Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and ...one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c. 400 000 years before present ( bp): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (greater-than-or-equal 99% Bayesian posterior probability); two that were more recently derived (rho estimate c. 20 000 bp) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c. 45 000 bp) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000-130 000 bp), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000-10 000 bp). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.
Microplastics are persistent environmental contaminants that to date have been studied primarily in aquatic systems, but few studies have examined their prevalence or impact in terrestrial trophic ...networks. A recent study documented microplastics in the gastrointestinal (GI) tracts of terrestrial raptors in central Florida. We used protocols based on that study to develop a baseline dataset of microplastics in the GI tracts of terrestrial raptors on the central coast of California. In 2021, Pacific Wildlife Care, a wildlife rehabilitation center in Morro Bay, CA, provided 16 raptor carcasses: three red-tailed hawks (Buteo jamaicensis), four red-shouldered hawks (Buteo lineatus), two great horned owls (Bubo virginianus), and seven barn owls (Tyto alba). We found microplastics in the GI tracts of all 16 birds, with a mean (± SE) of 12.25 (± 1.89) microplastic particles per bird. Of the 196 microplastic particles we observed, microfibers were the most abundant (58%), followed by microbeads (34%), and microfragments (8%). However, microbeads were the most prevalent, found in all 16 birds, followed by microfibers (15 birds), and microfragments (6 birds). The chemical composition and source of these contaminants remains unclear, along with the physiological and ecological implications to raptor populations and their ecosystems, and the extent to which microplastics occur in other terrestrial species and regions in California.
Species distribution models (SDMs) are commonly applied to predict species' responses to anticipated global change, but lack of data from future time periods precludes assessment of their ...reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high-confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900–1939) or modern (1970–2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the opposing time period and evaluated with data obtained from surveys conducted by Joseph Grinnell and his colleagues in the Sierra Nevada of California from 1900 to 1939 and modern resurveys from 2003 to 2011. Occupancy modeling was used to confidently assign absences at test sites where species were undetected. SDMs were evaluated using species' presences combined with this high-confidence absence (HCA) set, a low-confidence set in which non-detections were assumed to indicate absence (LCA), and randomly located ‘pseudoabsences’ (PSA). Model performance increased significantly with the quality of absences (mean AUC ± SE: 0.76 ± 0.01 for PSA, 0.79 ± 0.01 for LCA, and 0.81 ± 0.01 for HCA), and apparent differences between SDMs declined as the quality of test absences increased. Models projecting across time performed as well as when projecting within the same time period when assessed with threshold-independent metrics. However, accuracy of presence and absence predictions sometimes declined in cross-era projections. Although most variation in performance occurred among species, autecological traits were only weakly correlated with model accuracy. Our study indicates that a) the quality of evaluation data affects assessments of model performance; b) within-era performance correlates positively but unreliably with cross-era performance; and c) SDMs can be reliably but cautiously projected across time.
Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially ...replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in temperature better predicted the direction of shifts than change in precipitation, whereas the direction of shifts by low-elevation species was unpredictable by temperature or precipitation. While our results support previous findings of primarily upslope shifts in montane species, they also highlight the degree to which the responses of individual species vary across geographically replicated landscapes.
California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to ...multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911-1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F ST = -0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.
Island foxes (Urocyon littoralis) are listed as federally endangered on four of the six California Channel Islands to which they are endemic. The population on Santa Rosa Island declined by 99% ...during the 1990s due to golden eagle (Aguila chrysaetos) predation but is now recovering. This drastic population reduction provided an unprecedented opportunity to study home-range size and habitat use at very low levels of intraspecific competition. We used global positioning system (GPS) collars to track 14 adult male foxes from September 2009 through June 2010. On average, the collars operated for 16.5 wk, yielding 364 locations per fox. The 95% minimum convex polygon home ranges averaged 3.39 km2, which is several times larger than reported in previous studies conducted at higher population densities. We used Euclidean distance analysis to assess habitat selection within 95% kernel density isopleth (KDI) home ranges and 50% KDI core areas. The foxes used most of the available vegetation types but exhibited significant selection for valley bottoms and for bare areas and grassland at night. Our results, together with previous studies on island foxes, suggest an inverse relationship between home-range size and population density as has been shown for many other species. However, the pattern is confounded by differences among study areas and methods. We therefore recommend that this study be repeated when the Santa Rosa Island population recovers to its historic density of 4 adult foxes/km2 to better assess density-dependent changes in home-range size and habitat use.
Aim: The American pika (Ochotona princeps) appears to have experienced climatemediated upslope range contraction in the Great Basin of North America, but this result has not yet been extended to ...other portions of the pika's range. Our goals were: first, to determine the environmental parameters that most influence current pika distribution within California; second, to infer whether these constraints explain extirpations that have occurred in California; third, to predict future extirpations; and fourth, to advance methods for assessing the degree to which pikas and other climate-sensitive mammals are threatened by climate change. Location: Historical pika record locations in California, USA, spanning four degrees of latitude and longitude, from Mount Shasta to the southern Sierra Nevada. Methods: We identified 67 precise historical pika record locations and surveyed them exhaustively, over multiple years, to determine whether pika populations persist at those sites. We used an information theoretic approach and logistic regression to model current pika occupancy as a function of 16 environmental variables, tested our best-performing model as a predictor of historical occupancy, and then used our model to predict future pika occupancy given anticipated climate change. Results: Pikas no longer occurred at 10 of 67 (15%) historical sites in California. The best predictors of occupancy were average summer temperature and talus habitat area within a 1-km radius. A logistic model fitted to this relationship correctly predicted current occupancy at 94% of sites and correctly hindcasted past occupancy at 93% of sites, suggesting that the model has strong temporal transferability. Depending on the future climate scenario, our model projects that by 2070 pikas will be extirpated from 39% to 88% of these historical sites in California. Main conclusions: Our simple species distribution model for pikas performs remarkably well for both current and historical periods. Pika distribution appears to be governed primarily by behavioural restrictions mediated by summer temperature and by the configuration of talus habitat available to pikas locally. Pikas, and other montane species in the western USA, may be subjected to above-average exposure to climate change because summer temperature is projected to rise more than annual temperature.
Abstract
Carnivores play critical roles in ecosystems, yet many species are declining worldwide. The Sierra Nevada Red Fox (Vulpes vulpes necator; SNRF) is a rare and endangered subspecies of red fox ...limited to upper montane forests, subalpine, and alpine environments of California and Oregon, United States. Having experienced significant distribution contractions and population declines in the last century, the subspecies is listed as at-risk by relevant federal and state agencies. Updated information on its contemporary distribution and density is needed to guide and evaluate conservation and management actions. We combined 12 years (2009–2020) of detection and nondetection data collected throughout California and Oregon to model the potential distribution and density of SNRFs throughout their historical and contemporary ranges. We used an integrated species distribution and density modeling approach, which predicted SNRF density in sampled locations based on observed relationships between environmental covariates and detection frequencies, and then projected those predictions to unsampled locations based on the estimated correlations with environmental covariates. This approach provided predictions that serve as density estimates in sampled regions and projections in unsampled areas. Our model predicted a density of 1.06 (95% credible interval = 0.8–1.36) foxes per 100 km2 distributed throughout 22,926 km2 in three distinct regions of California and Oregon–Sierra Nevada, Lassen Peak, and Oregon Cascades. SNRFs were most likely to be found in areas with low minimum temperatures and high snow water equivalent. Our results provide a contemporary baseline to inform the development and evaluation of conservation and management actions, and guide future survey efforts.
Although biotic responses to contemporary climate change are spatially pervasive and often reflect synergies between climate and other ecological disturbances, the relative importance of climatic ...factors versus habitat extent for species persistence remains poorly understood. To address this shortcoming, we performed surveys for American pikas (Ochotona princeps) at > 910 locations in 3 geographic regions of western North America during 2014 and 2015, complementing earlier modern (1994–2013) and historical (1898–1990) surveys. We sought to compare extirpation rates and the relative importance of climatic factors versus habitat area for pikas in a mainland-versus-islands framework. In each region, we found widespread evidence of distributional loss— local extirpations, upslope retractions, and encounter of only old sign. Locally comprehensive surveys suggest extirpation of O. princeps from 5 of 9 new sites from the hydrographic Great Basin and from 11 of 29 sites in northeastern California. Although American pikas were recorded as recently as 2011 in Zion National Park and in 2012 from Cedar Breaks National Monument in Utah, O. princeps now appears extirpated from all reported localities in both park units. Multiple logistic regressions for each region suggested that both temperature-related and water-balance-related variables estimated from DAYMET strongly explained pika persistence at sites in the Great Basin and in Utah but not in the Sierra-Cascade “mainland” portion of northeastern California. Conversely, talus-habitat area did not predict American pika persistence in the Great Basin or Utah but strongly predicted persistence in the Sierra-Cascade mainland. These results not only add new areas to our understanding of long-term trend of the American pika's distribution, but also can inform decisions regarding allocation of conservation effort and management actions. Burgeoning research on species such as O. princeps has collectively demonstrated the heterogeneity and nuance with which climate can act on the distribution of mountain-dwelling mammals. Aunque las respuestas bióticas al cambio climático contemporáneo son espacialmente generalizadas y frecuentemente reflejan sinergias entre el clima y otros disturbios ecológicos, la importancia relativa de factores climáticos frente al área de hábitat para el mantenimiento de especies sigue siendo poco conocida. Para subsanar esta deficiencia, realizamos muestreos de la pika Americana (Ochotona princeps) en más de 910 sitios en 3 regiones geográficas del oeste de Norteamérica durante 2014 y 2015, complementando muestreos realizados en tiempos recientes (1994–2013) e históricos (1898–1990). Comparamos las tasas de extirpación para dilucidar la importancia relativa de los factores climáticos con respeto al área del hábitat disponible de las pikas bajo un marco conceptual de áreas continentales frente a zonas aisladas. En cada región, encontramos amplia evidencia en la pérdida de área de distribución - extinciones locales, desapariciones de las zonas bajas, y encuentro sólo de evidencia de ocupación pasada. Estudios localmente exhaustivos sugieren la extirpación de O. princeps en 5 de las 9 localidades nuevas muestreadas de la Gran Cuenca Hidrográfica (Great Basin), y en 11 de las 29 localidades en el noreste de California. Aunque las pikas todavía se encontraban en fechas recientes como en 2011 en el Parque Nacional Zion y en el Monumento Nacional Cedar Breaks en Utah en 2012, O. princeps ahora parece extirpada de todas las localidades donde fue encontrada anteriormente en ambos parques. Regresiones logísticas múltiples para cada región basados en factores ambientales como la temperatura y los factores relacionados con el balance del agua (ambos estimados por el DAYMET) explicaron claramente el patrón de persistencia de la pika en localidades de la Gran Cuenca y en Utah, pero no en el noreste de California, en el área “continental” de la montañas de Sierra Nevada y Cascades. Por el contrario, el hábitat de talud no predijo la persistencia de la pika en los sitios aislados en la Gran Cuenca y en Utah, pero lo predijo significativamente en el área continental (i.e., en las montañas de Sierra Nevada y Cascades). Estos resultados incrementan el conocimiento sobre la distribución histórica y la tendencia a largo plazo de la pika Americana. Este conocimiento también puede ayudar en la toma de decisiones sobre las prioridades en las acciones en conservación y manejo. El avance en conjunto en investigaciones de especies como O. princeps ha demostrado la heterogeneidad y la forma con que el clima actúa de diferente manera sobre la distribución de los mamíferos de montaña.
Red foxes (Vulpes vulpes) are native to boreal and western montane portions of North America but their origins are unknown in many lowland areas of the United States. Red foxes were historically ...absent from much of the East Coast at the time of European settlement and did not become common until the mid-1800s. Some early naturalists described an apparent southward expansion of native foxes that coincided with anthropogenic habitat changes in the region. Alternatively, red foxes introduced from Europe during Colonial times may have become established in the east and subsequently expanded their range westward. The red fox also was absent historically from most lowland areas of the western United States. Extant populations of red foxes in those areas are considered to have arisen from intentional introductions from the east (and by extension are putatively European), escapes or releases from fur farms, or range expansions by native populations. To test these hypotheses we compared mitochondrial DNA sequences (cytochrome b and D-loop) from 110 individuals from 6 recently established populations to 327 native (primarily historical) individuals from Eurasia, Alaska, Canada, the northeastern United States, and montane areas in the western contiguous United States, and to 38 individuals from fur farms. We found no Eurasian haplotypes in North America, but found native haplotypes in recently established populations in the southeastern United States and in parts of the western United States. Red foxes from the southeastern United States were closely related to native populations in eastern Canada and the northeastern United States, suggesting that they originated from natural range expansions, not from translocation of European lineages, as was widely believed prior to this study. Similarly, recently established populations in the Great Basin and in western Oregon originated primarily from native populations in western montane regions, but also contained a few nonnative North American haplotypes. In contrast, populations in western Washington and southern California contained nonnative, highly admixed stock that clearly resulted from intracontinental translocations. Several common haplotypes in these populations originated in regions where fur-farm stocks originated. Although European red foxes translocated to the eastern United States during Colonial times may have contributed genetically to extant populations in that region, our findings suggest that most of the matrilineal ancestry of eastern red foxes originated in North America.
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