John Perrine

California Polytechnic State University at San Luis Obispo, Biological Sciences, Faculty Member

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Papers by John Perrine

Extinction, Recovery, and the Endangered Species Act

Cambridge University Press eBooks, May 21, 2001

... Demographic stochasticity primarily affects populations with less than ﬁfty to one hundred in... more

Saving Lives and Training the Next Generation: State Route 101 Wildlife Corridor Safety Project

State Route (SR) 101 north of San Luis Obispo, California is a major regional traffic corridor wi... more State Route (SR) 101 north of San Luis Obispo, California is a major regional traffic corridor with peak weekday traffic volumes of approximately 4,000 vehicles per hour. State Route 101 also bisects a major wildlife corridor in and near the Los Padres National Forest in the central coast region of California. Animal-vehicle collisions (AVCs) with large mammals including mule deer (Odocoileus hemionus), black bear (Ursus americanus), mountain lion (Puma concolor), and feral pig (Sus scrofula) are a safety issue. Data provided by California Department of Fish and Wildlife indicates this section of highway may have a higher than normal AVC rate for black bear compared to other areas in the State. To develop solutions, Caltrans initiated an ongoing collaboration with California Polytechnic State University (Calpoly) in San Luis Obispo. Starting in 2009, students used automatic camera stations, trackplates and daily drive transects to document wildlife roadkills, roadside activity and use of existing underpasses for a wildlife connectivity study associated with a proposed median barrier project. Results from this study helped guide design decisions for a wildlife exclusion fence in a roadkill hotspot located in the same area. The project includes 2.5 miles of wildlife exclusion fence installed on both sides of SR 101, four jump-outs constructed at strategic locations to allow wildlife that become trapped along the roadway to escape from the highway corridor, and four electric mats installed as wildlife guards to discourage wildlife (bears in particular) from entering the highway corridor at unfenced roadways that intersect SR 101. The fencing project was funded through the Federal Highway Administration’s Transportation Enhancement Program in 2009 and was completed in April 2012. Currently, Calpoly students are monitoring the fence’s effectiveness at reducing roadkills while maintaining regional wildlife connectivity. Post-construction surveys began in summer 2012 and will continue for at least 12 months to allow for direct comparison with the 2009 pre-construction data. Students are conducting roadkill surveys to determine whether AVC rates have been reduced within the project area. Automatic camera stations have been deployed at the electric mats, jump-outs and undercrossings to quantify species-specific responses to these features. Initial results have documented the electric mats deterring bears from entering the road corridor, but suggest the design should be modified to better exclude deer. Results have also indicated that multiple species are using the undercrossings and deer are using the jump-outs. On-going monitoring and collaboration with partners has allowed Caltrans to integrate concerns about AVC rates and the preservation of wildlife habitat connectivity into the transportation planning process. The project received the Caltrans “Excellence in Transportation Award” in 2012 and the California Transportation Foundation 2013 Safety Project of the Year Award.

Documentation of microplastics in the gastrointestinal tracts of terrestrial raptors in central California, USA

California Fish and Wildlife Journal

Microplastics are persistent environmental contaminants that to date have been studied primarily ... more 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 microb...

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Right on track? Performance of satellite telemetry in terrestrial wildlife research

PLOS ONE, 2019

Satellite telemetry is an increasingly utilized technology in wildlife research, and current devi... more Satellite telemetry is an increasingly utilized technology in wildlife research, and current devices can track individual animal movements at unprecedented spatial and temporal resolutions. However, as we enter the golden age of satellite telemetry, we need an in-depth understanding of the main technological, species-specific and environmental factors that determine the success and failure of satellite tracking devices across species and habitats. Here, we assess the relative influence of such factors on the ability of satellite telemetry units to provide the expected amount and quality of data by analyzing data from over 3,000 devices deployed on 62 terrestrial species in 167 projects worldwide. We evaluate the success rate in obtaining GPS fixes as well as in transferring these fixes to the user and we evaluate failure rates. Average fix success and data transfer rates were high and were generally better predicted by species and unit characteristics, while environmental characteristics influenced the variability of performance. However, 48% of the unit deployments ended prematurely, half of them due to technical failure. Nonetheless, this study shows that the performance of satellite telemetry applications has shown improvements over time, and based on our findings, we provide further recommendations for both users and manufacturers.

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A hierarchical modeling approach to predict the distribution and density of Sierra Nevada Red Fox (Vulpes vulpes necator)

Journal of Mammalogy

Carnivores play critical roles in ecosystems, yet many species are declining worldwide. The Sierr... more 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...

format_quoteMinimum temperature and snow water equivalent were found to have 100% probability of negatively impacting SNRF density.format_quote

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Camera Study for Mammalian Carnivore Presence across Seasons in Montana de Oro State Park, San Luis Obispo County, CA

Montana de Oro (MDO) is one of the largest state parks in California. Little is known however abo... more Montana de Oro (MDO) is one of the largest state parks in California. Little is known however about its wildlife or their habits. Large predators such as mountain lion (Puma concolor) and black bear (Ursus americanus), and non-native species such as red fox (Vulpes vulpes) and feral pig (Sus scropha) are of management concern because of their potentially dramatic ecological roles. Cameras were deployed at 5 sites along the Coon Creek hiking trail in spring (May 3-June 7), summer (July 15-August 19), and fall (October 10-November 23) sessions with the goal of collecting a minimum of 28 survey nights of data. From this data species richness, latency to first detection, and activity patterns were examined. Overall, 19 different species of terrestrial vertebrates were detected: 8 species of birds, 11 species of mammals, and 7 species of mammalian carnivores (including the Virginia opossum (Didelphis virginiana), an introduced marsupial). Mountain lion was the only species of management concern detected, and it was only detected once during the summer session. ANVOA testing found no significant difference in species richness between seasons (α=0.05, P>0.05). Latency to first detection was too variable for statistical analysis, and there was no apparent trend for seasonal effect within any species. Daily activity patterns were analyzed using a chi-squared goodness of fit test (α=0.05) for striped skunk (Mephitis mephitis) (Pspring=0.41, n=8), mule deer (Odocoileus hemionus) (Pfall=0.03, n=10), and gray fox (Urocyon cinereoargenteus) (Pspring=0.032, n=16; Psummer<0.001, n=89; Pfall<0.001, n=59). All tests yielding significant P-values also indicated a preference for crepuscular activity. Contingency table analysis indicated there was an interaction between time of day and season for gray fox (P<0.001), with the strongest effect in dawn and spring, and night and fall. This interaction is unexplained. Lack of detection of black bear, red fox, and feral pig suggest that they are not present within the Coon Creek watershed of MDO. Additional studies on a larger spatial scale are required to determine their status throughout the park. Mountain lion likewise require further study on a larger scale to determine how they are using MDO habitat.

format_quoteGray fox showed significant crepuscular activity patterns across seasons, with P-values indicating strong preference for dawn in spring and dusk in summer.format_quote

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$Research paper thumbnail of Sierra Nevada Red Fox (\u3ci\u3eVulpes vulpes necator\u3c/i\u3e): A Conservation Assessment$

Sierra Nevada Red Fox (\u3ci\u3eVulpes vulpes necator\u3c/i\u3e): A Conservation Assessment

One goal of the Sierra Nevada Forest Plan Amendment (SNFPA) 2001 and 2004 Records of Decision was... more One goal of the Sierra Nevada Forest Plan Amendment (SNFPA) 2001 and 2004 Records of Decision was to protect and recover native Sierra Nevada red fox (Vulpes vulpes necator) populations in the Sierra Nevada (USDA Forest Service 2001 p. 14). To accomplish this goal, the ROD commits the U.S. Department of Agriculture (USDA) Forest Service to completing a conservation assessment for the Sierra Nevada red fox in cooperation with other federal, state, and local agencies, as well as Tribal governments. This conservation assessment synthesizes the best available scientific information and thought concerning habitat relationships, population status and trends, historical and current distributions, and key threats potentially affecting the distribution, abundance and persistence of the Sierra Nevada red fox. Biologists and resource managers from the Forest Service, US Department of the Interior (USDI) National Park Service, USDI Fish and Wildlife Service, US Geological Survey, University of ...

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$Research paper thumbnail of Meeting the Challenges: The Western Section\u27s Role in Developing Tomorrow\u27s Resource Management Professionals$

Meeting the Challenges: The Western Section\u27s Role in Developing Tomorrow\u27s Resource Management Professionals

The following is a slightly edited version of a plenary address delivered at the Western Section ... more The following is a slightly edited version of a plenary address delivered at the Western Section annual meeting in January 2009. The plenary theme was “The view from the future: wildlife management challenges and opportunities of the next 100 years.” Key references are listed at the end of the address. Readers will also be interested in the Winter 2009 (Vol. 3, No. 4) issue of The Wildlife Professional, which contains a special section on the preparation and training of future wildlife professionals

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Mammal use of undercrossings is influenced by openness and proximity to riparian corridors

Wildlife Research

Context: A central problem in road ecology is the need to minimise roadkill without exacerbating ... more Context: A central problem in road ecology is the need to minimise roadkill without exacerbating fragmentation. The best current solution to this problem is wildlife-exclusion fencing combined with crossing structures. However, because species vary in their propensity to use crossing structures, optimising their design for a suite of species remains a challenge. Aims: We investigated medium-and large-mammal use of undercrossings along Highway 101 in the Central Coast of California. Specifically, we quantified how undercrossing size, surrounding habitat, and the presence of a wildlife-exclusion fence, influenced overall species richness, as well as use by black bear, mule deer, puma, and bobcat. Methods: Using wildlife cameras, we documented mammal use at 11 undercrossings in our study area. We calculated the openness index of each undercrossing and remotely measured habitat features, such as percentage tree cover, and distance to nearest stream. We determined the relative importance of these factors on overall species richness, and the activity of focal species, using generalised linear mixed models in an information-theoretic framework. Key results: Mesocarnivores used a wider variety of undercrossings, and used them more frequently, than did larger mammals. Species richness and bear activity were greater closer to streams, and there was more bear activity at undercrossings within the wildlife-exclusion fence zone than outside it. Deer activity was strongly and positively related to undercrossing openness. Our puma and bobcat analyses were uninformative, likely because we detected puma too infrequently, and because bobcats showed little variation in use across sites. Conclusions: Our results support previous research highlighting natural travel corridors (e.g. riparian areas) as important places for wildlife crossings, both for a diversity of medium–large mammals and a low-density large carnivore. Ungulates may be the most selective taxa in respect to undercrossing use. Implications: Large, open undercrossings along natural travel routes accommodate the greatest diversity of medium–large mammal species.

MARK Occupancy Analysis Input File

This file contains the site-specific covariates and capture histories for the 34 occupancy-modele... more This file contains the site-specific covariates and capture histories for the 34 occupancy-modeled species. Each row contains a capture history for a species at a site along with that site's model covariates, including era, region, slope, elevation, elevation squared, T100 (number of traps x 100), and logT (log of the number of traps). There are also two columns for latitude ("lat") and longitude ("long"), but these were not used in the occupancy analysis. This file is formatted as it was used in the MARK analysis

Data from: Spatially heterogeneous impact of climate change on small mammals of montane California

Resurveys of historical collecting localities have revealed range shifts, primarily leading edge ... more 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

Spatially heterogeneous impact of climate change on small mammals of montane California

Proceedings of the Royal Society B: Biological Sciences, 2014

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Addressing biased occurrence data in predicting potential Sierra Nevada red fox habitat for survey prioritization

Endangered Species Research, 2011

The Sierra Nevada red fox Vulpes vulpes necator is listed as a threatened species under the Calif... more The Sierra Nevada red fox Vulpes vulpes necator is listed as a threatened species under the California Endangered Species Act. It originally occurred throughout California's Cascade and Sierra Nevada mountain regions. Its current distribution is unknown but should be determined in order to guide management actions. We used occurrence data from the only known population, in the Lassen Peak region of northern California, combined with climatic and remotely sensed variables, to predict the species' potential distribution throughout its historic range. These model predictions can guide future surveys to locate additional fox populations. Moreover, they allow us to compare the relative performances of presence-absence (logistic regression) and presence-only (maximum entropy, or Maxent) modeling approaches using occurrence data with potential false absences and geographical biases. We also evaluated the recently revised Maxent algorithm that reduces the effect of geographically biased occurrence data by subsetting background pixels to match biases in the occurrence data. Within the Lassen Peak region, all models had good fit to the test data, with high values for the true skill statistic (76-83%), percent correctly classified (86-92%), and area under the curve (0.94-0.96), with Maxent models yielding slightly higher values. Outside the Lassen Peak region, the logistic regression model yielded the highest predictive performance, providing the closest match to the fox's historic range and also predicting a site where red foxes were subsequently detected in autumn 2010. Subsetting background pixels in Maxent reduced but did not eliminate the effect that geographically biased occurrence data had on prediction results relative to the Maxent model using full background pixels.

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Evaluation of species distribution models by resampling of sites surveyed a century ago by Joseph Grinnell

Ecography, 2013

Species distribution models (SDMs) are commonly applied to predict species ' responses to anticip... more 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-confi dence 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 confi dently assign absences at test sites where species were undetected. SDMs were evaluated using species ' presences combined with this high-confi dence absence (HCA) set, a low-confi dence set in which non-detections were assumed to indicate absence (LCA), and randomly located ' pseudoabsences ' (PSA). Model performance increased signifi cantly with the quality of absences (mean AUC Ϯ SE: 0.76 Ϯ 0.01 for PSA, 0.79 Ϯ 0.01 for LCA, and 0.81 Ϯ 0.01 for HCA), and apparent diff erences 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 aff ects 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.

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Why Economics Matters for Endangered Species Protection

Conservation Biology, 1999

We offer three reasons why economics matters more to species protection than many people think an... more We offer three reasons why economics matters more to species protection than many people think and what this implies for the ongoing debate over the reauthorization of the Endangered Species Act of 1973. Economics matters because (1) human behavior generally, and economic parameters in particular, help determine the degree of risk to a species; (2) in a world of scarce resources, the opportunity cost of species protection-the costs of reduced resources for other worthwhile causes-must be taken into account in decision making; and (3) economic incentives are critical in shaping human behavior, and consequently the recovery of species. Endangered species protection that explicitly addresses these basic principles can avoid wasting valuable resources that yield no gain in species protection.

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Science and Uncertainty in Habitat Conservation Planning

American Scientist, 2001

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

Conservation Genetics, 2007

California is home to both the native statethreatened Sierra Nevada red fox (Vulpes vulpes necato... more California is home to both the native statethreatened 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.

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Examining the Impacts of State Route 101 on Wildlife Using Road Kill Surveys and Remote Cameras

Roads can negatively impact the survival of wildlife populations through additional mortality fro... more Roads can negatively impact the survival of wildlife populations through additional mortality from road kill and population fragmentation caused by road avoidance behaviors. The 11.9 mile section of State Route 101 between the towns of San Luis Obispo and Atascadero, CA, USA, crosses a mountain lion movement corridor and an area important to maintaining ecological connectivity between protected lands in the Los Padres National Forest to the north and south. I examined the spatial patterns and landscape and roadway factors associated with road kill occurrence for six taxa; large mammals, mesocarnivores, squirrels, rabbits, birds and raptors. road kills were documented using vehicle-based surveys. Small mammals were the most common road kill (58.3%), followed by mesocarnivores (10.9%), birds (10.6%), rabbits (5.1%), large mammals (3.3%) and raptors (3.2%). Twenty-nine large mammal road kills were observed; eighteen mule deer, six black bears and five feral pigs. Road kill was highest ...

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Meeting the Challenges: The Western Section's Role in Developing Tomorrow's Resource Management Professionals

Transactions of the Western Section of the Wildlife Society, 2010

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Conservation Assessment for the Sierra Nevada Red Fox (Vulpes vulpes necator)

This conservation assessment provides a science-based, comprehensive assessment of the status of ... more This conservation assessment provides a science-based, comprehensive assessment of the status of the Sierra Nevada red fox (Vulpes vulpes necator) and its habitat. It identifies and evaluates key risk factors affecting viability and describes general Conservation Options. The current distribution, abundance and population trend for Sierra Nevada red fox are uncertain, but there is little evidence of increase or expansion. It is unclear whether this native mountain fox persists outside of the Lassen Peak region.

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