The Coastal California Gnatcatcher (Polioptila californica californica), a federally threatened species, is a flagship species for regional conservation planning in southern California (USA). An inhabitant of coastal sage scrub vegetation, the gnatcatcher has declined in response to habitat loss and fragmentation, exacerbated by catastrophic wildfires. We documented the status of gnatcatchers throughout their California range and examined post-fire recovery of gnatcatchers and their habitat. We used GIS to develop a habitat suitability model for Coastal California Gnatcatchers using climate and topography covariates and selected over 700 sampling points in a spatially balanced manner. Bird and vegetation data were collected at each point between March and May in 2015 and 2016. Presence/absence of gnatcatchers was determined during three visits to points, using area searches within 150 x 150 m plots. We used an occupancy framework to generate Percent Area Occupied (PAO) by gnatcatchers, and analyzed PAO as a function of time since fire. At the regional scale in 2016, 23% of the points surveyed were occupied by gnatcatchers, reflecting the effect of massive wildfires in the last 15 years. Similarly, PAO in the post-fire subset of points was 24%, with the highest occupancy in unburned (last fire <2002) habitat. Positive predictors of occupancy included percent cover of California sagebrush (Artemisia californica), California buckwheat (Eriogonom fasciculatum), and sunflowers (Encelia spp., Bahiopsis laciniata), while negative predictors included laurel sumac (Malosma laurina) and total herbaceous cover; in particular, non-native grasses. Our findings indicate that recovery from wildfire may take decades, and provide information to speed up recovery through habitat restoration.

First posted May 17, 2024 For additional information, contact: Western Ecological Research CenterU.S. Geological Survey3020 State University Drive EastSacramento, California 95819 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.

Increasingly, genomic data are being used to supplement field-based ecological studies to help evaluate recovery status and trends in endangered species. We collected genomic data to address 2 related questions regarding the Least Bell's Vireo (Vireo bellii), an endangered migratory songbird restricted to southern California riparian habitat for breeding. First, we sought to delineate the range limits and potential overlap between Least Bell's Vireo and its sister subspecies, the Arizona Bell's Vireo, by analyzing samples from the deserts of eastern California, southwestern Nevada, Utah, and Arizona. Second, we evaluated genetic structure among Least Bell's Vireo populations in coastal California and estimated effective population size. Clustering analyses based on 10,571 single-nucleotide polymorphisms (SNPs) from 317 samples supported 2 major groups that aligned closely to the previously defined subspecies ranges. The first cluster included birds in the Central Valley, all coastal drainages, and westernmost deserts of California, with no further sub-structuring among coastal drainages. Almost all birds from the Amargosa River in eastern California and eastward assigned to the second cluster; however, low levels of gene flow were detected across the subspecies groups, with greater rates of gene flow from Arizona Bell's Vireo to Least Bell's Vireo than the reverse. Admixed individuals occurred in the California deserts; and although smaller than coastal populations, desert populations may be important for maintaining and replenishing genetic diversity and facilitating the movement of potentially adaptive genes between subspecies. Within Least Bell's Vireo, local populations in coastal drainages comprised a single genetic population, with some evidence of close relatives distributed across drainages, suggesting that these could function as a well-connected metapopulation. These results are consistent with previous Least Bell's Vireo banding studies that reported high rates of dispersal among drainages. Effective population size for both subspecies was high, suggesting that adaptive potential has been maintained despite previous declines. center dot Maintenance of genetic diversity is essential for species to be able to persist and adapt to changing environmental conditions.center dot We examined dispersal and genetic diversity in the endangered Least Bell's Vireo, a migratory songbird dependent upon riparian habitat for breeding, and in its closest subspecies, the Arizona Bell's Vireo.center dot Analysis of blood samples collected from vireos throughout southern California, Nevada, Utah, and Arizona revealed that in general birds from the Mojave Desert west are Least Bell's Vireos, while those to the east are Arizona Bell's Vireos. However, we found low levels of gene exchange across subspecies and that 9% of birds in the desert region were of mixed ancestry.center dot Occasional dispersal and successful breeding across the California desert could be a source of novel adaptive genetic variation that could increase the capacity of Least Bell's Vireo to adapt to climate change across its range. Cada vez mas, los datos genomicos se utilizan para complementar estudios ecologicos basados en el campo y ayudar a evaluar el estado de recuperacion y las tendencias en especies en peligro. Recolectamos datos genomicos para abordar dos preguntas relacionadas a Vireo bellii pusillus, un ave canora migratoria en peligro de extincion restringida para su reproduccion al habitat ribereno del sur de California. En primer lugar, buscamos delinear los limites de los rangos de distribucion y la posible superposicion entre V. b. pusillus y su subespecie hermana, V. b. arizonae, mediante el analisis de muestras de los desiertos del este de California, suroeste de Nevada, Utah y Arizona. En segundo lugar, evaluamos la estructura genetica entre las poblaciones de V. b. pusillus en la costa de California y estimamos el tamano efectivo de la poblacion. Los analisis de agrupamiento basados en 10.571 polimorfismos de nucleotido unico provenientes de 317 muestras respaldaron dos grupos principales que se alinearon estrechamente con los rangos previamente definidos de las subespecies. El primer grupo incluyo las aves en el Valle Central, todos los drenajes costeros y los desiertos mas occidentales de California, sin una subdivision adicional entre los drenajes costeros. Casi todas las aves del Rio Amargosa en el este de California y hacia el este se asignaron al segundo grupo; sin embargo, se detectaron bajos niveles de flujo genico entre los grupos de subespecies, con tasas de flujo genico mas altas desde V. b. arizonae hacia V. b. pusillus que al reves. Se encontraron individuos mestizos en los desiertos de California; y aunque mas pequenas que las poblaciones costeras, las poblaciones del desierto pueden ser importantes para mantener y reponer la diversidad genetica y facilitar el movimiento de genes potencialmente adaptativos entre las subespecies. Dentro de V. b. pusillus, las poblaciones locales en los drenajes costeros constituyeron una sola poblacion genetica, con algunas evidencias de parientes cercanos distribuidos a traves de los drenajes, lo que sugiere que estos podrian funcionar como una metapoblacion bien conectada. Estos resultados son consistentes con estudios anteriores de anillado de V. b. pusillus que informaron altas tasas de dispersion entre los drenajes. El tamano efectivo de la poblacion para ambas subespecies fue alto, lo que sugiere que el potencial adaptativo se ha mantenido a pesar de las disminuciones previas.

To cope with climate change, species may shift their distributions or adapt in situ to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher ( Empidonax traillii extimus ) through whole-genome comparisons between historical specimens, collected from 1888 to 1909 near San Diego, California, United States, and contemporary individuals from across the breeding range. Genomic analyses revealed that introgression into San Diego increased adaptive potential over time and shifted genome-wide population structure towards that of neighbouring populations. In contrast, loci linked to climate (dew point temperature and precipitation) shifted away from neighbouring populations and in a direction consistent with adaptation to climate change in southern California. This research highlights the role of admixture in facilitating adaptive shifts through its impact on genome-wide genetic variation and represents one of the few studies to document climate adaptation in a wild population.

First posted May 11, 2023 For additional information, contact: Western Ecological Research CenterU.S. Geological Survey3020 State University Drive EastSacramento, California 95819 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.