• Molecular methods to detect Mycoplasma spp. and testudinid herpesvirus 2 in desert tortoises (Gopherus agassizii) and implications for disease management

      Braun, Josephine; Schrenzel, Mark D.; Witte, Carmel L.; Gokool, Larisa; Burchell, Jennifer; Rideout, Bruce (2014)
      Mycoplasmas are an important cause of upper respiratory tract disease (URTD) in desert tortoises (Gopherus agassizii) and have been a main focus in attempts to mitigate disease-based population declines. Infection risk can vary with an animal's population of origin, making screening tests popular tools for determining infection status in individuals and populations…. Our findings suggest that mycoplasmas are not the only agents of concern and that a single M. agassizii ELISA or nasal flush qPCR alone failed to identify all potentially infected animals in a population….
    • Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae)

      Steiner, Cynthia C.; Charter, Suellen J.; Houck, Marlys L.; Ryder, Oliver A. (2014)
      Robertsonian (Rb) translocations, in particular centric fusions, are thought to play a primary role in evolution and speciation of the Bovidae family....This work studies chromosome variation in 72 captive individuals of 6 species of Alcelaphini (Antilopinae): The hartebeest (genus Alcelaphus), hirola (Beatragus), black and blue wildebeests (Connochaetes), and the topi and bontebok (Damaliscus)….
    • Mongoose lemur (Eulemur mongoz). The IUCN Red List of Threatened Species 2020

      Razafindramanana, J.; Eppley, Timothy M.; Rakotondrabe, R.; Roullet, D.; Irwin, M; King, T. (2020)
      There is a suspected population reduction of greater than or equal to 80% in this species over a three generation period (estimating the generation length to be 8 years). This time period includes both the past and the future. Causes of this reduction (which have not ceased) include continuing decline in area (through deforestation), extent and quality of habitat (selective logging), and exploitation through unsustainable levels of hunting. Furthermore, Eulemur mongoz has undergone hybridization with E. rufus in Western Betsiboka. Based on these premises, the species is listed as Critically Endangered.
    • Montane bias in lowland Amazonian peatlands: Plant assembly on heterogeneous landscapes and potential significance to palynological inference

      Householder, J. E.; Wittmann, F.; Tobler, Mathias W.; Janovec, J. P. (2015)
      Past temperature changes in tropical mountain regions are commonly inferred from vertical elevational shifts of montane indicator taxa in the palynological record.…To the extent that fossilization provides a better record of past vegetation that occurred proximate to the site of deposition, we suggest that habitat tracking of montane elements may introduce a cool bias in lowland paleo-temperature reconstructions based on pollen proxies.
    • Moore's woolly lemur (Avahi mooreorum). The IUCN Red List of Threatened Species 2020

      Eppley, Timothy M.; Borgerson, C.; Sawyer, R.M.; Fenosoa, Z.S.E. (2020)
      The extent of occurrence (EOO) of this species is 2,544 km2 . This geographic range is severely fragmented and undergoing continuing decline in area, extent and quality of habitat. The number of mature individuals is also suspected to be in decline. Based on these premises, the species is listed as Endangered
    • Morphology of the oxyurid nematodes Trypanoxyuris (T.) cacajao n. sp. and T. (T.) ucayalii n. sp. from the red uakari monkey Cacajao calvus ucayalii in the Peruvian Amazon

      Conga, D. F.; Giese, E. G.; Serra-Freire, N. M.; Bowler, Mark; Mayor, P. (2016)
      Cacajao calvus ucayalii (Thomas, 1928) (Primates: Pitheciidae), a subspecies endemic to the Peruvian Amazon, occurs in patchy and sometimes isolated populations in north-eastern Peru and is in a vulnerable situation, mainly due to habitat loss and hunting. This rareness and remote distribution means that, until now, parasitical studies have been limited. Based on optical and scanning electron microscopy of specimens of both sexes, we report two new species of Trypanoxyuris pinworms occurring in the large intestine of the Peruvian red uakari, namely Trypanoxyuris (Trypanoxyuris) cacajao and Trypanoxyuris (Trypanoxyuris) ucayalii. ...
    • Morphometrics and structure of complete baleen racks in gray whales (Eschrichtius robustus) From the eastern North Pacific ocean

      Young, Samantha; DeméRé, Thomas A.; Ekdale, Eric G.; Berta, Annalisa; Zellmer, Nicholas (2015)
      …In one of the first morphometric studies of the full baleen apparatus, we describe the morphology of complete baleen racks in neonate, yearling and adult gray whales (Eschrichtius robustus), and note morphometric variations between age groups as well as within individual racks… Histological examination of the epithelial base (Zwischensubstanz) and laminae showed basic epidermal layers, as well as gapping between layers and vacuoles
    • Movement patterns of cheetahs (Acinonyx jubatus) in farmlands in Botswana

      Van der Weyde, Leanne K.; Hubel, T. Y.; Horgan, J.; Shotton, J.; McKenna, R.; Wilson, A. M. (2017)
      Botswana has the second highest population of cheetah (Acinonyx jubatus) with most living outside protected areas. As a result, many cheetahs are found in farming areas which occasionally results in human-wildlife conflict. This study aimed to look at movement patterns of cheetahs in farming environments to determine whether cheetahs have adapted their movements in these human-dominated landscapes. We fitted high-time resolution GPS collars to cheetahs in the Ghanzi farmlands of Botswana. GPS locations were used to calculate home range sizes as well as number and duration of visits to landscape features using a time-based local convex hull method. Cheetahs had medium-sized home ranges compared to previously studied cheetah in similar farming environments. Results showed that cheetahs actively visited scent marking trees and avoided visiting homesteads. A slight preference for visiting game farms over cattle farms was found, but there was no difference in duration of visits between farm types. We conclude that cheetahs selected for areas that are important for their dietary and social needs and prefer to avoid human-occupied areas. Improved knowledge of how cheetahs use farmlands can allow farmers to make informed decisions when developing management practices and can be an important tool for reducing human-wildlife conflict.
    • Movement-based estimation and visualization of space use in 3D for wildlife ecology and conservation

      Tracey, Jeff A.; Sheppard, James; Zhu, Jun; Wei, Fuwen; Swaisgood, Ronald R.; Fisher, Robert N.; Sueur, Cédric; Sueur, Cédric (2014)
      Advances in digital biotelemetry technologies are enabling the collection of bigger and more accurate data on the movements of free-ranging wildlife in space and time. Although many biotelemetry devices record 3D location data with x, y, and z coordinates from tracked animals, the third z coordinate is typically not integrated into studies of animal spatial use. Disregarding the vertical component may seriously limit understanding of animal habitat use and niche separation. We present novel movement-based kernel density estimators and computer visualization tools for generating and exploring 3D home ranges based on location data. We use case studies of three wildlife species – giant panda, dugong, and California condor – to demonstrate the ecological insights and conservation management benefits provided by 3D home range estimation and visualization for terrestrial, aquatic, and avian wildlife research.
    • Moving towards greater success in translocations: recent advances from the herpetofauna

      Germano, Jennifer M.; Ewen, J. G.; Mushinsky, H.; McCoy, E.; Ortiz-Catedral, L. (2014)
      ...While the idea of moving an animal may seem simple at first glance, the reality is that translocations are inherently complex. In order to improve our rates of success, this complexity must be considered....
    • Multi-locus phylogeny of the tribe Tragelaphini (Mammalia, Bovidae) and species delimitation in bushbuck: Evidence for chromosomal speciation mediated by interspecific hybridization

      Hassanin, Alexandre; Houck, Marlys L.; Tshikung, Didier; Kadjo, Blaise; Davis, Heidi; Ropiquet, Anne (2018)
      The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species....
    • Multi-species occupancy modelling of a carnivore guild in wildlife management areas in the Kalahari

      Van der Weyde, Leanne K.; Mbisana, Christopher; Klein, Rebecca (Elsevier BV, 2018)
      It was hypothesised that land use type surrounding WMAs, human settlements and prey availability might affect carnivore distribution patterns. We conducted a camera-trap study with 96 stations in two WMAs in the Ghanzi district and used a Royles-Nichol multi-species occupancy model to test which factors influenced habitat use for nine carnivore species....
    • Mutual medication in capuchin monkeys–Social anointing improves coverage of topically applied anti-parasite medicines

      Bowler, Mark; Messer, Emily J. E.; Claidière, Nicolas; Whiten, Andrew (2015)
      Wild and captive capuchin monkeys will anoint themselves with a range of strong smelling substances including millipedes, ants, limes and onions. Hypotheses for the function of the behaviour range from medicinal to social. However, capuchin monkeys may anoint in contact with other individuals, as well as individually. The function of social anointing has also been explained as either medicinal or to enhance social bonding. By manipulating the abundance of an anointing resource given to two groups of tufted capuchins, we tested predictions derived from the main hypotheses for the functions of anointing and in particular, social anointing. Monkeys engaged in individual and social anointing in similar proportions when resources were rare or common, and monkeys holding resources continued to join anointing groups, indicating that social anointing has functions beyond that of gaining access to resources. The distribution of individual and social anointing actions on the monkeys’ bodies supports a medicinal function for both individual and social anointing, that requires no additional social bonding hypotheses. Individual anointing targets hard-to-see body parts that are harder to groom, whilst social anointing targets hard-to-reach body parts. Social anointing in capuchins is a form of mutual medication that improves coverage of topically applied anti-parasite medicines.
    • Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

      Krehenwinkel, Henrik; Pomerantz, Aaron; Henderson, James B.; Kennedy, Susan R.; Lim, Jun Y.; Swamy, Varun; Shoobridge, Juan D.; Patel, Nipam H.; Gillespie, Rosemary G.; Prost, Stefan (2019)
      Background: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Results: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. Conclusions: Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost effective, portable and universal approach for eukaryote DNA barcoding. Long rDNA amplicons scale up DNA barcoding by enabling the accurate recovery of taxonomic and phylogenetic diversity. However, bulk community analyses using long-read approaches may introduce biases and will require further exploration.
    • Nutrition and health in amphibian husbandry: Ex situ amphibian health and nutrition

      Ferrie, Gina M.; Alford, Vance C.; Atkinson, Jim; Baitchman, Eric; Barber, Diane; Blaner, William S.; Crawshaw, Graham; Daneault, Andy; Dierenfeld, Ellen; Finke, Mark; et al. (2014)
      Amphibian biology is intricate, and there are many inter‐related factors that need to be understood before establishing successful Conservation Breeding Programs (CBPs). Nutritional needs of amphibians are highly integrated with disease and their husbandry needs, and the diversity of developmental stages, natural habitats, and feeding strategies result in many different recommendations for proper care and feeding….
    • On the timing of an epidemic of amphibian chytridiomycosis in the highlands of Guatemala

      Mendelson, Joseph R.; Jones, Megan E. B.; Pessier, Allan P.; Toledo, Gabriela; Kabay, Edward H.; Campbell, Jonathan A. (2014)
      We analyzed museum specimens from two regions of Guatemala for the presence of the pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) using both histological and PCR-based assays. We determined that the pathogen was present at one site at low prevalence in 1980 and 1981, immediately preceding drastic declines of amphibian in the region by 1983….
    • Opportunities and challenges for conserving small populations: An emerging role for zoos in genetic rescue

      Ryder, Oliver A.; Minteer, Ben A.; Maienschein, Jane; Collins, James P. (University of Chicago PressChicago, IL, 2018)
      The growing commitment of zoos to address accelerated rates of extinction and losses of biodiversity utilizing the populations they manage has led to the exploration of options to rescue species from extinction, including advanced genetic and reproductive technologies. The availability of banked viable cell cultures, such as those held in collections like San Diego Zoo Global’s Frozen Zoo® and other facilities, may ultimately provide resources to reduce extinction risk of species for which appropriate samples have been collected....
    • Ovarian control and monitoring in amphibians

      Calatayud, Natalie E.; Stoops, M.; Durrant, Barbara S. (2018)
      Amphibian evolution spans over 350 million years ago, consequently this taxonomic group displays a wide, complex array of physiological adaptations and their diverse modes of reproduction are a prime example. Reproduction can be affected by taxonomy, geographic and altitudinal distribution, and environmental factors....
    • Ovulation induction in anovulatory southern white rhinoceros (Ceratotherium simum simum) without altrenogest

      Pennington, Parker M.; Marshall, Kira L.; Capiro, Jonnie M.; Felton, Rachel G.; Durrant, Barbara S. (2019)
      Lack of ovulation is common in captive southern white rhino females and contributes to poor reproductive success. We show that ovulation can be induced efficien
    • Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees

      Staes, Nicky; Stevens, Jeroen M. G.; Helsen, Philippe; Hillyer, Mia; Korody, Marisa L.; Eens, Marcel (2014)
      Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ~360 bp in this region (+/- DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.