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USGS2022

Distribution and demography of Southwestern Willow Flycatchers in San Diego County, 2015–19

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.

California↗
USGS2022

Distribution and abundance of Southwestern Willow Flycatchers (Empidonax traillii extimus) on the Upper San Luis Rey River, San Diego County, California—2021 data 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 2021. Surveys were completed at four locations: three downstream from Lake Henshaw, where surveys occurred from 2015 to 2020 (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 78 territorial flycatchers detected at 3 locations (RRR, CNF, VLH), and 1 transient flycatcher of unknown subspecies was detected at VID. Downstream from Lake Henshaw, five flycatchers, including three males and two females, were detected at RRR and CNF. In total, three territories were established, consisting of two pairs and one male of undetermined breeding status. At VLH, we detected 73 flycatchers, including 32 males, 38 females, and 3 flycatchers of unknown sex. In total, 43 territories were established, containing 38 pairs (22 monogamous pairings, 7 confirmed polygynous groups consisting of 7 males each pairing with 2 different females, and 1 suspected polygynous group consisting of 1 male and 2 females), and 5 flycatchers of undetermined breeding status (2 males and 3 flycatchers of unknown sex). Brown-headed cowbirds ( Molothrus ater ; cowbird) were detected at all four survey locations. Flycatchers used five habitat types in the survey area: (1) mixed willow riparian, (2) willow-cottonwood, (3) willow-oak, (4) willow-ash, and (5) sycamore-oak. Eighty-seven percent of the flycatchers were detected in habitat characterized as mixed willow riparian, and 94 percent of the flycatchers were detected in habitat with greater than 95-percent native plant cover. Exotic vegetation was not prevalent in the survey area. There were 15 nests incidentally located during surveys: 1 was successful, 2 were seen with eggs or nestlings on the last visit, 9 failed, and the outcome of the remaining 3 nests was unknown. Three of these nests were parasitized by cowbirds. There were 13 juveniles detected at VLH during surveys; no juveniles were detected at RRR or CNF. Of the 10 banded flycatchers detected during surveys, 7 were resighted and confirmed to be adults that held territories in previous years. Three flycatchers with a single dark blue federal band, indicating that they were banded as nestlings in the former demographic study area downstream from Lake Henshaw, were resighted during surveys. In 2021, we documented both adult and natal flycatchers moving from the former demographic study area downstream from Lake Henshaw upstream to the habitat surrounding Lake Henshaw. Three natal flycatchers that were originally banded as nestlings and three adults that previously held territories downstream dispersed to Lake Henshaw in 2021.

California↗
USGS2022

Distribution and demography of coastal Cactus Wrens (Campylorhynchus brunneicapillus) in southern San Diego County, California — 2021 Data summary

We surveyed for coastal Cactus Wren ( Campylorhynchus brunneicapillus ) in 378 established plots in southern San Diego County in 2021, encompassing 3 genetic clusters (Otay, Lake Jennings, and Sweetwater/Encanto). Two surveys were completed at each plot between March 1 and July 31. Cactus Wrens were detected in 130 plots (34 percent of plots), remaining virtually the same as the percentage of plots occupied in 2020 (35 percent). There were 113 Cactus Wren territories detected across all survey plots in 2021, an increase from 109 in 2020. At least 86 percent of Cactus Wren territories were occupied by pairs, and 50 fledglings were observed in 2021. We observed 48 color-banded Cactus Wrens in 2021, 44 of which we could identify to individual. Adults of known age ranged from 2 to at least 7 years old. Adult Cactus Wrens moved, on average, 0.1 kilometers (maximum 0.5 kilometers) from their 2020 territories to their 2021 territories. No known-identity Cactus Wrens moved between genetic clusters from 2020 to 2021. Vegetation at Cactus Wren plots typically was dominated by coastal sage scrub shrubs, such as California sagebrush ( Artemisia californica ), California buckwheat ( Eriogonum fasciculatum ), lemonadeberry ( Rhus integrifolia ), and San Diego sunflower ( Bahiopsis laciniata ). Twenty-nine percent of plots contained blue elderberry ( Sambucus nigra ssp. caerulea ), 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 more healthy cactus than plots that were not occupied by Cactus Wrens. Thirteen percent of plots had 5 percent or less of the cactus crowded or overtopped by vines and shrubs. Although in 2020, Cactus Wrens occupied proportionally more plots with 5 percent or less of cactus crowded or overtopped by vines and shrubs, this pattern was not found in 2021. Non-native annual cover was 5 percent or less at 29 percent of plots and, unlike in 2020, Cactus Wrens appeared to occupy proportionally more plots with less non-native annual cover than plots with more than 5-percent annual cover.

California↗
USGS2022

Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California

Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren ( Campylorhynchus brunneicapillus ) in San Diego County in 2011–2012 and again in 2017–2019, using 22 microsatellite loci. We found a significant decline in heterozygosity in one population (San Pasqual) and a decline in allelic richness and effective population size in another (Sweetwater). Genetic diversity in the remaining two populations was not significantly different over time. Local diversity declined despite evidence of dispersal among some populations. Approximately 12% of genetically determined family groups (parents, offspring, siblings) included one or more members sampled in different territories with distances ranging from 0.2 to 10 km. All but one inferred dispersal events occurred within the same genetic population. Population structure remained relatively stable, although genetic differentiation tended to increase in the later sampling period. Simulations suggest that at currently estimated effective sizes, populations of Cactus Wrens will continue to lose genetic diversity for many generations, even if gene flow among them is enhanced. However, the rate of loss of heterozygosity could be reduced with increased gene flow. Habitat restoration may help bolster local population sizes and allelic richness over the long term, whereas translocation efforts from source populations outside of San Diego may be needed to restore genetic diversity in the short term.

California↗
USGS2022

Least Bell's Vireos and Southwestern Willow Flycatchers at the San Luis Rey flood risk management project area in San Diego County, California: Breeding activities and habitat use—2021 Annual report

Executive Summary Surveys and monitoring for the endangered Least Bell’s Vireo ( Vireo bellii pusillus ; vireo) were done at the San Luis Rey Flood Risk Management Project Area (Project Area) in the city of Oceanside, San Diego County, California, between April 4 and August 4, 2021. We completed four protocol surveys during the breeding season, supplemented by weekly territory monitoring visits. We identified a total of 122 territorial male vireos; 111 were confirmed as paired and 8 were confirmed as single males. For the remaining three territories, we were unable to confirm pair status. Five transient vireos were detected in 2021. The vireo population in the Project Area decreased by 24 percent from 2020 to 2021. Vireo populations decreased across San Diego County, with a 14-percent decrease documented at Marine Corps Base Camp Pendleton (MCBCP); a 5-percent decrease on the Otay River; a 6-percent decrease on the middle San Luis Rey River; and a 44-percent decrease at Marine Corps Air Station (although this decrease was likely exaggerated by large-scale vegetation clearing that occurred prior to the 2021 breeding season). We used an index of treatment (Treatment Index) to evaluate the impact of on-going vegetation clearing on the Project Area vireo population. The Treatment Index measures the cumulative effect of vegetation treatment within a territory (since 2005) by using the percent area treated weighted by the number of years since treatment. We found that the Treatment Index for unoccupied habitat was more than two times that of occupied habitat, indicating that vireos selected less treated habitat in which to settle. We monitored vireo nests at three general site types: (1) within the flood channel where exotic and native vegetation removal has occurred regularly (Channel), (2) three sites next to the flood channel where limited exotic and native vegetation removal has occurred (Off-channel), and (3) three sites that have been actively restored by planting native vegetation (Restoration). Nesting activity was monitored in 85 territories, 8 of which were occupied by single males. Of the completed nests, 39 percent were successful, and nest success did not differ among the three sites. Clutch size was greater in the Channel than the Off-channel sites, and the proportion of hatchlings that fledged was greater in Off-channel sites than Channel and Restoration sites. There were no other nest-level differences detected among site types, nor were there any differences in territory-level measures of productivity (young fledged per pair, double-brooding) among the sites. Overall, breeding success and productivity were slightly lower in 2021 than in 2020, with 66 percent of pairs fledgling at least one young and pairs fledging an average of 1.9±1.7 young. To investigate if the cumulative years of treatment had an impact on vireo reproductive effort, we looked at the effects of the Treatment Index on reproductive parameters. Results from generalized linear models indicated that treatment did not have an effect on vireo nesting effort or the number of vireo fledglings per pair produced in 2021. Similarly, our analysis of nest survival for 2021 revealed no effect of Treatment Index on daily survival rate. Analysis of vegetation data collected at vireo nests from 2006 to 2021 did not indicate an effect of vegetation at the nest on daily survival rate. We also found no differences in nest-placement characteristics among site types or successful/unsuccessful nests. Red/arroyo willow ( Salix laevigata or Salix lasiolepis ) was the species most commonly selected for nesting by vireos in all three site types. Black willow ( Salix gooddingii ) and mule fat ( Baccharis salicifolia ) also were commonly used. Vireos used a wider variety of species for nesting in Channel and Off-channel sites (seven and eight species, respectively) compared with Restoration sites (three species).

California↗
USGS2022

Distribution and abundance of Least Bell’s Vireos ( Vireo bellii pusillus ) and Southwestern Willow Flycatchers ( Empidonax traillii extimus ) on the Middle San Luis Rey River, San Diego County, southern California—2021 Data summary

Executive Summary We surveyed for Least Bell’s Vireos ( Vireo bellii pusillus ; vireo) and Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) along the San Luis Rey River, between College Boulevard in Oceanside and Interstate 15 in Fallbrook, California (middle San Luis Rey River), in 2021. Surveys were conducted from April 13 to July 14 (vireo) and from May 18 to July 13 (flycatcher). We found 180 vireo territories, at least 125 of which were occupied by pairs. The vireo population size decreased by 6 percent from 2020 to 2021. In 2021, vireo territories decreased by 14 percent in the portion of the middle San Luis Rey River that burned in 2017 and decreased by 2 percent outside of the burned area. Vireos used six different habitat types in the survey area: (1) willow-cottonwood, (2) mixed willow riparian, (3) riparian scrub, (4) upland scrub, (5) willow-sycamore, and (6) non-native. Forty percent of the vireos were detected in habitat characterized as willow-cottonwood, and 97 percent of the vireos were detected in habitat with greater than 50-percent native plant cover. Of the 14 banded vireos detected in the survey area, 3 were resighted with a full color-band combination. There were 10 other vireos with single (natal) federal bands that were recaptured, identified, and color-banded in 2021. One vireo with a single dark blue federal band, indicating that it was banded as a nestling at the lower San Luis Rey River, could not be recaptured for identification. The 10 natal vireos that were recaptured on the middle San Luis Rey River dispersed from 2.0 to 11.7 kilometers from their natal territories. Banded vireos with a known age ranged from 1 to 7 years old. One resident flycatcher, of undetermined breeding status, was observed in the survey area in 2021. The resident flycatcher (male) was detected in a territory of mixed willow habitat with greater than 50-percent native plant cover. He was detected from May 20 to June 4, 2021, and no evidence of pairing or nesting was observed. The male flycatcher was resighted with a unique color-band combination and had occupied the same territory since 2018.

California↗
USGS2021

Distribution and abundance of Southwestern Willow Flycatchers (Empidonax traillii extimus) on the upper San Luis Rey River, San Diego County, California—2020 data 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 2020. Surveys were completed at four locations: three downstream from Lake Henshaw, where nest monitoring occurred from 2015 to 2019 (Rey River Ranch [RRR], Cleveland National Forest [CNF], Vista Irrigation District [VID]), and one at VID Lake Henshaw (VLH) that was previously surveyed in 2018 and 2019. There were 62 territorial flycatchers detected at 3 locations (RRR, CNF, VLH); no flycatchers were detected at VID. Within the former nest monitoring study area, 11 flycatchers, including 5 males and 6 females, were detected at RRR and CNF. In total, seven territories were established, consisting of six pairs (two polygynous groups consisting of two males each pairing with two different females) and one male of undetermined breeding status. Upstream from the former nest monitoring study area at VLH, we detected 51 flycatchers, including 24 males and 27 females. There were 28 territories established, containing 27 pairs (23 monogamous pairings and 4 confirmed polygynous pairings consisting of 1 male and 2 females) and 1 male of undetermined breeding status. Brown-headed cowbirds ( Molothrus ater ; cowbird) were detected at all four survey locations. Flycatchers used four different habitat types in the survey area: (1) mixed willow riparian, (2) willow-oak, (3) willow-ash, and (4) willow-sycamore. Eighty percent of the flycatchers were detected in habitat characterized as mixed willow riparian, and 83 percent of the flycatchers were detected in habitat with greater than 50-percent native plant cover. Exotic vegetation was not prevalent in the survey area. There were 17 flycatcher nests incidentally located during surveys: 2 were successful, 3 were seen with nestlings on the last visit, 10 failed, and the outcome of the remaining 2 nests was unknown. Five of these nests were parasitized by cowbirds. There were 10 juveniles detected during surveys: 2 at RRR and 8 at VLH. Of the 17 banded flycatchers detected during surveys, 8 were resighted and confirmed to be adults that held territories in previous years. Seven flycatchers with a single dark blue federal band, indicating that they were banded as nestlings in the former nest monitoring study area downstream from Lake Henshaw, were resighted during surveys; 86 percent of these “natal” flycatchers held territories at VLH. In 2020, we documented both adult and natal flycatchers moving from the former nest monitoring study area downstream from Lake Henshaw upstream to the habitat surrounding Lake Henshaw. Six natal flycatchers that were originally banded as nestlings and two adults that previously held territories downstream dispersed to Lake Henshaw in 2020.

California↗
USGS2021

Least Bell's Vireos and Southwestern Willow Flycatchers at the San Luis Rey flood risk management project area in San Diego County, California—Breeding activities and habitat use—2020 annual report

Executive Summary Surveys and monitoring for the endangered Least Bell’s Vireo ( Vireo bellii pusillus ; vireo) were done at the San Luis Rey Flood Risk Management Project Area (Project Area) in the city of Oceanside, San Diego County, California, between March 31 and July 20, 2020. We completed four protocol surveys during the breeding season, supplemented by weekly territory monitoring visits. We identified a total of 161 territorial male vireos; 145 were confirmed as paired and 4 were confirmed as single males. For the remaining 12 territories, we were unable to confirm pair status. Three transient vireos were detected in 2020. The vireo population in the Project Area increased by 26 percent from 2019 to 2020. Vireo populations increased across San Diego County, with a 39-percent increase documented at Marine Corps Base Camp Pendleton (MCBCP); a 58-percent increase at Marine Corps Air Station; a 78-percent increase on the Otay River; and a 7-percent increase in the population on the middle San Luis Rey River. We used an index of treatment (Treatment Index) to evaluate the impact of on-going vegetation clearing on the Project Area vireo population. The Treatment Index measures the cumulative effect of vegetation treatment within a territory (since 2005) by using the percent area treated weighted by the number of years since treatment. We found that the Treatment Index for unoccupied habitat was more than five times that of occupied habitat, indicating that vireos selected less disturbed habitat in which to settle. We monitored vireo nests at three general site types: (1) within the flood channel where exotic and native vegetation removal has occurred regularly (Channel), (2) three sites next to the flood channel where limited exotic and native vegetation removal has occurred (Off-channel), and (3) three sites that have been actively restored by planting native vegetation (Restoration). Nesting activity was monitored in 100 territories, 4 of which were occupied by single males. Hatching success was higher in the Channel relative to the Off-channel. We found no other differences between Channel, Off-channel, and Restoration nests in terms of clutch size or fledging success. There also was no difference in measures of productivity per pair between Channel, Off-channel, Restoration, and Mixed territories (territories that were classified as one site type but nesting occurred in another site type, or where multiple site types were used for nesting). Overall, breeding success and productivity were lower in 2020 than in 2019, with 69 percent of pairs fledgling at least one young and pairs fledging an average of 2.1±1.7 young. To investigate whether the cumulative years of treatment had an impact on vireo reproductive effort, we looked at the effects of the Treatment Index on reproductive parameters. Results from generalized linear models indicated that treatment did not have an effect on vireo nesting effort or the number of vireo fledglings per pair produced in 2020. Similarly, our analysis of nest survival for 2020 revealed no effect of Treatment Index on daily survival rate. Analysis of vegetation data collected at vireo nests from 2006 to 2020 revealed that vegetation at 1–2 meters (m) from the ground was the most important predictor of daily survival rate. There were differences in nest-placement characteristics among site types and successful/unsuccessful nests. Channel nests were placed higher in the vegetation than Off-channel or Restoration nests. Host plant height, distance to edge of host plant, and distance to edge of vegetation clump were greater at Channel sites compared with Off-channel sites, but were not different from Restoration sites. Within sites, we found only one difference between successful and unsuccessful nests. At Off-channel sites, successful nests were placed higher in the vegetation than unsuccessful nests. Red/arroyo willow ( Salix laevigata or Salix lasiolepis ) and mule fat ( Baccharis salicifolia ) were the species most commonly selected for nesting by vireos in all 3 site types. Vireos used a wider variety of species for nesting in Channel and Off-channel sites (7 and 10 species, respectively) compared to Restoration sites (3 species). Ninety-three vireos banded before the 2020 breeding season were resighted and identified at the Project Area in 2020, all of which were originally banded at the Project Area. Adult birds of known age ranged from 1 to 9 years old. A total of 171 vireos were newly banded in 2020. Twenty-eight adult vireos were banded with a unique color combination, and 143 nestlings were banded with a single dark blue numbered federal band on the left leg. Between 2006 and 2020, survivorship of males (67±10 percent) was consistently higher than females (59±11 percent). First-year birds from 2006 to 2020 had an average over-winter survivorship of 17±5 percent. First-year dispersal in 2020 averaged 2.9±2.9 kilometers (km), with the longest dispersal (13.5 km) by a female that was recaptured at Las Flores Creek, MCBCP. From 2007 to 2012, most returning first-year vireos returned to the Project Area, whereas from 2013 to 2017, the majority of returning birds dispersed to areas outside of the Project Area. In 2018, the trend shifted, and most first-year vireos returned to the Project area. This trend continued in 2020 with most first-year vireos returning to the Project Area; 77 percent of all re-encountered first-year birds returned to the Project Area and 23 percent dispersed to areas outside of the Project Area (upstream to the middle San Luis Rey River and to drainages on MCBCP). Most of the returning adult male vireos showed strong between-year site fidelity to their previous territories. Eighty percent of males (45/56) occupied a territory in 2020 that they had defended in 2019 (within 100 m). Thirty-three percent of females (2/6) detected in 2020 returned to a territory that they occupied in 2019. The average between-year movement for returning adult vireos was 0.1±0.5 km. We completed four protocol surveys for the endangered Southwestern Willow Fycatcher ( Empidonax traillii extimus ; flycatcher) at the Project Area between May 20 and July 20, 2020. No Willow Flycatchers were detected in the Project Area in 2020. A total of 46 vegetation transects (526 points) were sampled at the San Luis Rey Flood Risk Management Project Area in 2020. Seventy-one percent (376/526) of points were in the Channel and 22 percent (115/526) were at Upper Pond. The remaining 7 percent (35/526) were at the Whelan Restoration site. Foliage cover below 1 m was higher at the Channel points compared to Upper Pond and Whelan Restoration. Higher foliage cover in the Channel was attributed to the higher herbaceous component. However, foliage cover from 1 to 3 m was higher at the Whelan Restoration site compared to both Upper Pond and the Channel. Average canopy height was similar at all three site types and was 4.4 m or less. From 2006 to 2020, total foliage cover declined above 1 m in the Channel, from 4 to 5 m at Upper Pond, and above 8 m at Whelan Restoration. Within the Channel, the steepest declines occurred between 2009 and 2013 and between 2014 and 2016. Since 2016, we observed an increase in percent foliage between 0 and 2 m within the Channel, but for other height classes, percent cover remained below levels detected before 2009. Changes in cover at Upper Pond and Whelan Restoration appeared to be driven by the loss of tall tree cover. The vegetation mowing and treatment activities, in combination with lack of precipitation (especially between 2012 and 2016), may have contributed to the decline in foliage cover observed from 2006 to 2020. We sampled vegetation at 49 vireo nests and 49 random plots (“territory” plots) within territories in the Channel and Upper Pond following the 2020 breeding season. Vireos in the Channel selected territories with significantly more foliage cover above 2 m but less cover below 1 m relative to the available habitat. In contrast, Channel vireos selected nest sites within their territories with lower foliage cover above 3 m and were non-selective with regard to cover below 2 m. Vireos at Upper Pond generally were less selective with regard to territory and nest sites but tended to select territories with more foliage cover from 1 to 2 m and above 8 m, and they selected nest sites within their territories with greater foliage cover from 0 to 1 m.

California↗
USGS2021

Distribution and abundance of Least Bell's Vireos and Southwestern Willow Flycatchers on the middle San Luis Rey River, San Diego County, southern California—2020 data summary

We surveyed for Least Bell’s Vireos ( Vireo bellii pusillus ; vireo) and Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) along the San Luis Rey River, between College Boulevard in Oceanside and Interstate 15 in Fallbrook, California (middle San Luis Rey River), in 2020. Surveys were conducted from April 13 to July 13 (vireo) and from May 14 to July 13 (flycatcher). We found 192 vireo territories, at least 150 of which were occupied by pairs. Vireo territories increased by 40 percent from 2019 to 2020 in the portion of the middle San Luis Rey River that burned as a result of a wildfire in 2017. In contrast, vireo territories decreased by 5 percent from 2019 to 2020 in the unburned portion of the middle San Luis Rey River. Vireos used six different habitat types in the survey area: (1) willow-cottonwood, (2) mixed willow riparian, (3) riparian scrub, (4) upland scrub, (5) willow-sycamore, and (6) non-native. Forty-nine percent of the vireos were detected in habitat characterized as willow-cottonwood, and 93 percent of the vireos were detected in habitat with greater than 50-percent native plant cover. Of the 17 banded vireos detected in the survey area, 6 were resighted with a full color-band combination. Two other vireos with single (natal) federal bands were recaptured, identified, and color-banded in 2020. Eight vireos with a single dark blue federal band, indicating that they were banded as nestlings on the lower San Luis Rey River (LSLR), could not be recaptured for identification. One vireo with a single gold federal band, indicating that it was banded as a nestling at Marine Corps Base Camp Pendleton (MCBCP), could not be recaptured for identification. The two natal vireos that were recaptured on the middle San Luis Rey River dispersed from 2.6 to 6.2 kilometers (km) from their natal territories. Banded vireos with a known age ranged from 1 to 8 years old. One resident flycatcher was observed in the survey area in 2020. The resident flycatcher (male) was detected in a territory of mixed willow habitat with greater than 50-percent native plant cover. He was detected as a single male from May 27 to July 2, 2020, and no evidence of pairing or nesting was observed. The male flycatcher was resighted with a unique color-band combination and had occupied the same territory since 2018.

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USGS2021

Predictability of invasive Argentine ant distribution across Mediterranean ecoregions of southern California

The invasiveness of nonnative taxa can vary across a landscape due to environmental gradients, suggesting that location-dependent management strategies may be more effective at reducing spread compared to a “one size fits all” approach across the entire introduced range. Using bait stations placed along linear transects within habitat preserves, we tested for effects of ecoregion, vegetation, soil moisture, habitat edge type (i.e., moisture source), and distance from edges on the presence of the invasive Argentine ant Linepithema humile in San Diego County, California, a region with high indigenous biodiversity and numerous rare and protected species. Our results showed an inverse relationship between the presence of native ant species and the presence of the Argentine ant across ecoregions, with the latter reaching peak abundance in the coastal terrace. Argentine ant presence was negatively associated with distance from all edge types regardless of location, but the magnitude of this effect varied among ecoregions. In the xeric foothill and inland valleys, the probability of occurrence was nearly 0 at distances of 200 m and 750 m from moisture edges, respectively, whereas in the coastal terrace, the probability remained above 0.80 at distances up to 1.25 km. When compared to previous studies at different spatial scales, these findings provide an alternative perspective on the invasiveness of the Argentine ant at the landscape level. Our results further suggest that efforts to control spread in regions with a Mediterranean climate may be more successful in inland areas, where the ant is likely to have lower environmental tolerance and native ant species may be better able to generate biotic resistance. In contrast, different tactics and expectations may be necessary for coastal areas, where the same constraints are diminished or absent.

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USGS2020

Distribution and abundance of Least Bell’s Vireos (Vireo bellii pusillus) and Southwestern Willow Flycatchers (Empidonax traillii extimus) on the Middle San Luis Rey River, San Diego County, southern California—2019 data summary

We surveyed for Least Bell’s Vireos ( Vireo bellii pusillus ; vireo) along the San Luis Rey River, between College Boulevard in Oceanside and Interstate 15 in Fallbrook, California (middle San Luis Rey River), in 2019, and we surveyed and conducted nest monitoring for Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) in a survey area where breeding had historically been documented on the middle San Luis Rey River, in 2019. Surveys were conducted from April 11 to June 24 (vireo) and from May 16 to July 15 (flycatcher). We found 179 vireo territories, at least 124 of which were occupied by pairs. Vireo territories increased by 100 percent within the portion of the middle San Luis Rey River that burned as a result of a wildfire in 2017. In contrast, vireo territories increased by 5 percent within the unburned portion of the middle San Luis Rey River. Vireos used five different habitat types in the survey area: mixed willow riparian, willow-cottonwood, riparian scrub, willow-sycamore, and upland scrub. Fifty-two percent of the vireos were detected in habitat characterized as mixed willow, and 92 percent of the vireos were detected in habitat with greater than 50 percent native plant cover. Of the 12 banded vireos detected in the survey area, 5 were resighted with a full color-band combination. One adult female with a unique color-band combination immigrated to the middle San Luis Rey River from Marine Corps Base Camp Pendleton (MCBCP). Five other vireos with single (natal) federal bands were recaptured, identified, and color banded in 2019. Two vireos with a single dark blue federal band, indicating that they were banded as nestlings on the lower San Luis Rey River (LSLR), could not be recaptured for identification. The five natal vireos that were recaptured on the middle San Luis Rey River dispersed from 1.4 to 8.3 kilometers (km) from their natal territories. Banded vireos with a known age ranged from 1 to 11 years old. One resident flycatcher was observed in the survey area in 2019. The resident flycatcher (male) was detected in a territory of mixed willow habitat with greater than 50 percent native plant cover. He was detected as a single male from May 16 to July 17, 2019, and no evidence of pairing or nesting was observed. The male flycatcher with a unique color-band combination occupied the same territory in 2018 and 2019.

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USGS2019

DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)

Throughout the western United States, efforts are underway to better understand and preserve migration and movement corridors for mule deer and other big game and to minimize the impacts of development and other land-use change on populations. San Diego County is home to a unique non-migratory subspecies of mule deer, the Southern mule deer ( Odocoileus hemionus fuliginatus ; herein referred to as “mule deer”). Because it is the only large herbivorous mammal in San Diego, connectivity among mule deer groups is an important indicator of functional connectivity throughout San Diego County urban preserves and has therefore been monitored within central and eastern San Diego County using DNA fingerprinting since 2005. To continue this effort and to assess genetic connectivity in north San Diego County (herein “North County”), we genotyped scat samples from preserves in the area and tissue samples from Marine Corps Base Camp Pendleton (MCBCP). We used non-invasive capture/recapture analyses and pedigree analyses for assessing short-term movement and population clustering analyses to assess gene flow in North County. Additionally, we performed similar analyses on the combined San Diego County dataset, which was composed of the North County dataset collected for this study and a previously collected dataset from central and eastern San Diego County. Using recapture data, we found multiple instances of mule deer crossing roads in urban North County preserves, with several of these events occurring in areas where there are underpasses and culverts known to be used by mule deer. Corroborating previous studies in the region and statewide, pedigree and population structure analyses support the presence of two genetic clusters for mule deer in San Diego County—the “Coastal” and “Inland/Mountain” clusters. Low estimates of effective population size, especially in the Coastal cluster, suggest that to further understand potential vulnerabilities of mule deer in this region, it is important to continue to monitor connectivity, in particular, at the boundary between these two clusters.

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USGS2018

Population genomic surveys for six rare plant species in San Diego County, California

San Diego County is a hotspot of biodiversity, situated at the intersection of the Baja peninsula, the California floristic province, and the desert southwest. This hotspot is characterized by a high number of rare and endemic species, which persist alongside a major urban epicenter. San Diego County has implemented a strategic management plan that identifies species, based on low numbers of occurrences or high level of threat, for which management practices are recommended. In creating a management plan for rare species, it is important to strike a balance between preserving locally adapted traits and maintaining genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat fragmentation. This project, in partnership with the San Diego Natural History Museum, aims to provide a reference point for the current status of genetic diversity of rare plant species that will inform future preservation and restoration efforts. We focused on six threatened or endangered plant species: Acanthomintha ilicifolia , Baccharis vanessae , Chloropyron maritimum ssp. maritimum , Deinandra conjugens , Dicranostegia orcuttiana , and Monardella viminea . For each species, botanists from the San Diego Natural History Museum visited all known occurrences in San Diego County and collected leaf tissue for genetic and cytological analysis. We then developed a panel of genetic markers to estimate genetic diversity and population structure. This population genetic survey provided insight into the amount of genetic differentiation across each species’ range, identified isolated occurrences potentially subject to inbreeding or genetic bottlenecks, and identified areas that are rich sources of allelic diversity. Finally, we convened a panel of experts to review results and compatible management options for each species. A summary of the management workshop is included in this report. Overall, we found low genetic differentiation among occurrences across the San Diego region for all species, with the exception of A. ilicifolia . Relative inbreeding was low and consistent across sites, and genetic diversity across sites was variable, with noted exceptions. These findings allow for a wide array of management options that are compatible with panmictic population structure in five of the six surveyed species.

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USGS2018

Prioritizing conserved areas threatened by wildfire and fragmentation for monitoring and management

In many parts of the world, the combined effects of habitat fragmentation and altered disturbance regimes pose a significant threat to biodiversity. This is particularly true in Mediterranean-type ecosystems (MTEs), which tend to be fire-prone, species rich, and heavily impacted by human land use. Given the spatial complexity of overlapping threats and species’ vulnerability along with limited conservation budgets, methods are needed for prioritizing areas for monitoring and management in these regions. We developed a multi-criteria Pareto ranking methodology for prioritizing spatial units for conservation and applied it to fire threat, habitat fragmentation threat, species richness, and genetic biodiversity criteria in San Diego County, California, USA. We summarized the criteria and Pareto ranking results (from west to east) within the maritime, coastal, transitional, inland climate zones within San Diego County. Fire threat increased from the maritime zone eastward to the transitional zone, then decreased in the mountainous inland climate zone. Number of fires and fire return interval departure were strongly negatively correlated. Fragmentation threats, particularly road density and development density, were highest in the maritime climate zone, declined towards the east, and were positively correlated. Species richness criteria showed distributions among climate zones similar to those of the fire threat variables. When using species richness and fire threat criteria, most lower-ranked (higher conservation priority) units occurred in the coastal and transitional zones. When considering genetic biodiversity, lower-ranked units occurred more often in the mountainous inland zone. With Pareto ranking, there is no need to select criteria weights as part of the decision-making process. However, negative correlations and larger numbers of criteria can result in more units assigned to the same rank. Pareto ranking is broadly applicable and can be used as a standalone decision analysis method or in conjunction with other methods.

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USGS2018

Monitoring breeding and migration of neotropical migratory birds at Naval Base Coronado, Remote Training Site, Warner Springs, San Diego County, California, 5-year summary, 2013–17

We operated a bird banding station on the Naval Base Coronado, Remote Training Site, Warner Springs (RTSWS), in northeastern San Diego County, California, during the bird breeding season (spring/summer) from 2013 to 2017 and during migration (fall) from 2013 to 2016. The station was established in spring 2013 as part of the Monitoring Avian Productivity and Survivorship (MAPS) program and continued into the fall for the first 4 years as part of a long-term monitoring program for neotropical migratory birds. We captured 705 individuals of 58 species during the MAPS/breeding season from 2013 to 2017 (12–13 days each year in April through August), 79 percent of which were newly banded during the MAPS season (555), 8 percent of which were recaptures banded in previous years (57), and 13 percent of which we released unbanded (64 hummingbirds and 29 other birds that were released or escaped prior to banding). Sixty individuals were captured more than once within a year during MAPS. Bird capture rate averaged 19 ± 1 captures per 100 net-hours (range 17–20) across 5 years. Annual species richness ranged from 28 (2017) to 42 (2014). The average species richness per day was highest in 2014 (9 ± 3) and lowest in 2016 (6 ± 2). Bushtit ( Psaltriparus minimus ) was the most abundant breeding species captured, followed by Spotted Towhee ( Pipilo maculatus ), Oak Titmouse ( Baeolophus inornatus ), Anna’s Hummingbird ( Calypte anna ), House Wren ( Troglodytes aedon ), Ash-throated Flycatcher ( Myiarchus cinerascens ), California Scrub-jay ( Aphelocoma californica ), Bewick’s Wren ( Thryomanes bewickii ), Acorn Woodpecker ( Melanerpes formicivorus ), California Towhee ( Melozone crissalis ), and Western Bluebird ( Sialia mexicana ). Each of these 11 breeding species accounted for at least 5 percent of captures in any 1 year. Fifty-seven percent of known-sex captures were female and 43 percent were male. Thirty-three percent of known-age captures were juveniles. Peaks in number of birds captured were in the first and last weeks of April, and the greatest number of species was captured in early May.

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