• 113 Developing a cryopreservation protocol for desert tortoise sperm (Gopherus agassizzii)

      Ravida, Nicole; Young, C.; Gokool, L.; Durrant, Barbara S. (2017)
      The desert tortoise (Gopherus agassizzii) is listed as threatened by the USA Fish and Wildlife Service and population declines continue to occur throughout most of their range. This species’ low reproductive rate, combined with the advanced age at which they reach sexual maturity, makes them vulnerable to multiple threats....
    • 98 Efficacy of commercial equine semen freezing extenders for cryopreservation of southern white rhinoceros (Ceratotherium simum simum) sperm

      Young, Carly; Ravida, Nicole; Pennington, Parker M.; Durrant, Barbara S. (2019)
      Once nearly extinct in the wild, the southern white rhinoceros is currently listed as near threatened by IUCN. This status is likely to change as poaching continues to escalate....
    • A big data urban growth simulation at a national scale: Configuring the GIS and neural network based Land Transformation Model to run in a High Performance Computing (HPC) environment

      Pijanowski, B.C.; Tayyebi, A.; Douchette, J.; Pekin, Burak K.; Braun, D.; Plourde, J. (2014)
      The Land Transformation Model (LTM) is a Land Use Land Cover Change (LUCC) model which was originally developed to simulate local scale LUCC patterns…. This paper provides an overview of the new architecture which we discuss within the context of modeling LUCC that requires: (1) using an HPC to run a modified version of our LTM; (2) managing large datasets in terms of size and quantity of files; (3) integration of tools that are executed using different scripting languages; and (4) a large number of steps necessitating several aspects of job management.
    • A checklist of the iguanas of the world (Iguanidae; Iguaninae)

      Iguana Taxonomy Working Group (ITWG); Buckley, Larry J.; de Queiroz, Kevin; Grant, Tandora D.; Hollingsworth, Bradford D.; Iverson, John B.; Pasachnik, Stesha A.; Stephen, Catherine L.; Iverson, John B.; Grant, Tandora D.; et al. (2016)
      This annotated checklist of the world's iguanas (Iguanidae; Iguaninae) represents an update by the Iguana Taxonomy Working Group (ITWG) of its 2011 list. We recognize 44 extant species (19 subspecies across six species) in eight genera....
    • A comparison of walking rates Between wild and zoo African elephants

      Miller, Lance J.; Chase, Michael J.; Hacker, Charlotte E. (2016)
      The goal of the current study was to compare the walking rates of elephants in the wild versus elephants in zoos to determine if elephants are walking similar distances relative to their wild counterparts. Eleven wild elephants throughout different habitats and locations in Botswana were compared to 8 elephants at the San Diego Zoo Safari Park. Direct comparisons revealed no significant difference in average walking rates of zoo elephants when compared with wild elephants….
    • A comprehensive genomic history of extinct and living elephants

      Palkopoulou, Eleftheria; Lipson, Mark; Mallick, Swapan; Nielsen, Svend; Rohland, Nadin; Baleka, Sina; Karpinski, Emil; Ivancevic, Atma M.; To, Thu-Hien; Kortschak, R. Daniel; et al. (2018)
      Elephantids are the world’s most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ~120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths....
    • A diversity of biogeographies in an extreme Amazonian wetland habitat

      Householder, Ethan; Janovec, John; Tobler, Mathias W.; Wittmann, Florian; Myster, Randall W. (John Wiley & Sons, Ltd, 2017)
      Amazonian wetlands are associated with lower species diversity relative to surrounding terra firme forests, as well as compositional turnover along strong hydro-edaphic gradients. Because species differ in their ecophysiological response to soil waterlogging, hydrological regime is likely a major determinant of the local diversity, species distribution and assemblage of plant communities in wetland habitats....
    • A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species

      Sutton, Jolene; Helmkampf, Martin; Steiner, Cynthia C.; Bellinger, M. Renee; Korlach, Jonas; Hall, Richard; Baybayan, Primo; Muehling, Jill; Gu, Jenny; Kingan, Sarah; et al. (2018)
      Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications
    • A highly divergent picornavirus infecting the gut epithelia of zebrafish (Danio rerio) in research institutions worldwide

      Altan, Eda; Kubiski, Steven V.; Boros, Ákos; Reuter, Gábor; Sadeghi, Mohammadreza; Deng, Xutao; Creighton, Erica K.; Crim, Marcus J.; Delwart, Eric (2019)
      Zebrafish have been extensively used as a model system for research in vertebrate development and pathogen–host interactions. We describe the complete genome of a novel picornavirus identified during a viral metagenomics analysis of zebrafish gut tissue....
    • A management experiment evaluating nest-site selection by beach-nesting birds

      Swaisgood, Ronald R.; Nordstrom, Lisa A.; Schuetz, Justin G.; Boylan, Jeanette T.; Fournier, Joelle J.; Shemai, Barak (2018)
      It is important to understand nest-site selection in avian species to inform appropriate conservation management strategies. Studies of habitat selection alone, however, may be misleading unless the consequences for survival and reproduction are also documented....
    • 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 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 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 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.
    • 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.