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  • Institute for Conservation Research

    Peer reviewed and scientific works by SDZG's Institute for Conservation Research staff. Includes books, book sections, articles and conference publications and presentations.

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  • SDZG Research Publications

    Peer reviewed and scientific works by San Diego Zoo Global staff. Includes books, book sections, articles and conference publications and presentations.

Recent Submissions

  • 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.
  • Insights for reducing the consumption of wildlife: The use of bear bile and gallbladder in Cambodia

    Davis, Elizabeth Oneita; Veríssimo, Diogo; Crudge, Brian; Lim, Thona; Roth, Vichet; Glikman, Jenny A. (2020)
    Unsustainable wildlife use is one of the leading threats to earth's biodiversity. Historically, efforts to address this issue have been focused on increasing enforcement and anti-poaching measures. However, recognition that such supply-reduction measures may be inefficient has spurred a movement towards consumer research and behaviour change. Here, we used consumer research to investigate the consumption of bear bile and gallbladder in Cambodia. Our aim was to gather key consumer insights such as demographics, beliefs and the identification of trusted individuals and communication channels, which could be used to underpin future behaviour change efforts to reduce the consumption of bear bile and gallbladder. To accomplish this, we conducted 4,512 structured quantitative interviews and 132 qualitative, semi-structured interviews across Cambodia. We found that although the level of bear bile and gallbladder consumption varied across the country, consumers were largely homogenous in their beliefs and choice of trusted messengers. This indicates that behaviour change interventions grounded in these results may be effective in any of the eight areas surveyed. We believe our study strategy can be adapted and followed by other conservation organizations to ensure they are capturing essential information necessary for designing effective behaviour change campaigns. A free Plain Language Summary can be found within the Supporting Information of this article.
  • Usage, definition, and measurement of coexistence, tolerance and acceptance in wildlife conservation research in Africa

    Knox, Jillian; Ruppert, Kirstie; Frank, Beatrice; Sponarski, Carly C.; Glikman, Jenny A. (2021)
    The terms ‘coexistence’, ‘tolerance,’ and ‘acceptance’ appear frequently in conservation literature, but lack consistent characterization, making them difficult to apply across intervention frameworks. This review aims to describe the common characterizations of these three terms using Africa-based research as a case study….
  • Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore

    McLennan, E. A.; Grueber, Catherine E.; Wise, P.; Belov, K.; Hogg, Carolyn J. (2020)
    …We used an introduced population of Tasmanian devils Sarcophilus harrisii descended from two genetically differentiated source populations to illustrate the benefits of genetic admixture for translocation programmes. Devils are endangered due to an infectious cancer causing 80% population declines across their range since disease emergence in 1996…. As part of their conservation management, devils were introduced to Maria Island, Tasmania in an assisted colonization in 2012 with supplementations in 2013 and 2017….
  • Preference assessments as a tool to evaluate environmental enrichment

    Woods, Jocelyn M.; Lane, Erin K.; Miller, Lance J. (2020)
    …Ten-minute free operant, paired-choice preference assessments were implemented in Study 1 to determine the enrichment preferences of African lions (N = 3). Following Study 1, Study 2 was conducted, which examined the behavior of African lions with enrichment items over the course of 30, 24-hr trials to evaluate the relationship between preferences established in Study 1 and long-term interaction with the enrichment….
  • Giant panda conservation science: how far we have come

    Swaisgood, Ronald R.; Wei, Fuwen; Wildt, David E.; Kouba, Andrew J.; Zhang, Zejun (The Royal Society, 2009-10-28)
    ...Here we discuss recent advancements in conservation science for giant pandas and suggest that the way forward is more direct application of emerging science to management and policy.
  • Survey of geriatric elephant medical care, nutrition, husbandry, and welfare

    Greene, Whitney; Brenner, Deena J. (2020)
    Improvements in husbandry, veterinary care, and nutrition have led to increased longevity of animals in human care, including elephants. The goal of this study was to collect and synthesize information pertaining to geriatric elephant medicine, management, husbandry, and nutrition…..
  • 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....
  • Insights into medicinal wildlife consumption and bear part use in Rakhine, Myanmar

    Davis, Elizabeth Oneita; Gaffi, Lorenzo; Mussoni, Giulia; Zaw, Thet; Glikman, Jenny A. (2020)
    Myanmar is an area of high diversity with prolific illegal wildlife trade, including trade in bear products for medicine. We focused on Rakhine State, Myanmar, which retains sun bear (Helarctos malayanus) populations despite poaching….
  • Mating strategies

    Steyaert, Sam M.J.G.; Zedrosser, Andreas; Swaisgood, Ronald R.; Filipczykova, Eva; Crudge, Brian; Dutta, Trishna; Sharma, Sandeep; Ratnayeke, Shyamala; Koike, Shinsuke; Leclerc, Martin; et al. (Cambridge University PressCambridge, 2020)
    The mating system and mating strategies of a species refer to the behavioral strategies used to obtain reproductive partners and ensure reproductive success. Common determining factors of mating systems and strategies are: the manner of mate acquisition, the number of mates obtained by an individual, as well as the absence or presence and duration of parental care….
  • Evaluation of two doses of butorphanol-medetomidine-midazolam for the immobilization of wild versus captive black-footed cats (Felis nigripes)

    Eggers, Birgit; Tordiffe, Adrian S. W.; Lamberski, Nadine; Lawrenz, Arne; Sliwa, Alexander; Wilson, Beryl; Meyer, Leith C. R. (2020)
    The efficacy, safety, physiologic effects, and reversibility of butorphanol-medetomidine-midazolam (BMM) immobilization were evaluated in black-footed cats (Felis nigripes) and compared between captive and wild animals. Nine captive and 14 wild black-footed cats were hand injected into an accessible hind limb muscle group with the BMM combination…. The capture methods exerted a greater influence on the physiology of the immobilized animals than did the doses of the drugs used….
  • Giant panda (Ailuropoda melanoleuca)

    Swaisgood, Ronald R.; McShea, William M.; Wildt, David; Hull, Vanessa; Zhang, Jindong; Owen, Megan A.; Zhang, Zejun; Dvornicky-Raymond, Zachary; Valitutto, Marc; Li, Dihua; et al. (Cambridge University PressCambridge, 2020)
    This chapter comprises the following sections: names, taxonomy, subspecies and distribution, descriptive notes, habitat, movements and home range, activity patterns, feeding ecology, reproduction and growth, behavior, parasites and diseases, status in the wild, and status in captivity.
  • Managing for interpopulation connectivity of the world’s bear species

    Proctor, Michael F.; Dutta, Trishna; McLellan, Bruce N.; Rangel, Shaenandhoa Garcia; Paetkau, Dave; Swaisgood, Ronald R.; Zedrosser, Andreas; Melletti, Mario; Penteriani, Vincenzo (Cambridge University PressCambridge, 2020)
    … Here the current status of fragmentation, connectivity, methods, consequences, and management of the world’s eight bear species is reviewed. The metapopulation paradigm is also considered, i.e. are bears being forced into some form of functioning metapopulation or are they simply being fragmented into a series of isolated populations that, without conservation action, will likely be slowly extirpated, population by population?
  • How Is climate change affecting polar bears and giant pandas?

    Songer, Melissa; Atwood, Todd C.; Douglas, David C.; Huang, Qiongyu; Li, Renqiang; Pilfold, Nicholas W.; Xu, Ming; Durner, George M.; Melletti, Mario; Penteriani, Vincenzo (Cambridge University PressCambridge, 2020)
    Anthropogenic greenhouse gas emissions are the primary cause of climate change and an estimated increase of 3.7 to 4.8 °C is predicted by the year 2100 if emissions continue at current levels. Polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca) provide an interesting comparison study of the impact of climate change on bear species….
  • Highly accurate long-read HiFi sequencing data for five complex genomes

    Hon, Ting; Mars, Kristin; Young, Greg; Tsai, Yu-Chih; Karalius, Joseph W.; Landolin, Jane M.; Maurer, Nicholas; Kudrna, David; Hardigan, Michael A.; Steiner, Cynthia C.; et al. (2020)
    The PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10–25?kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria?×?ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
  • 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.
  • 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.
  • 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.
  • Climate suitability as a predictor of conservation translocation failure

    Bellis, Joe; Bourke, David; Maschinski, Joyce; Heineman, Katherine D.; Dalrymple, Sarah (2020)
    …We used species distribution models (SDMs) to predict the climate suitability of 102 release sites for amphibians, reptiles and terrestrial insects and compared suitability predictions between successful and failed attempts. We then quantified the importance of climate suitability relative to five other variables frequently considered in the literature to be important determinants of translocation success: number of release years, number of individuals released, life stage released, origin of the source population and position of the release site relative to the species’ range….
  • Initial sequence characterization of the rhabdoviruses of squamate reptiles including a novel rhabdovirus from a caiman lizard (Dracaena guianensis)

    Wellehan, J.F.X.; Pessier, Allan P.; Archer, L.; Childress, A.; Jacobson, E.R.; Tesh, R.B. (2012)
    Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis….

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