• 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 retrospective and prospective study of megaesophagus in the Parma wallaby (Macropus parma) at the San Diego Zoo, California, USA

      Burgdorf-Moisuk, Anne; Pye, Geoffrey W.; Smith, Joseph A.; Papendick, Rebecca; Ivy, Jamie A.; Hamlin-Andrus, Chris (2012)
      At the San Diego Zoo (California, USA), 22 cases of megaesophagus were diagnosed in the parma wallaby (Macropus parma); a prevalence of 21.1%. Parma wallabies often have no clinical signs until severe and chronic dilation of the esophagus is present....
    • Behavioral audiogram of the giant panda (Ailuropoda melanoleuca): Preliminary results

      Owen, Megan A.; Keating, Jennifer L.; Denes, Samuel L.; Hawk, Kathy; Boroski, Juli; Fiore, Angela; Swaisgood, Ronald R. (2011)
      We used behavioral techniques to assess the hearing sensitivity of four, critically endangered, giant pandas at the San Diego Zoo. Study subjects included one adult male (age 19), two adult females (ages 5 and 19), and one sub-adult female (age 3)…. Hearing sensitivity data will enhance the understanding of how anthropogenic noise may impact both free-ranging and captive giant pandas.
    • Cerebral Angiostrongylus cantonensis infection in a captive African pygmy falcon (Polihierax semitorquatus) in southern California

      Burns, Rachel E.; Bicknese, Elizabeth; Qvarnstrom, Yvonne; DeLeon-Carnes, Marlene; Drew, Clifton P.; Gardiner, Chris H.; Rideout, Bruce (2014)
      A 10-month-old, female African pygmy falcon (Polihierax semitorquatus) hatched and housed at the San Diego Zoo developed neurologic signs and died from a cerebral infection with the rat lungworm Angiostrongylus cantonensis…. To the authors’ knowledge, this infection has not previously been reported in a bird in the United States and has not been known to be naturally acquired in any species in this region of the world. The source of the infection was not definitively determined but was possibly feeder geckos (Hemidactylus frenatus) imported from Southeast Asia where the parasite is endemic.
    • Dietary specialization and Eucalyptus species preferences in Queensland koalas (Phascolarctos cinereus)

      Higgins, Alexis L.; Bercovitch, Fred B.; Tobey, Jennifer R.; Andrus, Chris Hamlin (2011)
      Koalas specialize on�Eucalyptus�leaves, but also feed selectively. Food choice is not random, but depends on various factors that are not well understood, although most research has focused on the role of secondary plant compounds. We studied the feeding choices of four adult male koalas housed at the San Diego Zoo....
    • Dietary specialization and Eucalyptus species preferences in Queensland koalas (Phascolarctos cinereus)

      Higgins, Alexis L.; Bercovitch, Fred B.; Tobey, Jennifer R.; Andrus, Chris Hamlin (2011)
      ...We studied the feeding choices of four adult male koalas housed at the San Diego Zoo. All subjects had a choice of nine types of Eucalyptus leaves over the eight‐week study....
    • Disentangling the mechanisms of mate choice in a captive koala population

      Brandies, Parice A.; Grueber, Catherine E.; Ivy, Jamie A.; Hogg, Carolyn J.; Belov, Katherine (2018)
      Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair’s age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
    • Does placental invasiveness lead to higher rates of malignant transformation in mammals?Response to: ‘Available data suggests positive relationship between placental invasion an malignancy’

      Boddy, Amy M.; Abegglen, Lisa M.; Aktipis, Athena; Schiffman, Joshua D.; Maley, Carlo C.; Witte, Carmel L. (2020)
      In our study, Lifetime cancer prevalence and life history traits in mammals, we reported the prevalence of neoplasia and malignancy in a select group of mammals housed at San Diego Zoo Global from 1964 to 1978 and 1987 to 2015 [1]. We also used these data to evaluate associations between life history traits and measures of population health. Our analysis showed placental invasiveness could not predict the proportion of animals diagnosed with neoplasia or malignancy. In a response to our article, Drs Wagner and colleagues describe a different calculation to test for a relationship between placental invasiveness and malignancy. They identified and included previously published veterinary neoplasia and malignancy data with our published dataset and suggest a positive relationship between placental invasiveness and development of malignancy (referred to as malignancy rate in Wagner and colleagues’ response). These data provided support for the Evolved Levels of Invasiveness (ELI) hypothesis [2]. We are pleased that other investigators find our data useful, and wholeheartedly agree with Drs Wagner and colleagues in the need to identify more data on cancer in a wide variety of species. Notwithstanding, this updated analysis brings up a number of topics that we would like to address....
    • Efforts to restore the California condor to the wild

      Wallace, Michael P. (2012)
      By the early 1980s new studies using radio telemetry and moult patterns to identify individuals indicated that only 21 California condors (Gymnogyps californianus) existed, with five pairs sporadically breeding. With continuous and poorly understood mortality, the decision was made to capture the remaining animals and in 1987 all 27 birds were placed in the protective custody of the San Diego and Los Angeles zoos, at which time the species was considered Extinct in the Wild....
    • Fat-soluble vitamin and mineral comparisons between zoo-based and free-ranging koalas (phascolarctos cinereus)

      Schmidt, Debra A.; Pye, Geoffrey W.; Hamlin-Andrus, Chris C.; Ellis, William A.; Ellersieck, Mark R.; Chen, Tai C.; Holick, Michael F. (2013)
      As part of a health investigation on koalas at San Diego Zoo, serum samples were analyzed from 18 free-ranging and 22 zoo-based koalas, Phascolarctos cinereus. Serum concentrations of calcium, chloride, cobalt, copper, iron, magnesium, manganese, molybdenum, phosphorus, potassium, selenium, sodium, zinc, and vitamins A, E, and 25(OH)D3 were quantified....
    • Gastrointestinal torsions and intussusception in Northern koalas (Phascolarctos cinereus) at San Diego Zoo (1976–2012)

      Joyce-Zuniga, Nicole M.; Roesler, Jennifer; Andrus, Chris Hamlin; Sutherland-Smith, Meg; Rideout, Bruce; Pye, Geoffrey W. (2014)
      The recent classification as threatened status of the northern koala (Phascolarctos cinereus) by the Australian Government highlights the importance of the conservation and health management of this iconic Australian marsupial. This case series describes gastrointestinal torsion and intussusception in six northern koalas (three males, three females, 2–11 yr old) at the San Diego Zoo from 1976 to 2012….
    • Herpesvirus surveillance and discovery in zoo-housed ruminants

      Partin, Teagen G.; Schrenzel, Mark D.; Braun, Josephine; Witte, Carmel L.; Kubiski, Steven V.; Lee, Justin; Rideout, Bruce (Public Library of Science (PLoS), 2021)
      Gammaherpesvirus infections are ubiquitous in captive and free-ranging ruminants and are associated with a variety of clinical diseases ranging from subclinical or mild inflammatory syndromes to fatal diseases such as malignant catarrhal fever. Gammaherpesvirus infections have been fully characterized in only a few ruminant species, and the overall diversity, host range, and biologic effects of most are not known. This study investigated the presence and host distribution of gammaherpesviruses in ruminant species at two facilities, the San Diego Zoo and San Diego Zoo Safari Park. We tested antemortem (blood, nasal or oropharyngeal swabs) or postmortem (internal organs) samples from 715 healthy or diseased ruminants representing 96 species and subspecies, using a consensus-based herpesvirus PCR for a segment of the DNA polymerase (DPOL) gene. Among the 715 animals tested, 161 (22.5%) were PCR and sequencing positive for herpesvirus, while only 11 (6.83%) of the PCR positive animals showed clinical signs of malignant catarrhal fever. Forty-four DPOL genotypes were identified of which only 10 have been reported in GenBank. The data describe viral diversity within species and individuals, identify host ranges of potential new viruses, and address the proclivity and consequences of interspecies transmission during management practices in zoological parks. The discovery of new viruses with wide host ranges and presence of co-infection within individual animals also suggest that the evolutionary processes influencing Gammaherpesvirus diversity are more complex than previously recognized.
    • Lifetime cancer prevalence and life history traits in mammals

      Boddy, Amy M.; Abegglen, Lisa M.; Pessier, Allan P.; Schiffman, Joshua D.; Maley, Carlo C.; Witte, Carmel L. (2020)
      Background Cancer is a common diagnosis in many mammalian species, yet they vary in their vulnerability to cancer. The factors driving this variation are unknown, but life history theory offers potential explanations to why cancer defense mechanisms are not equal across species. Methodology Here we report the prevalence of neoplasia and malignancy in 37 mammalian species, representing 11 mammalian orders, using 42 years of well curated necropsy data from the San Diego Zoo and San Diego Zoo Safari Park. We collected data on life history components of these species and tested for associations between life history traits and both neoplasia and malignancy, while controlling for phylogenetic history. Results These results support Peto’s paradox, in that we find no association between lifespan and/or body mass and the prevalence of neoplasia or malignancy. However, a positive relationship exists between litter size and prevalence of malignancy (P = 0.005, Adj. R2 = 0.212), suggesting that a species’ life history strategy may influence cancer vulnerabilities. Lastly, we tested for the relationship between placental invasiveness and malignancy. We find no evidence for an association between placental depth and malignancy prevalence (P = 0.618, Adj. R2 = 0.068). Conclusions Life history theory offers a powerful framework to understand variation in cancer defenses across the tree of life. These findings provide insight into the relationship between life history traits and cancer vulnerabilities, which suggest a trade-off between reproduction and cancer defenses. Lay summary Why are some mammals more vulnerable to cancer than others? We test whether life history trade-offs may explain this variation in cancer risk. Bigger, longer-lived animals do not develop more cancer compared to smaller, shorter-lived animals. However, we find a positive association between litter size and cancer prevalence in mammals.
    • Lineage identification and genealogical relationships among captive Galápagos tortoises

      Benavides, Edgar; Russello, Michael; Boyer, Donal; Wiese, Robert J.; Kajdacsi, Brittney; Marquez, Lady; Garrick, Ryan; Caccone, Adalgisa (2012)
      Genetic tools have become a critical complement to traditional approaches for meeting short‐ and long‐term goals of ex situ conservation programs. The San Diego Zoo (SDZ) harbors a collection of wild‐born and captive‐born Galápagos giant tortoises (n = 22) of uncertain species designation and unknown genealogical relationships. Here, we used mitochondrial DNA haplotypic data and nuclear microsatellite genotypic data to identify the evolutionary lineage of wild‐born and captive‐born tortoises of unknown ancestry, to infer levels of relatedness among founders and captive‐born tortoises, and assess putative pedigree relationships assigned by the SDZ studbook....
    • Pandemic (H1N1) 2009 virus in 3 wildlife species, San Diego, California, USA

      Schrenzel, Mark D.; Tucker, Tammy A.; Stalis, Ilse H.; Kagan, Rebecca A.; Burns, Russell P.; Denison, Amy M.; Drew, Clifton P.; Paddock, Christopher D.; Rideout, Bruce (2011)
      The influenza A pandemic (H1N1) 2009 virus rapidly created a global pandemic among humans and also appears to have strong infectivity for a broad range of animal species (1–3). The virus has been found repeatedly in swine and has been detected in a dog, cats, turkeys, and domestic ferrets and in nondomestic animals, including skunks, cheetahs, and giant anteaters (2–4). In some cases, animal-to-animal transmission may have occurred, raising concern about the development of new wildlife reservoirs. In 2009, the first recognized occurrence of pandemic (H1N1) 2009 in southern California in April was followed by a surge of cases during October through November (4). During this time, respiratory illness developed in a 12-year-old male American badger (Taxidea taxus taxus), a 19-year-old female Bornean binturong (Arctictis binturong penicillatus), and a 7-year-old black-footed ferret (Mustela nigripes) housed in a San Diego zoological garden....
    • Space use as an indicator of enclosure appropriateness in African wild dogs (Lycaon pictus)

      Hunter, Sally C.; Gusset, Markus; Miller, Lance J.; Somers, Michael J. (2014)
      A clear understanding of space use is required to more fully understand biological requirements of nonhuman animals in zoos, aid the design of exhibits, and maximize the animals' welfare. This study used electivity indexes to assess space use of two packs of African wild dogs (Lycaon pictus) and the appropriateness of two naturalistic, outdoor enclosures at the San Diego Zoo and Bronx Zoo....
    • Using microsatellite diversity in wild Anegada iguanas (Cyclura pinguis) to establish relatedness in a captive breeding group of this critically endangered species

      Mitchell, A.A.; Lau, J.; Chemnick, Leona G.; Thompson, E. A.; Alberts, Allison C.; Ryder, Oliver A.; Gerber, Glenn P. (2011)
      Awareness of the genealogical relationships between founder animals in captive breeding programs is essential for the selection of mating pairs that maintain genetic diversity. If captive founder relationships are unknown they can be inferred using genetic data from wild populations. Here, we report the results of such an analysis for six Cyclura pinguis (Sauria: Iguanidae) acquired as adults in 1999 by the San Diego Zoo Institute for Conservation Research to begin a captive breeding program for this critically endangered species....
    • Xantusia riversiana (island night lizard). Captive diet

      Baldwin, Brett; Fontaine, Jeremy; Lovich, Kim (2016)
      Xantusia riversiana has seldom been kept in zoological institutions, and very little is known about its diet in captivity. In the wild, X. riversiana has the broadest diet of all Xantusia species (Brattstrom 1952. Copeia 1952:168–172).…
    • Zoo and wildlife libraries: An international survey

      Coates, Linda L.; Tierney, Kaitlyn Rose; (2010)
      The conservation and well-being of exotic animals is core to the mission of zoos, aquariums and many small nonprofit wildlife groups. Increasingly, these organizations are committed to scientific research, both basic and applied. To ascertain the current state of the libraries that support their efforts, librarians at the San Diego Zoo conducted an international survey between June and August, 2008. Only 73 libraries responded to our request for information....