence interval of the odds ratio to determine the likelihood that the effect was significant. Where the confidence interval did not span 1, we concluded that we had 95-percent confidence that the covariate had a positive or negative effect on survival.

Site Fidelity and Movement

Site fidelity, between-year, and within-year movements of flycatchers were determined by measuring the distance between the center of a flycatcher’s breeding or natal territory in 2019 and the center of the same flycatcher’s breeding territory in 2020. Flycatchers showed site fidelity if they returned to within 100 m of their 2019 territory.

Data Comparisons

All data from previous years at MCBCP used in comparisons with current data can be found in Kus, 2001; Kus and Ferree, 2003; Kus and Kenwood, 2003, 2005, 2006a, 2006b313233; Kenwood and Kus, 2007; Rourke and others, 2008; Howell and Kus, 2009a, 2009b, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017131415161718192021; and Howell and others, 2018, 202023.

Results

Population Size and Distribution

Transients

Thirteen Willow Flycatchers of unknown subspecies were observed during protocol surveys and conspecific playback surveys (appendix 2, figs. 2.1–2.4). All transients were detected between May 12 and June 18. Transients were detected on four of the seven drainages surveyed in 2020. No Willow Flycatchers were detected on Fallbrook, Pilgrim, or San Mateo Creeks.

Residents

Two Southwestern Willow Flycatchers, including one male and one female, were detected throughout the 2020 breeding season (table 1; appendix 2, fig. 2.2; appendix 3, fig. 3.1). All residents were initially detected during conspecific playback surveys. One territory was established consisting of one monogamous pair. No single males or non-territorial floaters were observed in 2020. Overall, the resident flycatcher population on Base decreased by 33 percent (3 to 2 individuals) from 2019 to 2020 (fig. 3).

Table 1.    

Distribution of territorial Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2000–20.

[Drainage/breeding area: FC, Fallbrook Creek; LF, Las Flores Creek; PC, Pilgrim Creek; SO, San Mateo Creek; SR, Santa Margarita River. Refer to figure 1 for drainage/breeding areas]
Drainage/
breeding area		 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020
FC/Lake O'Neill 2 2 2 3 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0
LF/Las Flores 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PC/Pilgrim 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
SO/San Mateo 0 0 0 0 0 0 0 2 0 1 1 1 1 0 0 0 0 0 0 0 0
SR/Above Hospital 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Below Hospital 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Air Station 6 5 2 0 2 0 0 4 4 5 6 5 6 5 3 0 1 0 20 1 0
SR/Rifle Range 0 0 0 1 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Pump Road 2 6 6 5 11 9 6 8 3 3 3 2 11 2 0 0 0 0 0 0 0
SR/Treatment Ponds 1 1 0 0 0 1 5 4 2 4 4 3 3 4 3 4 2 0 20 0 0
SR/Pueblitos 4 7 6 9 8 4 9 2 5 3 11 1 0 11 2 11 0 0 3 2 2
SR/Ysidora Ponds 5 8 4 4 6 9 5 3 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Bell 4 4 6 3 10 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Vine 4 2 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SR/Stuart Mesa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 28 35 33 32 40 29 31 26 14 16 15 12 12 13 9 5 3 0 3 3 2
Table 1.    Distribution of territorial Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2000–20.
1

One male's territory overlapped two breeding areas, included in Treatment Ponds total.

2

Two different females used additional breeding areas (Air Station and Treatment Ponds) before settling in Pueblitos, included in Pueblitos total.

3. Stacked bar graph showing the annual number of flycatchers, separated by sex.
Figure 3.

Number of resident Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2000–20.

Resident flycatchers were restricted to the Santa Margarita River (appendix 2, fig. 2.2; appendix 3, fig. 3.1). In 2020, only one historical flycatcher breeding area along the Santa Margarita River was occupied: the northern part of Pueblitos (table 1). The Pueblitos breeding area was occupied by one pair. Overall, flycatcher distribution on the Santa Margarita River remained contracted relative to previous years. Multiple breeding areas along the Santa Margarita River that historically supported resident flycatchers (Vine, Bell, Ysidora Ponds, Pump Road, southern Pueblitos, and Treatment Ponds) were devoid of flycatcher territories in 2020, and for the first time in recent years, no breeding activity was detected in the Air Station breeding area (fig. 1; table 1).

Conspecific Playback Surveys

We detected breeding Willow Flycatchers in 14 percent (1/7) of conspecific playback plots and none of the control plots (figs. 4, 5). Of breeding flycatchers (one male, one female) detected on Base in 2020, 100 percent settled within 165 m of automated playback units. Transient flycatchers were detected in 43 percent (3/7) of conspecific playback plots and 14 percent (1/7) of control plots with no playback.

4. Transient flycatchers (blue circles) occurred in two of the four playback plots (green) and none of the three control plots (red) in this part of the study area. The one resident flycatcher pair detected in 2020 occupied a playback plot.
Figure 4.

Willow Flycatcher occupancy in conspecific playback and control survey plots at Santa Margarita River (upstream) and Lake O’Neill in Marine Corps Base Camp Pendleton, 2020.

5. Transient flycatchers (blue circles) occurred in one of the three playback plots (green) and one of the four control (red) plots.
Figure 5.

Willow Flycatcher occupancy in conspecific playback and control survey plots at Santa Margarita River (downstream) and Pilgrim Creek in Marine Corps Base Camp Pendleton, 2020.

Habitat Characteristics

A total of 43 percent (6/14) of all flycatcher sightings occurred in habitat classified as mixed willow riparian, 83 percent (5/6) of which occurred along the Santa Margarita River (table 2). Twenty-one percent (3/14) of locations were in riparian scrub, dominated by mule fat or sandbar willow. The remaining detections were located either in willow habitat co-dominated by cottonwood or sycamore (21 percent; 3/14), or upland scrub (14 percent; 2/14).

Table 2.    

Habitat characteristics of Willow Flycatcher locations at Marine Corps Base Camp Pendleton, 2020.

[Status: T, transient; P, breeding pair. Exotic cover class: 1, less than 5 percent; 2, 5–50 percent; 3, 51–95 percent. Dominant exotics: CON, poison hemlock (Conium maculatum); BRA, black mustard (Brassica nigra). Abbreviation: —, no data]
Bird identification Drainage Breeding status Habitat type Exotic cover class Dominant exotics
AL01F Aliso Creek T Upland scrub 2 CON
CC01F Cockleburr Canyon T Upland scrub 2 CON
UL01F Las Flores Creek T Willow/cottonwood 1 —
UL02F Las Flores Creek T Mixed willow 1 —
AH01F Santa Margarita River T Mixed willow 2 CON
AH02F Santa Margarita River T Willow/sycamore 2 CON
AH03F Santa Margarita River T Willow/sycamore 3 CON
ETC Santa Margarita River P Mixed willow 2 CON
HN701F Santa Margarita River T Riparian scrub 3 CON
HP301F Santa Margarita River T Mixed willow 3 CON
HP502F Santa Margarita River T Mixed willow 2 CON
HP601F Santa Margarita River T Riparian scrub 3 CON
HW01F Santa Margarita River T Mixed willow 1 —
HW02F Santa Margarita River T Riparian scrub 2 BRA
Table 2.    Habitat characteristics of Willow Flycatcher locations at Marine Corps Base Camp Pendleton, 2020.

Exotic vegetation was present in most flycatcher locations in 2020. The most common exotic plant in habitat used by flycatchers was poison hemlock (table 2). Of flycatcher locations, 50 percent (7/14) were composed of 5–50 percent exotic vegetation, and 29 percent (4/14) were dominated by exotic vegetation (percent cover of exotics greater than 50 percent).

Breeding Activities

Nesting was observed for one breeding pair. Nesting was initiated in late May (table 3). The earliest confirmed egg laying date was May 22 and the latest was July 16. Nesting continued into mid-August, with the last young fledging on August 15. Three nesting attempts by Southwestern Willow Flycatchers were documented during the 2020 breeding season; 33 percent (1/3) successfully fledged at least one flycatcher young. The first nest failed because of substrate failure, the second nest was depredated, and the final nest was successful. Mean clutch size (±standard deviation [SD]), calculated from three nests known to have full clutches, was 3.7±0.6 eggs. Two fledglings were produced, yielding a seasonal productivity of 2.0 young/pair.

Table 3.    

Nesting activity of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

[ID, identification; m-dd-yy, month-day-year; #, number; OTH, nest failed for other reasons that are known; PRE, nest failed as a result of predation; SUC, nest fledged at least one young]
Breeding territory ID Lay date
(m-dd-yy)		 # Eggs # Nestlings # Fledglings Nest fate Comments
ETC 5-22-20 4 0 0 OTH Host vegetation shifted; nest found tilted on side with two eggs on ground and two eggs in nest on 6-1-20. Next visit one egg in nest, eggshells on ground. No activity in nest area.
6-11-20 4 4 0 PRE No fledglings observed and no adults defending or present in area after expected fledge date. Nest lining pulled up.
7-16-20 3 2 2 SUC One egg did not hatch and was removed when nestlings were banded.
Table 3.    Nesting activity of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

Nest Site Characteristics

Flycatchers placed nests in two species of plants. Most nests (2/3) were in the native sandbar willow, while one was in the exotic poison hemlock (table 4). Nest height averaged 1.5±0.4 m, whereas host height averaged 2.2±0.9 m.

Table 4.    

Nest site characteristics of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

[All measurements are in meters. Abbreviation: ID, identification]
Pair ID Nest ID Host species Host height Nest height Distance to the edge of
Host plant Clump
ETC 1 Poison hemlock 1.2 1.0 0.0 3.0
ETC 2 Sandbar willow 2.7 1.7 0.0 2.5
ETC 3 Sandbar willow 2.8 1.7 0.9 1.2
Table 4.    Nest site characteristics of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

Cowbird Parasitism

All nests were checked for the presence of cowbird eggs. No nest parasitism of Southwestern Willow Flycatcher nests by cowbirds was documented in 2020.

Survivorship, Site Fidelity, and Movement

Overview of Banded Population

All Southwestern Willow Flycatchers were observed closely enough to confidently determine if they were banded (table 5). One hundred percent (2/2) of residents were banded in previous years on MCBCP. The resident female was banded as an adult in 2013, making her at least 8 years old. The resident male was banded as an adult in 2019, making him at least 2 years old. The male was originally banded with a white-black split band on the left leg, but post-2019, it was discovered that this was a duplicate band combination, and the band was replaced with a dark blue-red split in 2020. Additionally, the female was showing signs of possible leg injury (holding leg up, unsteady landing); consequently, the color band was removed, leaving the federal band intact for future identification.

Table 5.    

Band status of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

[See figure 1; appendix 2, figure 2.2; appendix 3, figure 3.1 for breeding area and territory locations. Band combinations: Msi, federal numbered aluminum band; dbre, dark blue-red split metal band; yepu, yellow-purple split metal band. Abbreviations: ID, identification; #, number of; P, breeding pair]
Territory/bird ID Status Male band combination
(left leg:right leg)		 Female band combination
(left leg:right leg)		 # Nestlings banded Comments
ETC P dbre:Msi yepu:Msi 6 Female banded in 2013 as an adult at Treatment Ponds. Male banded in 2019 as an adult at Pueblitos.
Table 5.    Band status of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

Six Southwestern Willow Flycatcher nestlings from two nests were banded in 2020 (appendix 4); only two successfully fledged.

Annual Survivorship

The recapture and resighting of banded birds allowed us to determine the proportion of Southwestern Willow Flycatchers previously documented on Base that returned to hold territories in 2020. Of the three uniquely banded adult flycatchers (two females, one male) present during the 2019 breeding season, 67 percent (2/3) returned to MCBCP in 2020. None of the seven nestlings banded in 2019 that survived to fledge were resighted or recaptured at MCBCP in 2020.

Survivorship Models—Adults-Only

Of the 8 models we built, the four highest ranked models were well supported, with AICc weights greater than 0.10 and the difference in AICc between each model and the best model (ΔAICc) within 2 units (table 6). Sex appeared in the top model, and the difference between female and male survival was significant (95-percent confidence interval of the odds ratio did not include 1; table 7). Based on the top model that included sex, female survival was 67 percent±4 percent, while male survival was 53 percent±5 percent. Detection probability for males (94 percent±4 percent [range of 79–98 percent]) was higher than for females (75 percent±6 percent [range of 62–84 percent]). Winter precipitation in varying time intervals (PrecipTW, PrecipLW, and PrecipEW) appeared in the remaining three of the top four models, although in all precipitation models, the 95-percent confidence intervals of the odds ratios included 1, and the odds ratios equaled 1, indicating that this variable had little effect on survival. Year appeared only in the two lowest ranked models and was not as well supported as the constant survival model.

Table 6.    

Logistic regression models for the effect of sex (male versus female), year, and winter precipitation variables on annual survival of adult Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

[The effect of sex on detection probability was included in all models. Models are ranked from best to worst based on Akaike’s Information Criterion for small samples (AICc), change in AICc (ΔAICc), and AICc weights. AICc is based on −2×loge likelihood and the number of parameters in the model. Models: PrecipTW, total winter precipitation from October 1 of the calendar year before the breeding season to March 31 of the breeding season year; PrecipLW, late winter precipitation from January 1 to March 31 of the breeding season year; PrecipEW, early winter precipitation from October 1 to December 31 of the calendar year before the breeding season. Abbreviations: #, number; +, plus]
Model AICc ΔAICc AICc weight Deviance # Parameters
Sex 50,005.0 0.0 0.32 49,770.2 4
PrecipTW 50,005.5 0.5 0.25 49,770.7 4
PrecipLW 50,006.8 1.8 0.13 49,772.0 4
PrecipEW 50,006.9 1.9 0.13 49,772.1 4
PrecipEW+PrecipLW 50,007.5 2.5 0.09 49,770.6 5
Constant 50,007.8 2.8 0.08 49,775.0 3
Sex+Year 50,017.7 12.7 0.00 49,741.4 23
Year 50,021.7 16.7 0.00 49,747.8 22
Table 6.    Logistic regression models for the effect of sex (male versus female), year, and winter precipitation variables on annual survival of adult Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

Table 7.    

Parameter estimate (β), standard error (SE), odds ratios, and 95-percent confidence intervals (CI) for top four models explaining annual survival of adult Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

[Models are in order of best-supported to least-supported. Models: PrecipTW, total winter precipitation from October 1 of the calendar year before the breeding season to March 31 of the breeding season year; PrecipLW, late winter precipitation from January 1 to March 31 of the breeding season year; PrecipEW, early winter precipitation from October 1 to December 31 of the calendar year before the breeding season]
Model Effect β SE Odds ratio 95-percent CI
Sex Intercept1 0.7 0.2 2.0 1.41–2.93
Male −0.6 0.3 0.6 20.33–0.94
PrecipTW Intercept −0.1 0.3 0.9 0.48–1.63
Precip TW 0.0 0.0 1.0 31.00–1.04
PrecipLW Intercept 0.0 0.3 1.0 0.62–1.75
Precip LW 0.0 0.0 1.0 31.00–1.05
PrecipEW Intercept 0.1 0.2 1.1 0.68–1.75
PrecipEW 0.0 0.0 1.0 0.99–1.07
Table 7.    Parameter estimate (β), standard error (SE), odds ratios, and 95-percent confidence intervals (CI) for top four models explaining annual survival of adult Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.
1

Intercept includes females.

2

The 95-percent confidence interval of the odds ratio does not span 1. Bold indicates a significant effect.

3

Value prior to rounding up was below 1.00.

Survivorship Models—Adults Versus First-Year Flycatchers

Of the eight models built to examine the effects of age, year, and winter precipitation on annual survival of all flycatchers, the top model included age (table 8). This model had an AICc weight greater than 0.99, well above any other model in the model set. In this top model, survival differences between first-year and adult flycatchers were significant (95-percent confidence interval of the odds ratio did not include 1; table 9). Based on the top model that included age, adult survival was 60 percent±3 percent, while first-year survival was 20 percent±3 percent.

Table 8.    

Logistic regression models for the effect of age (first-year versus adult), year, and winter precipitation variables on survival of Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

[The effect of age on detection probability was included in all models. Models are ranked from best to worst based on Akaike’s Information Criterion for small samples (AICc), change in AICc (ΔAICc), and AICc weights. AICc is based on −2×loge likelihood and the number of parameters in the model. Models: PrecipEW, early winter precipitation from October 1 to December 31 of the calendar year before the breeding season; PrecipTW, total winter precipitation from October 1 of the calendar year before the breeding season to March 31 of the breeding season year; PrecipLW, late winter precipitation from January 1 to March 31 of the breeding season year. Abbreviations: #, number; +, plus]
Model AICc ΔAICc AICc weight Deviance # Parameters
Age 836.8 0.0 1.00 300.8 4
Age+Year 854.5 17.7 0.00 278.5 23
PrecipEW 883.6 46.8 0.00 347.6 4
Constant 883.6 46.8 0.00 349.6 3
PrecipTW 884.5 47.8 0.00 348.5 4
PrecipLW 885.3 48.6 0.00 349.3 4
PrecipEW+PrecipLW 885.6 48.8 0.00 347.6 5
Year 901.1 64.4 0.00 327.4 22
Table 8.    Logistic regression models for the effect of age (first-year versus adult), year, and winter precipitation variables on survival of Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

Table 9.    

Parameter estimate (β), standard error (SE), odds ratios and 95-percent confidence intervals (CI) for the top model explaining annual survival of Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.

[The intercept includes first-year flycatchers. All other effects values are the difference between that parameter and the intercept]
Model Effect β SE Odds ratio 95-percent CI
Age Intercept −1.4 0.2 0.3 0.18–0.36
Adult 1.8 0.2 5.9 13.77–9.25
Table 9.    Parameter estimate (β), standard error (SE), odds ratios and 95-percent confidence intervals (CI) for the top model explaining annual survival of Southwestern Willow Flycatchers on Marine Corps Base Camp Pendleton, 2000–20.
1

The 95-percent confidence interval of the odds ratio does not span 1. Bold indicates a significant effect.

Site Fidelity and Movement

Southwestern Willow Flycatchers at MCBCP generally settle into historically occupied breeding areas to establish territories (fig. 1). Resighting banded birds allowed us to examine between-year and within-year site fidelity. Of the two banded birds (one male, one female) seen in both 2019 and 2020, both returned to the same breeding area last occupied (table 10). The male has occupied this area since 2019 and may have also been present in 2018 as an unbanded male. The female has occupied this area since 2018, after she moved mid-season from the Treatment Ponds area where she nested from 2013 to 2015. The female was not detected in 2016 or 2017.

Table 10.    

Between-year, between-area movement of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

[See figure 1; appendix 2, figure 2.2; appendix 3, figure 3.1 for breeding area and territory locations. Band combinations: Msi, federal aluminum band; dbre, dark blue-red split metal band; yepu, yellow-purple split metal band. Sex: M, male; F, female. Abbreviations: km, kilometers; ≥, greater than or equal to]
Year last detected Breeding area
(territory last detected)		 Breeding area
(territory in 2020)		 Distance moved
(km)		 Band combination
(left leg:right leg)		 Age in 2020 Sex
2019 Pueblitos (ETC) Pueblitos (ETC) 0.0 dbre:Msi ≥2 yrs. M
2019 Pueblitos (ETC) Pueblitos (ETC) 0.0 yepu:Msi ≥8 yrs. F
Table 10.    Between-year, between-area movement of Southwestern Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020.

No instances of movement by adult Southwestern Willow Flycatchers within the 2020 breeding season were observed.

Discussion

The resident population of Southwestern Willow Flycatchers on MCBCP in 2020 (two individuals) decreased 33 percent compared to 2019. There were no unpaired males or non-territorial floaters detected on Base during the 2020 breeding season. Although it is encouraging that breeding continues on Base, the population is in a critical state; the current population has declined 95 percent from the record high of 42 individuals in 2004. An overall downward trend began in 2005, characterized by several stepwise population declines where the resident population dropped more than 24 percent from one year to the next (2004–05, 24 percent; 2007–08, 42 percent; 2013–14, 47 percent; 2014–15, 44 percent; and 2015–16, 40 percent).

The number of transients detected annually in the core and non-core group A survey area since 2002 has varied greatly, despite consistent survey scope and effort, from a low of 4 in 2019 to a high of 65 in 2016. Although factors influencing the migratory route and variable timing of transient Willow Flycatchers are unclear, it remains clear that MCBCP provides important stop-over habitat for migrating Willow Flycatchers.

Breeding flycatchers were limited to the Santa Margarita River in 2020, whereas transient flycatchers were also found on Aliso Creek, Cockleburr Canyon, and Las Flores Creek. Habitat use by breeding flycatchers also differed from transient flycatchers; breeding birds settled only in mixed willow riparian habitat, in contrast to transient flycatchers, which were also found in riparian scrub, willow-sycamore, willow-cottonwood, and upland scrub habitats. Exotic vegetation was also dominant in several transient locations, whereas resident locations had less than 50 percent exotic vegetation present.

Of the seven core breeding areas on the Santa Margarita River historically occupied by flycatchers, only the northern section of Pueblitos was occupied in 2020. This area has been occupied by breeding birds most years since 2000, although since 2009, occupancy has fluctuated between zero and one pair before hosting two pairs in 2018. In both 2019 and 2020, one pair occupied the northern part of Pueblitos. Between-year site fidelity in 2020 was 100 percent, with the 2019 ETC pair returning to the same area and territory in 2020. Between-year site fidelity has been highly variable, ranging from a low of 40 percent in 2008 to a high of 100 percent in 2018 and 2020. Apart from 2016, site fidelity has been high since 2009 (75–100 percent), suggesting that the occupied areas represent the most suitable habitat available on Base.

All other breeding areas more recently occupied by Southwestern Willow Flycatchers on MCBCP remained vacant in 2020, including the Treatment Ponds breeding area. The Treatment Ponds breeding area was last occupied by breeding birds in 2018; the area hosted one to four breeding pairs from 2006 to 2016, was unoccupied in 2017 (when no breeding birds were detected anywhere on Base), and was occupied by one female at the beginning of the 2018 breeding season before she moved to northern Pueblitos. The reasons for decline in the Treatment Ponds breeding area are unclear, but may include habitat senescence, changes in vegetation composition and structure, or hydrologic changes.

Two additional breeding areas were affected by fire in the recent past, which may have played a role in their occupancy status. The Air Station breeding area was unoccupied for the first time in 2020. The Air Station breeding area has been occupied by breeding birds on and off since 2000 and provided habitat for one to five breeding pairs in most years before the 2014 Las Pulgas fire, which burned approximately 350 hectares (ha) of riparian habitat along the Santa Margarita River. The Air Station breeding area has not had a male present since the fire; however, an unpaired breeding female attempted to nest in the area in 2016 and 2018, building a nest and laying infertile eggs both years. In 2018, the breeding female remained for approximately 1 month before moving to northern Pueblitos. In 2019, the breeding female returned to the Air Station breeding area and successfully fledged young. In 2020, no breeding flycatchers were detected in the Air Station breeding area.

The Pump Road breeding area was last occupied in 2013, before the 2014 Las Pulgas wildfire, and the habitat may still be recovering. Based on habitat recovery after previous fires in Southwestern Willow Flycatcher-occupied habitat in other locations, a minimum of 3–5 years is necessary for burned habitat to become suitable for breeding again (Paxton and others, 2007). However, burned areas may take more than a decade to regain suitability for flycatchers after a catastrophic wildfire and may not recover at all. A site along the San Pedro River in Arizona that burned in June 1996 still had not been reoccupied after 10 years (Durst and others, 2008); the lack of suitable habitat regeneration was suggested as the reason for extirpation (English and others, 2006). Habitat recovery after fire depends on many factors including hydrologic conditions during regrowth; drought, reduced groundwater, and altered river flow may impede recovery (Smith and others, 2009). Before the fire, occupancy at the Pump Road breeding area had been declining, from a high of 11 individuals in 2004 down to 2 individuals the year before the fire. Possible reasons for the decline include habitat senescence, changes in vegetation composition and structure, or hydrologic changes.

The three remaining historically occupied breeding areas along the Santa Margarita River (Vine, Bell, and Ysidora Ponds) have been unoccupied since 2004, 2007, and 2008, respectively. The decline in these areas may have been related to prolonged overgrowth of exotic vegetation and poor recovery of the riparian habitat after removal. Exotic vegetation (giant reed and saltcedar) was removed from these areas in 2008 and 2009; however, the areas remain unoccupied. It is possible that drought conditions experienced in San Diego County slowed habitat recovery after exotic vegetation removal. In the past, flycatchers have reoccupied areas on Base after exotic vegetation removal within 5–7 years. The Pump Road area had exotic vegetation removal in 1996 and supported multiple breeding pairs by 2001, the Air Station area had exotic vegetation removal in 2000 and had returned to pre-removal occupancy by 2007, and the Treatment Ponds area had exotic vegetation removal in 2001 with recolonization by 2006. Mean (±SD) annual precipitation for the first 5 years after exotic vegetation removal for the Pump Road, Air Station, and Treatment Ponds breeding areas was 41.9±23.9, 42.8±29, and 40.5±29.9 centimeters (cm), respectively (Office of Water Resources 2020). In contrast, the mean annual precipitation for the first 5 years after exotics removal in 2008 (Ysidora Pond) and 2009 (Bell and Vine) was 33.7±13.3 and 31.8±12.2 cm, respectively. Reduced precipitation in the post-removal years may have suppressed natural regrowth of riparian vegetation after removal. Although more precipitation was seen in recent years (2017, 2019, and 2020), providing some relief from the drought, the 2018 bio-year produced less than half the average rainfall, perpetuating drought conditions that do not favor vegetation growth. It will likely take multiple years with adequate rainfall for the vegetation to regrow to levels sufficient for breeding flycatchers.

Although adequate rainfall occurred during the 2020 bio-year (44.7 cm; Office of Water Resources 2020), creating lush vegetation throughout the flycatcher breeding season that may have encouraged maximum clutch sizes in early breeding season nests, this did not translate into an overall increase in productivity because of multiple nest failures. Average clutch size (3.7 eggs per nest) was less than 2019 (4.0 eggs per nest), but still above the annual mean clutch size (3.2 eggs per nest). However, overall nest success decreased to 33 percent during the 2020 breeding season, significantly lower than in 2019 (100 percent), and lower than the mean annual nest success (54±21 percent; 2001–19, excluding the partial 2011 season). Predation and substrate failure accounted for the two nest failures. Seasonal productivity decreased to 2.0 young per pair, compared to 3.5 young per breeding female in 2019 but was comparable to the annual mean (1.9 young per pair) from 2001 to 2019.

The return rate of banded adults between 2019 and 2020 (67 percent) was higher than the mean annual return rate (52±25 percent). Before 2020, the return rate had fluctuated from a low of 25 percent in 2001 to a high of 100 percent in 2018 and 2019. Both the male and female breeding in the 2019 ETC territory returned in 2020; however, the banded female present in the Air Station breeding area did not return. The use of RMark to model annual survival allowed us to account for years when flycatchers survived but were not detected and to control for differences in detectability between males and females. Our estimates of adult survival using RMark were slightly higher in most years and less variable from year to year than previously calculated estimates that did not account for imperfect detectability.

Adult flycatcher annual survival and detection probabilities both varied by sex, with females having higher survival and lower detectability than males. Survival models also included winter precipitation as a possible effect on survival, although its effect was essentially neutral (the odds ratio was 1, indicating no positive or negative effect). It may have been a nuisance variable in that it coincidentally carried some values that the models selected as useful, or it may have been confounded by an unknown factor. Overall, first-year survival was lower than adult survival. Adult survival was 60 percent±3 percent, while first-year survival was 20 percent±3 percent.

None of the fledglings banded in 2019 were detected on Base in 2020. First-year survival calculated with RMark was slightly higher than traditional calculations (19±7 percent [2001–12; adjusted for birds that returned in later years]). Because RMark factors in detection probabilities, survival estimates were higher than zero for all years after 2012, despite the reality that no MCBCP fledglings have recruited into the breeding population since 2013. From 2001 to 2012, one to six MCBCP natal birds annually recruited into their natal site and established their first breeding territory. Since 2013, no juveniles that hatched at MCBCP have returned in subsequent years to breed anywhere on Base. The reasons for this are unclear, but it is possible that first-year flycatchers since 2013 encountered habitat conditions that were unsuitable, such as habitat burned by the 2014 Las Pulgas fire. First-year flycatchers that attempted to recruit in 2014 would have encountered a large expanse of burned habitat, which may have prompted them to settle elsewhere. Two MCBCP natal birds that fledged between 2013 and 2018 have been detected in other areas of San Diego County. A single male was discovered at the Otay River in 2014, 86 km from his 2013 natal site, and a female was discovered breeding on the Upper San Luis Rey River near Lake Henshaw in 2015, 55 km from her 2013 natal site. First-year flycatchers have been documented dispersing as far as 444 km to establish their first breeding territory (Paxton and others, 2007). Because survival estimates cannot separate annual mortality from permanent emigration, especially in studies that only cover a small geographic area, it is possible that first-year survival is not low; the birds simply dispersed elsewhere. The lack of recruitment to MCBCP may be a result of low first-year survival, young birds dispersing to areas outside the Base, or both. While the small number of fledglings produced in the past 8 years may be contributing to the metapopulation in southern California as a whole, the failure of any recruits to return to MCBCP and perpetuate local breeding, for whatever reason, increases the likelihood of local extirpation in the near future.

While it remains unclear what is driving the decline of breeding flycatchers on MCBCP, several measures have been initiated in recent years to better understand the declines, including a comparative vegetation study of historical breeding territories carried out by USGS in 2018 and 2019. The study determined that less than half of the historically occupied habitat was still considered suitable for breeding flycatchers (Howell and others, 2018, 2020). Vegetation at the territory level is likely not the only factor driving the decline in occupancy of Southwestern Willow Flycatchers on MCBCP. There may be other larger scale or non-vegetation factors that affect settling patterns, such as the distance to surface water or proximity to a source population. Lack of occupancy may simply be linked to a decline in the overall Southwestern Willow Flycatcher population. If there are fewer birds, then fewer birds will be available to occupy the plot, regardless of habitat suitability. However, the information gained from vegetation comparisons could be used to guide future restoration efforts in historic breeding areas that are no longer occupied.

Additional efforts to increase occupancy on Base included using conspecific attraction to facilitate recolonization of historically occupied breeding areas. An experimental study using conspecific playback was initiated in 2018 and has continued annually through 2020 (Howell and others, 2018, 2020). Conspecific attraction, the tendency for individuals of a species to settle near one another, has been successfully used as a tool for recolonizing restored Sierra Nevada meadows by Willow Flycatchers (Schofield and others, 2018). All breeding flycatchers (one pair) detected on Base in 2020 settled within 165 m of automated playback stations; however, because the sample size was so small, it is impossible to know for certain if the birds were attracted to the playback. The breeding area where the pair settled in 2020 was recolonized in 2018 after a 1-year vacancy in 2017. None of the breeding areas with conspecific playback broadcasts that had been vacant for more than two breeding years have been recolonized since the playback study was initiated. In 2020, site fidelity rather than conspecific attraction may have affected where the pair settled, given that they nested within 52 m of their 2019 nest location.

The seep enhancement project initiated by AC/S Environmental Security to augment surface water in historically occupied habitat is an important step in attempting to mitigate declines in the flycatcher population on Base that could be related to changes in surface water. In 2020, no breeding flycatchers were observed using the area adjacent to the seep; however, the additional surface water provided by the seep is likely to have future effects on the riparian habitat, especially in drought years. Although increasing surface water may seem less important in years with sufficient rainfall, such as the 2020 bio-year, it may lessen the severity of drought effects in years with less than average rainfall. The additional water may serve to aid in vegetation recovery after drought years and assist in creating desirable habitat conditions for breeding flycatchers. A combination of habitat restoration, seep enhancement, and subsequent conspecific broadcasts in restored and still suitable areas could be the key to augmenting the Southwestern Willow Flycatcher population on MCBCP.

Conclusions

The Southwestern Willow Flycatcher population in California appears to be experiencing a statewide decline not isolated to Marine Corps Base Camp Pendleton (MCBCP or “Base”). Populations on the Kern River (Mary Whitfield, Southern Sierra Research Station, written commun., 2020) and the lower San Luis Rey River (Houston and others, 2021) have experienced steep declines or have been extirpated in recent years. Declines continued at Bonsall on the San Luis Rey River, which has been devoid of breeding flycatchers since 2017, after 10 years of occupancy from 2006 to 2016 (Allen and Kus, 2021). The Upper San Luis Rey River near Lake Henshaw also experienced declines in 2019; the number of territories fell by 22 percent between 2018 (18) and 2019 (14; Howell and others, 2022). Although breeding Willow Flycatchers are still occupying MCBCP, the population is at a critical low, declining 95 percent from the high in 2004. Habitat loss from fire, changes in habitat composition, and prolonged drought have been detrimental to the long-term persistence of this endangered species on Base. It is unlikely that the population on Base will persist unless additional suitable habitat becomes available either through restoration efforts or natural regrowth, or through occupation of suitable but currently unoccupied habitat. Until that time, any projects that alter the habitat in occupied areas would best be given careful consideration. Restoration activities, such as planting and watering of burned habitats in historically occupied areas, may increase the chances of recolonization by Southwestern Willow Flycatchers. The creation or restoration of water sources, such as holding ponds near historically occupied areas and in areas that our vegetation model predicts are suitable for occupancy, may increase the retention of Southwestern Willow Flycatchers and lead to a population increase that enhances recovery of flycatchers on Base and in the region.

Based upon our long-term observations of Southwestern Willow Flycatchers breeding under a variety of environmental conditions, the following actions have high potential for enhancing habitat suitability and availability on Base, thereby contributing to flycatcher recovery:

  1. 1. Evaluating potential changes in vegetation structure and composition that may have reduced the suitability of historically occupied areas by comparing vegetation data collected previously (in 2001 and 2002) with new data describing current habitat conditions (carried out in 2018 and 2019).

  2. 2. Implementing habitat restoration in previously burned (Pump Road) breeding areas.

  3. 3. Implementing habitat restoration in historically occupied breeding areas (Vine, Bell, and Ysidora Ponds) where exotic removal took place, but the vegetation has not yet regenerated, with priority given to areas closest to currently occupied habitat.

  4. 4. Creating or restoring water sources at the following locations (World Geodetic System of 1984) in or adjacent to historically occupied breeding areas and considering controlled release to mimic seasonal flooding.

    1. a. Settling Ponds (33.28351, −117.37373; 33.26235, −117.37162)

    2. b. Canal/Ditch (33.28254, −117.37361 (initiated in 2018); 33.28053, −117.37371; 33.27817, −117.37476; 33.25122, −117.37616)

    3. c. Pooling (33.29325, −117.36784; 33.27908, −117.37424; 33.27874, −117.37338; 33.28443, −117.37991; 33.25797, −117.37241)

With the continued decline of Southwestern Willow Flycatchers on Base, communication between the AC/S Environmental Security and other military departments may become increasingly important. Our findings and experience indicate that impacts to active territories can be minimized when maintenance activities, such as clearing vegetation, are coordinated among personnel. This coordination and cooperation among various departments could help maintain a balance among the sometimes competing land uses on Base, including military activities, recreation, habitat protection, and endangered species management.

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Appendix 1. Southwestern Willow Flycatcher Survey Areas at Marine Corps Base Camp Pendleton, California, 2020

1.1. Overview of the study area with yellow polygons indicating core survey areas.
Figure 1.1.

Willow Flycatcher survey areas at Marine Corps Base Camp Pendleton, 2020: Santa Margarita River (upstream) and Fallbrook Creek.

1.2 Overview of the study area with yellow polygons indicating core survey areas and red polygons representing non-core survey areas.
Figure 1.2.

Willow Flycatcher survey areas at Marine Corps Base Camp Pendleton, 2020: Aliso Creek, Cockleburr Canyon, and Santa Margarita River (downstream).

1.3. Overview of the study area with yellow polygons indicating core survey areas and red polygons representing non-core survey areas.
Figure 1.3.

Willow Flycatcher survey areas at Marine Corps Base Camp Pendleton, 2020: Las Flores Creek.

1.4. Overview of the study area with yellow polygons indicating core survey areas.
Figure 1.4.

Willow Flycatcher survey areas at Marine Corps Base Camp Pendleton, 2020: San Mateo Creek.

1.5. Overview of the study area with yellow polygons indicating core survey areas.
Figure 1.5.

Willow Flycatcher survey areas at Marine Corps Base Camp Pendleton, 2020: Pilgrim Creek.

Appendix 2. Locations of Willow Flycatchers at Marine Corps Base Camp Pendleton, California, 2020

2.1. Overview of the study area with core survey areas shown in yellow, one conspecific playback plot shown as a green circle, and transient flycatchers shown as yellow diamonds.
Figure 2.1.

Locations of Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020: Santa Margarita River (upstream).

2.2. Overview of the study area with core survey areas shown in yellow and non-core survey areas shown in red. Multiple conspecific playback plots (green) and control plots (red) are located along the length of this river reach. One resident flycatcher (red diamond) was detected near a playback plot. Transient flycatchers (yellow diamonds) occurred near both playback and control plots.
Figure 2.2.

Locations of Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020: Santa Margarita River (downstream).

2.3. Overview of the study area with non-core survey areas shown in red. Only two transients (yellow diamonds) were detected in these areas.
Figure 2.3.

Locations of Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020: Aliso Creek and Cockleburr Canyon.

2.4. Overview of the study area with core survey areas shown in yellow. Only two transients (yellow diamonds) were detected in the northeast section of this survey area.
Figure 2.4.

Locations of Willow Flycatchers at Marine Corps Base Camp Pendleton, 2020: Las Flores Creek.

Appendix 3. Southwestern Willow Flycatcher Territory Locations at Marine Corps Base Camp Pendleton, California, 2020

3.1. Overview of the study area showing the territory boundary, territory ID, and nest locations of a pair of breeding flycatchers.
Figure 3.1.

Southwestern Willow Flycatcher territories at Marine Corps Base Camp Pendleton, California, 2020: Pueblitos Breeding Area, Santa Margarita River.

Appendix 4. Band Combinations and Identification of Southwestern Willow Flycatcher Nestlings Banded on Marine Corps Base Camp Pendleton, California, 2020

Table 4.1.    

Band combinations and identification of Southwestern Willow Flycatcher nestlings banded on Marine Corps Base Camp Pendleton, 2020.

[ID, identification. Band combinations: left leg:right leg; Msi, federal numbered aluminum band; none, no bands present]
Territory ID Nest ID Nestling band combination Federal band number Nestling fledged?
ETC 1 Msi:none 287073580 No
ETC 1 Msi:none 287073581 No
ETC 1 Msi:none 287073582 No
ETC 1 Msi:none 287073583 No
ETC 2 Msi:none 287073584 Yes
ETC 2 Msi:none 287073585 Yes
Table 4.1.    Band combinations and identification of Southwestern Willow Flycatcher nestlings banded on Marine Corps Base Camp Pendleton, 2020.

Conversion Factors

International System of Units to U.S. customary units

Multiply By To obtain
Length
centimeter (cm) 0.3937 inch (in.)
meter (m) 3.281 foot (ft)
kilometer (km) 0.6214 mile (mi)
Area
hectare (ha) 2.471 acre
hectare (ha) 0.003861 square mile (mi2)
kilometer per hour (km/hr) 0.6214 mile per hour (mi/hr)

Datum

Coordinate information is referenced to the World Geodetic System of 1984 (WGS 84).

Abbreviations

AICC

Akaike’s Information Criterion for small sample size

MCBCP or Base

Marine Corps Base Camp Pendleton

PrecipEW

Precipitation total for early winter (October to December)

PrecipLW

Precipitation total for late winter (January to March)

For more information concerning the research in this report, contact the

Director, Western Ecological Research Center

U.S. Geological Survey

3020 State University Drive East

Sacramento, California 95819

https://www.usgs.gov/centers/werc

Publishing support provided by the Science Publishing Network,

Sacramento Publishing Service Center

Disclaimers

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested Citation

Howell, S.L., and Kus, B.E., 2024, Distribution, abundance, and breeding activities of the Southwestern Willow Flycatcher at Marine Corps Base Camp Pendleton, California—2020 annual report: U.S. Geological Survey Open-File Report 2024–1005, 35 p., https://doi.org/10.3133/ofr20241005.

ISSN: 2331-1258 (online)

Study Area

Publication type Report
Publication Subtype USGS Numbered Series
Title Distribution, Abundance, and Breeding Activities of the Southwestern Willow Flycatcher at Marine Corps Base Camp Pendleton, California—2020 Annual Report
Series title Open-File Report
Series number 2024-1005
DOI 10.3133/ofr20241005
Year Published 2024
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Ecological Research Center
Description viii, 35 p.
Country United States
State California
Other Geospatial Marine Corps Base Camp Pendleton
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
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