Study Area

Surveys for the Southwestern Willow Flycatcher were completed in 2024 at six locations in San Diego County: two along the middle San Luis Rey River near Bonsall and four along the upper San Luis Rey River near Santa Ysabel (fig. 1). The middle San Luis Rey River survey area consisted of an approximately 3.8-kilometer (km) reach of the San Luis Rey River downstream from Interstate 15 (I–15; fig. 1). Two locations along the middle San Luis Rey River were surveyed for flycatchers, including Bonsall (BO) and Rincon (RIN); both were last surveyed in 2021 (Allen and Kus, 2022). The survey area included property managed by the City of Oceanside, County of San Diego Department of Parks and Recreation, and the State of California Department of Transportation. Surveys were done from County of San Diego managed property and public access right-of-way. Riparian habitat in this section included a mix of mature willow (Salix spp.) and Fremont’s cottonwood (Populus fremontii), with some mule fat (Baccharis salicifolia) present. Understory vegetation included native vegetation such as poison oak (Toxicodendron diversilobum) and stinging nettle (Urtica dioica) interspersed with non-native giant reed (Arundo donax), poison hemlock (Conium maculatum), milk thistle (Silybum marinum), and black mustard (Brassica nigra).

The upper San Luis Rey River survey area consisted of an approximately 6.9-km reach of the San Luis Rey River downstream from Lake Henshaw and the habitat surrounding Lake Henshaw (fig. 1). Four locations along the upper San Luis Rey River were surveyed for flycatchers in 2024, including three locations downstream from the Henshaw dam that have been surveyed annually since 2015 (Rey River Ranch [RRR], Cleveland National Forest [CNF], and Vista Irrigation District [VID]) and one location upstream from the Henshaw dam that has been surveyed annually since 2018 (VID Lake Henshaw [VLH]). The survey area included property managed by Vista Irrigation District, Cleveland National Forest, and private property downstream from the U.S. Forest Service property. Surface flows were regulated by a dam at Lake Henshaw operated by the Vista Irrigation District, and water was present year-round. In most years, spring and summer flows were swift, and slow-moving backwater/marshy habitats were absent. The flood plain in the downstream part of the study area was narrow and bordered by steep slopes that supported chaparral vegetation. Riparian habitat downstream included a diverse mix of mature willow (Salix spp.) woodland and coast live oak (Quercus agrifolia) woodland, dominated by coast live oak, willow, velvet ash (Fraxinus velutina), California sycamore (Platanus racemosa), and white alder (Alnus rhombifolia). Thick understory vegetation was present, including California wildrose (Rosa californica), poison oak, stinging nettle, and California blackberry (Rubus ursinus) interspersed with patches of open habitat dominated by annual grasses and bracken fern (Pteridium sp.). The habitat surrounding Lake Henshaw was dominated by Goodding’s black willow (Salix gooddingii), with some arroyo willow (Salix lasiolepis), red willow (Salix laevigata), Fremont’s cottonwood, and coast live oak where the west fork of the San Luis Rey River and several other minor creeks flowed into the lake. There were several patches of non-native tamarisk (Tamarix ramosissima) present. In 2023, above-average precipitation (114.5 centimeters [cm], 172 percent of mean from 1960 to 2022 [66.7 cm]; J. Sherwood, Vista Irrigation District, written commun., 2024) resulted in a lake level that partially inundated flycatcher habitat at Lake Henshaw. All understory vegetation was submerged, but the tops of mature willow, cottonwood, and tamarisk trees extended above the water line in some sections. Although the lake level lowered in 2024 after a year of average precipitation (67.2 cm; J. Sherwood, Vista Irrigation District, written commun., 2024), most of the flycatcher habitat continued to be submerged, and evidence of tree death was prominent. This habitat decline was especially apparent among cottonwood and tamarisk trees; most specimens of these two species were not leafed out and appeared to be dead. Black willow, a dominant tree species at Lake Henshaw, were affected at the high water line and many snapped and fell over; however, some vertical shoots emerged from the horizontal trunks, indicating that the trees were still alive. Large numbers of horizontal trees prevented surveyors from accessing the interior habitat, which may have resulted in an underestimate of the number of flycatcher territories present in some habitat patches.

Surveys

U.S. Geological Survey biologists Lisa Allen, Annabelle Bernabe, Abigail Boylan, Alexandra Houston, Scarlett Howell, W. Paul Kessler, Barbara Kus, Suellen Lynn, Jessica Medina, Shannon Mendia, Maia Nguyen, and Aaron Spiller completed flycatcher surveys following a standardized call-back survey protocol for Southwestern Willow Flycatchers (Sogge and others, 2010). The survey protocol is designed to increase the likelihood of detecting Southwestern Willow Flycatchers and aid in determining their breeding status by performing repeated surveys during the early to mid-nesting season, with three to four surveys carried out at least 5 days apart during three consecutive survey periods between May 15 and July 31. One survey was done between May 15 and May 31, one survey between June 1 and June 24, and one to two surveys between June 25 and July 31. Flycatcher surveys were completed under U.S. Fish and Wildlife Service (USFWS) 10(a)1(A) Recovery Permit ESPER0004080_0.3. Surveys were done between dawn and early afternoon, avoiding periods of inclement weather such as temperatures below freezing, rain, or strong winds that inhibit detection of flycatchers. Surveys were done by walking next to the river or lake, using caution to avoid disturbing the habitat or damaging nests. In wider stands, observers traversed the habitat, choosing routes that permitted detection of all birds throughout its extent, such as multiple straight transects, serpentine, zig-zag, or crisscross routes. In flooded habitat, surveys were done by boat, primarily by moving along the outside edge of the habitat patch and entering the interior habitat whenever possible.

Upon initiation of the survey, investigators stood quietly for 1–2 minutes, listening for spontaneously singing flycatchers and acclimating to surrounding conditions, such as road and river noise. During boat surveys, investigators stopped the boat engine and floated quietly during the listening period. If there were no birds detected during the initial listening period, investigators broadcasted the flycatcher song (“fitz-bew”) using an MP3 player or Android phone and an amplified speaker at the volume of typical bird songs for approximately 10–15 seconds and then looked and listened for approximately 1 minute for a response. Flycatchers typically responded by moving silently toward the song, singing in response to the song, or producing some other call or vocalization. Song playback was ceased immediately upon detection of a flycatcher. Additional flycatcher vocalizations were broadcasted occasionally during boat-based surveys to elicit response and confirm flycatcher presence. This procedure was repeated (including a 10-second quiet pre-broadcast listening period) every 20–30 m throughout land-based survey sites or 80–100 m throughout boat-based survey sites and more frequently if background noise was loud. If a flycatcher was detected, the investigator moved approximately 50–80 m beyond the detection before additional playback occurred to avoid double counting birds. At most flycatcher territories, flycatchers in adjacent territories could be heard vocalizing simultaneously.

For each flycatcher encountered, observers recorded age (adult or juvenile), sex (male, female, or unknown), breeding status (paired, undetermined, or transient), and whenever possible, if the bird was banded. Flycatcher age was determined by physical appearance of plumage (for example, juveniles [fledged young-of-the-year] exhibited buffy wing bars) combined with behavioral cues, such as territorial defense or singing. Sex determination was based on behavioral observations detected during each survey visit. For example, males often continuously broadcast song from conspicuous perches, whereas females only sing occasionally (Seutin, 1987; Sedgwick and Knopf, 1989). Females perform most of the nest building, incubation (U.S. Fish and Wildlife Service, 2002), and so forth. If we could not confidently assign a field sex, the flycatcher’s sex remained unknown. Breeding status was also based on the culmination of behavioral observations observed over multiple visits. Flycatchers were considered paired if (1) a second flycatcher was present and unchallenged by the territorial male during more than one survey period, (2) male/female interactions were observed, (3) an adult flycatcher was observed carrying nesting material or food, (4) an active flycatcher nest was located, or (5) adults were observed actively feeding fledglings. To avoid overcounting male flycatchers, observers also attempted to determine pairing type (monogamous or polygynous). Monogamous pairings consisted of one male paired with one female, whereas polygynous pairings consisted of one male paired with more than one female. Behaviors used to establish polygyny included males interacting with more than one female simultaneously or sequentially. For example, during a territory visit, observers often documented a male/female interaction in territory “A,” while simultaneously hearing a third flycatcher vocalizing (for example, whitting) in the adjacent territory “B,” and when the territory A interaction ended, a male/female interaction was subsequently heard in territory B, and the female in territory A simultaneously began vocalizing. Flycatcher breeding status was considered undetermined when behaviors such as spontaneous singing or other territory defense were observed during the non-migration period (approximately from June 15 to July 20; Sogge and others, 2010), but no pair behaviors were confirmed. A flycatcher was considered transient if detected only once, or if twice, was detected over two successive survey periods in which detections were less than 2 weeks apart. Adult flycatcher locations were mapped using Environmental Systems Research Institute (commonly known as “Esri”) Field Maps (Esri, 2024) on Samsung Galaxy XCover6 Pro mobile phones with Android operating systems and built in Global Positioning System to determine geographic coordinates (World Geodetic System of 1984). Habitat was characterized by visual inspection within 50 m of each flycatcher location. Dominant native and exotic plants were recorded at each location, and percent cover of native vegetation was estimated using cover categories of less than 5 percent, 5–50 percent, 51–95 percent, and greater than 95 percent. Overall habitat type was specified according to the following categories:

Nest Monitoring

From May 17 to August 23, U.S. Geological Survey biologists Scarlett Howell and Suellen Lynn monitored nesting attempts of paired flycatchers at Lake Henshaw to determine nest success, productivity, and cowbird parasitism rate (percentage of nests parasitized). Pairs were observed for evidence of nesting, and when vegetation structure allowed access, their nests were located and monitored following standard protocol (Rourke and others, 1999). To minimize the chances of leading predators or cowbirds to nest sites, nests were visited only as frequently as needed to collect sufficient data, and nests were not approached while predators or cowbirds were present (Rourke and others, 1999). Typically, there were three to four visits per nest, corresponding to about one visit per week. The first visits were timed to determine the number of eggs (cowbird and flycatcher) laid; subsequent visits were to determine if eggs had hatched and age of young, and the last visit to confirm fledging. Whenever possible, cowbird eggs were removed from parasitized nests and destroyed to promote nest success because parasitized flycatcher nests are rarely successful in fledging host young (Rothstein and others, 2003). Because flycatchers readily renest after failure, biologists frequently located and monitored more than one nest in a flycatcher territory.

Nests were assigned six possible fates based on the following parameters. Nests that fledged at least one young were considered successful (SUC). Fledging was confirmed by detection of young outside the nest. Unsuccessful nests were placed into one of five nest fate categories. Nests found empty or destroyed prior to the estimated fledge date and where the adult flycatchers were not found tending fledgling(s) were considered depredated (PRE). Previously active nests that were subsequently abandoned by adult flycatchers after one or more cowbird eggs were laid in the nest were considered to have failed because of nest parasitism (PAR). Any nests that fledged cowbird young without fledging flycatcher young were also considered to have failed because of nest PAR. Nests failing for reasons such as poor nest construction, the collapse of a host plant that caused a nest’s contents to be dumped onto the ground, or the presence of a clutch of infertile eggs were classified as “failing” because of other causes that were known (OTH). Nests that appeared intact and undisturbed but were abandoned with flycatcher eggs before the earliest hatch date or nests that were completed but failed before flycatcher eggs could be confirmed were classified as having “failed” because of unknown causes (UNK). Nests that were found empty and intact after the estimated fledge date, but no fledgling(s) could be confirmed, and no adults were detected in the territory, were also classified as “UNK.” Finally, nests that were seen during the construction phase but were never completed or that showed evidence of being dismantled before flycatcher eggs were confirmed in the nest were classified as “incomplete” (INC).

We used information collected during territory and nest visits to determine nest initiation dates (date first egg laid), apparent nest success (the proportion of completed nests that fledged young), productivity (the number of young fledged per pair), and fledge dates (the date on which at least one fledgling was detected outside the nest, estimated based on nest chronology). We used the presence of cowbird eggs in flycatcher nests that contained at least one flycatcher egg to calculate parasitism rate (percentage of nests parasitized) based on nests in which the contents were observed. If cowbird eggs were removed from a nest, apparent nest success and productivity were calculated again treating parasitized nests as failed, even if they were rescued and ultimately successful.

Banded Bird Resighting

Flycatchers were banded at three locations (RRR, CNF, and VID) as part of a separate demographic study from 2015 to 2019 (Howell and others, 2022). In that study, adults were captured at monitored territories using mist nets and song playback and were banded with a unique color-band combination. Nestlings from accessible nests were banded with a single metal dark-blue band on the left or right leg. In subsequent years, flycatchers that were resighted with a single dark-blue band (natal) were recaptured using the same methods described for adults and given a second leg band to yield a unique color-band combination. In 2024, we attempted to resight all flycatchers to identify individuals based on color-band combinations. If banded birds were detected, color-band resighting data were used to determine age and document movement from banding sites.

Abundance and Distribution

In 2024, there were a minimum of 47 territorial flycatchers and 6 transient flycatchers of unknown subspecies observed during surveys along the San Luis Rey River (figs. 2, 3; tables 1, 2). The flycatcher population at the upper San Luis Rey River decreased 36 percent from 2023 (74 territorial flycatchers; Howell and Kus, 2022b, 2024a) to 2024 (Howell and Kus, 2022b). No territorial flycatchers were detected at any of the survey locations downstream from Lake Henshaw; all territorial detections were at VLH. There were 30 territories established at VLH, containing 21 pairs (17 males and 21 females) and 9 male flycatchers of undetermined breeding status. Of the 21 pairs, 13 were monogamous pairings, and 8 were polygynous pairings consisting of 4 males each pairing with 2 different females. Of the six transient flycatchers, one was detected at BO, one was detected at CNF, one was detected at VID, and three were detected at VLH (figs. 2, 3; tables 1, 2).

The distribution of flycatcher territories along the upper San Luis Rey River has shifted since 2018 when Lake Henshaw was first surveyed. From 2018 to 2023, the combined population of flycatchers downstream from Lake Henshaw (CNF, RRR, VID) decreased annually before falling to zero territories in 2023, whereas the population upstream from Henshaw dam (VLH) increased from 2018 to 2021, declined slightly in 2022, increased in 2023, and declined in 2024 (fig. 4).

Flycatchers used four habitat types along the San Luis Rey River in 2024. Of the flycatcher locations, 86 percent (31/36) were in habitat characterized as mixed willow riparian, 8 percent (3/36) in willow riparian habitat co-dominated by cottonwood, and the remaining 6 percent equally divided between willow riparian habitat co-dominated by either oak or sycamore (table 3). The most frequently recorded dominant vegetation species at flycatcher locations was Goodding’s black willow. Exotic vegetation was not prevalent in the survey area; 97 percent (35/36) of flycatcher locations occurred in habitat with greater than 95-percent native plant cover (table 3).

Nest Monitoring

Of the 21 territories at VLH that contained paired flycatchers, 13 were monitored during the 2024 breeding season. There were 22 flycatcher nests located, and of these, 41 percent (9) successfully fledged young. Of the 13 failed nests, 62 percent were depredated (8), 23 percent failed for unknown reasons (3), and 15 percent failed because of cowbird parasitism (2). There were 22 fledglings confirmed, yielding a seasonal productivity of 1.7 young/pair (22 young/13 monitored pairs). An additional four fledglings were confirmed during territory visits to unmonitored territories at VLH (table 2).

Brown-headed Cowbirds

Cowbirds were detected at all six survey locations. During nest monitoring activities, we were able to observe the contents of 19 flycatcher nests during the egg stage. Three of these nests (16 percent) were parasitized, each containing one cowbird egg (table 4). Of the three nests, two were abandoned, and one nest was ultimately successful after the cowbird egg disappeared (MLH02F nest 2; table 4).

Banded Birds

No banded flycatchers present in previous years were observed in 2024. However, flooded conditions made entering the interior habitat difficult, and we were unable to access the exact territory locations where banded birds were last observed in 2022.