• A management experiment evaluating nest-site selection by beach-nesting birds

      Swaisgood, Ronald R.; Nordstrom, Lisa A.; Schuetz, Justin G.; Boylan, Jeanette T.; Fournier, Joelle J.; Shemai, Barak (2018)
      It is important to understand nest-site selection in avian species to inform appropriate conservation management strategies. Studies of habitat selection alone, however, may be misleading unless the consequences for survival and reproduction are also documented....
    • A multi-model approach to guide habitat conservation and restoration for the endangered San Bernardino kangaroo rat

      Chock, Rachel Y.; Hennessy, Sarah McCullough; Wang, Thea B.; Gray, Emily; Shier, Debra M. (2020)
      The San Bernardino kangaroo rat (Dipodomys merriami parvus) is a federally listed endangered species endemic to Southern California and limited to three remaining populations. Its native habitat of alluvial fan sage scrub faces many anthropogenic threats, including urban and agricultural development, and the resulting flood control and fire suppression. With the loss of natural processes such as scouring or burning from floods and fires, the mosaic of seral stages across the landscape has shifted to dense vegetation, and active restoration may be necessary to provide suitable habitat for the San Bernardino kangaroo rat. Species distribution modeling using the partitioned Mahalanobis distance method on all occurrence points collected in the past 16 years revealed that alluvial scrub cover and fluvent soils were most strongly associated with San Bernardino kangaroo rat occupancy. Through surveys at 14 locations across the species’ range, we identified non-native grass cover, shrub cover, bare ground and sandy soils as microhabitat features related to San Bernardino kangaroo rat abundance. We also calculated the optimal range of cover for each habitat type that was correlated with higher kangaroo rat abundance. The results of this multiple-model approach can be used by the agencies to assess the value of conserved habitat, set targets for microhabitat enhancement to facilitate population growth and expansion, or identify receiver sites should translocation be required for recovery. This work lays the foundation for more coordinated and strategic restoration efforts, given the compressed and rigid timelines of development projects that continue to impact remaining San Bernardino kangaroo rat populations.
    • Capturing pests and releasing ecosystem engineers: translocation of common but diminished species to re-establish ecological roles

      Swaisgood, Ronald R.; Montagne, J.P.; Lenihan, C. M.; Wisinski, Colleen L.; Nordstrom, Lisa A.; Shier, Debra M. (2019)
      Translocation of abundant but declining ecologically important species for re-establishing more sustainable ecosystem function is a neglected but promising form of conservation intervention. Here, we developed a translocation program in which we capture pests and release ecosystem engineers, by relocating California ground squirrels Otospermophilus beecheyi from areas where they are unwanted to conserved lands where they can perform ecosystem services such as burrowing and vegetation alteration. We accomplished this using an experimental approach in which some factors were measured or experimentally manipulated, while others were held constant. We translocated 707 squirrels and examined survival and movement patterns as a function of several translocation tactics and ecological factors. We released squirrels at 9 different plots with varying ecological contexts and at each plot experimentally manipulated post-release habitat using mowing, mowing plus the use of augers to establish starter burrows, and controls that remained unmanipulated. The most influential variables affecting short-term survival, dispersal, and long-term persistence were factors relating to soils and vegetation structure. Translocated squirrels had higher initial survival on plots where dense exotic grasses were experimentally altered, greater dispersal when released at sites with less friable clay soils, and improved long-term persistence at sites characterized by more friable soils associated with metavolcanic than alluvial geological layers. Squirrel persistence was also improved when translocations supplemented previous translocation sites than during initial translocations to sites containing no resident squirrels. Our results demonstrate how California ground squirrels can be successfully translocated as part of a larger objective to favorably alter ecological function in novel grassland ecosystems dominated by non-native vegetation. In broader context, our study highlights the importance of testing release strategies, and examining habitat variables and restoration techniques more closely when selecting release sites to improve translocation outcomes.
    • Chilled frogs are hot: hibernation and reproduction of the Endangered mountain yellow-legged frog Rana muscosa

      Santana, Frank E.; Swaisgood, Ronald R.; Lemm, Jeffrey M.; Fisher, Robert N.; Clark, Rulon W. (2015)
      In the face of the sixth great extinction crisis, it is imperative to establish effective breeding protocols for amphibian conservation breeding programs. Captive efforts should not proceed by trial and error, nor should they jump prematurely to assisted reproduction techniques, which can be invasive, difficult, costly, and, at times, counterproductive. Instead, conservation practitioners should first look to nature for guidance, and replicate key conditions found in nature in the captive environment, according to the ecological and behavioral requirements of the species. We tested the effect of a natural hibernation regime on reproductive behaviors and body condition in the Endangered mountain yellow-legged frog Rana muscosa. Hibernation had a clear positive effect on reproductive behavior, manifesting in vocal advertisement signaling, female receptivity, amplexus, and oviposition. These behaviors are critical components of courtship that lead to successful reproduction. Our main finding was that captive R. muscosa require a hibernation period for successful reproduction, as only hibernated females produced eggs and only hibernated males successfully fertilized eggs. Although hibernation also resulted in a reduced body condition, the reduction appeared to be minimal with no associated mortality. The importance of hibernation for reproduction is not surprising, since it is a major component of the conditions that R. muscosa experiences in the wild. Other amphibian conservation breeding programs can also benefit from a scientific approach that tests the effect of natural ecological conditions on reproduction. This will ensure that captive colonies maximize their role in providing genetic reservoirs for assurance and reintroduction efforts.
    • Conserving San Diego’s endemic geophytes

      Davitt, Joe (2017)
      The Mediterranean climate and diverse habitats that typify San Diego County have resulted in both the highest number of plant taxa found in any county in the United States, and plants with adaptations that make species assessment challenging. Geophytes are perennial plants with underground storage structures such as bulbs, corms, and rhizomes, which are particularly common in Mediterranean climates. With the goal of capturing the breadth of a species’ genetic diversity in the seed bank, we must assess a species population size across its entire range. Yet the ability of geophytes to remain dormant underground for prolonged periods of time make their assessment very difficult. The problem is further exacerbated by drought and the inherent unpredictability of future weather as a result of climate change. Because of this we must monitor and make seed collections from rare geophyte populations across many different years and under different climatic conditions.
    • Effects of artificial light at night on the foraging behavior of an endangered nocturnal mammal

      Shier, Debra M.; Bird, Alicia K.; Wang, Thea B. (2020)
      ...The endangered Stephens’ kangaroo rat (SKR), Dipodomys stephensi, is a nocturnal rodent threatened by habitat destruction from urban expansion. The degree to which ALAN impacts their recovery is unknown....
    • Experimental habitat restoration for conserved species using ecosystem engineers and vegetation management

      Hennessy, Sarah McCullough; Deutschman, D. H.; Shier, Debra M.; Nordstrom, Lisa A.; Lenihan, C.; Montagne, J.P.; Wisinski, Colleen L.; Swaisgood, Ronald R. (2016)
      We manipulated vegetation and the ecosystem engineer California ground squirrel, Otospermophilus beecheyi, in a replicated, large-scale field experiment for 2 years, and monitored through a third year…. The overarching goal of this experiment was to provide conservation managers with a cost-effective tool for restoring degraded habitats to a hybrid ecosystem state with improved suitability for species of conservation concern, in this case, the western burrowing owl Athene cunicularia hypugaea.
    • Fitness costs associated with ancestry to isolated populations of an endangered species

      Wilder, Aryn P.; Navarro, Asako Y.; King, Shauna N. D.; Miller, William B.; Thomas, Steven M.; Steiner, Cynthia C.; Ryder, Oliver A.; Shier, Debra M. (2020)
      ... The endangered Pacific pocket mouse (Perognathus longimembris pacificus) persists in three isolated populations in southern California. Mitochondrial and microsatellite data indicated that effective population sizes were extremely small (Ne< 50), and continued declines prompted a conservation breeding program founded by individuals from each population....
    • Hepatitis and splenitis due to systemic tetratrichomoniasis in an American white pelican (Pelecanus erythrorhynchos)

      Burns, Rachel E.; Braun, Josephine; Armién, Aníbal G.; Rideout, Bruce (2013)
      A free-ranging, young adult, female American white pelican (Pelecanus erythrorhynchos), found dead on the grounds of the San Diego Zoo Safari Park in Southern California, had severe multifocal to coalescing necrotizing hepatitis and splenitis on postmortem examination. Histologically, within the large areas of necrosis were myriad pleomorphic, 5–20 µm in diameter, protozoal organisms with 1 to multiple nuclei. Ultrastructurally, the organisms were consistent with a trichomonad flagellate. Polymerase chain reaction and sequencing of the small subunit ribosomal RNA gene identified nucleotide sequences with 99% identity to Tetratrichomonas gallinarum, which is a common inhabitant of the intestinal tract of galliform and anseriform birds that has occasionally been associated with disease, including typhlitis and hepatitis. Damage to the cecal mucosa in the pelican from trematodes and secondary bacterial infection could have allowed invasion and systemic dissemination of the organism. Exposure of the pelican to a variety of native and exotic anseriform and galliform birds at the zoological institution could have led to cross-species infection and severe manifestation of disease in a novel host.
    • Hierarchical dominance structure in reintroduced California condors: correlates, consequences, and dynamics

      Sheppard, James; Walenski, Matthew; Wallace, Michael P.; Vargas Velazco, J.J.; Porras, C.; Swaisgood, Ronald R. (2013)
      Populations of reintroduced California condors (Gymnogyps californianus) develop complex social structures and dynamics to maintain stable group cohesion, and birds that do not successfully integrate into group hierarchies have highly impaired survivability. Consequently, improved understanding of condor socioecology is needed to inform conservation management strategies…
    • Histopathologic findings in free-ranging California hummingbirds, 1996–2017

      Magagna, Michelle; Noland, Erica; Tell, Lisa A.; Purdin, Guthrum; Rideout, Bruce; Lipman, Max W.; Agnew, Dalen (2018)
      A histopathologic study of free-ranging hummingbirds in California was performed to identify mortality trends. Tissues from 61 wild hummingbirds representing five native California species collected by the San Diego Zoo from 1996 to 2016 or the Lindsay Wildlife Experience from 2015 to 2017 were histologically examined....
    • Historical and geographical patterns in Knemidocoptes mite infestations in Southern California birds

      Clark, Kevin B.; Rideout, Bruce; Garrett, Kimball L.; Unitt, Philip; O’Connor, Barry (2019)
      We investigated the causes of toe and foot loss and other deformities long observed in urban Brewer’s Blackbirds (Euphagus cyanocephalus) in southern California. Histopathologic evaluation showed that afflicted individuals suffered from infestations of mites compatible with Knemidokoptes spp. (scaly-leg mites). We developed a case definition based on gross lesions in confirmed cases and the scientific literature to search two large ornithological collections for specimens exhibiting these lesions. In evaluating specimens among seven species of the family Icteridae, we found 34 specimens in the two collections with lesions consistent with Knemidokoptes spp. Species afflicted included the Red-winged Blackbird (Agelaius phoeniceus; 12 of 978 specimens), Brewer’s Blackbird (10/337 specimens), Tricolored Blackbird (A. tricolor; 4/101 specimens), Brown-headed Cowbird (Molothrus ater; 4/828 specimens), and Great-tailed Grackle (Quiscalus mexicanus; 4/224 specimens). The earliest cluster of California specimens dated to 1962. Fourteen of the 34 specimens exhibiting the condition were collected since 1999. No specimens of the Yellow-headed Blackbird (Xanthocephalus xanthocephalus; 0 of 214 specimens) or Western Meadowlark (Sturnella neglecta; 0/278) were found with the condition.
    • Lead in ammunition: A persistent threat to health and conservation

      Johnson, C. K.; Kelly, T. R.; Rideout, Bruce (2013)
      Many scavenging bird populations have experienced abrupt declines across the globe, and intensive recovery activities have been necessary to sustain several species, including the critically endangered California condor (Gymnogyps californianus). Exposure to lead from lead-based ammunition is widespread in condors and lead toxicosis presents an immediate threat to condor recovery, accounting for the highest proportion of adult mortality….
    • Personality assessment in African elephants (Loxodonta africana): Comparing the temporal stability of ethological coding versus trait rating

      Horback, Kristina M.; Miller, Lance J.; Kuczaj, Stan A. (2013)
      The consistency of personality assessment was addressed in this study of 12 zoological African elephants living at the San Diego Zoo Safari Park in Escondido, CA, USA during the 2010 and 2011 summer seasons. Using 480 h of observational behavior data, three personality traits were determined based on behavior events, with the most significant correlations (two-tailed rs > 0.77, P < 0.005) being playful, curious, and sociable….
    • Reconsidering habitat associations in the Anthropocene

      Hennessy, Sarah McCullough; Marczak, Susanne A.; Nordstrom, Lisa A.; Swaisgood, Ronald R. (2018)
      The California ground squirrel (Otospermophilus beecheyi) is generally undervalued despite serving as an ecosystem engineer in grassland ecosystems. Evidence of significant engineering effects by squirrels indicates that population reductions have cascading effects on other species, including several conservation-dependent species. While the theory and practices behind habitat association studies are already well established, our application of this approach helped identify priority management options in degraded grasslands expected to change further under shifts in climate. In this study we conducted surveys for California ground squirrels throughout San Diego County grasslands and examined habitat covariates to determine the ecological variables currently associated with occurrence. The primary objectives were to 1) improve our understanding of the habitat variables associated with squirrel presence, and 2) develop a predictive model for squirrel habitat suitability at a local scale. The most predictive models included significant main effects for percent sand (as a component of soil texture) and vegetation cover. A 10% increase in vegetation cover was associated with 1.3 fold lower odds of squirrel presence, whereas a 10% increase in percent sand was associated with 2.0 times higher odds of squirrel presence. Comparison of the predictive accuracy of soil texture data at two scales (fine-scale field vs. landscape scale GIS layers) showed fine-scale field sampling has greater predictive strength. Because soil type is a logistically non-malleable factor for wildlife managers, it is important to categorize management sites by soil type to identify the potential for promoting fossorial species on the landscape. With the prospect of shifting landscape ecotones due to climate change, it is as important to understand the basic habitat requirements of keystone species as for rare species.
    • Rediscovery of the horseshoe shrimp Lightiella serendipita Jones, 1961 (Cephalocarida: Hutchinsoniellidae) in San Francisco Bay, California, USA, with a key to the worldwide species of Cephalocarida

      Garcia, Crystal; Woo, Isa; Rogers, D. Christopher; Flanagan, Alison M.; De La Cruz, Susan E. W.
      Lightiella serendipitaJones, 1961 was first discovered in San Francisco Bay, California in 1953, but it had not been observed since 1988. In 2017, a total of 13 adult L. serendipita specimens were found as part of a study in central San Francisco Bay, nearly doubling the total number of specimens ever collected. We measured vertical distribution of macroinvertebrates and environmental variables, including grain size and chemical composition of sediment samples, to evaluate potential features associated with the habitat of the species. Specimens were generally found in sediments with low organic matter (1.7–3%), high sulfate concentrations (594.6–647 ppm SO4), fine grain size (12.8–36.2% sand, 35.6–58% silt, 22.8–37.6% clay) and were mostly found in deep core sections (4–10 cm). Specimens were also consistently observed in cores containing tube-forming Polychaeta (i.e., Sabaco elongatus (Verrill, 1873) and Capitellidae), suggesting L. serendipita may have a commensal relationship with sedentary polychaetes, as do other cephalocaridans such as Lightiella incisaGooding, 1963. We provide a scanning electron micrograph of L. serendipita and the first complete key to the species in class Cephalocarida to help elucidate the taxonomy of this rare crustacean taxon. The perceived absence of L. serendipita in previous surveys of the Bay may be attributable to its rarity; however, additional research is needed to fully understand habitat requirements and population size of this unique endemic species.
    • Social learning in captive African elephants (Loxodonta africana africana)

      Greco, Brian J.; Brown, Tracey K.; Andrews, Jeff R. M.; Swaisgood, Ronald R.; Caine, Nancy G. (2013)
      …Social learning is assumed to be important for elephants, but evidence in support of that claim is mostly anecdotal. Using a herd of six adult female African bush elephants (Loxodonta africana africana) at the San Diego Zoo’s Safari Park, we evaluated whether viewing a conspecific’s interactions facilitated learning of a novel task….
    • Spatial and temporal response of wildlife to recreational activities in the San Francisco Bay ecoregion

      Reilly, M. L.; Tobler, Mathias W.; Sonderegger, D. L.; Beier, P. (2017)
      Non-motorized human recreation may displace animals from otherwise suitable habitat; in addition, animals may alter their activity patterns to reduce (or increase) interactions with recreationists. We investigated how hiking, mountain biking, equestrians, and recreationists with domestic dogs affected habitat use and diel activity patterns of ten species of medium and large-sized mammals in the San Francisco Bay ecoregion....
    • Using spatially-explicit population models to evaluate habitat restoration plans for the San Diego cactus wren (Campylorhynchus brunneicapillus sandiegensis)

      Conlisk, Erin; Motheral, Sara; Chung, Rosa; Wisinski, Colleen L.; Endress, Bryan A. (2014)
      A long-standing debate within conservation is how best to allocate limited management resources: should reserve area be increased, should anthropogenic disturbances be mitigated, or should connectivity be increased? We explore these issues for the San Diego cactus wren, a California Species of Special Concern…. Our modeling approach provides insight into the relative benefit of several realistic restoration scenarios, providing an important tool for species conservation and habitat restoration on complex landscapes.