• Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

      Krehenwinkel, Henrik; Pomerantz, Aaron; Henderson, James B.; Kennedy, Susan R.; Lim, Jun Y.; Swamy, Varun; Shoobridge, Juan D.; Patel, Nipam H.; Gillespie, Rosemary G.; Prost, Stefan (2019)
      Background: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Results: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. Conclusions: Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost effective, portable and universal approach for eukaryote DNA barcoding. Long rDNA amplicons scale up DNA barcoding by enabling the accurate recovery of taxonomic and phylogenetic diversity. However, bulk community analyses using long-read approaches may introduce biases and will require further exploration.
    • Nutrition and health in amphibian husbandry: Ex situ amphibian health and nutrition

      Ferrie, Gina M.; Alford, Vance C.; Atkinson, Jim; Baitchman, Eric; Barber, Diane; Blaner, William S.; Crawshaw, Graham; Daneault, Andy; Dierenfeld, Ellen; Finke, Mark; et al. (2014)
      Amphibian biology is intricate, and there are many inter‐related factors that need to be understood before establishing successful Conservation Breeding Programs (CBPs). Nutritional needs of amphibians are highly integrated with disease and their husbandry needs, and the diversity of developmental stages, natural habitats, and feeding strategies result in many different recommendations for proper care and feeding….
    • 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….
    • 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....
    • 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.
    • 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.
    • Personality assessment in African elephants (Loxodonta africana): Comparing the temporal stability of ethological coding versus trait rating

      Horback, Kristina M.; Miller, Lance J.; Kuczaj, Stan A. (2013)
      The consistency of personality assessment was addressed in this study of 12 zoological African elephants living at the San Diego Zoo Safari Park in Escondido, CA, USA during the 2010 and 2011 summer seasons. Using 480 h of observational behavior data, three personality traits were determined based on behavior events, with the most significant correlations (two-tailed rs > 0.77, P < 0.005) being playful, curious, and sociable….
    • Peters anomaly in a red kangaroo (macropus rufus)

      Suedmeyer, Wm. Kirk; Pearce, Jacqueline; Persky, Meredith; Houck, Marlys L. (2014)
      A 10-mo-old female red kangaroo (Macropus rufus) presented with a unilateral congenital corneal opacity OD…. The maternal and paternal adult pairing has been discontinued in an effort to prevent future offspring anomalies.
    • Peyrieras' woolly lemur (Avahi peyrierasi). The IUCN Red List of Threatened Species 2020

      Eppley, Timothy M.; Patel, E. (2020)
      A population reduction of greater than or equal to 30% is predicted to occur over a three-generation time period (30 years) in the future, based on continuing and projected decline in area, extent and quality of habitat, in addition to ongoing and projected exploitation through unsustainable hunting pressure. The extent of occurrence (EOO) of this species is 6,991 km2 and extremely fragmented. Based on these premises, the species is listed as Vulnerable.
    • Phenotypic plasticity in the timing of reproduction in Andean bears

      Appleton, R. D.; Van Horn, Russell C.; Noyce, K. V.; Spady, T. J.; Swaisgood, Ronald R.; Arcese, P. (2018)
      Many factors influence whether mammals reproduce seasonally or continuously but disentangling them can be challenging in free‐living species that are hard to observe. We described the seasonality of reproduction in Andean bears (Tremarctos ornatus) in NW Peru (6°26′S, 79°33′W) to test for phenotypic plasticity in response to extrinsic cues.
    • Phenotypic variability along a climatic gradient in a perennial afrotropical rainforest understorey herb

      Ley, Alexandra C.; Herzog, Patrick; Lachmuth, Susanne; Abwe, Abwe E.; Christian, Mbella F.; Sesink Clee, Paul R.; Abwe, Ekwoge E.; Morgan, Bethan J.; Gonder, Mary K. (2018)
      Plants evolved in response to climatic conditions, which shaped their geographic distribution, functional traits and genetic composition. In the face of climatic changes, plants have to react by either genetic adaptation, phenotypic plasticity or geographic range shift....
    • Photos provide information on age, but not kinship, of Andean bear

      Van Horn, Russell C.; Zug, Becky; Appleton, Robyn D.; Velez-Liendo, Ximena; Paisley, Susanna; LaCombe, Corrin (2015)
      Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs <6 months old, we evaluated the degree to which visual information may be used to estimate bears’ ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤6 months old may be estimated from their size relative to their mothers with an average error of <0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥10 years old may be estimated from the proportion of their nose that is pink with an average error of <0.01 ± 3.5 years (n = 41). We also show that similarity among the bears’ natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R2 < 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species.
    • Phylogeography of the endangered Lesser Antillean iguana, Iguana delicatissima: a recent diaspora in an archipelago known for ancient herpetological endemism

      Martin, Jessica L.; Knapp, Charles R.; Gerber, Glenn P.; Thorpe, Roger S; Welch, Mark E. (2015)
      Iguana delicatissima is an endangered endemic of the Lesser Antilles in the Caribbean. Phylogeographic analyses for many terrestrial vertebrate species in the Caribbean, particularly lizards, suggest ancient divergence times. Often, the closest relatives of species are found on the same island, indicating that colonization rates are so low that speciation on islands is often more likely to generate biodiversity than subsequent colonization events…. Despite the great distances between islands and habitat heterogeneity within islands, this species is characterized by low haplotype diversity.
    • Pitheciins: Use of time and space

      Setz, E.Z.F.; Pinto, L.P.; Bowler, Mark; Barnett, A.A.; Vie, J.C.; Barnett, A.A.; Veiga, L.M.; Ferrari, S.F.; Norconk, M.A. (Cambridge University PressCambridge, 2013)