• 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 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 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 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.
    • 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 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....
    • 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….
    • Animal Welfare in Conservation Breeding: Applications and Challenges

      Greggor, Alison L.; Vicino, Greg A.; Swaisgood, Ronald R.; Fidgett, Andrea; Brenner, Deena J.; Kinney, Matthew E.; Farabaugh, Susan M.; Masuda, Bryce M.; Lamberski, Nadine (2018)
      Animal welfare and conservation breeding have overlapping and compatible goals that are occasionally divergent. Efforts to improve enclosures, provide enriching experiences, and address behavioral and physical needs further the causes of animal welfare in all zoo settings. However, by mitigating stress, increasing behavioral competence, and enhancing reproduction, health, and survival, conservation breeding programs must also focus on preparing animals for release into the wild. Therefore conservation breeding facilities must strike a balance of promoting high welfare, while minimizing the effects of captivity to increase population sustainability. As part of the Hawaii Endangered Bird Conservation Program, San Diego Zoo Global operates two captive breeding facilities that house a number of endangered Hawaiian bird species. At our facilities we aim to increase captive animal welfare through husbandry, nutrition, behavior-based enrichment, and integrated veterinary practices. These efforts help foster a captive environment that promotes the development of species-typical behaviors. By using the “Opportunities to Thrive” guiding principles, we outline an outcome-based welfare strategy, and detail some of the related management inputs, such as transitioning to parental rearing, and conducting veterinary exams remotely. Throughout we highlight our evidence-based approach for evaluating our practices, by monitoring welfare and the effectiveness of our inputs. Additionally we focus on some of the unique challenges associated with improving welfare in conservation breeding facilitates and outline concrete future steps for improving and evaluating welfare outcomes that also meet conservation goals.
    • Applying SNP-derived molecular coancestry estimates to captive breeding programs

      Ivy, Jamie A.; Putnam, Andrea S.; Navarro, Asako Y.; Gurr, Jessica; Ryder, Oliver A. (2016)
      ...Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs...
    • Approaches to management and care of the neonatal nondomestic ruminant

      Wolfe, B.A.; Lamberski, Nadine (2012)
      ...These differences become apparent quickly when the nondomestic neonate requires treatment, and an understanding of the special needs and risks involved can prevent unnecessary problems and losses. The aim of this article is to discuss the unique challenges presented by nondomestic ruminants and approaches to management of neonatal and pediatric cases.
    • Are any populations ‘safe’? Unexpected reproductive decline in a population of Tasmanian devils free of devil facial tumour disease

      Farquharson, Katherine A.; Gooley, Rebecca M.; Fox, S.; Huxtable, Stewart J.; Belov, Katherine; Pemberton, David; Hogg, Carolyn J.; Grueber, Catherine E. (2018)
      Conservation management relies on baseline demographic data of natural populations. For Tasmanian devils (Sarcophilus harrisii), threatened in the wild by two fatal and transmissible cancers (devil facial tumour disease DFTD: DFT1 and DFT2), understanding the characteristics of healthy populations is crucial for developing adaptive management strategies to bolster populations in the wild....
    • Assessing possible hybridization among managed Nubian ibex in North America

      Putnam, Andrea S.; Nguyen, Tram N.; Mott, Alison; Korody, Marisa L.; Ryder, Oliver A. (2020)
      Hybridization among closely related species is a concern in zoo and aquarium populations where unpedigreed animals are frequently exchanged with the private sector. In this study, we examine possible hybridization in a group of Nubian ibex (Capra nubiana) imported into the Association of Zoos and Aquariums’ (AZA) Species Survival Program (SSP) from a private institution....
    • Attempted Predation by Nigeria-Cameroon Chimpanzees (Pan troglodytes ellioti) on Preuss's Red Colobus (Procolobus preussi) in the Ebo Forest, Cameroon

      Morgan, Bethan J.; Suh, J.N.; Abwe, Ekwoge E. (2012)
      We describe the first observation of a predation attempt by Nigerian-Cameroon chimpanzees (Pan troglodytes ellioti) on Preuss’s red colobus (Procolobus preussi) in the Ebo forest, Cameroon. The activity, which was observed for 15 min, primarily involved 1 chimpanzee and 1 red colobus individual, with a further 2 chimpanzees observing the event....
    • Behavioral diversity as a potential indicator of positive animal welfare

      Miller, Lance J.; Vicino, Greg A.; Sheftel, Jessica; Lauderdale, Lisa K. (2020)
      Modern day zoos and aquariums continuously assess the welfare of their animals and use evidence to make informed management decisions. Historically, many of the indicators of animal welfare used to assess the collection are negative indicators of welfare, such as stereotypic behavior. However, a lack of negative indicators of animal welfare does not demonstrate that an individual animal is thriving. There is a need for validated measures of positive animal welfare and there is a growing body of evidence that supports the use of behavioral diversity as a positive indicator of welfare. This includes an inverse relationship with stereotypic behavior as well as fecal glucocorticoid metabolites and is typically higher in situations thought to promote positive welfare. This review article highlights previous research on behavioral diversity as a potential positive indicator of welfare. Details are provided on how to calculate behavioral diversity and how to use it when evaluating animal welfare. Finally, the review will indicate how behavioral diversity can be used to inform an evidence-based management approach to animal care and welfare.
    • Beyond masking: Endangered Stephen's kangaroo rats respond to traffic noise with footdrumming

      Shier, Debra M.; Lea, Amanda J.; Owen, Megan A. (2012)
      ... Roads and road margins on and off reserves serve as dispersal corridors and refugia for SKR and other semifossorial taxa; these areas may therefore function as ecological traps if anthropogenic roadway noise negatively affects population persistence.
    • Beyond masking: Endangered Stephen’s kangaroo rats respond to traffic noise with footdrumming

      Shier, Debra M.; Lea, Amanda J.; Owen, Megan A. (2012)
      ...Because many species rely on low-frequency signals to communicate with conspecifics, they are likely to be especially vulnerable to signal masking and the concomitant biological effects associated with exposure to traffic noise. Here, we show that the spectral characteristics of traffic noise overlap extensively with footdrumming signals of the endangered Stephens’ kangaroo rat (Dipodomys stephensi; SKR)....