• 117 Cryopreservation of snake semen: Are we frozen in time?

      Zacariotti, R.; Guimarães, M.; Jensen, Thomas; Durrant, Barbara S. (2011)
      The increasing number of endangered snake species, isolation of small fragmented populations with associated inbreeding and mating or conception problems in captivity underscore the need to develop assisted reproductive techniques such as semen cryopreservation and artificial insemination to enhance conservation efforts. However, no efficient protocols for semen evaluation, cooling, or freezing are described in the 4 known publications on snake semen cryopreservation. In this initial study, semen was collected noninvasively from 4 live adult red diamond rattlesnakes (Crotalus ruber) by ventral massage....
    • A comparative genomics multitool for scientific discovery and conservation

      Genereux, Diane P.; Serres, Aitor; Armstrong, Joel; Johnson, Jeremy; Marinescu, Voichita D.; Murén, Eva; Juan, David; Bejerano, Gill; Casewell, Nicholas R.; Chemnick, Leona G.; et al. (2020)
      The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
    • A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations

      Ivy, Jamie A.; Lacy, Robert C. (2012)
      Captive breeding programs aim to maintain populations that are demographically self-sustaining and genetically healthy. It has been well documented that the best way for managed breeding programs to retain gene diversity (GD) and limit inbreeding is to select breeding pairs that minimize a population's average kinship....
    • A high density snp array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies

      McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; et al. (2012)
      An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ?43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of -750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
    • Activation of southern white rhinoceros (Ceratotherium simum simum) estrogen receptors by phytoestrogens: Potential role in the reproductive failure of captive-born females?

      Tubbs, Christopher W.; Hartig, P.; Cardon, M.; Varga, Nicole; Milnes, Matthew R. (2012)
      The captive southern white rhinoceros (SWR; Ceratotherium simum simum) population serves as an important genetic reservoir critical to the conservation of this vulnerable species. Unfortunately, captive populations are declining due to the poor reproductive success of captive-born females....
    • Advancing laboratory-based zoo research to enhance captive breeding of southern white rhinoceros

      Tubbs, Christopher W.; Minteer, Ben A.; Maienschein, Jane; Collins, James P. (University of Chicago PressChicago, IL, 2018)
      The captive southern white rhinoceros (SWR) is not currently self-sustaining because of low fertility of captive-born females. The cause of this phenomenon is believed to be high dietary levels of phytoestrogens; endocrine disrupting chemicals (EDCs) produced by plants that can mimic the reproductive hormone estrogen....
    • Alsophis sibonius (NCN) copulation

      Knapp, Charles R.; Shirk, P.L.; (2010)
      Alsophis sibonius is a diurnal, actively foraging snake inhabiting the Commonwealth of Dominica, West Indies....Here we report a field observation of copulation for A. sibonius from the Caribbean side of Dominica....
    • Altered gonadal expression of TGF-beta superfamily signaling factors in environmental contaminant-exposed juvenile alligators

      Moore, B.C.; Milnes, Matthew R.; Kohno, S.; Katsu, Y.; Iguchi, T. (2011)
      Environmental contaminant exposure can influence gonadal steroid signaling milieus; however, little research has investigated the vulnerability of non-steroidal signaling pathways in the gonads. Here we use American alligators (Alligator mississippiensis) hatched from field-collected eggs to analyze gonadal mRNA transcript levels of the activin–inhibin–follistatin gene expression network and growth differentiation factor 9....
    • AMPHIBIAN DISEASES-Batrachochytrium dendrobatidis in Adult Notophthalmus viridescens in North-Central Alabama, USA

      Bakkegard, K. A.; Pessier, Allan P.; (2010)
      ...We report on a haphazard collection of dead adult Notophthalmus viridescens discovered during a field zoology class trip conducted by KAB in Birmingham, Alabama....
    • An interdisciplinary systems approach to study sperm physiology and evolution

      Shi, L.Z.; Nascimento, J.; Botvinick, E.; Durrant, Barbara S.; Berns, M.W. (2011)
      Optical trapping is a noninvasive biophotonic tool that has been developed to study the physiological and biomechanical properties of cells…. A real‐time automated tracking and trapping system (RATTS) is described that provides a remote user‐friendly robotic interface…. This combination of photonic physical and engineering tools has been used to examine the evolutionary effect of sperm competition in primates….
    • Andean Bear Priority Conservation Units in Bolivia and Peru: Results of the Binational Workshop for the Conservation of the Andean Bear in Bolivia and Peru, November 8th & 9th 2008, held as part of the II International Symposium on the Andean Bear in Lima, Peru.

      Pitman, Renata Leite; Reinaga, A.; Siles, T.; Baiker, J.; Goldstein, B.; Ríos-Uzeda, R.; Van Horn, Russell C.; Vargas, X.; ADD MORE (2014)
      ...Given the importance of the Andean bear for conservation efforts across the Tropical Andes and the lack of systematized information regarding distribution and ecology, an effort was made at the beginning of the millennium to gather and collectively analyze existing Andean bear data for the Northern Andes. Lead by the World Wildlife Fund (WWF), with institutional support from a number of other conservation NGO’s, particularly the Wildlife Conservation Society (WCS) and Ecociencia, this exercise encompassed the entire known northern range for the species in Colombia, Ecuador and Venezuela, as well as the extreme northern portions of Peru (Rodríguez et al., 2003). A parallel analysis of these results were also published in an internationally recognized journal (Kattan et al., 2004), and the fIndings and recommendations have been widely cited (Garcia-Rangel, 2012) and incorporated into conservation planning efforts across the range covered by the analysis (Peralvo et al., 2005)....
    • Appendix 4: Annotated bibliography of books, journals, and web sites on captive management.

      Kenyon Barboza, K.; Coates, Linda L.; Kleiman, Devra G. (University of Chicago Press, 2010)
      ...Wild Mammals in Captivity presents the most current thinking and practice in the care and management of wild mammals in zoos and other institutions. In one comprehensive volume, the editors have gathered the most current information from studies of animal behavior; advances in captive breeding; research in physiology, genetics, and nutrition; and new thinking in animal management and welfare.....
    • Assessing potential impacts of solar power facilities on wildlife utilizing animal behavior research

      Chock, Rachel Y.; Clucas, B.; Peterson, E.K.; Blackwell, B.F.; Blumstein, D.T.; Church, K.; Fernández-Juricic, E.; Francescoli, G.; Greggor, A.L.; Kemp, P.; et al. (Virtual, 2021)
      Utility-scale solar power is a rapidly expanding renewable energy source with great potential to help meet increasing global energy demands. Solar facilities have large footprints across previously undeveloped habitat, particularly the American Southwest. Despite the scale of this industry, research is scarce on how construction and operation of facilities affect wildlife. We conducted a research-prioritization process to identify key questions to better understand how wildlife is affected by solar facilities and how behavioral data can be used to mitigate negative impacts. Behavioral responses are often the most visible signs of detrimental effects, as behavioral shifts are usually an animal’s first response to environmental change. We asked professionals in the fields of ecology, conservation, and energy to identify important research questions, then held a workshop to reduce and clarify these questions. The priority research areas that emerged included animal perception of solar facilities, movement, habitat use, and interspecific interactions.
    • Benefits of overwintering in the conservation breeding and translocation of a critically endangered amphibian

      Calatayud, Natalie E.; Hammond, Talisin T.; Gardner, Nicole R.; Curtis, Michelle J.; Swaisgood, Ronald R.; Shier, Debra M. (2020)
      At high altitudes, amphibians brumate (over winter) during the winter months, an adaptation that provides protection from harsh weather and minimizes metabolic demand when food resources are scarce. However, brumation in ex situ populations is often avoided due to concerns regarding slow growth rates, compromised immunity, and increased morbidity, and to accelerate growth and sexual maturation. Running counter to these ideas is the hypothesis that husbandry that mimics the environmental conditions under which a species evolved may benefit animal health and reproduction. This may be particularly critical for animals slated for release into the wild. Here, we evaluated the effects of brumation on juvenile southern mountain yellow-legged frogs (Rana muscosa) in a conservation breeding and release program. Growth measurements, (weight and snout-urostyle length [SUL]), were examined in three experimental groups: Nonbrumated, 1 or 3-month brumation. Postrelease survival was also analyzed and compared between nonbrumated and 3-month brumated frogs. This study indicates that brumated R. muscosa juveniles grow to sizes and weights similar to controls within 3 to 4 months following brumation. Mark-recapture models suggested that short-term postrelease survival was not lower and in fact, may be higher in brumated compared to nonbrumated frogs. Results of this study indicate that although brumation entails short-term costs to growth, this species possesses compensatory growth mechanisms following brumation which allow them to attain similar body size to nonbrumated conspecifics in time for the next winter and that for frogs destined for translocation to the wild, brumation could improve survival outcomes.
    • Body size and sexual selection in the koala

      Ellis, William A.; Bercovitch, Fred B. (2011)
      ...Koalas are sexually dimorphic in multiple domains, yet are absent from the literature on sexual selection and the structure of their mating system is unclear. We provide the first documentation of the strength of sexual selection in koalas by using microsatellite markers to identify sires....
    • Body size, demography, and body condition in Utila spiny-tailed iguanas, Ctenosaura bakeri

      Pasachnik, Stesha A.; Montgomery, Chad E; Martinez, Andrea; Belal, Nardiah; Clayson, Steve; Faulkner, Shane (2012)
      Utila Spiny-tailed Iguanas, Ctenosaura bakeri, are listed as Critically Endangered by the IUCN Redlist Assessment and are listed under Appendix II of CITES. This species occupies a portion of Utila, a small continental island located off the northern coast of Honduras, in the Bay Islands chain. Habitat destruction and overharvesting for consumption and the pet trade are among the top threats facing this species. Though first described in 1901 (Stejneger) and currently the focus of a local conservation program, little is known concerning that basic biology of this species. Combining data from six years we examined body size, sexual size dimorphism, and changes in demography and body condition over the study period. Our results indicate that males are larger and heavier than females on average, and have a longer tail for a given snout-vent length, as is the case with most iguanas. Over the study period we found an increase in the ratio of males to females, suggesting that female biased hunting pressure is increasing. This is consistent with an increase in the human population size and a preference for consuming gravid females. The body condition of both males and females declined over the duration of the study, which is suggestive of a decrease in habitat quality. These results indicate that the situation for this endangered species is becoming increasingly threatening. Conservation measures should focus on alleviating these threats through increased law enforcement, outreach, and education.
    • Bringing the Tiger Back from the Brink—The Six Percent Solution

      Walston, Joe; Robinson, John G.; Bennett, Elizabeth L.; Breitenmoser, Urs; Fonseca, Gustavo A. B. da; Goodrich, John; Gumal, Melvin; Hunter, Luke; Johnson, Arlyne; Karanth, K. Ullas; et al. (2010)
      ...Wild tiger numbers are at an historic low. There is no evidence of breeding populations of tigers in Cambodia, China, Vietnam, and DPR Korea. Current approaches to tiger conservation are not slowing the decline in tiger numbers [1]–[3], which has continued unabated over the last two decades. While the scale of the challenge is enormous, we submit that the complexity of effective implementation is not: commitments should shift to focus on protecting tigers at spatially well-defined priority sites, supported by proven best practices of law enforcement, wildlife management, and scientific monitoring. Conflict with local people needs to be mitigated. We argue that such a shift in emphasis would reverse the decline of wild tigers and do so in a rapid and cost-efficient manner....
    • Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

      Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; et al. (2020)
      The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
    • Camera settings and biome influence the accuracy of citizen science approaches to camera trap image classification

      Egna, Nicole; O'Connor, David; Stacy-Dawes, Jenna; Tobler, Mathias W.; Pilfold, Nicholas W.; Neilson, Kristin; Simmons, Brooke; Davis, Elizabeth Oneita; Bowler, Mark; Fennessy, Julian; et al. (2020)
      Scientists are increasingly using volunteer efforts of citizen scientists to classify images captured by motion-activated trail cameras. The rising popularity of citizen science reflects its potential to engage the public in conservation science and accelerate processing of the large volume of images generated by trail cameras. While image classification accuracy by citizen scientists can vary across species, the influence of other factors on accuracy is poorly understood. Inaccuracy diminishes the value of citizen science derived data and prompts the need for specific best-practice protocols to decrease error. We compare the accuracy between three programs that use crowdsourced citizen scientists to process images online: Snapshot Serengeti, Wildwatch Kenya, and AmazonCam Tambopata. We hypothesized that habitat type and camera settings would influence accuracy. To evaluate these factors, each photograph was circulated to multiple volunteers. All volunteer classifications were aggregated to a single best answer for each photograph using a plurality algorithm. Subsequently, a subset of these images underwent expert review and were compared to the citizen scientist results. Classification errors were categorized by the nature of the error (e.g., false species or false empty), and reason for the false classification (e.g., misidentification). Our results show that Snapshot Serengeti had the highest accuracy (97.9%), followed by AmazonCam Tambopata (93.5%), then Wildwatch Kenya (83.4%). Error type was influenced by habitat, with false empty images more prevalent in open-grassy habitat (27%) compared to woodlands (10%). For medium to large animal surveys across all habitat types, our results suggest that to significantly improve accuracy in crowdsourced projects, researchers should use a trail camera set up protocol with a burst of three consecutive photographs, a short field of view, and determine camera sensitivity settings based on in situ testing. Accuracy level comparisons such as this study can improve reliability of future citizen science projects, and subsequently encourage the increased use of such data.
    • Can science save the giant panda (Ailuropoda melanoleuca)? Unifying science and policy in an adaptive management paradigm

      Swaisgood, Ronald R.; Wei, Fuwen; Mcshea, William J.; Wildt, David E.; Kouba, Andrew J.; Zhang, Zejun (2011)
      …Here, we review recent developments in giant panda conservation science and propose a strategic plan for moving panda conservation forward…. Specific threats, such as habitat destruction, anthropogenic disturbance and fragmented nonviable populations, need to be addressed simultaneously by researchers, managers and policy-makers working in concert to understand and overcome these obstacles to species recovery. With the backing of the Chinese Government and the conservation community, the giant panda can become a high-profile test species for this much touted, but rarely implemented, approach to conservation management….