• 98 Efficacy of commercial equine semen freezing extenders for cryopreservation of southern white rhinoceros (Ceratotherium simum simum) sperm

      Young, Carly; Ravida, Nicole; Pennington, Parker M.; Durrant, Barbara S. (2019)
      Once nearly extinct in the wild, the southern white rhinoceros is currently listed as near threatened by IUCN. This status is likely to change as poaching continues to escalate....
    • A big data urban growth simulation at a national scale: Configuring the GIS and neural network based Land Transformation Model to run in a High Performance Computing (HPC) environment

      Pijanowski, B.C.; Tayyebi, A.; Douchette, J.; Pekin, Burak K.; Braun, D.; Plourde, J. (2014)
      The Land Transformation Model (LTM) is a Land Use Land Cover Change (LUCC) model which was originally developed to simulate local scale LUCC patterns…. This paper provides an overview of the new architecture which we discuss within the context of modeling LUCC that requires: (1) using an HPC to run a modified version of our LTM; (2) managing large datasets in terms of size and quantity of files; (3) integration of tools that are executed using different scripting languages; and (4) a large number of steps necessitating several aspects of job management.
    • A highly divergent picornavirus infecting the gut epithelia of zebrafish (Danio rerio) in research institutions worldwide

      Altan, Eda; Kubiski, Steven V.; Boros, Ákos; Reuter, Gábor; Sadeghi, Mohammadreza; Deng, Xutao; Creighton, Erica K.; Crim, Marcus J.; Delwart, Eric (2019)
      Zebrafish have been extensively used as a model system for research in vertebrate development and pathogen–host interactions. We describe the complete genome of a novel picornavirus identified during a viral metagenomics analysis of zebrafish gut tissue....
    • 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.
    • Assessment of in situ nest decay rate for chimpanzees (Pan troglodytes ellioti Matschie, 1914) in Mbam-Djerem National Park, Cameroon: implications for long-term monitoring

      Kamgang, Serge Alexis; Carme, Tuneu Corral; Bobo, Kadiri Serge; Abwe, Ekwoge E.; Gonder, Mary Katherine; Sinsin, Brice (Springer, 2020)
      Accurate assessment of great ape populations is a prerequisite for conservation planning. Indirect survey methods using nest and dung, and a set of conversion parameters related to nest decay rates, are increasingly used. Most surveys use the standing crop nest count (SCNC) method, whereby nests are counted along transects and the estimated nest density is converted into chimpanzee density using an often non-local nest decay rate. The use of non-local decay rate is thought to introduce substantial bias to ape population estimates given that nest decay rates vary with location, season, rainfall, nest shape, and tree species used. SCNC method has previously been applied in Mbam-Djerem National Park (MDNP) in Cameroon, for chimpanzee surveys using a non-local nest decay rate. This current study aimed to measure a local nest decay rate for MDNP and implications for chimpanzee population estimates in the MDNP. The mean nest decay rate estimated using a logistic regression analysis was 127 [95% CI (100–160)] days. Moreover, the results suggested that rainfall strongly influenced the nest decay rate over the early stage of the lifetime of the nests. The study confirms that estimates of chimpanzee density and abundance using non-local decay rates should be treated with caution. Our research emphasized the importance of using local nest decay rates and other survey methods which do not depend on decay rates to obtain more accurate estimates of chimpanzee densities in order to inform conservation strategies of these great apes in MDNP.
    • Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding

      Tollington, S.; Greenwood, A.; Jones, C.G.; Hoeck, Paquita; Chowrimootoo, A.; Smith, D.; Richards, H.; Tatayah, V.; Groombridge, J.J. (2015)
      Infectious diseases are widely recognized to have substantial impact on wildlife populations. These impacts are sometimes exacerbated in small endangered populations, and therefore, the success of conservation reintroductions to aid the recovery of such species can be seriously threatened by outbreaks of infectious disease. Intensive management strategies associated with conservation reintroductions can further compound these negative effects in such populations. Exploring the sublethal effects of disease outbreaks among natural populations is challenging and requires longitudinal, individual life‐history data on patterns of reproductive success and other indicators of individual fitness. Long‐term monitoring data concerning detailed reproductive information of the reintroduced Mauritius parakeet (Psittacula echo ) population collected before, during and after a disease outbreak was investigated. Deleterious effects of an outbreak of beak and feather disease virus (BFDV ) were revealed on hatch success, but these effects were remarkably short‐lived and disproportionately associated with breeding pairs which took supplemental food. Individual BFDV infection status was not predicted by any genetic, environmental or conservation management factors and was not associated with any of our measures of immune function, perhaps suggesting immunological impairment. Experimental immunostimulation using the PHA (phytohaemagglutinin assay) challenge technique did, however, provoke a significant cellular immune response. We illustrate the resilience of this bottlenecked and once critically endangered, island‐endemic species to an epidemic outbreak of BFDV and highlight the value of systematic monitoring in revealing inconspicuous but nonetheless substantial ecological interactions. Our study demonstrates that the emergence of such an infectious disease in a population ordinarily associated with increased susceptibility does not necessarily lead to deleterious impacts on population growth and that negative effects on reproductive fitness can be short‐lived.
    • Estimating mammalian species richness and occupancy in tropical forest canopies with arboreal camera traps

      Bowler, Mark; Tobler, Mathias W.; Endress, Bryan A.; Gilmore, Michael P.; Anderson, Matthew J. (2017)
      Large and medium-bodied rainforest canopy mammals are typically surveyed using line transects, but these are labour intensive and usually ignore nocturnal species. Camera traps have become the preferred tool for assessing terrestrial mammal communities, but have rarely been used for arboreal species. Here, we compare the efficiency of arboreal camera trapping with line transects for inventorying medium and large-sized arboreal mammals, and assess the viability of using camera traps in trees to model habitat occupancy. We installed 42 camera traps, spaced 2 km apart, in the canopy of the Maijuna-Kichwa Regional Conservation Area, Peru and walked 2014 km of diurnal line transects on 22 trails at the same site. We compared the efficiency of each method using species accumulation curves. We applied a multi-species occupancy model, while examining the effect of camera height on detection probabilities, including the distance from a village and from a river as covariates to examine variability in habitat occupancy. In 3147 camera days, 18 species of arboreal medium and large-sized mammals were detected by cameras, while 11 species were recorded on line transects. Ten of these species were detected by both methods. Diurnal species were detected more quickly and with less effort using arboreal camera trapping than using diurnal line transects at the same site, although some species were more easily detected during line transects. Habitat occupancy was positively correlated with distance from the village for two species, and negatively correlated with distance from the river for one. Detection probabilities increased modestly with camera height. Practical limitations of arboreal camera trapping include the requirement for specialized climbing techniques, as well as increased potential for false triggers, requiring extended processing time. Arboreal camera trapping is an efficient method for inventorying arboreal mammals and a viable option for studying their distribution relative to environmental or anthropogenic variables when abundance or density estimates are not required.
    • Habitat differentiation among three Nigeria–Cameroon chimpanzee (Pan troglodytes ellioti) populations

      Abwe, Ekwoge E.; Morgan, Bethan J.; Tchiengue, Barthelemy; Kentatchime, Fabrice; Doudja, Roger; Ketchen, Marcel E.; Teguia, Eric; Ambahe, Ruffin; Venditti, Dana M.; Mitchell, Matthew W.; et al. (2019)
      Ecological niche models (ENMs) are often used to predict species distribution patterns from datasets that describe abiotic and biotic factors at coarse spatial scales. Ground-truthing ENMs provide important information about how these factors relate to species-specific requirements at a scale that is biologically relevant for the species. Chimpanzees are territorial and have a predominantly frugivorous diet. The spatial and temporal variation in fruit availability for different chimpanzee populations is thus crucial, but rarely depicted in ENMs. The genetic and geographic distinction within Nigeria–Cameroon chimpanzee (Pan troglodytes ellioti) populations represents a unique opportunity to understand fine scale species-relevant ecological variation in relation to ENMs. In Cameroon, P. t. ellioti is composed of two genetically distinct populations that occupy different niches: rainforests in western Cameroon and forest–woodland–savanna mosaic (ecotone) in central Cameroon. We investigated habitat variation at three representative sites using chimpanzee-relevant environmental variables, including fruit availability, to assess how these variables distinguish these niches from one another. Contrary to the assumption of most ENM studies that intact forest is essential for the survival of chimpanzees, we hypothesized that the ecotone and human-modified habitats in Cameroon have sufficient resources to sustain large chimpanzee populations. Rainfall, and the diversity, density, and size of trees were higher at the rainforest. The ecotone had a higher density of terrestrial herbs and lianas. Fruit availability was higher at Ganga (ecotone) than at Bekob and Njuma. Seasonal variation in fruit availability was highest at Ganga, and periods of fruit scarcity were longer than at the rainforest sites. Introduced and secondary forest species linked with anthropogenic modification were common at Bekob, which reduced seasonality in fruit availability. Our findings highlight the value of incorporating fine scale species-relevant ecological data to create more realistic models, which have implications for local conservation planning efforts.
    • Joint species distribution models with species correlations and imperfect detection

      Tobler, Mathias W.; Kéry, Marc; Hui, Francis K. C.; Guillera-Arroita, Gurutzeta; Knaus, Peter; Sattler, Thomas (2019)
      Spatiotemporal patterns in biological communities are typically driven by environmental factors and species interactions. Spatial data from communities are naturally described by stacking models for all species in the community....
    • Progress in the ecology and conservation of giant pandas

      Wei, Fuwen; Swaisgood, Ronald R.; Hu, Yibo; Nie, Yonggang; Yan, Li; Zhang, Zejun; Qi, Dunwu; Zhu, Lifeng (2015)
      Giant panda (Ailuropoda melanoleuca) conservation is a possible success story in the making. If extinction of this iconic endangered species can be avoided, the species will become a showcase program for the Chinese government and its collaborators. We reviewed the major advancements in ecological science for the giant panda, examining how these advancements have contributed to panda conservation….
    • Recursive movement patterns: Review and synthesis across species

      Berger-Tal, Oded; Bar-David, Shirli (2015)
      Recursive movement—returns to previously visited areas—is a widespread phenomenon exhibited by a large range of species from bees and birds to primates and large felines, at different spatial scales. Nevertheless, the wide scope and generality of this phenomenon remain underestimated by the scientific community. This limited appreciation for the pervasiveness of recursive movement can be attributed to its study by parallel lines of research, with different methodologies and nomenclature, and almost no cross referencing among them. Among these lines of studies are traplining behavior in foraging ecology, path recursions in movement ecology and the ecology of fear in predator–prey studies. We synthesize these three lines of research, to underline the mechanisms driving these patterns and create a conceptual model for recursive movement behavior across species and spatio-temporal scales. The emergence and complexity of recursive movement patterns are determined by the rate of resource recovery, environmental heterogeneity, the predictability of resource recovery, and the animal's cognitive capabilities. Our synthesis can be used to generate predictions within and among systems, as well as to promote the sharing of knowledge and methodologies gained in each sub-field. Such sharing can greatly advance our understanding of behavioral and ecological processes and provide novel opportunities for future research.
    • Refining reproductive parameters for modelling sustainability and extinction in hunted primate populations in the Amazon

      Bowler, Mark; Anderson, Matthew J.; Montes, Daniel; Pérez, Pedro; Mayor, Pedro; Fenton, Brock; Fenton, Brock (2014)
      Primates are frequently hunted in Amazonia. Assessing the sustainability of hunting is essential to conservation planning. The most-used sustainability model, the ‘Production Model’, and more recent spatial models, rely on basic reproductive parameters for accuracy. These parameters are often crudely estimated. To date, parameters used for the Amazon’s most-hunted primate, the woolly monkey (Lagothrix spp.), come from captive populations in the 1960s, when captive births were rare. Furthermore, woolly monkeys have since been split into five species. We provide reproductive parameters calculated by examining the reproductive organs of female Poeppig’s woolly monkeys (Lagothrix poeppigii), collected by hunters as part of their normal subsistence activity. Production was 0.48–0.54 young per female per year, and an interbirth interval of 22.3 to 25.2 months, similar to parameters from captive populations. However, breeding was seasonal, which imposes limits on the maximum reproductive rate attainable. We recommend the use of spatial models over the Production Model, since they are less sensitive to error in estimated reproductive rates. Further refinements to reproductive parameters are needed for most primate taxa. Methods like ours verify the suitability of captive reproductive rates for sustainability analysis and population modelling for populations under differing conditions of hunting pressure and seasonality. Without such research, population modelling is based largely on guesswork.
    • Signalling behaviour is influenced by transient social context in a spontaneously ovulating mammal

      Owen, Megan A.; Swaisgood, Ronald R.; Zhou, Xiaoping; Blumstein, Daniel T. (2016)
      ...Using female giant pandas at the Wolong Breeding Centre in Sichuan, China, we explored the interaction between social context and reproductive status on signalling and maintenance behaviours. To do so, we used linear mixed models and an information-theoretic approach to assess the temporal relationship between signalling behaviours and the timing of first mating....
    • 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.
    • The exploration-exploitation dilemma: A Multidisciplinary framework

      Berger-Tal, Oded; Nathan, Jonathan; Meron, Ehud; Saltz, David (2014)
      The trade-off between the need to obtain new knowledge and the need to use that knowledge to improve performance is one of the most basic trade-offs in nature, and optimal performance usually requires some balance between exploratory and exploitative behaviors. Researchers in many disciplines have been searching for the optimal solution to this dilemma. Here we present a novel model in which the exploration strategy itself is dynamic and varies with time in order to optimize a definite goal, such as the acquisition of energy, money, or prestige. Our model produced four very distinct phases: Knowledge establishment, Knowledge accumulation, Knowledge maintenance, and Knowledge exploitation, giving rise to a multidisciplinary framework that applies equally to humans, animals, and organizations. The framework can be used to explain a multitude of phenomena in various disciplines, such as the movement of animals in novel landscapes, the most efficient resource allocation for a start-up company, or the effects of old age on knowledge acquisition in humans.
    • 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.
    • Variation in reproductive success across captive populations: Methodological differences, potential biases and opportunities

      Griffith, Simon C.; Crino, Ondi L.; Andrew, Samuel C.; Nomano, Fumiaki Y.; Adkins-Regan, Elizabeth; Alonso-Alvarez, Carlos; Bailey, Ida E.; Bittner, Stephanie S.; Bolton, Peri E.; Boner, Winnie; et al. (2017)
      ...The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency….