• Ganzhorna's mouse lemur (Microcebus ganzhorni). The IUCN Red List of Threatened Species 2020

      Ganzhorn, J.; Donati, G; Eppley, Timothy M.; Hyde Roberts, S; Poelstra, J.W; Rakotondranary, S.J.; Ramanamanjato, J.-B.; Randriantafika, F.M.; Refaly, E.; Tsagnangara, C.; et al. (2020)
      Up to 2016, the south-eastern subpopulation of Grey Mouse Lemurs has been considered to represent a disjunct population of Microcebus murinus (Mittermeier et al. 2010). Based on samples from the littoral forest of Mandena a new form has been separated from M. murinus and been named as M. ganzhorni based on genetic grounds (Hotaling et al. 2016). Morphologically M. ganzhorni is indistinguishable from M. murinus and difficult to distinguish from M. griseorufus (M. griseorufus has a white belly with white underfur while M. murinus and M. ganzhorni have greyish underfur) and thus, taxonomic assignments in the field remain uncertain without genetic analyses. Given these uncertainty, the Extent of Occurrence was unclear at the time the species was described. New genetic analyses showed that M. ganzhorni does not occur in Andohahela National Park (Tiley, Poelstra, Yoder et al., unpubl. data) and does not move up the coastal mountains as this is the range of M. tanosi and M. manitatra (Rasoloarison et al. 2013, Donati et al. 2019). M. ganzhorni thus seems to be restricted to littoral forests east and possibly west of Fort Dauphin. In any case, the area of occupancy (AOO) is estimated to be above 10 km� but below 500 km�. These forests are severely fragmented with the largest fragments measuring less than 2 km�. The size of most forest fragments is declining and forests are being degraded. The species tolerates forest degradation and occurs in a wide range of different habitats, including gardens....
    • Gastric pneumatosis with associated eosinophilic gastritis in four black and white ruffed lemurs (Varecia variegata variegata)

      Niederwerder, M.C.; Stalis, Ilse H.; Campbell, G.A.; Backues, K.A. (2013)
      Pneumatosis cystoides intestinalis (PCI) with associated eosinophilic inflammation was documented in the gastric tissues of four black and white ruffed lemurs (Varecia variegata variegata). Pneumatosis cystoides intestinalis is an uncommon disease described in humans and characterized by multilocular gas-filled cystic spaces located within the wall of the gastrointestinal tract. These cystic spaces can occur in any location along the gastrointestinal tract as well as within the associated connective and lymphatic tissues…
    • Gastrointestinal torsions and intussusception in Northern koalas (Phascolarctos cinereus) at San Diego Zoo (1976–2012)

      Joyce-Zuniga, Nicole M.; Roesler, Jennifer; Andrus, Chris Hamlin; Sutherland-Smith, Meg; Rideout, Bruce; Pye, Geoffrey W. (2014)
      The recent classification as threatened status of the northern koala (Phascolarctos cinereus) by the Australian Government highlights the importance of the conservation and health management of this iconic Australian marsupial. This case series describes gastrointestinal torsion and intussusception in six northern koalas (three males, three females, 2–11 yr old) at the San Diego Zoo from 1976 to 2012….
    • 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 aspects of equids with particular reference to their hybrids

      Benirschke, Kurt; Ryder, Oliver A.; (1985)
      This paper gives a brief review of the cytogenetic knowlege of equine species, the chromosomal errors currently known to exist, and an account of the interspecific hybrids that have served man during the 4500 years of domestication of horse and donkey.
    • Genetic characterization and epidemiology of Helicobacters in non-domestic animals

      Schrenzel, Mark D.; Witte, Carmel L.; Bahl, J.; Tucker, Tammy A.; Fabian, Niora; Greger, Heidi; Hollis, Chrissie; Hsia, Gary; Siltamaki, Erin; Rideout, Bruce; et al. (2010)
      ... To better understand the ecology of helicobacters, we did a PCR survey and epidemiologic analysis of 154 captive or wild vertebrate taxa originating from 6 continents....
    • Genetic connectivity across marginal habitats: the elephants of the Namib Desert

      Ishida Yasuko; Van Coeverden de Groot Peter J.; Leggett Keith E. A.; Putnam, Andrea S.; Fox Virginia E.; Lai Jesse; Boag Peter T.; Georgiadis Nicholas J.; Roca Alfred L. (2016)
      Locally isolated populations in marginal habitats may be genetically distinctive and of heightened conservation concern. Elephants inhabiting the Namib Desert have been reported to show distinctive behavioral and phenotypic adaptations in that severely arid environment. The genetic distinctiveness of Namibian desert elephants relative to other African savanna elephant (Loxodonta africana ) populations has not been established. To investigate the genetic structure of elephants in Namibia, we determined the mitochondrial (mt) DNA control region sequences and genotyped 17 microsatellite loci in desert elephants (n = 8) from the Hoanib River catchment and the Hoarusib River catchment. We compared these to the genotypes of elephants (n = 77) from other localities in Namibia. The mtDNA haplotype sequences and frequencies among desert elephants were similar to those of elephants in Etosha National Park, the Huab River catchment, the Ugab River catchment, and central Kunene, although the geographically distant Caprivi Strip had different mtDNA haplotypes. Likewise, analysis of the microsatellite genotypes of desert‐dwelling elephants revealed that they were not genetically distinctive from Etosha elephants, and there was no evidence for isolation by distance across the Etosha region. These results, and a review of the historical record, suggest that a high learning capacity and long‐distance migrations allowed Namibian elephants to regularly shift their ranges to survive in the face of high variability in climate and in hunting pressure.
    • Genetic guidelines for acquiring a conservation collection

      Maschinski, Joyce; Walters, Christina; Guerrant, Ed; Murray, Sheila; Havens, Kayri; Font, Jeremie; Kramer, Andrea; Vitt, Pati; Neale, Jennifer Ramp; Guerrant Jr., Edward O.; et al. (Center for Plant ConservationEscondido, California, 2019)
      Planning the quantities to collect from one population and across the range of species will improve the chance of maximizing the genetic diversity of the conservation collection. Maintain maternal lines separately to help approximate potential genetic diversity and allow flexibility for use in future conservation translocations. Collect no more than 10% of a population’s seed crop in a single year and no more than 5 years out of 10.
    • Genetic guidelines for acquiring, maintaining, and using a conservation collection: Introduction

      Maschinski, Joyce; Havens, Kayri; Font, Jeremie; Kramer, Andrea; Vitt, Pati; Neale, Jennifer Ramp; Guerrant Jr., Edward O.; Edwards, Christine; Steele, Stephanie; Center for Plant Conservation (CPC) (Center for Plant ConservationEscondido, California, 2019)
      Essential to plant conservation practice of the Center for Plant Conservation is taking action that will benefit species’ survival and reduce the extinction risk of globally and/or regionally rare plant species. CPC participating institutions make conservation collections for this purpose....
    • Genetic guidelines for maintaining a conservation collection

      Maschinski, Joyce; Havens, Kayri; Font, Jeremie; Kramer, Andrea; Vitt, Pati; Neale, Jennifer Ramp; Guerrant Jr., Edward O.; Edwards, Christine; Steele, Stephanie; Center for Plant Conservation (CPC) (Center for Plant ConservationEscondido, California, 2019)
      While the conservation collection grows in the nursery, take care to maintain genetic diversity. Keeping records and labels on aternal lines will help track the potential genetic diversity represented in the collection and can be used to equalize family lines for reintroductions or other conservation translocations.
    • Genetic guidelines for maintaining a conservation collection

      Maschinski, Joyce; Havens, Kayri; Font, Jeremie; Kramer, Andrea; Vitt, Pati; Neale, Jennifer Ramp; Guerrant Jr., Edward O.; Edwards, Christine; Steele, Stephanie; Maschinski, Joyce; et al. (Center for Plant ConservationEscondido, California, 2019)
      Give your reintroduced population a good chance for survival by starting with adequate numbers of plants or seeds at the beginning. Determine the source of the plants or seeds. Determine whether the source should consist of seeds or plants from a single population or from mixed populations.
    • 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….
    • Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus)

      Ting, Nelson; Astaras, Christos; Hearn, Gail; Honarvar, Shaya; Corush, Joel; Burrell, Andrew S.; Phillips, Naomi; Morgan, Bethan J.; Gadsby, Elizabeth L.; Raaum, Ryan; et al. (2012)
      It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.
    • Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

      Brandt, Jessica R.; van Coeverden de Groot, Peter J.; Witt, Kelsey E.; Engelbrektsson, Paige K.; Helgen, Kristofer M.; Malhi, Ripan S.; Ryder, Oliver A.; Roca, Alfred L. (2018)
      The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples....
    • Genetic structure of Rhinoceros Rock Iguanas, Cyclura cornuta, in the Dominican Republic, with insights into the impact of captive facilities and the taxonomic status of Cyclura on Mona Island

      Pasachnik, Stesha A.; Colosimo, Giuliano; Carreras-De León, Rosanna; Gerber, Glenn P. (2020)
      …To better understand the population structure of this species, we used a combination of mtDNA and nuclear markers to elucidate the genetic variation of wild populations across 13 sampling regions in the Dominican Republic (DR), as well as neighboring Mona Island, home to a Cyclura population of uncertain taxonomic status…. Our results suggest that the captive facilities may pose a threat to wild populations and increased regulation of these facilities is needed….
    • Genetic tools: maintaining genetic diversity in the Tasmanian devil metapopulation

      Grueber, Catherine E.; McLennan, Elspeth A.; Hogg, Carolyn J.; Fox, Samantha; Pemberton, David; Belov, Katherine (CSIROClayton South, Australia, 2019)
    • Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers

      Mohammadabadi, M.R.; Nikbakhti, M.; Mirzaee, H.R.; Shandi, A.; Saghi, D.A.; Romanov, Michael N.; Moiseyeva, I.G.; (2010)
      This paper represents the results of a study on the genetic diversity in three native chicken populations (Barred, Brown and Black) of Khorasan, a province in northeastern Iran, by using four microsatellite markers (MCW0005, MCW0016, MCW0018 and MCW0034). Average number of alleles was found to be 5.25 per locus across all populations....
    • Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

      Steiner, Cynthia C.; Houck, Marlys L.; Ryder, Oliver A. (2018)
      The Sumatran rhinoceros (Dicerorhinus sumatrensis) is the smallest and one of the most endangered rhinoceros species, with less than 100 individuals estimated to live in the wild. It was originally divided into three subspecies but only two have survived, D. sumatrensis sumatrensis (Sumatran subspecies), and D. s. harrissoni (Bornean)....
    • Genome-wide characterization of centromeric satellites from multiple mammalian genomes

      Alkan, C.; Cardone, M. F.; Catacchio, C. R.; Antonacci, F.; O'Brien, S. J.; Ryder, Oliver A.; Purgato, S.; Zoli, M.; Della Valle, G.; Eichler, E. E.; et al. (2011)
      ...We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes....
    • Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range

      Kjeldsen, Shannon R.; Zenger, Kyall R.; Leigh, Kellie; Ellis, William A.; Tobey, Jennifer R.; Phalen, David; Melzer, Alistair; FitzGibbon, Sean; Raadsma, Herman W. (2016)
      The koala (Phascolarctos cinereus) is an iconic Australian species that is currently undergoing a number of threatening processes, including disease and habitat loss. A thorough understanding of population genetic structuring and genomic variability of this species is essential to effectively manage populations across the species range. Using a reduced representation genome sequencing method known as double digest restriction-associated sequencing, this study has provided the first genome-wide SNP marker panel in the koala. In this study, 33,019 loci were identified in the koala and a filtered panel of 3060 high-utility SNP markers, including 95 sex-linked markers, were used to provide key insights into population variability and genomic variation in 171 koalas from eight populations across their geographic range. Broad-scale genetic differentiation between geographically separated populations (including sub-species) was assessed and revealed significant differentiation between all populations (FST range = 0.01–0.28), with the largest divergence observed between the three geographically distant subgroups (QLD, NSW and VIC) along the east coast of Australia (average FST range = 0.17–0.23). Sub-group divergence appears to be a reflection of an isolation by distance effect and sampling strategy rather than true evidence of sub-speciation. This is further supported by low proportions of AMOVA variation between sub-species groups (11.19 %). Fine-scale analysis using genome-wide SNP loci and the NETVIEW pipeline revealed cryptic genetic sub-structuring within localised geographic regions, which corresponded to the hierarchical mating system of the species. High levels of genome-wide SNP heterozygosity were observed amongst all populations (He = 0.25–0.35), and when evaluating across the species to other vertebrate taxa were amongst the highest values observed. This illustrates that the species as a whole still retains high levels of diversity which is comparable to other outbred vertebrate taxa for genome-wide SNPs. Insights into the potential for adaptive variation in the koala were also gained using outlier analysis of genome-wide SNPs. A total of 10 putative outlier SNPs were identified indicating the high likelihood of local adaptations within populations and regions. This is the first use of genome-wide markers to assess population differentiation at a broad-scale in the koala and the first time that sex-linked SNPs have been identified in this species. The application of this novel genomic resource to populations across the species range will provide in-depth information allowing informed conservation priorities and management plans for in situ koalas across Australia and ex situ around the world.