California Gnatcatcher Research Articles

Rangewide occupancy of a flagship species, the Coastal California Gnatcatcher (Polioptila californica californica) in southern California: Habitat associations and recovery from wildfire.

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.

Foraging preferences of the threatened coastal California Gnatcatcher ( Polioptila californica ) during the non-breeding season

We studied the foraging behavior of the federally threatened coastal California Gnatcatcher (<em>Polioptila californica</em>), an obligate insectivore, during the non-breeding season, a period of reduced survivorship for this non-migratory passerine due to seasonal aridity and the onset of cold winter storms. During the seasonal dry period in fall (October–November), California Gnatcatchers preferentially foraged in fall-blooming shrubs such as coyote brush (<em>Baccharis pilularis</em>), and California brickelbush (<em>Brickellia californica</em>). Upon the onset of the wet winter period (December–January), foraging California Gnatcatchers demonstrated a seasonal shift toward drought deciduous shrubs then leafing out, especially coastal sagebrush (<em>Artemisia californica</em>). Our findings suggest that California Gnatcatchers shift their foraging preferences seasonally to track available food resources. Additionally, our findings point to the value of floristic diversity within California Gnatcatcher habitat to provide year-round foraging opportunities for this obligate insectivore.

Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation.

Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica, is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. Lack of congruence among morphological subspecies hypotheses and lack of measurable genetic structure found in a few genetic markers led to questions about the validity of subspecies within P. californica and the listing status of the coastal California gnatcatcher, P. c. californica. As a U.S. federally threatened subspecies, P. c. californica is recognized as a flagship for coastal sage scrub conservation throughout southern California. We used restriction site‐associated DNA sequencing to develop a genomic dataset for the California gnatcatcher. We sampled throughout the species' range, examined genetic structure, gene–environment associations, and demographic history, and tested for concordance between genetic structure and morphological subspecies groups. Our data support two distinct genetic groups with evidence of restricted movement and gene flow near the U.S.‐ Mexico international border. We found that climate‐associated outlier loci were more strongly differentiated than climate neutral loci, suggesting that local climate adaptation may have helped to drive differentiation after Holocene range expansions. Patterns of habitat loss and fragmentation are also concordant with genetic substructure throughout the southern California portion of the range. Finally, our genetic data supported the morphologically defined P. c. californica as a distinct group, but there was little evidence of genetic differentiation among other previously hypothesized subspecies in Baja California. Our data suggest that retaining and restoring connectivity, and protecting populations, particularly at the northern range edge, could help preserve existing adaptive potential to allow for future range expansion and long‐term persistence of the California gnatcatcher.

Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence

Comparative phylogeography explores the historical congruence of co-distributed species to understand the factors that led to their current genetic and phenotypic structures. Even species that span the same biogeographic barrier can exhibit different phylogeographic structures owing to differences in effective population sizes, genetic marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers, including the Vizcaíno Desert and Sierra de la Laguna (Cape District), that have left phylogeographic patterns in some but not all species. We used genome-wide SNP data to test the hypothesis that the diverse phylogeographic patterns inferred from prior studies were supported. We found that mitochondrial DNA, single nuclear gene, and genome-wide SNP data show that the cactus wren and LeConte’s thrasher have a concordant historical division at or near the Vizcaíno Desert in north-central Baja California, the Gila woodpecker is at an intermediate stage of divergence, and the California gnatcatcher lacks phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeConte’s thrasher. We also analyzed mtDNA data on samples of nine other species that span the Vizcaíno Desert, with four showing no apparent division, and six additional species from the Sierra de la Laguna, all but one of which are differentiated. Reasons for contrasting phylogeographic patterns among these species should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaíno desert is well known in other vertebrate species, and our study further corroborates the extent, profound effect, and importance of this biogeographic boundary. The areas north and south of the Vizcaíno Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation.

A spatially explicit model for estimating risks of pesticide exposure to bird populations.

Pesticides are used widely in agriculture and have the potential to affect non-target organisms, including birds. We developed an integrated modeling system to allow for spatially-explicit evaluation of potential impacts to bird populations following exposures to pesticides. Our novel methodology builds upon three existing models: the Terrestrial Investigation Model (TIM), the Markov Chain Nest Productivity Model (MCnest), and HexSim to simulate population dynamics. We parameterized the integrated modeling system using information required under the Federal Insecticide, Fungicide, and Rodenticide Act, together with species habitat and life history data available from the scientific literature as well as landcover data representing agricultural areas and species habitat. Our case study of the federally threatened California Gnatcatcher (Polioptila californica) illustrates how the integrated modeling system can estimate the population-scale consequences of pesticide applications. We simulated impacts from two insecticides applied to wheat: one causing mortality (survival stressor), and the other causing reproductive failure (reproductive stressor). We observed declines in simulated gnatcatcher abundance and changes in the species’ distribution following applications of each pesticide; however, the impacts of the two pesticides were different. Our methodology attempts to strike a balance between biological realism and model complexity and should be applicable to a wide array of species, systems, and stressors.

The Current Northernmost Breeding Pair of the California Gnatcatcher

The Current Northernmost Breeding Pair of the California Gnatcatcher

Distinguishing recent dispersal from historical genetic connectivity in the coastal California gnatcatcher

Habitat loss and fragmentation are primary threats to biodiversity worldwide. We studied the impacts of habitat loss and fragmentation on genetic connectivity and diversity among local aggregations of the California gnatcatcher (Polioptila californica californica) across its U.S. range. With a dataset of 268 individuals genotyped at 19 microsatellite loci, we analyzed genetic structure across the range using clustering analyses, exact tests for population differentiation, and a pedigree analysis to examine the spatial distribution of first-order relatives throughout the study area. In addition, we developed a habitat suitability model and related percent suitable habitat to genetic diversity indices within aggregations at two spatial scales. We detected a single genetic cluster across the range, with weak genetic structure among recently geographically isolated aggregations in the northern part of the range. The pedigree analysis detected closely related individuals across disparate aggregations and across large geographic distances in the majority of the sampled range, demonstrating that recent long-distance dispersal has occurred within this species. Genetic diversity was independent of suitable habitat at a local 5-km scale, but increased in a non-linear fashion with habitat availability at a broader, 30-km scale. Diversity declined steeply when suitable habitat within 30-km fell below 10%. Together, our results suggest that California gnatcatchers retain genetic connectivity across the majority of the current distribution of coastal sage scrub fragments, with the exception of some outlying aggregations. Connectivity may help support long-term persistence under current conservation and management strategies. However, emerging structure among more remote aggregations and associations between available habitat and genetic diversity also suggest that continued loss of habitat could threaten diversity and connectivity in the future.

Restoring habitat for coastal California Gnatcatchers (Polioptila californica californica)

ABSTRACT One goal of Habitat Conservation Plans is to protect viable populations of animal species. Management actions included in such plans often focus on vegetation restoration to benefit the target animal species. Yet, such restoration activities are often uninformed by fine-scale animal survey data. Using the California Gnatcatcher (Polioptila californica californica), we demonstrate how survey data can guide restoration toward the goal of improving gnatcatcher viability by identifying habitat conditions most favorable for gnatcatcher occupancy. We found that gnatcatcher presence and colonization probabilities tripled as the coverage of coastal sagebrush (Artemisia californica) increased from 10% to 40%. Coastal sagebrush was more likely to be present at low elevations, and was most closely associated with soil texture of 5%–20% clay, 40%–70% sand, and 20%–40% silt. Higher gnatcatcher extinction probabilities were associated with closed, dense habitat; optimal conditions were between 30% and 40% open...

Accessibility drives species exposure to recreation in a fragmented urban reserve network

Outdoor recreation is a valuable ecosystem service permitted in most protected areas globally. Land-use planners and managers are often responsible for providing access to natural areas for recreation while avoiding environmental impacts such as declines of threatened species. Since recreation can have harmful effects on biodiversity, reliable information about protected-area visitation patterns is vital for managers. Our goal was to quantify recreational use in a fragmented urban reserve network and identify factors that influenced visitation. We empirically measured visitation rates at 18 reserves in San Diego County, California. Using random forest models, we identified biophysical and socioeconomic factors that influenced spatial variation in visitation rates and made projections to 27 additional reserves, validating with an expert opinion survey. Visitation rates varied widely across the reserve network. Accessibility variables, such as numbers of housing units and parking lots, were key explanatory variables that had positive relationships with visitation rates. To illustrate the applications of our models, we assessed the exposure of 7 species and subspecies of conservation concern to recreation by comparing predicted occurrence to projected visitation intensities. We found that several species and subspecies, including the orange-throated whiptail (Aspidoscelis hyperythra), western spadefoot (Spea hammondii), and the federally-threatened coastal California gnatcatcher (Polioptila californica californica), are likely exposed to high levels of recreational activity. Our results can be used to identify species for further research, highlight areas with potential conflict between recreation and conservation objectives, and forecast future changes in visitation.

Environmental change, shifting distributions, and habitat conservation plans: A case study of the California gnatcatcher.

Many species have already experienced distributional shifts due to changing environmental conditions, and analyzing past shifts can help us to understand the influence of environmental stressors on a species as well as to analyze the effectiveness of conservation strategies. We aimed to (1) quantify regional habitat associations of the California gnatcatcher (Polioptila californica); (2) describe changes in environmental variables and gnatcatcher distributions through time; (3) identify environmental drivers associated with habitat suitability changes; and (4) relate habitat suitability changes through time to habitat conservation plans. Southern California's Western Riverside County (WRC), an approximately 4,675 km2 conservation planning area. We assessed environmental correlates of distributional shifts of the federally threatened California gnatcatcher (hereafter, gnatcatcher) using partitioned Mahalanobis D 2 niche modeling for three time periods: 1980–1997, 1998–2003, and 2004–2012, corresponding to distinct periods in habitat conservation planning. Highly suitable gnatcatcher habitat was consistently warmer and drier and occurred at a lower elevation than less suitable habitat and consistently had more CSS, less agriculture, and less chaparral. However, its relationship to development changed among periods, mainly due to the rapid change in this variable. Likewise, other aspects of highly suitable habitat changed among time periods, which became cooler and higher in elevation. The gnatcatcher lost 11.7% and 40.6% of highly suitable habitat within WRC between 1980–1997 to 1998–2003, and 1998–2003 to 2004–2012, respectively. Unprotected landscapes lost relatively more suitable habitat (−64.3%) than protected landscapes (30.5%). Over the past four decades, suitable habitat loss within WRC, especially between the second and third time periods, was associated with temperature‐related factors coupled with landscape development across coastal sage scrub habitat; however, development appears to be driving change more rapidly than climate change. Our study demonstrates the importance of providing protected lands for potential suitable habitat in future scenarios.

Status of the California Gnatcatcher at the Northern Edge of Its Range

Status of the California Gnatcatcher at the Northern Edge of Its Range

A comparison of point-count and area-search surveys for monitoring site occupancy of the Coastal California Gnatcatcher (Polioptila californica californica)

ABSTRACT Improving the efficiency of monitoring protocols prescribed by conservation plans can release typically limited funding for other management and conservation activities. We present an approach for optimizing protocols that considers the precision of parameter estimates, costs of implementation, and broader monitoring-program goals. In a case study of the Coastal California Gnatcatcher (Polioptila californica californica), we compared the efficiency of point-count surveys (with and without playbacks of vocalizations) and area-search surveys (with playbacks) for estimating site occupancy. Conducting an area-search survey of a 2.25 ha plot required an average of 19 min longer than conducting an 18-min point-count survey (15 min of silent observation followed by 3 min of playbacks) at the same location. However, the estimated detection probability (p) during a single visit was lower for point counts (0.41 ± 0.05) than for area searches (0.69 ± 0.05), while both methods generated similar occupancy (Ψ)...

Geographic variation, null hypotheses, and subspecies limits in the California Gnatcatcher: A response to McCormack and Maley

ABSTRACT We interpreted the results of nuclear DNA sequencing to be inconsistent with the recognition of California Gnatcatcher (Polioptila californica) subspecies. McCormack and Maley (2015) suggested that our data did support 2 taxa, one of which was P. c. californica, listed as Threatened under the Endangered Species Act (ESA). We summarize here how 2 sets of researchers with access to the same data reached different conclusions by including different analyses. We included the southern subspecies' boundary from the taxonomy of Atwood (1991), the taxonomic basis for the ESA listing, which resulted in an Analysis of Molecular Variance that provided no support for subspecies. In contrast, using a novel taxonomic hypothesis without precedent in the literature, McCormack and Maley (2015) found statistically significant FST values for 2 loci, which they suggested supports P. c. californica. We propose that our mitochondrial and nuclear data had sufficient power to capture geographical structure at either the...

Subspecies and the philosophy of science

Phylogenetic methods increasingly are brought to bear on questions of subspecies taxonomy, but several recent examples highlight the need for a clear and consistent philosophical approach to how genetic data are used to assess subspecies limits. Such standards are crucial conceptually, whether or not taxonomic decisions affect conservation decisions, as they might in a recent study focused on the California Gnatcatcher (Polioptila californica), a taxon currently protected under the U.S. Endangered Species Act. It is also crucial that any adopted framework allows each of a full range of alternatives to be either supported or rejected. In this spirit, in addition to recommending best practices, I propose an amendment to the phylogenetic species concept to include a subspecies category.

Interpreting negative results with taxonomic and conservation implications: Another look at the distinctness of coastal California Gnatcatchers

ABSTRACT A recent study by Zink et al. (2013) raises questions about how to interpret negative results in studies when the distinctness of a species of conservation concern is in question. Zink et al. found no evidence for genetic or ecological distinctness of the coastal California Gnatcatcher (Polioptila californica californica). We discuss why the genetic markers they chose were not well suited to the question of distinctness and how they overinterpreted negative results in their genetic and ecological analyses. We reanalyze their genetic data and find evidence that several genetic loci show significant differentiation in the coastal California Gnatcatchers. We provide recommendations for best practices in determining distinctness in phenotype, genetics, and ecology for California Gnatcatchers and other populations of conservation concern.

Predicting the impact of fire on a vulnerable multi-species community using a dynamic vegetation model

Conservation management under human-induced changes to disturbance requires tools that can balance the needs of multiple species with different life histories and habitat requirements. Despite this urgent conservation need, landscape management typically focuses on single species and rarely includes the influence of disturbance-dependent vegetation transitions on multiple target species. In this paper, we describe a simulation model that achieves these goals, ranking possible fire management strategies from the viewpoint of protecting endangered coastal Southern Californian wildlife. The model involves the direct and indirect effects of fire on four animal species of conservation concern (coastal cactus wren, California gnatcatcher, Stephens’ kangaroo rat, and Pacific pocket mouse) and five vegetation types (grass, coastal sage scrub, obligate seeding and resprouting chaparral, resprouting-only chaparral, and woodlands). Using historical fire records for the region, we predicted spatially-explicit fire frequencies and ignition probabilities. For these predictions, we simulated the location and extent of fires. Combining fire history and vegetation transition data from 1933 to 2003, we specified vegetation change probabilities under simulated fire regimes. Fire occurrence in a location altered habitat suitability, directly for each of the animal species and indirectly by changing the vegetative community. For some open-habitat species, such as the Stephens’ kangaroo rat and Pacific pocket mouse, fairly frequent fire is required to reduce the density of invasive grasses and herbs. For other species, such as the coastal cactus wren and California gnatcatcher, frequent fire destroys the mature coastal sage scrub on which these species depend. The model includes a management component, allowing us to rank fire management actions. Over a 50-year time horizon, we find that populations of California gnatcatchers and Pacific pocket mouse are highly variable, and the pocket mouse is particularly prone to decline, despite prescribed burns designed to boost population viability. California gnatcatchers were also likely to be extirpated in the model, with relatively small extirpation risks for the cactus wren and Stephens’ kangaroo rat. Despite conflicting requirements with respect to fire and differing life history traits among the four animals, we identified a beneficial strategy for our four target species, namely, controlling fire in coastal sage scrub.

Effects of habitat quality and wildfire on occupancy dynamics of Coastal California Gnatcatcher (Polioptila californica californica)

ABSTRACT Habitat Conservation Plans (HCPs) are a mechanism used for conserving land and often have an umbrella species associated with them. We conducted occupancy surveys for an umbrella species, the Coastal California Gnatcatcher (Polioptila californica californica), from 2004 to 2009 in San Diego County, California, focusing on preserve lands associated with HCPs. We investigated the effects of habitat quality classification, elevation, distance to coast, and heat load on gnatcatcher occupancy, extinction, and colonization probabilities. Our work focused on these factors throughout the range of this species in San Diego County where, through conservation agreements, a preserve system has been assembled addressing management considerations at a landscape scale. In addition, a large wildfire in 2003 burned 17,044 ha, roughly 1/3 of preserve lands, thus we were able to investigate the recolonization process associated with this event. We found that occupancy increased with habitat quality and over time, b...

Phylogeography of the California Gnatcatcher (Polioptila californica) using multilocus DNA sequences and ecological niche modeling

ABSTRACT. An important step in conservation is to identify whether threatened populations are evolutionarily discrete and significant to the species. A prior mitochondrial DNA (mtDNA) phylogeographic study of the California Gnatcatcher (Polioptila californica) revealed no geographic structure and, thus, did not support the subspecies validity of the threatened coastal California Gnatcatcher (P. c. californica). The U.S. Fish and Wildlife Service concluded that mtDNA data alone were insufficient to test subspecies taxonomy. We sequenced eight nuclear loci to search for historically discrete groupings that might have been missed by the mtDNA study (which we confirmed with new ND2 sequences). Phylogenetic analyses of the nuclear loci revealed no historically significant groupings and a low level of divergence (G ST = 0.013). Sequence data suggested an older population increase in southern populations, consistent with niche modeling that suggested a northward range expansion following the Last Glacial Maximum...

Using California Gnatcatcher to Test Underlying Models in Habitat Conservation Plans

Abstract: Habitat Conservation Plans are a widely used strategy to balance development and preservation of species of concern and have been used in southern California, USA, to protect the coastal California gnatcatcher (Polioptila californica). Few data exist on gnatcatcher abundance and distribution, and existing data have problems with issues of closure (i.e., sampling occurs in a short enough time period such that abundance or distribution are not changing), detectability, and proper attention to probability‐based sampling schemes. Thus, a habitat model has been relied upon in reserve design. California gnatcatchers are the flagship and umbrella species of many plans and we provide the first estimates that incorporate probabilistic sampling and test predictions from the habitat model. Probability of occurrence was 26% (SĚ = 0.06); however, occupancy varied by modeled habitat quality with slopes &lt;40%, warm, and wet sagebrush habitat having higher occupancy probabilities. Interpreting abundance and occupancy probabilities by vegetation type was complicated by error detected in Geographic Information System vegetation metadata files. The slope (1.08, SĚ = 0.66), temperature (0.79, SĚ = 0.70), and precipitation (—2.62, SĚ = 1.21) variables associated with habitat models were stronger influences on occupancy than was patch size (0.48, SĚ = 0.66). Previous models weight patch size equal to slope and climate. Our work demonstrates that probabilistic sampling can be carried out on a large scale and the results provide better information for managers to make decisions about their reserves.

Type I errors linked to faulty statistical analyses of endangered subspecies classifications

Legal issues related to subspecies identification frequently occur through the im plementation of the 1973 Endangered Species Act (ESA). A listing under the ESA requires management actions to ensure the continued existence of the taxa. However, these actions often have important social, economic, and political implications. We ex amined the statistical methods of morphological analysis used in subspecies identifica tion. Methods are illustrated using the California gnatcatcher (Polioptila californica), which was incorrectly listed under the ESA due to misinterpretation of morphological data. We found that inferences based on tests of sample means (i.e., ?-test, Hotelling's T2-statistic), cluster analysis, and discriminant analysis were subject to high rates of false positives (identification of subspecies when none exist; Type I error). These sim ple tests ignore the common occurrence of spatial clines in animal tracts. Alternatively, spline-regression and step-regression procedures were found to be quite robust yet had high resolution in finding subspecies break locations.