• Soil and species effects on bark nutrient storage in a premontane tropical forest

      Jones, Jennifer M.; Heineman, Katherine D.; Dalling, James W. (2019)
      Background and aims Bark contains a substantial fraction of the nutrients stored in woody biomass, however the degree of functional coordination of bark, wood, and foliar nutrient pools, and its relationship to soil nutrient availability remains poorly understood....
    • Sound transmission in a bamboo forest and its implications for information transfer in giant panda ( Ailuropoda melanoleuca ) bleats

      Charlton, Benjamin D.; Owen, Megan A.; Keating, Jennifer L.; Martin-Wintle, Meghan S.; Zhang, Hemin; Swaisgood, Ronald R. (2018)
      Although mammal vocalisations signal attributes about the caller that are important in a range of contexts, relatively few studies have investigated the transmission of specific types of information encoded in mammal calls. In this study we broadcast and re-recorded giant panda bleats in a bamboo plantation, to assess the stability of individuality and sex differences in these calls over distance, and determine how the acoustic structure of giant panda bleats degrades in this species’ typical environment. Our results indicate that vocal recognition of the caller’s identity and sex is not likely to be possible when the distance between the vocaliser and receiver exceeds 20 m and 10 m, respectively. Further analysis revealed that the F0 contour of bleats was subject to high structural degradation as it propagated through the bamboo canopy, making the measurement of mean F0 and F0 modulation characteristics highly unreliable at distances exceeding 10 m. The most stable acoustic features of bleats in the bamboo forest environment (lowest % variation) were the upper formants and overall formant spacing. The analysis of amplitude attenuation revealed that the fifth and sixth formant are more prone to decay than the other frequency components of bleats, however, the fifth formant still remained the most prominent and persistent frequency component over distance. Paired with previous studies, these results show that giant panda bleats have the potential to signal the caller’s identity at distances of up to 20 m and reliably transmit sex differences up to 10 m from the caller, and suggest that information encoded by F0 modulation in bleats could only be functionally relevant during close-range interactions in this species’ natural environment.
    • Space use as an indicator of enclosure appropriateness in African wild dogs (Lycaon pictus)

      Hunter, Sally C.; Gusset, Markus; Miller, Lance J.; Somers, Michael J. (2014)
      A clear understanding of space use is required to more fully understand biological requirements of nonhuman animals in zoos, aid the design of exhibits, and maximize the animals' welfare. This study used electivity indexes to assess space use of two packs of African wild dogs (Lycaon pictus) and the appropriateness of two naturalistic, outdoor enclosures at the San Diego Zoo and Bronx Zoo....
    • 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....
    • Spatial mapping shows that some African elephants use cognitive maps to navigate the core but not the periphery of their home ranges

      Presotto, Andrea; Fayrer-Hosken, Richard; Curry, Caitlin; Madden, Marguerite (2019)
      Strategies of navigation have been shown to play a critical role when animals revisit resource sites across large home ranges. The habitual route system appears to be a sufficient strategy for animals to navigate while avoiding the cognitive cost of traveling using the Euclidean map....
    • Spatio-temporal patterns of Mauritia flexuosa fruit extraction in the Peruvian Amazon: Implications for conservation and sustainability

      Horn, Christa M.; Vargas Paredes, Victor H.; Gilmore, Michael P.; Endress, Bryan A. (2018)
      In the Amazon Basin, some non-timber forest products (NTFPs), such as the ecologically and economically important palm Mauritia flexuosa, are extracted intensively and across large areas – the ecological effect of which is unclear. In this study, we sought to better understand the scale and scope of M. flexuosa fruit harvest in the Peruvian Amazon, the destructive harvest of which has caused conservation concern for decades, by collecting data on the amounts and origins of the fruit entering the city of Iquitos, Peru – making harvest patterns spatially and temporally explicit for the first time....
    • Spatiotemporal hierarchical modelling of species richness and occupancy using camera trap data

      Tobler, Mathias W.; Zúñiga Hartley, Alfonso; Carrillo-Percastegui, Samia E.; Powell, George V. N. (2015)
      * Over the last two decades, a large number of camera trap surveys have been carried out around the world and camera traps have been proposed as an ideal tool for inventorying and monitoring medium to large-sized terrestrial vertebrates. However, few studies have analysed camera trap data at the community level. * We developed a multi-session multi-species occupancy model that allows us to obtain estimates for species richness and occupancy combining data from multiple camera trap surveys (sessions). By estimating species presence at the session-level and modelling detection probability and occupancy for each species and sessions as nested random effects, we could improve parameter estimates for each session, especially for species with sparse data. We developed two variants of our model: one was a binary latent states model while the other used a Royle–Nichols formulation for the relationship between detection probability and abundance. * We applied both models to data from eight camera trap surveys from south-eastern Peru including six study sites, 263 camera stations and 17 423 camera days. Sites covered protected areas, a logging concession and Brazil nut concessions. We included habitat (terra firme vs. floodplain) as a covariate for occupancy and trail vs. off-trail as a covariate for detection. * Among-camera heterogeneity was a serious problem for our data and the Royle–Nichols variant of our model had a much better fit than the binary-state variant. Both models resulted in similar species richness estimates showing that most of the sites contained intact large mammal communities. Detection probabilities and occupancy values were more variable across species than across sessions within species. Three species showed a habitat preference and four species showed preference or avoidance of trails. * Synthesis and applications. Our multi-session multi-species occupancy model provides improved estimates for species richness and occupancy for a large data set. Our model is ideally suited for integrating large numbers of camera trap data sets to investigate regional and/or temporal patterns in the distribution and composition of mammal communities in relation to natural or anthropogenic factors or to monitor mammal communities over time.
    • Spatiotemporal network structure among “friends of friends” reveals contagious disease process

      Witte, Carmel L.; Hungerford, Laura L.; Rideout, Bruce; Papendick, Rebecca; Fowler, James H. (2020)
      Disease transmission can be identified in a social network from the structural patterns of contact. However, it is difficult to separate contagious processes from those driven by homophily, and multiple pathways of transmission or inexact information on the timing of infection can obscure the detection of true transmission events. Here, we analyze the dynamic social network of a large, and near-complete population of 16,430 zoo birds tracked daily over 22 years to test a novel “friends-of-friends” strategy for detecting contagion in a social network. The results show that cases of avian mycobacteriosis were significantly clustered among pairs of birds that had been in direct contact. However, since these clusters might result due to correlated traits or a shared environment, we also analyzed pairs of birds that had never been in direct contact but were indirectly connected in the network via other birds. The disease was also significantly clustered among these friends of friends and a reverse-time placebo test shows that homophily could not be causing the clustering. These results provide empirical evidence that at least some avian mycobacteriosis infections are transmitted between birds, and provide new methods for detecting contagious processes in large-scale global network structures with indirect contacts, even when transmission pathways, timing of cases, or etiologic agents are unknown.
    • Species concepts for conservation – Reply to Russello and Amato

      Frankham, Richard; Lacy, Robert C.; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D.B.; Fenster, Charles B.; Mendelson, Joseph R.; Porton, Ingrid J.; Ralls, Katherine; Ryder, Oliver A. (2014)
      There are two critical steps required in assessing the taxonomic identity of populations (especially fragmented ones) for conservation purposes. The first is to define the criteria for distinguishing species and the second is to implement the delineation....
    • Splitting samples for safety duplication storage and testing

      Maschinski, Joyce; Walters, Christina; McCue, Kim; Remucal, David; Ritchie, James; Meyer, Evan; Wesley, Robert; Way, Michael; Chapman, Suzzanne; Fitch, Ryan; et al. (Center for Plant ConservationEscondido, California, 2019)
      The old adage “Don’t put all your eggs in one basket” applies to seed banking. Divide each accession and store each half at a different safe seed banking facility. Create curation packages to place inside storage packages. Seeds in curation packages can be used for testing initial and long-term viability. Seeds in storage packages are intended to be stored long-term.
    • Spring fasting behavior in a marine apex predator provides an index of ecosystem productivity

      Rode, Karyn D.; Wilson, Ryan R.; Douglas, David C.; Muhlenbruch, Vanessa; Atwood, Todd C.; Regehr, Eric V.; Richardson, Evan S.; Pilfold, Nicholas W.; Derocher, Andrew E.; Durner, George M.; et al. (2018)
      The effects of declining Arctic sea ice on local ecosystem productivity are not well understood but have been shown to vary inter-specifically, spatially, and temporally. Because marine mammals occupy upper trophic levels in Arctic food webs, they may be useful indicators for understanding variation in ecosystem productivity. Polar bears (Ursus maritimus) are apex predators that primarily consume benthic and pelagic-feeding ice-associated seals. As such, their productivity integrates sea ice conditions and the ecosystem supporting them. Declining sea ice availability has been linked to negative population effects for polar bears but does not fully explain observed population changes. We examined relationships between spring foraging success of polar bears and sea ice conditions, prey productivity, and general patterns of ecosystem productivity in the Beaufort and Chukchi Seas (CSs). Fasting status (?7 days) was estimated using serum urea and creatinine levels of 1,448 samples collected from 1,177 adult and subadult bears across three subpopulations. Fasting increased in the Beaufort Sea between 1983–1999 and 2000–2016 and was related to an index of ringed seal body condition. This change was concurrent with declines in body condition of polar bears and observed changes in the diet, condition and/or reproduction of four other vertebrate consumers within the food chain. In contrast, fasting declined in CS polar bears between periods and was less common than in the two Beaufort Sea subpopulations consistent with studies demonstrating higher primary productivity and maintenance or improved body condition in polar bears, ringed seals, and bearded seals despite recent sea ice loss in this region. Consistency between regional and temporal variation in spring polar bear fasting and food web productivity suggests that polar bears may be a useful indicator species. Furthermore, our results suggest that spatial and temporal ecological variation is important in affecting upper trophic-level productivity in these marine ecosystems.
    • Stereotypic behaviour predicts reproductive performance and litter sex ratio in giant pandas

      Martin, Meghan S.; Owen, Megan A.; Wintle, Nathan J. P.; Zhang, Guiquan; Zhang, Hemin; Swaisgood, Ronald R. (2020)
      Breeding and welfare problems confront many conservation breeding programs. Stereotypies—repetitive, unvarying, functionless behaviours —are common abnormal behaviours that often arise in suboptimal conditions. While the role of stereotypies in welfare assessment is well studied, few investigations address the relationship between stereotypic behaviour and reproduction. We examined the correlation between stereotypic behaviour and reproductive performance in 101 giant pandas (Ailuropoda melanoleuca). High stereotyping males copulated more and produced more cubs, suggesting that highly sexually motivated males were prone to stereotypy but also had high reproductive competence. Female stereotypies were negatively associated with all reproductive measures closely tied to behavioural competence: high stereotyping females were less likely to copulate, less likely to mother-rear cubs, and—probably a result of poor maternal care—had lower cub survival. However, females that exhibited stereotypies were more likely to produce a cub, suggesting stereotypies are tied to behavioural but not physiological competence. High stereotyping female pandas also displayed strong and consistent bias toward production of female offspring while paternal relationship to sex allocation was the reverse. These results are consistent with stress-mediated sex allocation theory. Our findings raise concern about differential reproductive success among high and low stereotyping pandas, and possible genetic adaptation to captivity.
    • Strongylid infection varies with age, sex, movement and social factors in wild African elephants

      Parker, Jenna M.; Goldenberg, Shifra Z.; Letitiya, David; Wittemyer, George (2019)
      Comparing parasitic infection among individuals of wildlife populations can provide insight into factors that influence wildlife disease ecology. Strongylids are parasitic worms that infect the intestinal tract of vertebrates, and infection with strongylids can be approximated by counting strongylid eggs in dung samples....
    • Strongylid infection varies with age, sex, movement and social factors in wild African elephants

      Parker, Jenna M.; Goldenberg, Shifra Z.; Letitiya, David; Wittemyer, George (2020)
      Comparing parasitic infection among individuals of wildlife populations can provide insight into factors that influence wildlife disease ecology. Strongylids are parasitic worms that infect the intestinal tract of vertebrates, and infection with strongylids can be approximated by counting strongylid eggs in dung samples....
    • Sumatran tiger survival threatened by deforestation despite increasing densities in parks

      Luskin, Matthew Scott; Albert, Wido Rizki; Tobler, Mathias W. (2017)
      The continuing development of improved capture–recapture (CR) modeling techniques used to study apex predators has also limited robust temporal and cross-site analyses due to different methods employed. We develop an approach to standardize older non-spatial CR and newer spatial CR density estimates and examine trends for critically endangered Sumatran tigers (Panthera tigris sumatrae) using a meta-regression of 17 existing densities and new estimates from our own fieldwork. We find that tiger densities were 47% higher in primary versus degraded forests and, unexpectedly, increased 4.9% per yr from 1996 to 2014, likely indicating a recovery from earlier poaching. However, while tiger numbers may have temporarily risen, the total potential island-wide population declined by 16.6% from 2000 to 2012 due to forest loss and degradation and subpopulations are significantly more fragmented. Thus, despite increasing densities in smaller parks, we conclude that there are only two robust populations left with >30 breeding females, indicating Sumatran tigers still face a high risk of extinction unless deforestation can be controlled.
    • Survey of Plasmodium spp. in free-ranging neotropical primates from the Brazilian Amazon region impacted by anthropogenic actions

      Bueno, Marina G.; Rohe, Fabio; Kirchgatter, Karin; Di Santi, Silvia M. F.; Guimarães, Lilian O.; Witte, Carmel L.; Costa-Nascimento, Maria J.; Toniolo, Christina R. C.; Catão-Dias, José Luiz (2013)
      This study investigated Plasmodium spp. infection in free-ranging neotropical primates from Brazilian Amazon regions under the impact of major anthropogenic actions. Blood samples from 19 new world primates were collected and analyzed with microscopic and molecular procedures. The prevalence of Plasmodium infection was 21.0% (4/19) and PCR positive samples were identified as P. brasilianum. Considering the social-economic changes that the Amazon is facing, the prevalence of P. brasilianum infection highlights the necessity to closely monitor the movement of both human and non-human primate populations, in order to mitigate pathogen exposure and the introduction of new agents into previously naïve areas.
    • Systematic evidence synthesis as part of a larger process: a response to comments on Berger-Tal et al

      Berger-Tal, Oded; Greggor, Alison L.; Macura, Biljana; Adams, Carrie Ann; Blumenthal, Arden; Bouskila, Amos; Candolin, Ulrika; Doran, Carolina; Fernández-Juricic, Esteban; Gotanda, Kiyoko M.; et al. (2018)
      We are encouraged that the prospect of generating systematic reviews and maps (Berger-Tal et al. 2019) has stirred enthusiasm among our peers. The resulting discussion brings up a number of valid points that share a vision for a field with greater internal rigor and external impact....
    • Systematic reviews and maps as tools for applying behavioral ecology to management and policy

      Berger-Tal, Oded; Greggor, Alison L.; Macura, Biljana; Adams, Carrie Ann; Blumenthal, Arden; Bouskila, Amos; Candolin, Ulrika; Doran, Carolina; Fernández-Juricic, Esteban; Gotanda, Kiyoko M.; et al. (2019)
      We describe the utility of conducting formal systematic reviews and maps to synthesize behavioral evidence in a way that enhances its utility to managers, polic
    • Systemic amyloid A amyloidosis in island foxes (Urocyon littoralis): Severity and risk factors

      Gaffney, Patricia M.; Witte, Carmel L.; Clifford, D. L.; Imai, D. M.; O’Brien, T. D.; Trejo, M.; Liberta, F.; Annamalai, K.; Fändrich, M.; Masliah, E.; et al. (2016)
      ...Here we define the severity of glomerular and medullary renal amyloid and identify risk factors for AA amyloidosis in 321 island foxes necropsied from 1987 through 2010. In affected kidneys, amyloid more commonly accumulated in the medullary interstitium than in the glomeruli (98% [n = 78 of 80] vs 56% [n = 45], respectively; P < .0001), and medullary deposition was more commonly severe (19% [n = 20 of 105]) as compared with glomeruli (7% [n = 7]; P = .01)....
    • Systemic amyloidosis in an African tiger snake (Telescopus semiannulatus)

      Burns, Rachel E.; Gaffney, Patricia M.; Nilsson, K. P. R.; Armién, A. G.; Pessier, Allan P. (2017)
      Summary An adult male African tiger snake (Telescopus semiannulatus) was diagnosed with disseminated mycobacteriosis and a hepatic biliary cystadenocarcinoma. Histologically, the spleen was largely replaced by extracellular deposits of eosinophilic, fibrillar to hyaline material....