• A molecular phylogeny of the Pacific clade of Cyrtandra (Gesneriaceae) reveals a Fijian origin, recent diversification, and the importance of founder events

      Johnson, Melissa A.; Clark, John R.; Wagner, Warren L.; McDade, Lucinda A. (2017)
      Cyrtandra (Gesneriaceae) is among the largest genera of flowering plants in the remote oceanic islands of the Pacific, with an estimated 175 species distributed across an area that extends from the Solomon Islands, east to the Marquesas Islands, and north to the Hawaiian Islands. The vast majority of species are single-island endemics that inhabit upland rainforests....
    • A multi-model approach to guide habitat conservation and restoration for the endangered San Bernardino kangaroo rat

      Chock, Rachel Y.; Hennessy, Sarah McCullough; Wang, Thea B.; Gray, Emily; Shier, Debra M. (2020)
      The San Bernardino kangaroo rat (Dipodomys merriami parvus) is a federally listed endangered species endemic to Southern California and limited to three remaining populations. Its native habitat of alluvial fan sage scrub faces many anthropogenic threats, including urban and agricultural development, and the resulting flood control and fire suppression. With the loss of natural processes such as scouring or burning from floods and fires, the mosaic of seral stages across the landscape has shifted to dense vegetation, and active restoration may be necessary to provide suitable habitat for the San Bernardino kangaroo rat. Species distribution modeling using the partitioned Mahalanobis distance method on all occurrence points collected in the past 16 years revealed that alluvial scrub cover and fluvent soils were most strongly associated with San Bernardino kangaroo rat occupancy. Through surveys at 14 locations across the species’ range, we identified non-native grass cover, shrub cover, bare ground and sandy soils as microhabitat features related to San Bernardino kangaroo rat abundance. We also calculated the optimal range of cover for each habitat type that was correlated with higher kangaroo rat abundance. The results of this multiple-model approach can be used by the agencies to assess the value of conserved habitat, set targets for microhabitat enhancement to facilitate population growth and expansion, or identify receiver sites should translocation be required for recovery. This work lays the foundation for more coordinated and strategic restoration efforts, given the compressed and rigid timelines of development projects that continue to impact remaining San Bernardino kangaroo rat populations.
    • A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

      Farré, Marta; Li, Qiye; Zhou, Yang; Damas, Joana; Chemnick, Leona G.; Kim, Jaebum; Ryder, Oliver A.; Ma, Jian; Zhang, Guojie; Larkin, Denis M.; et al. (2018)
      Background The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Findings Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Conclusions Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
    • A novel herpesvirus of the proposed genus chelonivirus from an asymptomatic bowsprit tortoise (Chersina angulata)

      Bicknese, Elizabeth; Childress, April L.; Wellehan, James F. X.; (2010)
      A wild-caught Bowsprit tortoise (Chersina angulata) was received into quarantine and appeared clinically normal. Oral swabs for consensus herpesvirus polymerase chain reaction (PCR) and sequencing were obtained during routine quarantine, and a novel herpesvirus was identified....
    • A recovering flagship: Giant otters, communities and tourism in northern Peru

      Recharte, Maribel; Bride, Ian G.; Bowler, Mark (2015)
      We investigate attitudes towards giant otters in rural northern Peru, to see whether negative perceptions towards the species are mitigated by involvement in tourism…. We highlight the need for research into the value of otters to tourism, and to disseminate the results in rural areas where otter tourism may benefit local people.
    • A reliable method for sexing giant otters (Pteronura brasiliensis) in the wild

      Groenendijk, Jessica; Hajek, Frank (2015)
      ...Here, we present a reliable method of sexing wild Giant otters of all ages and sexual status, tested with known sex individuals.
    • A reservoir species for the emerging amphibian pathogen Batrachochytrium dendrobatidis thrives in a landscape decimated by disease.

      Reeder, N.M.M.; Pessier, Allan P.; Vredenburg, V.T. (2012)
      Chytridiomycosis, a disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is driving amphibian declines and extinctions in protected areas globally. The introduction of invasive reservoir species has been implicated in the spread of Bd but does not explain the appearance of the pathogen in remote protected areas. In the high elevation (>1500 m) Sierra Nevada of California, the native Pacific chorus frog, Pseudacris regilla, appears unaffected by chytridiomycosis while sympatric species experience catastrophic declines. We investigated whether P. regilla is a reservoir of Bd by comparing habitat occupancy before and after a major Bd outbreak and measuring infection in P. regilla in the field, monitoring susceptibility of P. regilla to Bd in the laboratory, examining tissues with histology to determine patterns of infection, and using an innovative soak technique to determine individual output of Bd zoospores in water. Pseudacris regilla persists at 100% of sites where a sympatric species has been extirpated from 72% in synchrony with a wave of Bd. In the laboratory, P. regilla carried loads of Bd as much as an order of magnitude higher than loads found lethal to sympatric species. Histology shows heavy Bd infection in patchy areas next to normal skin, a possible mechanism for tolerance. The soak technique was 77.8% effective at detecting Bd in water and showed an average output of 68 zoospores per minute per individual. The results of this study suggest P. regilla should act as a Bd reservoir and provide evidence of a tolerance mechanism in a reservoir species....
    • 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....
    • A road map for 21st century genetic restoration: Gene pool enrichment of the black-footed ferret

      Wisely, S. M.; Ryder, Oliver A.; Santymire, R. M.; Engelhardt, J. F.; Novak, B. J. (2015)
      Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species.
    • A scoping review into the impact of animal imagery on pro-environmental outcomes

      Thomas-Walters, Laura; McNulty, Claire; Veríssimo, Diogo (2020)
      With the recognition that most global environmental problems are a result of human actions, there is an increasing interest in approaches which have the potential to influence human behaviour. Images have a powerful role in shaping persuasive messages, yet research on the impacts of visual representations of nature is a neglected area in biodiversity conservation. We systematically screened existing studies on the use of animal imagery in conservation, identifying 37 articles. Although there is clear evidence that images of animals can have positive effects on people’s attitudes to animals, overall there is currently a dearth of accessible and comparable published data demonstrating the efficacy of animal imagery. Most existing studies are place and context-specific, limiting the generalisable conclusions that can be drawn. Transdisciplinary research is needed to develop a robust understanding of the contextual and cultural factors that affect how animal images can be used effectively for conservation purposes.
    • A suite of microsatellite markers optimized for amplification of DNA from addax (Addax nasomaculatus) blood preserved on FTA cards: Microsatellites for addax on FTA cards

      Heim, Brett C.; Ivy, Jamie A.; Latch, Emily K. (2012)
      The addax (Addax nasomaculatus) is a critically endangered antelope that is currently maintained in zoos through regional, conservation breeding programs. As for many captive species, incomplete pedigree data currently impedes the ability of addax breeding programs to confidently manage the genetics of captive populations and to select appropriate animals for reintroduction. Molecular markers are often used to improve pedigree resolution, thereby improving the long‐term effectiveness of genetic management....
    • A systematic survey of the integration of animal behavior into conservation

      Berger-Tal, Oded; Blumstein, Daniel T.; Carroll, Scott; Fisher, Robert N.; Mesnick, Sarah L.; Owen, Megan A.; Saltz, David; St. Clair, Colleen Cassady; Swaisgood, Ronald R. (2016)
      The role of behavioral ecology in improving wildlife conservation and management has been the subject of much recent debate. We sought to answer 2 foundational questions about the current use of behavioral knowledge in conservation: To what extent is behavioral knowledge used in wildlife conservation and management, and how does the use of animal behavior differ among conservation fields in both frequency and types of use? We searched the literature for intersections between key fields of animal behavior and conservation and created a systematic heat map (i.e., graphical representation of data where values are represented as colors) to visualize relative efforts. Some behaviors, such as dispersal and foraging, were commonly considered (mean [SE] of 1147.38 [353.11] and 439.44 [108.85] papers per cell, respectively). In contrast, other behaviors, such as learning, social, and antipredatory behaviors were rarely considered (mean [SE] of 33.88 [7.62], 44.81 [10.65], and 22.69 [6.37] papers per cell, respectively). In many cases, awareness of the importance of behavior did not translate into applicable management tools. Our results challenge previous suggestions that there is little association between the fields of behavioral ecology and conservation and reveals tremendous variation in the use of different behaviors in conservation. We recommend that researchers focus on examining underutilized intersections of behavior and conservation themes for which preliminary work shows a potential for improving conservation and management, translating behavioral theory into applicable and testable predictions, and creating systematic reviews to summarize the behavioral evidence within the behavior-conservation intersections for which many studies exist.
    • A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

      Tomaszkiewicz, Marta; Rangavittal, Samarth; Cechova, Monika; Sanchez, Rebeca Campos; Fescemyer, Howard W.; Harris, Robert; Ye, Danling; O'Brien, Patricia C. M.; Chikhi, Rayan; Ryder, Oliver A.; et al. (2016)
      The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
    • Abomasal impaction in captive bongo (Tragelaphus eurycerus)

      Gyimesi, Zoltan S.; Burns, Roy B.; Campbell, Mark; Knightly, Felicia; Kramer, Lynn W.; Wack, Raymund F.; Zuba, Jeffery R.; Rings, D. Michael (2011)
      Fatal abomasal impaction, often combined with omasal impaction, was diagnosed in 11 bongo (Tragelaphus eurycerus) from five different zoologic collections in the United States between 1981 and 2009. Nine of 11 cases occurred in young females (10 mo–7 yr old) and typical clinical signs prior to diagnosis or death included partial or complete anorexia, dehydration, and scant fecal production....
    • Acoustic recordings provide detailed information regarding the behavior of cryptic wildlife to support conservation translocations

      Yan, Xiao; Zhang, Hemin; Li, Desheng; Wu, Daifu; Zhou, Shiqiang; Sun, Mengmeng; Hu, Haiping; Liu, Xiaoqiang; Mou, Shijie; He, Shengshan; et al. (2019)
      For translocated animals, behavioral competence may be key to post-release survival. However, monitoring behavior is typically limited to tracking movements or inferring behavior at a gross scale via collar-mounted sensors. Animal-bourne acoustic monitoring may provide a unique opportunity to monitor behavior at a finer scale. The giant panda is an elusive species of Ursid that is vulnerable to extinction. Translocation is an important aspect of the species’ recovery, and survival and recruitment for pandas likely hinge on behavioral competence. Here we tested the efficacy of a collar-mounted acoustic recording unit (ARU) to remotely monitor the behavior of panda mothers and their dependent young. We found that trained human listeners could reliably identify 10 behaviors from acoustic recordings. Through visual inspection of spectrograms we further identified 5 behavioral categories that may be detectable by automated pattern recognition, an approach that is essential for the practical application of ARU. These results suggest that ARU are a viable method for remotely observing behaviors, including feeding. With targeted effort directed towards instrumentation and computing advances, ARU could be used to document how behavioral competence supports or challenges post-release survival and recruitment, and allow for research findings to be adaptively integrated into future translocation efforts.
    • Activation of southern white rhinoceros (Ceratotherium simum simum) estrogen receptors by phytoestrogens: Potential role in the reproductive failure of captive-born females?

      Tubbs, Christopher W.; Hartig, P.; Cardon, M.; Varga, Nicole; Milnes, Matthew R. (2012)
      The captive southern white rhinoceros (SWR; Ceratotherium simum simum) population serves as an important genetic reservoir critical to the conservation of this vulnerable species. Unfortunately, captive populations are declining due to the poor reproductive success of captive-born females....
    • Advances and constraints in somatic embryogenesis of Araucaria angustifolia, Acca sellowiana, and Bactris gasipaes

      Stefenon, Valdir Marcos; Ree, Joseph Francis; Pinheiro, Marcos Vinicius Marques; Goeten, Daniela; Steiner, Neusa; Guerra, Miguel Pedro (2020)
      Somatic embryogenesis (SE) is a useful biotechnological tool to promote the conservation of plant genetic resources. Araucaria angustifolia, Acca sellowiana, and Bactris gasipaes are forest species with recognized ecological, cultural, and economic importance in the subtropical Atlantic Forest and the tropical Amazon Forest…. Here we reviewed and discussed the advancements and continuing constraints in the SE of these species, pointing out the more successful procedures….
    • Advances in conservation endocrinology: The application of molecular approaches to the conservation of endangered species

      Tubbs, Christopher W.; McDonough, C. E.; Felton, Rachel G.; Milnes, Matthew R. (2014)
      …In this review we examine various in vitro approaches we have used to compare estrogen receptor binding and activation by endogenous hormones and phytoestrogens in two species of rhinoceros; southern white and greater one-horned. We have found many of these techniques valuable and practical in species where access to research subjects and/or tissues is limited due to their conservation status....
    • Advancing laboratory-based zoo research to enhance captive breeding of southern white rhinoceros

      Tubbs, Christopher W.; Minteer, Ben A.; Maienschein, Jane; Collins, James P. (University of Chicago PressChicago, IL, 2018)
      The captive southern white rhinoceros (SWR) is not currently self-sustaining because of low fertility of captive-born females. The cause of this phenomenon is believed to be high dietary levels of phytoestrogens; endocrine disrupting chemicals (EDCs) produced by plants that can mimic the reproductive hormone estrogen....