• Obituary to Kupe Cowboy

      Morgan, Bethan J. (2020)
      Simon ‘Kupe’ Ngwese, better known as ‘Kupe Cowboy’, lived a full life. Born in around 1940, to a poor family in Kupe village, near Tombel, Kupe-Muanenguba division of South West Region, Cameroon, like many around him he grew up as a farmer and opportunistic hunter. Later in life, he worked as a research assistant to the then San Diego Zoo Global project at Mount Kupe in Bakossiland....
    • Old-growth forest is what giant pandas really need

      Zhang, Zejun; Swaisgood, Ronald R.; Zhang, S.; Nordstrom, Lisa A.; Wang, H.; Gu, X.; Hu, J.; Wei, F. (2011)
      …Here, we use an information-theoretic approach to analyse the largest, landscape-level dataset on panda habitat use to date, and challenge the prevailing wisdom about panda habitat needs. We show that pandas are associated with old-growth forest more than with any ecological variable other than bamboo….
    • On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

      Yu, Li; Peng, Dan; Liu, Jiang; Luan, Pengtao; Liang, Lu; Lee, Hang; Lee, Muyeong; Ryder, Oliver A.; Zhang, Yaping (2011)
      Background Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems. Results The combined nuclear intron and mt genome analyses both robustly support that Taxidiinae diverged first, followed by Melinae. Lutrinae and Mustelinae are grouped together in all analyses with strong supports. The position of Helictidinae, however, is enigmatic because the mt genome analysis places it to the clade uniting Lutrinae and Mustelinae, whereas the nuclear intron analysis favores a novel view supporting a closer relationship of Helictidinae to Martinae. This finding emphasizes a need to add more data and include more taxa to resolve this problem. In addition, the molecular dating provides insights into the time scale of the origin and diversification of the Mustelidae subfamilies. Finally, the phylogenetic performances and limits of nuclear introns and mt genes are discussed in the context of Mustelidae phylogeny. Conclusion Our study not only brings new perspectives on the previously obscured phylogenetic relationships among Mustelidae subfamilies, but also provides another example demonstrating the effectiveness of nuclear non-coding loci for reconstructing evolutionary histories in a group that has undergone rapid bursts of speciation.
    • On the timing of an epidemic of amphibian chytridiomycosis in the highlands of Guatemala

      Mendelson, Joseph R.; Jones, Megan E. B.; Pessier, Allan P.; Toledo, Gabriela; Kabay, Edward H.; Campbell, Jonathan A. (2014)
      We analyzed museum specimens from two regions of Guatemala for the presence of the pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) using both histological and PCR-based assays. We determined that the pathogen was present at one site at low prevalence in 1980 and 1981, immediately preceding drastic declines of amphibian in the region by 1983….
    • On the trail of primate scent signals: A field analysis of callitrichid scent-gland secretions by portable gas chromatography-mass spectrometry

      Poirier, Alice C.; Waterhouse, John S.; Watsa, Mrinalini; Erkenswick, Gideon A.; Moreira, Laís A. A.; Tang, Jia; Dunn, Jacob C.; Melin, Amanda D.; Smith, Andrew C. (2021)
      …We present the first use of the Torion® portable gas chromatography-mass spectrometry (GC-MS) instrument for in situ chemical analysis of primate scents. We collected and analyzed swab samples from the scent glands and skin from 13 groups (57 individuals) of two sympatric species of wild emperor tamarins, Saguinus imperator, and Weddell's saddleback tamarins, Leontocebus weddelli (Callitrichidae). In total, 11 compounds of interest (i.e., probably derived from the animals) could be detected in the samples, with 31 of 215 samples containing at least one compound of interest….
    • Opportunities and challenges for conserving small populations: An emerging role for zoos in genetic rescue

      Ryder, Oliver A.; Minteer, Ben A.; Maienschein, Jane; Collins, James P. (University of Chicago PressChicago, IL, 2018)
      The growing commitment of zoos to address accelerated rates of extinction and losses of biodiversity utilizing the populations they manage has led to the exploration of options to rescue species from extinction, including advanced genetic and reproductive technologies. The availability of banked viable cell cultures, such as those held in collections like San Diego Zoo Global’s Frozen Zoo® and other facilities, may ultimately provide resources to reduce extinction risk of species for which appropriate samples have been collected....
    • Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers

      Walker, Jerilyn A.; Konkel, Miriam K.; Ullmer, Brygg; Monceaux, Christopher P.; Ryder, Oliver A.; Hubley, Robert; Smit, Arian FA; Batzer, Mark A. (2012)
      Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition.
    • Ovarian control and monitoring in amphibians

      Calatayud, Natalie E.; Stoops, M.; Durrant, Barbara S. (2018)
      Amphibian evolution spans over 350 million years ago, consequently this taxonomic group displays a wide, complex array of physiological adaptations and their diverse modes of reproduction are a prime example. Reproduction can be affected by taxonomy, geographic and altitudinal distribution, and environmental factors....
    • Ovulation induction in anovulatory southern white rhinoceros (Ceratotherium simum simum) without altrenogest

      Pennington, Parker M.; Marshall, Kira L.; Capiro, Jonnie M.; Felton, Rachel G.; Durrant, Barbara S. (2019)
      Lack of ovulation is common in captive southern white rhino females and contributes to poor reproductive success. We show that ovulation can be induced efficien
    • Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees

      Staes, Nicky; Stevens, Jeroen M. G.; Helsen, Philippe; Hillyer, Mia; Korody, Marisa L.; Eens, Marcel (2014)
      Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ~360 bp in this region (+/- DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.
    • Panda downlisted but not out of the woods

      Swaisgood, Ronald R.; Wang, Dajun; Wei, Fuwen (2018)
      The giant panda (Ailuropoda melanoleuca) is no longer Endangered on the International Union for the Conservation of Nature's (IUCN) storied Red List. The decision to downlist the panda to Vulnerable has its foundation in a systematic assessment of population parameters as determined by China State Forestry Administration's circa decadal national survey and other scientific outputs, compared to standardized criteria used by IUCN to determine the status of all species. This decision has not been without controversy and disagreement, perhaps reflecting disparities between how people view the term “Endangered” and the criteria established by the IUCN. Here, we explore the architecture of recovery of this iconic “Endangered” species, make transparent the process of the IUCN downlisting decision, evaluate emerging threats to pandas on the horizon, and contemplate the meaning of this milestone for endangered species conservation. Through this revelation, we find profound reasons for hope for species conservation everywhere, and a useful example of success in the making. However, this positive message comes with measured caution. The Chinese government and conservation community must maintain its focus and investment on panda conservation, and contend with strategies to address new threats. If they do not, the panda will return to “Endangered” status once again.
    • 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....
    • Past experiences and future expectations generate context-dependent costs of foraging

      Berger-Tal, Oded; Embar, Keren; Kotler, Burt P.; Saltz, David (2014)
      We released Allenby’s gerbils (Gerbillus andersoni allenbyi) into an enclosure containing rich patches with equal amounts of food and manipulated the quality of the environment over time by reducing the amount of food in most (but not all) food patches and then increasing it again…. Specifically, in the second rich period, the gerbils spent more time foraging and harvested more food from the patches. Thus, seemingly identical environments can be treated as strikingly different by foragers as a function of their past experiences and future expectations.
    • Pathogenesis, diagnosis, and treatment of amphibian chytridiomycosis

      Baitchman, Eric J.; Pessier, Allan P. (2013)
      Amphibian chytridiomycosis, caused by the chytridiomycete fungus, Batrachochytrium dendrobatidis (Bd), is responsible for a global pandemic that has dramatically reduced global amphibian populations and diversity. Species declines, extirpations, and extinctions attributed to chytridiomycosis have occurred in Australia, Europe, Latin America, and the United States….
    • Pathologic changes associated with suspected hypovitaminosis A in amphibians under managed care

      Rodríguez, Carlos E.; Pessier, Allan P. (2014)
      Vitamin A deficiency is a recently recognized nutritional disease in amphibians fed insect-based diets…. This review highlights the need to establish standardized guidelines for optimal postmortem tissue sampling of amphibians in order to maximize the accurate diagnosis of pathologic lesions that may be associated with hypovitaminosis A.
    • Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat (Dipodomys merriami parvus) and implications for conservation management

      Hendricks, Sarah; Navarro, Asako Y.; Wang, Thea B.; Wilder, Aryn P.; Ryder, Oliver A.; Shier, Debra M. (2020)
      ...We examined the genetic diversity, population structure, and phylogeography of this subspecies using partial mitochrondrial DNA sequencing and microsatellite genotyping. Our study indicates that currently, the three remaining populations seem to be highly fragmented....
    • Patterns of mortality in free-ranging California condors (Gymnogyps californianus)

      Rideout, Bruce; Stalis, Ilse H.; Papendick, Rebecca; Pessier, Alan P.; Puschner, B.; Finkelstien, M.E.; Smith, D.R.; Johnson, M.; Mace, Michael E.; Stroud, R.; et al. (2012)
      We document causes of death in free-ranging California Condors (Gymnogyps californianus) from the inception of the reintroduction program in 1992 through December 2009 to identify current and historic mortality factors that might interfere with establishment of self-sustaining populations in the wild. A total of 135 deaths occurred from October 1992 (the first post-release death) through December 2009, from a maximum population-at-risk of 352 birds, for a cumulative crude mortality rate of 38%. A definitive cause of death was determined for 76 of the 98 submitted cases, 70%(53/76) of which were attributed to anthropogenic causes. Trash ingestion was the most important mortality factor in nestlings (proportional mortality rate [PMR] 73%; 8/11), while lead toxicosis was the most important factor in juveniles (PMR 26%; 13/50) and adults (PMR 67%; 10/15). These results demonstrate that the leading causes of death at all California Condor release sites are anthropogenic. The mortality factors thought to be important in the decline of the historic California Condor population, particularly lead poisoning, remain the most important documented mortality factors today. Without effective mitigation, these factors can be expected to have the same effects on the sustainability of the wild populations as they have in the past.
    • Peatlands of the Madre de Dios River of Peru: Distribution, geomorphology, and habitat diversity

      Householder, J. Ethan; Janovec, John P.; Tobler, Mathias W.; Page, Susan; Lähteenoja, Outi (2012)
      We present results of research concerning the distribution, depth, volume, geomorphology, and habitat diversity of peatlands in the southern Peruvian Amazon. We identified 295 peatlands covering 294 km2 and ranging in size from 10 to 3,500 ha….
    • Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species

      Farquharson, Katherine A.; Hogg, Carolyn J.; Grueber, Catherine E. (2017)
      Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals....