• 113 Developing a cryopreservation protocol for desert tortoise sperm (Gopherus agassizzii)

      Ravida, Nicole; Young, C.; Gokool, L.; Durrant, Barbara S. (2017)
      The desert tortoise (Gopherus agassizzii) is listed as threatened by the USA Fish and Wildlife Service and population declines continue to occur throughout most of their range. This species’ low reproductive rate, combined with the advanced age at which they reach sexual maturity, makes them vulnerable to multiple threats....
    • 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 time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

      Tomaszkiewicz, Marta; Rangavittal, Samarth; Cechova, Monika; Sanchez, Rebeca Campos; Fescemyer, Howard W.; Harris, Robert; Ye, Danling; O'Brien, Patricia C. M.; Chikhi, Rayan; Ryder, Oliver A.; et al. (2016)
      The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
    • Advances in conservation endocrinology: The application of molecular approaches to the conservation of endangered species

      Tubbs, Christopher W.; McDonough, C. E.; Felton, Rachel G.; Milnes, Matthew R. (2014)
      …In this review we examine various in vitro approaches we have used to compare estrogen receptor binding and activation by endogenous hormones and phytoestrogens in two species of rhinoceros; southern white and greater one-horned. We have found many of these techniques valuable and practical in species where access to research subjects and/or tissues is limited due to their conservation status....
    • Amdoparvovirus Infection in Red Pandas (Ailurus fulgens)

      Alex, Charles E.; Kubiski, Steven V.; Li, Linlin; Sadeghi, Mohammadreza; Wack, Raymund F.; McCarthy, Megan A.; Pesavento, Joseph B.; Delwart, Eric; Pesavento, Patricia A. (2018)
      Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda (Ailurus fulgens), discovered using viral metagenomics....
    • Androgen and glucocorticoid production in the male killer whale (Orcinus orca): influence of age, maturity, and environmental factors

      O'Brien J. K.; Steinman K. J.; Fetter, G. Alan; Robeck T. R. (2016)
      Circulating concentrations of testosterone and its precursor androstenedione, as well as dehydroepiandrosterone (DHEA ) and the adrenal hormones cortisol and corticosterone were measured at monthly intervals in 14 male killer whales (Orcinus orca ) aged 0.8–38 years. Analyses were performed for examination of the relationships of age, sexual maturation status (STATUS ), season, and environmental temperature (monthly air ambient temperature, A‐TEMP ) with hormone production using a mixed effects linear regression model with animal ID as the random variable....
    • Animal cytogenetics

      Houck, Marlys L.; Lear, Teri L.; Charter, Suellen J.; Arsham, Marilyn S.; Barch, Margaret J.; Lawce, Helen J. (John Wiley & Sons, Inc., 2017)
      Chromosome karyotyping and gene mapping has been carried out for a wide variety of animal species and continues to expand. Cross-species chromosome painting, or Zoo-FISH, for example, can now be used to identify genome segments originating from a common ancestor that have been conserved between species for millions of years....
    • Approaches to studying behavior in captive sloth bears through animal keeper feedback

      Khadpekar, Yaduraj; Whiteman, John P.; Durrant, Barbara S.; Owen, Megan A.; Prakash, Sant (2018)
      Animal keepers at zoos and wildlife rescue centers often possess in-depth knowledge of the health and behavior of the individuals under their care. While it is often not feasible for keepers to regularly collect behavior data through formal scientific methods, efforts should be made to find alternative means to capture this knowledge.....
    • Assessment and validation of miniaturized technology for the remote tracking of critically endangered Galápagos pink land iguana (Conolophus marthae)

      Loreti, Pierpaolo; Bracciale, Lorenzo; Colosimo, Giuliano; Vera, Carlos; Gerber, Glenn P.; De Luca, Massimiliano; Gentile, Gabriele (2020)
      Background: Gathering ecological data for species of conservation concern inhabiting remote regions can be daunting and, sometimes, logistically infeasible. We built a custom-made GPS tracking device that allows to remotely and accurately collect animal position, environmental, and ecological data, including animal temperature and UVB radiation. We designed the device to track the critically endangered Galápagos pink land iguana, Conolophus marthae. Here we illustrate some technical solutions adopted to respond to challenges associated with such task and present some preliminary results from controlled trial experiments and feld implementation. Results: Our tests show that estimates of temperature and UVB radiation are affected by the design of our device, in particular by its casing. The introduced bias, though, is systematic and can be corrected using linear and quadratic regressions on collected values. Our data show that GPS accuracy loss, although introduced by vegetation and orientation of the devices when attached to the animals, is acceptable, leading to an average error gap of less than 15 m in more than 50% of the cases. Conclusions: We address some technical challenges related to the design, construction, and operation of a custom made GPS tracking device to collect data on animals in the wild. Systematic bias introduced by the technological implementation of the device exists. Understanding the nature of the bias is crucial to provide correction models. Although designed to track land iguanas, our device could be used in other circumstances and is particularly useful to track organisms inhabiting locations that are diffcult to reach or for which classic telemetry approaches are unattainable.
    • 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.
    • Assessment of mammal reproduction for hunting sustainability through community-based sampling of species in the wild

      Mayor, Pedro; El Bizri Hani; Bodmer Richard E.; Bowler, Mark (2017)
      ...researchers face severe difficulties in obtaining reproductive data in the wild, so these assessments often rely on classic reproductive rates calculated mostly from studies of captive animals conducted 30 years ago. The result is a flaw in almost 50% of studies, which hampers management decision making....
    • Challenges in the development of semen cryopreservation protocols for snakes

      Young, Carly; Ravida, Nicole; Durrant, Barbara S. (2019)
    • Chemical signatures of femoral pore secretions in two syntopic but reproductively isolated species of Galápagos land iguanas (Conolophus marthae and C. subcristatus)

      Colosimo, Giuliano; Di Marco, Gabriele; D’Agostino, Alessia; Gismondi, Angelo; Vera, Carlos A.; Gerber, Glenn P.; Scardi, Michele; Canini, Antonella; Gentile, Gabriele (Springer Science and Business Media LLC, 2020)
      The only known population of Conolophus marthae (Reptilia, Iguanidae) and a population of C. subcristatus are syntopic on Wolf Volcano (Isabela Island, Galápagos). No gene flow occurs suggesting that effective reproductive isolating mechanisms exist between these two species. Chemical signature of femoral pore secretions is important for intra- and inter-specific chemical communication in squamates. As a first step towards testing the hypothesis that chemical signals could mediate reproductive isolation between C. marthae and C. subcristatus, we compared the chemical profiles of femoral gland exudate from adults caught on Wolf Volcano. We compared data from three different years and focused on two years in particular when femoral gland exudate was collected from adults during the reproductive season. Samples were processed using Gas Chromatography coupled with Mass Spectrometry (GC–MS). We identified over 100 different chemical compounds. Non-Metric Multidimensional Scaling (nMDS) was used to graphically represent the similarity among individuals based on their chemical profiles. Results from non-parametric statistical tests indicate that the separation between the two species is significant, suggesting that the chemical profile signatures of the two species may help prevent hybridization between C. marthae and C. subcristatus. Further investigation is needed to better resolve environmental influence and temporal reproductive patterns in determining the variation of biochemical profiles in both species.
    • Collecting and maintaining exceptional species in tissue culture and cryopreservation

      Pence, Valerie; Westwood, Murphy; Maschinski, Joyce; Powell, Christy; Sugii, Nellie; Fish, Diana; McGuinness, Julianne; Raven, Pat; Duval, Julian; Herrera-Mishler, Tomas; et al. (Center for Plant ConservationEscondido, California, 2019)
      Tissue culture and cryopreservation are alternative storage methods for exceptional species that produce few seeds or seed that are intolerant to drying or freezing. Adequately storing exceptional species requires specialized expertise, infrastructure, and greater resources than conventional seed storage....
    • Comparative pathology of ranaviruses and diagnostic techniques

      Miller, D.L.; Pessier, Allan P.; Hick, P.; Whittington, R.J.; Gray M.; Chinchar V. (SpringerNew York, 2015)
      Recognizing the pathological changes caused by ranaviruses, understanding how to properly collect test samples, and knowing what diagnostic tools to choose are key to detecting ranaviruses and in determining whether they are a factor in morbidity and mortality events. Whether infection occurs in fish, reptiles, or amphibians, clinical disease is typically acute and can affect a high proportion of the population. Among ectothermic vertebrates, affected individuals can present with hemorrhages, edema, and necrosis. Generally, microscopic examination reveals intracytoplasmic inclusion bodies and necrosis of hematopoietic tissues, vascular endothelium, and epithelial cells. Ultimately, the type and severity of the lesions that develop vary depending upon the host species, type of ranavirus, or environmental factors. Our ability to identify lesions caused by ranaviruses is improving because of the knowledge gained from laboratory experiments and the improvement of existing, or development of new diagnostic tests. There is no single Gold Standard test for ranavirus detection, rather the diagnostic test chosen depends on the question asked. For example, a surveillance study may use quantitative real-time PCR (qPCR) to detect ranaviruses, but an investigation of a mortality event may use virus isolation, qPCR, histopathology, electron microscopy, and bioassay. To date, a treatment for ranavirus infections has not been found; however, vaccine development against iridoviruses is showing promise for both DNA and live vaccines within the aquaculture industry.
    • Conservation genetics of Roatán Spiny-tailed Iguanas, Ctenosaura oedirhina.

      Pasachnik, Stesha A.; Hudman, S.; Iverson, John B.; Grant, Tandora D.; Knapp, Charles R.; Pasachnik, Stesha A. (2016)
      Roatán Spiny-tailed Iguanas, Ctenosaura oedirhina, are assessed as Endangered by the IUCN Red List of Threatened Species and listed in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Occurring in less than 1% of the available habitat on Roatán, due primarily to hunting... pressure, this species faces severe fragmentation.
    • Derivation of induced pluripotent stem cells from orangutan skin fibroblasts

      Ramaswamy, Krishna; Yik, Wing Yan; Wang, Xiao-Ming; Oliphant, Erin N.; Lu, Wange; Shibata, Darryl; Ryder, Oliver A.; Hacia, Joseph G. (2015)
      Background Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. Along with the African great apes, orangutans are among the closest living relatives to humans. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved somatic cells obtained from captive orangutans. Results Primary skin fibroblasts from two Sumatran orangutans were transduced with retroviral vectors expressing the human OCT4, SOX2, KLF4, and c-MYC factors. Candidate orangutan iPSCs were characterized by global gene expression and DNA copy number analysis. All were consistent with pluripotency and provided no evidence of large genomic insertions or deletions. In addition, orangutan iPSCs were capable of producing cells derived from all three germ layers in vitro through embryoid body differentiation assays and in vivo through teratoma formation in immune-compromised mice. Conclusions We demonstrate that orangutan skin fibroblasts are capable of being reprogrammed into iPSCs with hallmark molecular signatures and differentiation potential. We suggest that reprogramming orangutan somatic cells in genome resource banks could provide new opportunities for advancing assisted reproductive technologies relevant for species conservation efforts. Furthermore, orangutan iPSCs could have applications for investigating the phenotypic relevance of genomic changes that occurred in the human, African great ape, and/or orangutan lineages. This provides opportunities for orangutan cell culture models that would otherwise be impossible to develop from living donors due to the invasive nature of the procedures required for obtaining primary cells.
    • 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.
    • Detection of neopterin in the urine of captive and wild platyrrhines

      Sacco, Alexandra J.; Mayhew, Jessica A.; Watsa, Mrinalini; Erkenswick, Gideon; Binder, April K. (Springer Science and Business Media LLC, 2020)
      Background: Non-invasive biomarkers can facilitate health assessments in wild primate populations by reducing the need for direct access to animals. Neopterin is a biomarker that is a product of the cell-mediated immune response, with high levels being indicative of poor survival expectations in some cases. The measurement of urinary neopterin concentration (UNC) has been validated as a method for monitoring cell-mediated immune system activation in multiple catarrhine species, but to date there is no study testing its utility in the urine of platyrrhine species. In this study, we collected urine samples across three platyrrhine families including small captive populations of Leontopithecus rosalia and Pithecia pithecia, and larger wild populations of Leontocebus weddelli, Saguinus imperator, Alouatta seniculus, and Plecturocebus toppini, to evaluate a commercial enzyme-linked immunosorbent assay (ELISA) for the measurement of urinary neopterin in platyrrhines. Results: Our results revealed measured UNC fell within the sensitivity range of the assay in all urine samples collected from captive and wild platyrrhine study species via commercial ELISA, and results from several dilutions met expectations. We found significant differences in the mean UNC across all study species. Most notably, we observed higher UNC in the wild population of L. weddelli which is known to have two filarial nematode infections compared to S. imperator, which only have one. Conclusion: Our study confirms that neopterin is measurable via commercial ELISA in urine collected from captive and wild individuals of six genera of platyrrhines across three different families. These findings promote the future utility of UNC as a promising biomarker for field primatologists conducting research in Latin America to non-invasively evaluate cell-mediated immune system activation from urine. Keywords: Neopterin, Health monitoring, Platyrrhines, Immune function, Biomarker