• Andros iguana: Conservation action plan, 2005-2011

      Knapp, Charles; Pagni, Lee (IUCN/SSC Iguana Specialist GroupGland, Switzerland, 2011)
      The endangered Andros iguana, Cyclura cychlura cychlura, is the largest native terrestrial vertebrate, and the only iguana (of 3 species) in the Bahamas that is not confined presently to small cays. The Andros iguana is unique to Andros Island and despite the recent formation of a national park on North Andros Island in 2002, the population is declining. This document presents a comprehensive plan for conservation measures considered essential to the long-term survival of this flagship species in the wild. It combines the knowledge and expertise of highly qualified experts from government and non-government organizations within The Bahamas with the collective conservation experience and scientific expertise of the IUCN/SSC Iguana Specialist Group.
    • Animal Welfare in Conservation Breeding: Applications and Challenges

      Greggor, Alison L.; Vicino, Greg A.; Swaisgood, Ronald R.; Fidgett, Andrea; Brenner, Deena J.; Kinney, Matthew E.; Farabaugh, Susan M.; Masuda, Bryce M.; Lamberski, Nadine (2018)
      Animal welfare and conservation breeding have overlapping and compatible goals that are occasionally divergent. Efforts to improve enclosures, provide enriching experiences, and address behavioral and physical needs further the causes of animal welfare in all zoo settings. However, by mitigating stress, increasing behavioral competence, and enhancing reproduction, health, and survival, conservation breeding programs must also focus on preparing animals for release into the wild. Therefore conservation breeding facilities must strike a balance of promoting high welfare, while minimizing the effects of captivity to increase population sustainability. As part of the Hawaii Endangered Bird Conservation Program, San Diego Zoo Global operates two captive breeding facilities that house a number of endangered Hawaiian bird species. At our facilities we aim to increase captive animal welfare through husbandry, nutrition, behavior-based enrichment, and integrated veterinary practices. These efforts help foster a captive environment that promotes the development of species-typical behaviors. By using the “Opportunities to Thrive” guiding principles, we outline an outcome-based welfare strategy, and detail some of the related management inputs, such as transitioning to parental rearing, and conducting veterinary exams remotely. Throughout we highlight our evidence-based approach for evaluating our practices, by monitoring welfare and the effectiveness of our inputs. Additionally we focus on some of the unique challenges associated with improving welfare in conservation breeding facilitates and outline concrete future steps for improving and evaluating welfare outcomes that also meet conservation goals.
    • 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, 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.
    • California condor North American studbook (Gymnogyps californianus)

      Mace, Michael E.; (Zoological Society of San DiegoEscondido, CA, 2010)
    • California Condor Studbook

      Mace, Michael E. (Zoological Society of San DiegoSan Diego, 2011)
    • Characterization of cultured adult Corturnix japonica testicular germ stem cells using seven stem cell markers.

      Jensen, Thomas; Poling, Matthew; Charter, Suellen; Durrant, Barbara S.; (2010)
      ...The large avian oocyte and the inability to consistently superovulate birds make techniques such as cloning and oocyte cryopreservation unlikely tools for avian conservation. Instead, the use of domestic birds as hosts to produce sperm of exotic species for use in artificial insemination may be a practical approach to conserve avian germplasm....
    • Comparative and demographic analysis of orang-utan genomes

      Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; et al. (2011)
      ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
    • Comparison of beak and feather disease virus prevalence and immunity-associated genetic diversity over time in an island population of red-crowned parakeets

      Knafler, Gabrielle J.; Ortiz-Catedral, Luis; Jackson, Bethany; Varsani, Arvind; Grueber, Catherine E.; Robertson, Bruce C.; Jamieson, Ian G. (2016)
      …Beak and feather disease virus (BFDV) was detected for the first time in an island population of red-crowned parakeets (Cyanoramphus novaezelandiae) in 2008 on Little Barrier Island (Hauturu-o-Toi) of New Zealand. By 2013, the prevalence of the viral infection had significantly decreased within the population….
    • Conservation genetics of the black rhinoceros, Diceros bicornis bicornis, in Namibia

      Van Coeverden de Groot, Peter J.; Putnam, Andrea S.; Erb, Peter; Scott, Candace; Melnick, Don; O’Ryan, Colleen; Boag, Peter T. (2011)
      Poaching and habitat destruction across sub-Saharan Africa brought the black rhinoceros (Diceros bicornis) close to extinction. Over the past few decades, however, one of four subspecies, D. b. bicornis, has experienced a significant population increase as a consequence of its protection within Etosha National Park (ENP), Namibia. We report here on the level and spatial distribution of black rhinoceros genetic diversity within ENP….
    • Conservation genomics of threatened animal species

      Steiner, Cynthia C.; Putnam, Andrea S.; Hoeck, Paquita E. A.; Ryder, Oliver A. (2013)
      The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation.…
    • Conservation implications of inaccurate estimation of cryptic population size: Inaccurate estimation of cryptic population size

      Katzner, T. E.; Ivy, Jamie A.; Bragin, E. A.; Milner-Gulland, E.J.; DeWoody, J. A. (2011)
      ...Estimating population size is central to species‐oriented conservation and management. However, in spite of recent development in monitoring protocols, there are gaps in our ability to accurately and quickly estimate numbers of individuals present, especially for the cryptic and often non‐breeding components of structured vertebrate populations. Yet knowing the size and growth trajectory of all stage classes of a population is critical for species conservation. Here we use data from 2 years of non‐invasive genetic sample collection from the cryptic, non‐breeding component of an endangered bird of prey population to evaluate the impact of variability in population estimates on demographic models that underpin conservation efforts....
    • Cryptic population size and conservation: consequences of making the unknown known: Cryptic population size and conservation reponse

      Katzner, T. E.; Ivy, Jamie A.; Bragin, E. A.; Milner-Gulland, E. J.; DeWoody, J. A. (2011)
      ...Our two papers use non‐invasive genetic sampling and population modeling to highlight how far off our original estimate of imperial eagle Aquila heliaca population size was (Rudnick et al., 2008), and to allow us to begin to consider the consequences, for monitoring and for conservation, of changing an known unknown into a known known (Katzner et al., 2011)....
    • Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population

      Wright, Belinda; Morris, Katrina; Grueber, Catherine E.; Willet, Cali E.; Gooley, Rebecca; Hogg, Carolyn J.; O’Meally, Denis; Hamede, Rodrigo; Jones, Menna; Wade, Claire; et al. (2015)
      The Tasmanian devil (Sarcophilus harrisii) has undergone a recent, drastic population decline due to the highly contagious devil facial tumor disease. The tumor is one of only two naturally occurring transmissible cancers and is almost inevitably fatal. In 2006 a disease-free insurance population was established to ensure that the Tasmanian devil is protected from extinction. The insurance program is dependent upon preserving as much wild genetic diversity as possible to maximize the success of subsequent reintroductions to the wild. Accurate genotypic data is vital to the success of the program to ensure that loss of genetic diversity does not occur in captivity. Until recently, microsatellite markers have been used to study devil population genetics, however as genetic diversity is low in the devil and potentially decreasing in the captive population, a more sensitive genotyping assay is required.
    • Developmental stability of foraging behavior: evaluating suitability of captive giant pandas for translocation

      Swaisgood, Ronald R.; Martin-Wintle, Meghan S.; Owen, Megan A.; Zhou X.; Zhang H. (2018)
      The behavioral competence of captive-bred individuals - an important source population for translocation programs - may differ from that of wild-born individuals and these differences may influence post-release survival. Some behaviors will be more robust, or developmentally stable, than others in the face of the environmental novelties of captivity. Here, we investigated developmental stability of foraging behavior by quantifying bamboo feeding behavior in captive-bred and wild-born giant pandas, Ailuropoda melanleuca. As an energy-limited species adapted to a low-nutrition diet, any reductions in feeding efficiency may compromise post-release survival. Using video of 22 captive pandas, we measured several components of the panda's elaborate bamboo feeding behavior repertoire. We found that captive-born and wild-born pandas displayed the same repertoire of feeding behaviors, suggesting developmental stability in these motor patterns, but that they employed them differently with different parts of the bamboo. Captive-born pandas devoted less time and effort to handling and chewing leaves while allocating more effort to the consumption of large culms than did wild?born pandas. Captive-born pandas also handled small culm and stripped small culms to prepare them for consumption less often than did wild?born pandas. All of these behavioral differences indicate that wild-born pandas in captivity behave in a manner more similar to wild pandas, and focus their behavioral effort on more nutritious bamboo. Thus, these aspects of captive-born panda feeding behavior may be compromised, and were not developmentally stable in the captive environment. These behavioral differences are cause for concern and should be the subject of future study to determine whether they forecast compromised fitness in translocations. Evaluating developmental stability and behavioral competence should be a key component of captive-release translocation programs, serving to guide pre-release training and selection of individuals to be released.
    • Disorders of sexual development in wild and captive exotic animals

      Mastromonaco, G. F.; Houck, Marlys L.; Bergfelt, D. R. (2012)
      ...Compared to the wealth of information available on humans and domestic species, a better understanding of the factors influencing sexual development in wildlife is essential for developing and improving population management or conservation plans. This review attempts to bring together the different facets of DSDs as studied in the fields of reproductive physiology, endocrinology, ecotoxicology, wildlife biology, and environmental health.