• 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 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 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.
    • Alternatives to conventional seed banking: Introduction

      Maschinski, Joyce; Pence, Valerie; Center for Plant Conservation (CPC) (Center for Plant ConservationEscondido, California, 2019)
      For exceptional (or non-orthodox) plants that cannot be conserved long-term using conventional seed banking methods, three alternatives traditionally used by botanical gardens are tissue culture, cryogenic storage, and field genebanks. (See Overview.) Each requires different institutional commitment to space, resources, staff time, and expertise....
    • An autonomous GPS geofence alert system to curtail avian fatalities at wind farms

      Sheppard, James; McGann, Andrew; Lanzone, Michael; Swaisgood, Ronald R. (2015)
      Wind energy developments are increasingly proliferating as nations seek to secure clean and renewable energy supplies. Wind farms have serious impacts on avifauna populations through injuries sustained by collisions with turbines. Our aim was to develop new biotelemetric technologies to minimize collision risks, particularly for threatened and endangered bird species whose ranges overlap with current and future wind farm sites.
    • Animal cytogenetics

      Houck, Marlys L.; Lear, Teri L.; Charter, Suellen J.; Arsham, Marilyn S.; Barch, Margaret J.; Lawce, Helen J. (John Wiley & Sons, Inc., 2017)
      Chromosome karyotyping and gene mapping has been carried out for a wide variety of animal species and continues to expand. Cross-species chromosome painting, or Zoo-FISH, for example, can now be used to identify genome segments originating from a common ancestor that have been conserved between species for millions of years....
    • Assessment and validation of miniaturized technology for the remote tracking of critically endangered Galápagos pink land iguana (Conolophus marthae)

      Loreti, Pierpaolo; Bracciale, Lorenzo; Colosimo, Giuliano; Vera, Carlos; Gerber, Glenn P.; De Luca, Massimiliano; Gentile, Gabriele (2020)
      Background: Gathering ecological data for species of conservation concern inhabiting remote regions can be daunting and, sometimes, logistically infeasible. We built a custom-made GPS tracking device that allows to remotely and accurately collect animal position, environmental, and ecological data, including animal temperature and UVB radiation. We designed the device to track the critically endangered Galápagos pink land iguana, Conolophus marthae. Here we illustrate some technical solutions adopted to respond to challenges associated with such task and present some preliminary results from controlled trial experiments and feld implementation. Results: Our tests show that estimates of temperature and UVB radiation are affected by the design of our device, in particular by its casing. The introduced bias, though, is systematic and can be corrected using linear and quadratic regressions on collected values. Our data show that GPS accuracy loss, although introduced by vegetation and orientation of the devices when attached to the animals, is acceptable, leading to an average error gap of less than 15 m in more than 50% of the cases. Conclusions: We address some technical challenges related to the design, construction, and operation of a custom made GPS tracking device to collect data on animals in the wild. Systematic bias introduced by the technological implementation of the device exists. Understanding the nature of the bias is crucial to provide correction models. Although designed to track land iguanas, our device could be used in other circumstances and is particularly useful to track organisms inhabiting locations that are diffcult to reach or for which classic telemetry approaches are unattainable.
    • Challenges in the development of semen cryopreservation protocols for snakes

      Young, Carly; Ravida, Nicole; Durrant, Barbara S. (2019)
    • Collecting and maintaining exceptional species in tissue culture and cryopreservation

      Pence, Valerie; Westwood, Murphy; Maschinski, Joyce; Powell, Christy; Sugii, Nellie; Fish, Diana; McGuinness, Julianne; Raven, Pat; Duval, Julian; Herrera-Mishler, Tomas; et al. (Center for Plant ConservationEscondido, California, 2019)
      Tissue culture and cryopreservation are alternative storage methods for exceptional species that produce few seeds or seed that are intolerant to drying or freezing. Adequately storing exceptional species requires specialized expertise, infrastructure, and greater resources than conventional seed storage....
    • Comparative genomics reveals insights into avian genome evolution and adaptation

      Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; et al. (2014)
      Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades....
    • Derivation of induced pluripotent stem cells from orangutan skin fibroblasts

      Ramaswamy, Krishna; Yik, Wing Yan; Wang, Xiao-Ming; Oliphant, Erin N.; Lu, Wange; Shibata, Darryl; Ryder, Oliver A.; Hacia, Joseph G. (2015)
      Background Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. Along with the African great apes, orangutans are among the closest living relatives to humans. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved somatic cells obtained from captive orangutans. Results Primary skin fibroblasts from two Sumatran orangutans were transduced with retroviral vectors expressing the human OCT4, SOX2, KLF4, and c-MYC factors. Candidate orangutan iPSCs were characterized by global gene expression and DNA copy number analysis. All were consistent with pluripotency and provided no evidence of large genomic insertions or deletions. In addition, orangutan iPSCs were capable of producing cells derived from all three germ layers in vitro through embryoid body differentiation assays and in vivo through teratoma formation in immune-compromised mice. Conclusions We demonstrate that orangutan skin fibroblasts are capable of being reprogrammed into iPSCs with hallmark molecular signatures and differentiation potential. We suggest that reprogramming orangutan somatic cells in genome resource banks could provide new opportunities for advancing assisted reproductive technologies relevant for species conservation efforts. Furthermore, orangutan iPSCs could have applications for investigating the phenotypic relevance of genomic changes that occurred in the human, African great ape, and/or orangutan lineages. This provides opportunities for orangutan cell culture models that would otherwise be impossible to develop from living donors due to the invasive nature of the procedures required for obtaining primary cells.
    • Differential success in obtaining gametes between male and female Australian temperate frogs by hormonal induction: A review

      Clulow, John; Pomering, Melissa; Herbert, Danielle; Upton, Rose; Calatayud, Natalie E.; Clulow, Simon; Mahony, Michael J.; Trudeau, Vance L. (2018)
      Most Australian frogs fall into two deeply split lineages, conveniently referred to as ground frogs (Myobatrachidae and Limnodynastidae) and tree frogs (Pelodryadidae). Species of both lineages are endangered because of the global chytrid pandemic, and there is increasing interest and research on the endocrine manipulation of reproduction to support the use of assisted reproductive technologies in conservation....
    • Ecological scale and seasonal heterogeneity in the spatial behaviors of giant pandas

      Zhang, Zejun; Sheppard, James; Swaisgood, Ronald R.; Wang, Guan; Nie, Yonggang; Wei, Wei; Zhao, Naxun; Wei, Fuwen (2014)
      We report on the first study to track the spatial behaviors of wild giant pandas (Ailuropoda melanoleuca ) using high‐resolution global positioning system (GPS) telemetry.... Despite a high degree of spatial overlap between panda home ranges, particularly in winter, we detected neither avoidance nor attraction behavior between conspecifics.
    • Efficient 3D movement-based kernel density estimator and application to wildlife ecology

      Tracey, J.A.; Sheppard, James; Lockwood, G.K.; Chourasia, A.; Tatineni, M.; Fisher, R.N.; Sinkovits, R.S. (Association for Computing MachineryAtlanta (GA), 2014)
    • Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells

      Tunstall, Tate S.; Kock, Richard; Vahala, Jiri; Diekhans, Mark; Fiddes, Ian; Armstrong, Joel; Paten, Benedikt; Ryder, Oliver A.; Steiner, Cynthia C. (2018)
      The critically endangered northern white rhinoceros is believed to be extinct in the wild, with the recent death of the last male leaving only two remaining individuals in captivity. Its extinction would appear inevitable, but the development of advanced cell and reproductive technologies such as cloning by nuclear transfer and the artificial production of gametes via stem cells differentiation offer a second chance for its survival. In this work, we analyzed genome-wide levels of genetic diversity, inbreeding, population history, and demography of the white rhinoceros sequenced from cryopreserved somatic cells, with the goal of informing how genetically valuable individuals could be used in future efforts toward the genetic rescue of the northern white rhinoceros. We present the first sequenced genomes of the northern white rhinoceros, which show relatively high levels of heterozygosity and an average genetic divergence of 0.1% compared with the southern subspecies. The two white rhinoceros subspecies appear to be closely related, with low genetic admixture and a divergent time <80,000 yr ago. Inbreeding, as measured by runs of homozygosity, appears slightly higher in the southern than the northern white rhinoceros. This work demonstrates the value of the northern white rhinoceros cryopreserved genetic material as a potential gene pool for saving this subspecies from extinction.
    • Generation of induced pluripotent stem cells from mammalian endangered species

      Ben-Nun, Inbar Friedrich; Montague, Susanne C.; Houck, Marlys L.; Ryder, Oliver A.; Loring, Jeanne F.; Verma P.; Sumer H. (Humana PressNew York, NY, 2015)
      For some highly endangered species there are too few reproductively capable animals to maintain adequate genetic diversity, and extraordinary measures are necessary to prevent their extinction. Cellular reprogramming is a means to capture the genomes of individual animals as induced pluripotent stem cells (iPSCs), which may eventually facilitate reintroduction of genetic material into breeding populations. Here, we describe a method for generating iPSCs from fibroblasts of mammalian endangered species.
    • Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

      Buchalski, Michael R.; Navarro, Asako Y.; Boyce, Walter M.; Winston, Vickers T.; Tobler, Mathias W.; Nordstrom, Lisa A.; García, Jorge Alaníz; Gille, Daphne A.; Penedo, Maria Cecilia T.; Ryder, Oliver A.; et al. (2015)
      …Within the United States (US), Peninsular bighorn sheep (Ovis canadensis nelsoni, PBS) are listed as federally endangered…. Patterns of genetic spatial structure indicate gene flow throughout the ranges is common, and construction of a US–Mexico border fence or wind energy infrastructure would disrupt connectivity of the metapopulation….
    • Hot monkey, cold reality: surveying rainforest canopy mammals using drone-mounted thermal infrared sensors

      Kays, Roland; Sheppard, James; Mclean, Kevin; Welch, Charlie; Paunescu, Cris; Wang, Victor; Kravit, Greg; Crofoot, Meg (2018)
      Animals of the rainforest canopies are often endangered by deforestation or hunting but are difficult to survey and study because of the inaccessibility of the treetops, combined with the visual camouflage of many species. Drone-based thermal sensors have the potential to overcome these hurdles by rapidly scanning large forested areas from above, detecting and mapping wildlife based on the contrast between their warm body temperatures and the cool tree canopies....
    • Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

      Zimkus, Breda M; Hassapakis, Craig L; Houck, Marlys L. (2018)
      Global amphibian declines associated with anthropogenic causes, climate change, and amphibianspecific infectious diseases (e.g., chytridiomycosis) have highlighted the importance of biobanking amphibian genetic material. Genetic resource collections were the first to centralize the long-term storage of samples for use in basic science, including disciplines such as molecular evolution, molecular genetics, phylogenetics, and systematics. Biobanks associated with conservation breeding programs put a special emphasis on the cryopreservation of viable cells. These cell lines have a broader application, including the potential for genetic rescue and use in species propagation for population enhancement, such as captive breeding and reintroduction programs. We provide an overview of the most commonly used methods for the preservation of genetic resources, identify ways to standardize collection processes across biobanks, and provide decision trees to assist researchers in maximizing the potential use of their samples for both scientific research and the practice of species conservation. We hope that the collection and deposition of tissues preserved using methods that enable eventual cell line establishment will become routine practice among researchers, particularly herpetologists working in the field. While many major museums do not yet cryopreserve reproductive cells or cell lines, they contain the infrastructure and staff to maintain these collections if protocols and procedures are adapted. Collaboration between organizations can play an important future role in the conservation of amphibians, especially biobanks associated with research institutions and those pioneering techniques used in breeding programs.