• 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....
    • 117 Cryopreservation of snake semen: Are we frozen in time?

      Zacariotti, R.; Guimarães, M.; Jensen, Thomas; Durrant, Barbara S. (2011)
      The increasing number of endangered snake species, isolation of small fragmented populations with associated inbreeding and mating or conception problems in captivity underscore the need to develop assisted reproductive techniques such as semen cryopreservation and artificial insemination to enhance conservation efforts. However, no efficient protocols for semen evaluation, cooling, or freezing are described in the 4 known publications on snake semen cryopreservation. In this initial study, semen was collected noninvasively from 4 live adult red diamond rattlesnakes (Crotalus ruber) by ventral massage....
    • 2013 Reporte Manu: Pasión por la Investigación en la Amazonia Peruana

      San Diego Zoo Global PERU; Servicio Nacional de Áreas Naturales Protegidas (Peru); Groenendijk, Jessica; Tovar, Antonio; Wust Edicciones; San Diego Zoo Global PERU; Servicio Nacional de Áreas Naturales Protegidas (Peru) (San Diego Zoo Global Peru : SERNANPLima, 2013)
      Summarizes the main findings of research carried out at Cocha Cashu and the wider Manu Biosphere Reserve, roughly since 2000, with sections on forest and aquatic ecology, fauna, and the human dimension.
    • 5.3 Grazing

      Becchetti, Theresa; Barry, Sheila; Honey, Marc; Ozeran, Rebecca; Defreese, Denise; de la Rosa, Charlie; Rao, Devii; Freese, Robert; Principe, Zach; Shomo, Brian (California Invasive Plant Council (Cal-IPC), 2021)
      ...The information in this guide is organized into sections based on similarities in the certain techniques— either how they are applied or how they control a weed.... Grazing by cattle, sheep, and goats can be used as a technique for controlling weeds. There are differences in effectiveness among grazers depending on weed species and environments being targeted, but in general grazing (herbivory) for weed control varies more by the plants being grazed than the animals grazing them....
    • 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 comparative genomics multitool for scientific discovery and conservation

      Genereux, Diane P.; Serres, Aitor; Armstrong, Joel; Johnson, Jeremy; Marinescu, Voichita D.; Murén, Eva; Juan, David; Bejerano, Gill; Casewell, Nicholas R.; Chemnick, Leona G.; et al. (2020)
      The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
    • A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations

      Ivy, Jamie A.; Lacy, Robert C. (2012)
      Captive breeding programs aim to maintain populations that are demographically self-sustaining and genetically healthy. It has been well documented that the best way for managed breeding programs to retain gene diversity (GD) and limit inbreeding is to select breeding pairs that minimize a population's average kinship....
    • 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 demonstration of conservation genomics for threatened species management

      Wright, Belinda R.; Farquharson, Katherine A.; McLennan, Elspeth A.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2020)
      ... We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced‐representation sequencing (RRS) of 98 founders of the same programme. A subset of the WGS samples was also sequenced by RRS, allowing us to directly compare genome‐wide heterozygosity with estimates from RRS data. We found good congruence in interindividual variation and gene‐ontology classifications between the two data sets, indicating that our RRS data reflect the genome well....
    • 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 density snp array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies

      McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; et al. (2012)
      An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ?43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of -750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
    • 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 massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

      Goto, Hiroki; Ryder, Oliver A.; Fisher, Allison R.; Schultz, Bryant; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton; Makova, Kateryna D. (2011)
      The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered—two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117–0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.
    • A meta-analysis of birth-origin effects on reproduction in diverse captive environments

      Farquharson, Katherine A.; Hogg, Carolyn J.; Grueber, Catherine E. (2018)
      Successfully establishing captive breeding programs is a priority across diverse industries to address food security, demand for ethical laboratory research animals, and prevent extinction. Differences in reproductive success due to birth origin may threaten the long-term sustainability of captive breeding. Our meta-analysis examining 115 effect sizes from 44 species of invertebrates, fish, birds, and mammals shows that, overall, captive-born animals have a 42% decreased odds of reproductive success in captivity compared to their wild-born counterparts. The largest effects are seen in commercial aquaculture, relative to conservation or laboratory settings, and offspring survival and offspring quality were the most sensitive traits. Although a somewhat weaker trend, reproductive success in conservation and laboratory research breeding programs is also in a negative direction for captive-born animals. Our study provides the foundation for future investigation of non-genetic and genetic drivers of change in captivity, and reveals areas for the urgent improvement of captive breeding.