We surveyed for Southwestern Willow Flycatchers (Empidonax traillii extimus; flycatcher) at 33 locations along multiple drainages in San Diego County, including portions of Agua Hedionda Creek, Cottonwood Creek, Escondido Creek, Los Penasquitos Creek, Otay River, San Diego River, San Dieguito River, San Luis Rey River, Sweetwater River, and Tijuana River. Resident flycatchers were only found on two drainages in San Diego County, at San Dieguito and San Luis Rey Rivers, with 99 percent occurring on the San Luis Rey River. Resident flycatchers were detected at 18 percent of survey locations (Bonsall, Cleveland National Forest, Rey River Ranch, San Dieguito, and Vista Irrigation District [VID], and VID Lake Henshaw). Resident flycatchers were documented for the first time at Lake Henshaw, the only new location surveyed that supported flycatchers. We detected a minimum of 80 resident flycatchers from 2015 to 2019, most of these were upstream and downstream from Lake Henshaw. Transient flycatchers were found at 42 percent of survey locations; 38 transient individuals were detected at Agua Hedionda Creek, Otay River, San Diego River, San Dieguito River, and the San Luis Rey River.

Over the course of this study, 11 locations historically occupied by resident flycatchers were resurveyed; only 5 were found to have resident flycatchers: (1) Bonsall, (2) Cleveland National Forest, (3) Rey River Ranch, (4) San Dieguito, and (5) Vista Irrigation District. The number of resident flycatchers declined from previous high counts at all five locations. Collectively, the number of resident flycatcher territories within the historically occupied area of the upper San Luis Rey River downstream from Lake Henshaw (Cleveland National Forest, Rey River Ranch, and Vista Irrigation District) declined 71 percent between 1999 (48) and 2019 (14); 42 percent of the decline occurred between 1999 and 2016, with an additional decline (50 percent) occurring between 2016 and 2019. In 2016, the distribution of flycatcher territories at the historically occupied area of the upper San Luis Rey River changed relative to the distribution in 1999: the proportion of territories at Cleveland National Forest and Rey River Ranch decreased to 36 percent each, while Vista Irrigation District increased to 29 percent, creating a more equal distribution of territories across the historically occupied area. By 2019, the distribution changed relative to 2016, with most of the territories spread equally between Cleveland National Forest and Rey River Ranch (43 percent each), while the proportion of territories at Vista Irrigation District declined to 14 percent.

During countywide surveys, we documented the dispersal of two natal banded flycatchers; both were females that were originally banded as nestlings at Marine Corps Base Camp Pendleton and were seen for the first time as breeding adults. One of the females dispersed to San Dieguito, a distance of 41 kilometers, and a second female dispersed to Cleveland National Forest, a distance of 55 kilometers. We also documented the within-season movement of a uniquely banded male that was seen at the beginning of the 2017 breeding season at Bonsall and was later documented at San Dieguito, a movement distance of 31 kilometers.

We completed nest monitoring activities along the upper San Luis Rey River near Lake Henshaw in Santa Ysabel, California from 2016 to 2019. Monitoring occurred at three locations: (1) Cleveland National Forest, (2) Rey River Ranch, and (3) Vista Irrigation District, collectively the upper San Luis Rey River monitoring area. The number of flycatcher territories monitored each year ranged from 14 to 27. We observed polygynous pairings (one male paired with multiple females) in all years, with the lowest rate of polygyny (number of polygynous pairs/total number of pairs) observed in 2016 (10 percent) and the highest in 2017 (70 percent). The proportion of paired males that were polygynous ranged from 5 to 54 percent between 2016 and 2019.

We monitored the nesting activity of 14–27 pairs annually during the course of the study. Most of the first nesting attempts were initiated during late May and early June. We monitored 18–41 Southwestern Willow Flycatcher nests per year from 2016 to 2019. Apparent nest success ranged from 11 to 37 percent and differed significantly by year, with higher success in 2016 and 2017 compared to 2018 and 2019. Predation was the presumed to be the primary source of nest failure, with 63–84 percent of failures annually attributed to predation. Although none of the failures were attributed to Brown-headed cowbird (Molothrus ater) parasitism, 4–27 percent of nests were parasitized annually from 2016 to 2019, with increased parasitism rates observed in 2018 and 2019 compared to 2016 and 2017. We “rescued” 11 parasitized nests between 2016 and 2019 by removing cowbird eggs; if those nests had been allowed to fail, apparent nest success would have been up to 45 percent lower annually.

Flycatcher egg clutch size ranged from 2.8±0.8 to 3.1±0.8 annually and did not vary significantly between years. The number of fledglings per pair ranged from 0.5±1.0 to 1.6±1.5 annually from 2016 to 2019. There was a significant difference in the number of young fledged per pair between years, with pairs in 2016 producing more than three times the number of fledglings compared to 2019. The percent of pairs fledging at least one young ranged from 18 to 62 percent annually but did not vary significantly by year.
Analysis of flycatcher daily nest survival rates suggested that both early and late winter precipitation influenced nest survival, with increases in early winter precipitation positively influencing nest survival and later winter precipitation negatively influencing nest survival. The second-best supported model included year, with the lowest daily nest survival occurring in 2018 and 2019.

A total of 119 flycatchers were newly banded over the course of this study; 36 adult flycatchers were banded with a unique color combination, and 83 nestlings (57 of which survived to fledging) were banded with a single band on the left or right leg. In addition, two adults that were banded before 2015 were observed in the monitoring area. Between 2015 and 2019, we accumulated 94 resights of 49 individual color-banded adult flycatchers that ranged in age from 1 to 8 years old.

Banding allowed us to examine differences in annual survivorship among flycatchers of different ages and sexes. We estimated annual survivorship of adult males to be 69±7 percent, which is higher than estimates of female survivorship (45±10 percent). Annual survivorship of first-year flycatchers ranged from 24 to 41 percent, which is roughly half the estimates calculated for adult flycatchers (52–75 percent). We found no evidence that precipitation in the previous breeding year had an effect on flycatcher survival.

We were also able to observe dispersal and movement among adults and first-year flycatchers. Average first-year dispersal distance was 3.1±2.6 kilometers, with the longest dispersal (8.5 kilometers) by a natal female dispersing from the monitoring area to Lake Henshaw. Of the first-year flycatchers, 65 percent returned to the monitoring area to establish an adult breeding territory, while the remaining 35 percent dispersed to Lake Henshaw.

Territory fidelity among adult flycatchers was high with 69±13 percent of returning adults occupying the same territory (or within 100 meters) from the previous year. There was no significant difference in territory fidelity between males and females, or across years. Nesting success in the previous year appeared to be a strong driver of territory fidelity, with adults more likely to return to the same territory following years when they successfully fledged young. The average between-year movement for returning adult flycatchers was 0.5±0.8 km. We documented the movement of two adult males from the monitoring area to Lake Henshaw. Between-year movement distances did not differ by sex or year.

Resident flycatchers in the upper San Luis Rey River monitoring area used five habitat types from 2016 to 2019: (1) willow-oak, (2) willow-ash, (3) oak-sycamore, (4) mixed willow riparian, and (5) willow-sycamore, with willow-oak the most commonly used habitat type. The most commonly recorded dominant species at flycatcher territories included coast live oak (Quercus agrifolia), red or arroyo willow (Salix laevigata or Salix lasiolepis), California sycamore (Platanus racemosa), and velvet ash (Fraxinus velutina).

In 2018, we anecdotally began to observe dead and dying oaks in the monitoring area, which we believe to be the result of goldspotted oak borer (Agrilus auroguttatus) infestation. At the conclusion of this study, we investigated the overall change in normalized difference vegetation index (NDVI) in flycatcher territories within the monitoring area. The greatest negative change in NDVI occurred in territories closest to Lake Henshaw, and many of the affected territories were no longer occupied in the later years of the study.

Flycatchers used 13 plant species for nesting at the monitoring area from 2016 to 2019; 70 percent of all nests were placed in coast live oak. None of the nest characteristics including host height, nest height, distance to the edge of the host, or distance to the edge of the vegetation clump where the nest was placed differed between years. In 2016, successful nests were placed higher than unsuccessful nests; no other within-year differences were observed.