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Distribution, abundance, and breeding activities of Southwestern Willow Flycatchers ( Empidonax traillii extimus ) on the San Dieguito River and upper San Luis Rey River, San Diego County, California—2025 data summary

Executive Summary We surveyed for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) at the San Dieguito River and the upper San Luis Rey River in 2025. Surveys were completed at five locations: one along the San Dieguito River (San Dieguito [SD]), which was last surveyed in 2016, and four along the upper San Luis Rey River, including three downstream from Lake Henshaw that have been surveyed annually since 2015 (Rey River Ranch [RRR], Cleveland National Forest [CNF], Vista Irrigation District [VID]), and one upstream at VID Lake Henshaw (VLH) that has been surveyed annually since 2018. There was a minimum of 57 territorial flycatchers (22 male, 35 female) and 3 transient flycatchers of unknown subspecies detected at 1 location (VLH). In total, 37 territories were established, containing 35 pairs (20 males and 35 females) and 2 male flycatchers of undetermined breeding status. Of the 35 pairs, 12 were monogamous pairings, and 23 were polygynous pairings consisting of 3 males each pairing with 2 different females [6 pairs], 3 males each pairing with 3 different females [9 pairs], and 2 males each pairing with 4 different females [8 pairs]). No territorial flycatchers were detected downstream from Lake Henshaw or along the San Dieguito River. Brown-headed Cowbirds ( Molothrus ater ; cowbird) were detected at all five survey locations. No banded flycatchers were detected during surveys. Flycatchers used only one habitat type at VLH, mixed willow riparian. All flycatcher locations were in habitat characterized as mixed willow riparian dominated by Goodding’s black willow ( Salix gooddingii ), and 93 percent were in habitat with greater than 95-percent native plant cover. We monitored flycatcher nests at VLH to collect baseline data on nest success, productivity, and cowbird parasitism rate. There were 33 completed nests monitored in 26 territories; 10 were successful (30 percent). Of the 23 failed nests, 14 were depredated, 5 failed for unknown reasons, and 4 failed because of cowbird parasitism. There were 33 fledglings confirmed in monitored territories, yielding a seasonal productivity of 1.3 young/pair (33 young/26 monitored pairs). One additional fledgling was confirmed in an unmonitored territory during surveys at VLH. Based on 31 nests in which the contents were observed during the egg stage, 23 percent of nests in 2025 were parasitized. In two additional territories where nests were not located, adult flycatchers were observed feeding a cowbird fledgling.

California

Genetic analysis of Harbison’s Dun Skipper to inform population management and restoration on conserved lands in San Diego County

This report details the development and analysis of single nucleotide polymorphic loci to understand population genetic structure and diversity among local populations of the Harbison’s dun skipper, Euphyes vestris harbisoni , primarily in San Diego County, California, USA. We developed a set of 2984 SNPs. Local populations were clustered into two to three regional genetic clusters throughout the San Diego County study area: a southeast cluster, an admixed northeast cluster, and a cluster comprised of the two local populations sampled west of Interstate 15 in Lake Hodges and Elfin Forest. Increasing genetic isolation with geographic distance was significant among local populations. While effective population size estimates calculated for the 2016 cohorts in the Southeast and Lake Hodges clusters were both high (point estimates above 500), individual heterozygosity appeared to decline in both clusters over time, and notably so in the Lake Hodges cluster after 2016, suggesting that this cluster may have lost genetic diversity over time. The Southeast cluster appears to have the highest observed heterozygosity across all surveyed areas, but sample sizes in the Northeast cluster were low which may affect these estimates. Future collection efforts may benefit from additional sampling in the Northeast cluster to improve representation. The management plan for Harbison’s dun skipper encourages restoration and re-establishment efforts in unoccupied or recently extirpated sites, particularly in the central portion of the range. Re-establishment efforts could target individuals from large and annually stable local populations in the Southeast portion of the range for transplant, as these populations were also the most genetically diverse.

California

Non-native invasive beetle alters structure of a riparian bird community in a biodiversity hotspot

A serious emerging threat to southern California riparian ecosystems is the invasive shot hole borer ( Euwallacea spp.; SHB), a non-native beetle that cultivates a pathogenic fungus that kills trees of 66 reproductive host species. We examined the response of the bird community at the Tijuana River, California, to a massive SHB infestation in 2015 using data from a Monitoring Avian Productivity and Survivorship (MAPS) station operated during 7 pre-infestation (2009-15) and 7 post-infestation (2017-23) years. Species richness did not change between pre- and immediate (2017-18) post-SHB periods, but average annual adult captures declined by 27%. Among the species making up ≥ 5% of the total individuals caught in any one year (n=15), abundance declined by up to 76% in 10 species, including those most abundant at the station (Bushtit ( Psaltriparus minimus ), Song Sparrow ( Melospiza melodia ), Common Yellowthroat ( Geothlypis trichas ), Orange-crowned Warbler ( Leiothlypis celata ), and Wilson’s Warbler ( Cardellina pusilla )). Mean annual abundance increased slightly for the endangered Least Bell’s Vireo ( Vireo bellii pusillus ) and Northern Yellow Warbler ( Setophaga aestiva ) and doubled for House Finch ( Haemorhous mexicanus ) and Western Warbling-Vireo ( V. swainsoni ). We compared species trends at the Tijuana River to those at a nearby uninfested MAPS station on the Santa Margarita River to isolate the effect of SHB from other factors influencing annual abundance. The contribution of SHB to changes in abundance post-SHB was high (63-80%) for 7 declining species, moderate (22-45%) for 4 species, and weakly to moderately positive (18-40%) for 3 species. By 2019, the SHB infestation at the Tijuana River had abated and canopy cover was recovering through resprouting of mature willows ( Salix spp.) and seedling establishment. Bird abundance tracked this regrowth, with all of the species strongly affected by SHB increasing between 2019-23. The rapid recovery of the Tijuana River habitat and the associated response by the bird community are encouraging signs that the threat of the invasive shot hole borer to regional biodiversity may not be as great as originally anticipated.

California

Southwestern Willow Flycatcher ( Empidonax traillii extimus ) surveys at the city of Carlsbad Preserve, San Diego County, California—2025 data summary

Executive Summary We surveyed for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) at five survey areas within the City of Carlsbad Preserve, Carlsbad, California, in 2025. Three flycatcher surveys were completed between May 16 and June 30, 2025. One transient flycatcher was observed at the Lake Calavera survey area in the City of Carlsbad Preserve in 2025.

California

Distribution, abundance, and habitat characteristics of Coastal Cactus Wrens (Campylorhynchus brunneicapillus) in San Diego County, California—2024 data summary

Executive Summary We surveyed for coastal Cactus Wren ( Campylorhynchus brunneicapillus ) in 507 established plots in San Diego County in 2024, encompassing four genetic clusters (Otay, Lake Jennings, Sweetwater/Encanto, and San Pasqual). Of the 507 plots, 376 have been surveyed every year starting in 2020. Two surveys were completed at each plot between March 1 and July 31, 2024. Cactus Wrens were detected in 216 plots (43 percent of plots). Cactus Wrens were detected in 34 percent of the plots that have been consistently surveyed since 2020, indicating a higher plot occupancy rate than in 2023 (26 percent) and a similar plot occupancy rate to 2022 (31 percent), 2021 (34 percent), and 2020 (35 percent). There were 175 Cactus Wren territories detected across all survey plots in 2024. We documented 111 territories in the plots that have been consistently surveyed since 2020, which is an increase from 85 territories in 2023 and from 94 territories in 2022, and similar to the number of territories documented in 2021 (113) and 2020 (109). The number of territories declined from 2023 to 2024 in the San Pasqual genetic cluster but increased in the Otay, Lake Jennings, and Sweetwater/Encanto genetic clusters. At least 86 percent of Cactus Wren territories were occupied by pairs, and 176 fledglings were observed in 2024. We observed six banded Cactus Wrens in 2024, all of which we could identify individually by color band combination. Adults of known age ranged from 5 to 8 years old. All individually identifiable adult Cactus Wrens occupied the same territory in 2024 that they occupied during 2022 or 2023. We detected no movement of banded Cactus Wrens between genetic clusters during 2024. Vegetation at Cactus Wren survey plots was dominated by coastal sage scrub shrubs, such as California sagebrush ( Artemisia californica ), California buckwheat ( Eriogonum fasciculatum ), lemonade berry ( Rhus integrifolia ), San Diego County sunflower ( Bahiopsis laciniata ), and laurel sumac ( Malosma laurina ). Cactus Wrens preferentially occupied plots dominated by California buckwheat in the Otay genetic cluster and avoided plots dominated by lemonade berry (results of this test were marginally significant). Cactus Wrens also appeared to prefer plots dominated by broom baccharis ( Baccharis sarothroides ) in the Sweetwater/Encanto cluster and plots dominated by California buckwheat in the San Pasqual genetic cluster, although these preferences were marginally statistically significant. No definitive signs of fungal pathogens were observed on cactus within and around survey plots. Blue elderberry ( Sambucus mexicana ) was detected at 43 percent of plots, and Cactus Wrens preferentially occupied more plots with elderberry than were available. Very little dead or unhealthy cactus was observed within all survey plots, and Cactus Wrens preferentially occupied plots with lower amounts of dead and unhealthy cactus than were available. Over 80 percent of plots had more than 5 percent of cactus crowded or overtopped by vines and shrubs, and Cactus Wren occupied plots in proportion to the degree of shrub and vine crowding or overtopping. Non-native annual cover was less prevalent in survey plots in 2024 than in 2023, and Cactus Wrens preferentially occupied plots with less non-native cover.

California

Survival of captive-raised light-footed Ridgway’s rails is influenced by release date and time in wild

Captive breeding and translocation programs are an increasingly common conservation tool and management strategy used for some of the rarest and most endangered species in the world. These programs come at a high cost, and many translocation programs fail to monitor animals after release. Light-footed Ridgway’s rails ( Rallus obsoletus levipes ) are federally endangered marsh birds endemic to coastal wetlands of southern California and northern Mexico. Juvenile captive-raised light-footed Ridgway’s rails have been released into marshes within their U.S. range for >20 yr, but little effort has been devoted to post-release tracking of their movement and survival. We used satellite GPS transmitters to track survival of 46 juvenile captive-released and 42 juvenile wild-caught light-footed Ridgway’s rails from 2020–2022. Our results suggest that juvenile captive-released rails had lower initial daily survival probability (0.979) compared with that of juvenile wild-caught rails (0.994). Survival probability of captive-released rails increased with time in the wild, matching that of wild birds at about 100 d post-release. Survival of captive-released birds was most influenced by the date birds were released (releases in early summer had the highest survival). Our study emphasizes the importance of post-release monitoring as part of any captive breeding and translocation program and provides important insight into management strategies that may improve captive-released rail survival in the wild.

California

Distribution, abundance, and breeding activities of Southwestern Willow Flycatchers (Empidonax traillii extimus) at select locations on the San Luis Rey River, San Diego County, California—2024 data summary

We surveyed for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) at select locations along the San Luis Rey River, including along the middle San Luis Rey River near Bonsall and the upper San Luis Rey River near Santa Ysabel, California, in 2024. Surveys were completed at six locations: two along the middle San Luis Rey River (Bonsall [BO] and Rincon), which were last surveyed in 2021, and four along the upper San Luis Rey River, including three downstream from Lake Henshaw that have been surveyed annually since 2015 (Rey River Ranch, Cleveland National Forest [CNF] , Vista Irrigation District [VID] ), and one upstream at VID Lake Henshaw (VLH) that has been surveyed annually since 2018. There were a minimum of 47 territorial flycatchers (26 male, 21 female) detected at 1 location (VLH) and 6 transient flycatchers of unknown subspecies detected at 3 locations (BO, CNF, and VLH). In total, 30 territories were established, containing 21 pairs and 9 flycatchers of undetermined breeding status. Of the 21 pairs, 13 pairs were monogamous (1 male and 1 female), and 8 pairs were polygynous (1 male paired with more than 1 female). No territorial flycatchers were detected downstream from Lake Henshaw or along the middle San Luis Rey River. Brown-headed Cowbirds ( Molothrus ater ; cowbird) were detected at all six survey locations. No banded flycatchers were detected during surveys. Flycatchers used four habitat types in the survey area: (1) mixed willow riparian, (2) willow-cottonwood, (3) willow-oak, and (4) willow-sycamore. Of the flycatcher locations, 86 percent were in habitat characterized as mixed willow riparian, and 97 percent were in habitat with greater than 95-percent native plant cover. We monitored flycatcher nests at VLH to collect baseline data on nest success, productivity, and parasitism rate. There were 22 nests monitored in 13 territories; 9 were successful. Of the 13 failed nests, 8 were depredated, 3 failed for unknown reasons, and 2 failed because of cowbird parasitism. We confirmed 26 juvenile flycatchers in 2024, which included 22 from monitored nests, and an additional 4 juveniles detected in unmonitored territories. Based on 19 nests in which the contents were observed during the egg stage, 16 percent of nests in 2024 were parasitized.

California

Science support for recovery of Southwestern Willow Flycatcher (Empidonax traillii extimus) on conserved lands in San Diego County

This document was developed based on the results of scientific research to support management and recovery of the endangered Southwestern Willow Flycatcher ( Empidonax traillii extimus ) and its habitat in San Diego County, California. A migratory species restricted to riparian habitat for breeding, the flycatcher is present in southern California from May to August. The flycatcher has declined over the last several decades primarily in response to habitat loss, and possibly Brown-headed Cowbird ( Molothrus ater ) parasitism. This document compiles and analyzes data collected by USGS scientists on population size, distribution, demography, and breeding habitat condition and uses this information to evaluate potential management options and locations relative to several variables including spatial proximity to currently occupied locations, historical occupation, and potential for restoration that would benefit the flycatcher and expand populations. Location-specific management options and habitat restoration opportunities are ranked based on the contribution of each location to promoting regional flycatcher persistence. The results of these analyses can be used by land and resource managers to develop their habitat management projects and priorities and promote flycatcher recovery.

California

Quantification of threats to bats at localized spatial scales for conservation and management

In a rapidly changing world, where species conservation needs vary by local habitat, concentrated conservation efforts at small spatial scales can be critical. Bats provide an array of value to the ecosystems they inhabit; many bat species are also of conservation concern. San Diego County, California, contains 22 of the 41 bat species that occur in the United States, 16 of which are on conservation watchlists. Thus, management of bat communities in San Diego County is a pressing need. Because bats exploit vast areas of the landscape and historical sampling strategies have shifted over time, a standardized way of prioritizing areas of the landscape for management would provide an integral asset to bat conservation. We leveraged long-term bat community survey data from sampling areas across San Diego County to prioritize areas with the most management need. We calculated two types of scores: species scores and threat scores. Species scores incorporated richness and conservation status, and threat scores included landscape level threats that bats could encounter. We found that urbanization, the presence of artificial lights, and areas sampled on unconserved land were all significantly associated with decreases in species richness. Further, using species and threat scores, each sampling area was placed into one of four conservation categories, in order from greatest to least conservation need, ranging from highest priority (high species score, high threat score) to lowest (low species score, low threat score). Additionally, we focused on sampling areas in which Townsend’s big-eared bat ( Corynorhinus townsendii ) and/or pallid bat ( Antrozous pallidus ) occurred. These two species are of exceptional conservation concern in San Diego County and across the western United States. We identified urbanization, the presence of artificial lights, and areas sampled on unconserved land as threats that were all significantly associated with the absence of Townsend’s big-eared bat, but not pallid bat. The strategy, methodology, and solutions proposed in our study should assist bat conservation and management efforts wherever bats occur, and can be extended to other species that require conservation attention.

California

Distribution, abundance, and habitat characteristics of Coastal Cactus Wrens (Campylorhynchus brunneicapillus) in San Diego County, California—2023 Data Summary

Executive Summary We surveyed for coastal Cactus Wren ( Campylorhynchus brunneicapillus ) in 507 established plots in San Diego County in 2023, encompassing 4 genetic clusters (Otay, Lake Jennings, Sweetwater/Encanto, and San Pasqual). Two surveys were completed at each plot between March 1 and July 31. Cactus Wrens were detected in 181 plots (36 percent of plots). Cactus Wrens were detected in 26 percent of plots that have been consistently surveyed since 2020, indicating lower plot occupancy than in 2022 (31 percent), 2021 (34 percent), and 2020 (35 percent). There were 158 Cactus Wren territories detected across all survey plots in 2023. In plots that have been consistently surveyed since 2020, we documented 85 territories, which is a decrease from 94 territories in 2022, 113 territories in 2021, and 109 territories in 2020. The number of territories declined from 2022 to 2023 in the Lake Jennings, Sweetwater/Encanto, and San Pasqual genetic clusters but remained virtually the same in the Otay genetic cluster. At least 80 percent of Cactus Wren territories were occupied by pairs, and 125 fledglings were observed in 2023. We observed 14 banded Cactus Wrens in 2023, 9 of which we could identify individually by color band combination. Adults of known age ranged from 4 to 7 years old. All individually identifiable adult Cactus Wrens occupied the same territory in 2023 that they occupied in 2022, and we detected no movement of banded Cactus Wrens between genetic clusters. Vegetation at Cactus Wren survey plots was dominated by coastal sage scrub shrubs, such as California sagebrush ( Artemisia californica ), California buckwheat ( Eriogonum fasciculatum ), lemonade berry ( Rhus integrifolia ), jojoba ( Simmondsia chinensis ), and San Diego viguiera ( Bahiopsis laciniata ). No definitive signs of fungal pathogens were observed on cactus within and around survey plots. Blue elderberry ( Sambucus mexicana ) was detected at 41 percent of plots, and Cactus Wrens occupied proportionally more plots with elderberry than plots without elderberry. Very little dead or unhealthy cactus was observed within all survey plots, and Cactus Wren occupancy did not differ between plots with high or low amounts of dead or unhealthy cactus. Almost 90 percent of plots had more than 5 percent of cactus crowded or overtopped by vines and shrubs, and Cactus Wren occupancy did not differ between plots with high or low amounts of cactus crowded or overtopped by vines and shrubs. Non-native annual cover was more prevalent in survey plots in 2023 than in 2022. Cactus Wrens did not select or avoid plots with more non-native cover.

California

Distribution and abundance of Southwestern Willow Flycatchers ( Empidonax traillii extimus ) on the Upper San Luis Rey River, San Diego County, California—2023 data summary

Executive Summary We surveyed for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) along the upper San Luis Rey River near Lake Henshaw in Santa Ysabel, California, in 2023. Surveys were completed at four locations: three downstream from Lake Henshaw, where surveys previously occurred from 2015 to 2022 (Rey River Ranch [RRR], Cleveland National Forest [CNF], Vista Irrigation District [VID]), and one at VID Lake Henshaw (VLH) that has been surveyed annually since 2018. There were a minimum of 74 territorial flycatchers detected at 1 location (VLH), and 12 transient flycatchers of unknown subspecies detected at 2 locations (CNF and VLH). At VLH, we detected a minimum of 31 males, 40 females, and 3 flycatchers of unknown sex. In total, 51 territories were established, containing 40 pairs and 11 flycatchers of undetermined breeding status (8 males and 3 flycatchers of unknown sex). Of the 40 pairs, 9–11 pairs were monogamous (1 male and 1 female), and 29–31 pairs were polygynous (1 male paired with more than 1 female). For the first time since annual surveys began in 2015, no territorial flycatchers were detected downstream from Lake Henshaw. Brown-headed cowbirds ( Molothrus ater ; cowbird) were detected at all four survey locations. No banded flycatchers were detected during surveys. Flycatchers used three habitat types in the survey area: (1) mixed willow riparian, (2) willow-cottonwood, and (3) oak-sycamore. Of the flycatcher locations, 86 percent were in habitat characterized as mixed willow riparian, and 95 percent were in habitat with greater than 95-percent native plant cover. Exotic vegetation was not prevalent in the survey area. There were five nests incidentally located during surveys: one failed, one was seen with eggs on the last visit, and the outcome of the remaining three nests was unknown. One of these nests was parasitized by cowbirds, and a second nest was suspected to contain a cowbird nestling. Adult flycatchers in two territories were observed feeding cowbird fledglings. No juvenile flycatchers were detected during surveys.

California

Variation in dietary ecology of two invasive American Bullfrog (Lithobates catesbeianus) populations in Southern California

Invasive American Bullfrogs (Lithobates catesbeianus) are a threat to native species in riparian ecosystems worldwide. They are indiscriminate predators consuming both vertebrate and invertebrate prey, negatively affecting biodiversity. Documenting the diet and feeding ecology of invasive L. catesbeianus can help management agencies identify affected species and facilitate eradication efforts. We present a dietary analysis of two invasive L. catesbeianus populations over multiple breeding seasons (2016–2020), elucidating ontogenetic changes in diet and dietary differences between sexes and habitats. This is the first study to analyze dietary variation from contemporary populations of invasive L. catesbeianus occupying different watersheds in Southern California, an area where their invasion presents acute conservation challenges. Our analysis of 667 gut contents shows that adult females had more prey in their guts than adult males, even though male and female body size was not significantly different. Adults were more likely than juveniles to consume vertebrate prey, and juveniles were more likely than adults to have empty stomachs. We also found that invasive Red Swamp Crayfish (Procambarus clarkii), made up a substantial portion of the diet of adult L. catesbeianus at the site where they were present. These results provide an important ecological context for designing mitigation actions that ameliorate the impacts of invasive L. catesbeianus.

California

2023-2024 Coastal sage scrub and chaparral community monitoring for western San Diego County

Western San Diego County is dominated by shrublands supporting biologically diverse native plant and animal communities. Widespread urbanization has led to regional habitat loss and fragmentation, and many species in these shrubland communities are rare, threatened, or endangered. Large-scale, multiple-species conservation planning has resulted in a regional preserve system that focuses on these shrubland communities. Several large-scale threats are leading to type conversion from shrub-dominated to non-native invasive annual grass-dominated vegetation. To understand the changes that are occurring to native shrublands, we have developed a vegetation monitoring program with several components at multiple spatial scales, focused on quantifying coastal sage scrub (CSS) and chaparral vegetation community characteristics. Several drivers of change associated with type conversion of native shrubland to non-native annual grassland have been identified by previous research including increasing fire frequency, nitrogen deposition from air pollution, and prolonged and intense drought associated with changing climate. Loss of ecological integrity indices have been proposed as useful measures of the threat of degradation and type conversion of shrublands in San Diego County. For this study, ecological integrity is defined as a system’s ability to maintain species’ relationships and functions comparable to natural habitat in the region. Previous studies have identified the percent cover of invasive non-native annual grasses as a proxy for overall ecological degradation (loss of integrity) that is consistent across native taxonomic groups. Increased cover of non-native grass is associated with lower integrity of the shrubland vegetation community as shrub-associated plant and animal species are replaced by species preferring grassy and disturbed habitats. The objectives of this CSS and chaparral vegetation community monitoring plan are to: 1) Determine the distribution, composition, structure, and integrity of CSS and chaparral vegetation communities on conserved lands in western San Diego County, 2) Identify whether these attributes of the vegetation communities are changing over time, and 3) Evaluate relationships of known drivers of change (threats) and environmental factors in association with changes in vegetation community attributes. The CSS and chaparral vegetation community monitoring program is divided into four components: 1) vegetation mapping, 2) GIS/remote sensing office analysis of landscape-scale data, 3) permanent field plots using Unmanned Aerial Systems (UAS) and field data collections, and 4) animal and target species surveys and rapid assessment protocols. The first component, which is not detailed in this vegetation monitoring plan, aims to map vegetation communities every 10-15 years based on a classification developed for western San Diego County. High resolution aerial imagery will be used to update the 2012 vegetation map and expand it across the entire study area. The second component uses remote sensing models to annually track ecological integrity of shrublands across the study area and will include a map of areas of change and areas of stability over several decades. These landscape-scale integrity classifications will be used to analyze ecological processes, threats, and abiotic factors relative to changes to shrubland ecological integrity over time and space. The third component includes field surveys of 100 permanent plots across areas historically mapped as shrublands. Surveys in the 1930s mapped vegetation types using plot data. By using this historical classification map, we included areas that have already type-converted from shrubland to non-native annual grassland. The plots were split between CSS (55 plots) and chaparral (45 plots) and stratified into four geographical eco-subregions to guarantee coverage over small patches of habitat along the heavily developed coast. Surveys will include the collection of UAS imagery at a very high resolution. Species-level identifications will be made from the imagery based on a plant list compiled of all species detected in the plot during a thorough field survey by botanists, combined with geo-referenced samples of plant species locations. In addition, herbaceous cover will be estimated in the field using nine 1-m diameter circles (one per subplot) to obtain ocular estimates of cover for each plant species within the circle frame. Soil samples will be collected and analyzed for important element compositions. These data will be analyzed to evaluate plot-level ecological integrity based on species composition and cover. Repeated monitoring will allow evaluation of changes in vegetation attributes over time with known drivers or threats and other environmental factors. In addition, analyses will focus on indicator species and various measures of biological diversity for the vegetation communities. Finally, animal species and rare plants will be assessed using either taxa-based rapid assessment protocols or specialized species-specific protocols for rarer species. The purpose of these assessments is to document the status, habitat, and threat covariates of specific species and confirm the species composition and diversity of animal taxonomic groups (e.g., pollinators). Diversity and abundance of animal species at vegetation plots will be used to refine measures and thresholds of ecological integrity. Rapid assessment protocols for animal taxonomic groups can include multiple detection methods such as, camera traps, cover boards, and bird point counts. Pollinators will be monitored at plots using a protocol currently being developed in conjunction with but separately from this plan. Target rare plant species will be monitored using the regional Inspect and Manage (IMG) protocol that measures the status of rare plant occurrences and habitat and threat covariates over time. Species-specific animal survey methods will be refined as these species are prioritized for future monitoring. The goal of this monitoring program is to classify CSS and chaparral vegetation community integrity, identify areas of degradation across western San Diego County, and characterize drivers, and environmental factors associated with loss of ecological integrity. A combination of vegetation mapping, landscape-scale remote sensing, and field plots will be used to address all the aspects of our research questions. Data compiled and collected will be available to conservation partners to help inform future management decisions.

California

Monitoring Avian Productivity and Survivorship (MAPS) 6-year summary, Naval Outlying Landing Field, Imperial Beach, southwestern San Diego County, California, 2014–20

Executive Summary From 2014 to 2020, a Monitoring Avian Productivity and Survivorship (MAPS) banding station (station) was operated at the Naval Outlying Landing Field (NOLF), Imperial Beach, in southwestern San Diego County, California. The station was established as part of a long-term monitoring program of Neotropical migratory bird populations on NOLF and helps Naval Base Coronado (NOLF is a component) meet the goals and objectives of the Department of Defense Partners in Flight program and the Birds and Migratory Birds Management Strategies of the Naval Base Coronado Integrated Natural Resources Management Plan. The station was established in 2009 and has been in operation during the spring and summer since 2009 except for 2016 when it was not funded. The station was operated by AMEC Earth and Environmental, Inc., from 2009 to 2011, by the U.S. Geological Survey from 2012 to 2015, the San Diego Natural History Museum in 2017, and the U.S. Geological Survey again from 2018 to 2023. This report synthesizes results from 2014 to 2020. A prior report presents summaries and analyses from 2009 to 2013. The banding station at NOLF was operated according to the standard MAPS protocol with some exceptions. Ten mist nets used to capture birds were erected in fixed locations that remained consistent between and within years, with few minor relocations. Nets were open for 6 hours per day, once every 10 days (a netting period) for 13 netting periods starting April 1 each year. Occasionally, poor weather conditions (for example, rain, wind, or excessive heat) prevented net operation or forced nets to be closed early (or, rarely, late). Nets were checked periodically throughout the day and birds were removed, processed (leg bands affixed, measurements recorded), and released. From 2014 to 2020, we had 3,543 captures (including initial captures and recaptures) of a maximum of 3,264 year-unique captures (543±143 year-unique captures [the total number of individual birds captured for the first time each year]). The count of year-unique captures included 2,702 newly banded birds, 258 individuals that were recaptured from previous years, and 304 birds that were released unbanded (218 hummingbirds and 86 other birds that were intentionally released unbanded [game birds, and so forth] or escaped before banding). Individuals of 68 species were captured, 39 of which breed at or in the immediate vicinity of the MAPS banding station. Bird capture rate averaged 43±30 captures per day (corrected to account for variation in effort) for all years (range 7–163 effort-corrected captures per day) and species richness per year averaged 43±4. Bushtit ( Psaltriparus minimus ) was the most abundant species captured, followed by Orange-crowned Warbler ( Leiothlypis celata ), Wilson’s Warbler ( Cardellina pusilla ), House Finch ( Haemorhous mexicanus ), Song Sparrow ( Melospiza melodia ), and Common Yellowthroat ( Geothlypis trichas ). The mean adult sex ratio of all species combined across all years was 54:46 male:female. Adults averaged 73±12 percent of known age captures per year (range 59–94 percent), and juveniles averaged 27±12 percent (range 6–41 percent). Nineteen sensitive species were detected at NOLF (12 captured and 7 observed only). During 2014–20, we captured one State and federally endangered species, Least Bell’s Vireo ( Vireo bellii pusillus ); one federally threatened species, California Gnatcatcher ( Polioptila californica ); one State endangered species, Willow Flycatcher ( Empidonax traillii ); and two State species of concern, Yellow-breasted Chat ( Icteria virens ) and Yellow Warbler ( Setophaga petechia ). One additional State species of concern, Northern Harrier ( Circus hudsonius ), was observed at the MAPS banding station but not captured. Peregrine Falcon ( Falco peregrinus ) and White-tailed Kite ( Elanus leucurus ), California State fully protected species, also were observed at the MAPS banding station. Seven federal bird species of conservation concern—Calliope Hummingbird ( Selasphorus calliope ), Rufous Hummingbird ( Selasphorus rufus ), Allen’s Hummingbird ( Selasphorus sasin ), Nuttall’s Woodpecker ( Dryobates nuttallii ), Wrentit ( Chamaea fasciata ), California Thrasher ( Toxostoma redivivum ), and Lawrence’s Goldfinch ( Spinus lawrencei )—also were captured, and four additional federal bird species of conservation concern—Willet ( Tringa semipalmata ), Western Gull ( Larus occidentalis ), California Gull ( Larus californicus ), and Bullock’s Oriole ( Icterus bullockii )—were observed but not captured. Local population trends varied among species and years. From 2012 to 2019, year-round residents Bushtit, Song Sparrow, and Common Yellowthroat significantly decreased, whereas the migrant Least Bell’s Vireo increased. The total number of captures for all species except Least Bell’s Vireo was lowest in 2017, corresponding to the habitat damage caused by Kuroshio shot hole borer beetle ( Euwallacea kuroshio ) in the Tijuana River Valley. Annual productivity and annual adult survival were calculated for seven breeding species based on criteria used by the Institute for Bird Populations (Least Bell’s Vireo, Bushtit, Wrentit, House Wren [ Troglodytes aedon ], Song Sparrow, Orange-crowned Warbler, and Common Yellowthroat). Productivity was highest for most species in 2010 and 2019, years with high precipitation, and lowest in 2014 and 2018, years with low precipitation. Song Sparrow demonstrated the highest productivity among species and Least Bell’s Vireo had the lowest productivity. Annual adult survival was generally high from 2011 to 2012 and from 2018 to 2019. Bushtit had higher annual survival with lower late winter precipitation. Either temperature or precipitation was associated with productivity for all species except Wrentit, and with survival for all species except Least Bell’s Vireo and Common Yellowthroat. For most species, productivity was positively associated with precipitation, and both productivity and survival were negatively associated with temperature. Other studies have found that higher temperatures led to increased predation by snakes and birds and also increased vector-borne disease transmission, such as West Nile virus. Predicted regional increases in temperature over the next 30 years will likely affect the demographics of these species. The Song Sparrow population increased with higher breeding productivity during the previous year, and the Bushtit population increased with higher annual survival and higher productivity during the previous year. Aside from a possible positive association between survivorship and Common Yellowthroat population growth, productivity and survival rates did not appear to influence population change for other focal species.

California

Southwestern Willow Flycatcher (Empidonax traillii extimus) surveys at the city of Carlsbad Preserve, San Diego County, California—2022 data summary

Executive Summary We surveyed for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) at five survey areas within the City of Carlsbad Preserve, Carlsbad, California, in 2022. Three flycatcher surveys were completed between May 18 and June 29, 2022. Territorial or transient flycatchers were not observed at the City of Carlsbad Preserve in 2022.

California

Distribution and demography of coastal Cactus Wrens ( Campylorhynchus brunneicapillus ) in San Diego County, California—2022 data summary

We surveyed for coastal Cactus Wren ( Campylorhynchus brunneicapillus ) in 507 established plots in San Diego County in 2022, encompassing 4 genetic clusters (Otay, Lake Jennings, Sweetwater/Encanto, and San Pasqual). Two surveys were completed at each plot between March 1 and July 31. Cactus Wrens were detected in 214 plots (42 percent of plots). Cactus Wrens were detected in 31 percent of plots that have been consistently surveyed since 2020, indicating less plot occupancy than in 2021 (34 percent) and 2020 (35 percent). There were 202 Cactus Wren territories detected across all survey plots in 2022. In plots that have been consistently surveyed since 2020, we documented 94 territories, which is a decrease from 113 territories in 2021 and 109 in 2020. The number of territories declined from 2021 to 2022 in the Lake Jennings and Otay genetic clusters but remained virtually the same in the Sweetwater/Encanto genetic cluster. At least 78 percent of Cactus Wren territories were occupied by pairs, and 134 fledglings were observed in 2022. We observed 24 banded Cactus Wrens in 2022, 20 of which we could identify individually by band combination. Adults of known age ranged from 3 to at least 7 years old. All individually identifiable adult Cactus Wrens remained on the same territory in 2022 that they occupied in 2021, and we detected no movement of banded Cactus Wrens between genetic clusters. Vegetation at Cactus Wren survey plots was dominated by coastal sage scrub shrubs, such as California sagebrush ( Artemisia californica ), California buckwheat ( Eriogonum fasciculatum ), lemonadeberry ( Rhus integrifolia ), jojoba ( Simmondsia chinensis ), and San Diego sunflower ( Bahiopsis laciniata ). No definitive signs of fungal pathogens were observed on cactus within and around survey plots. Blue elderberry ( Sambucus nigra ssp. caerulea ) was detected at 39 percent of plots, and Cactus Wrens occupied proportionally more plots with elderberry than plots without elderberry. Very little dead or unhealthy cactus was observed within all survey plots, and the plots that were occupied by Cactus Wrens were likely to contain fewer dead cactus than plots that were not occupied by Cactus Wrens. Almost 80 percent of plots had more than 5 percent of cactus crowded or overtopped by vines and shrubs. Similar to 2020, Cactus Wrens occupied proportionally more plots with 5 percent or less of cactus crowded or overtopped by vines and shrubs, although this pattern was not observed in 2021. Non-native annual cover was less prevalent in survey plots in 2022 than in 2021, and Cactus Wrens did not preferentially occupy survey plots with 5 percent or less non-native annual cover than plots with more non-native cover.

California

Prioritizing the risk and management of introduced species in a landscape with high indigenous biodiversity

Risk analysis protocols for prioritizing the management of non-native species are numerous, yet few incorporate risk and management in the same analysis or accommodate a broad diversity of taxa outside of a specific geographic area. We adapted a protocol that accounts for these factors to address non-native animal species in the Southern California/Northern Baja California Coast Ecoregion near the international border in San Diego County, an area with high indigenous biodiversity and high numbers of species of conservation concern. This stepwise, semi-quantitative protocol is applicable to any animal group in any predefined geographic area, relies on consensus-building among taxonomic experts, and has been vetted through previous use and in peer-reviewed literature. Our results show that the final prioritization was driven mainly by management feasibility, with top-ranked species having multitrophic effects that favor other non-native invaders over native residents. Conditions within the assessment area required some modification to the protocol as it was originally designed, namely a shift in emphasis from eradication to control, given that eradication is implausible for most non-native species in the assessment area. We call attention to taxon-specific issues that surfaced during the analysis, identify areas for improvement in this first-ever risk assessment for invasive animal species in the Natural Communities Conservation Plan/Habitat Conservation Plan (NCCP/HCP) reserve system of San Diego County, and provide suggestions for further refinement of the protocol. This study builds on the effort to standardize risk analysis for invasive species globally, given that many of the same invaders present threats to indigenous biodiversity worldwide.

California