• 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, Isle 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…
    • 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 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; Center for Plant Conservation (CPC) (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 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 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 SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range

      Kjeldsen, Shannon R.; Zenger, Kyall R.; Leigh, Kellie; Ellis, William; 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.
    • Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation

      Yu, Li; Wang, Guo-Dong; Ruan, Jue; Chen, Yong-Bin; Yang, Cui-Ping; Cao, Xue; Wu, Hong; Liu, Yan-Hu; Du, Zheng-Lin; Wang, Xiao-Ping; et al. (2016)
      The snub-nosed monkey genus Rhinopithecus includes five closely related species distributed across altitudinal gradients from 800 to 4,500 m. Rhinopithecus bieti, Rhinopithecus roxellana, and Rhinopithecus strykeri inhabit high-altitude habitats, whereas Rhinopithecus brelichi and Rhinopithecus avunculus inhabit lowland regions. We report the de novo whole-genome sequence of R. bieti and genomic sequences for the four other species. Eight shared substitutions were found in six genes related to lung function, DNA repair, and angiogenesis in the high-altitude snub-nosed monkeys. Functional assays showed that the high-altitude variant of CDT1 (Ala537Val) renders cells more resistant to UV irradiation, and the high-altitude variants of RNASE4 (Asn89Lys and Thr128Ile) confer enhanced ability to induce endothelial tube formation in vitro. Genomic scans in the R. bieti and R. roxellana populations identified signatures of selection between and within populations at genes involved in functions relevant to high-altitude adaptation. These results provide valuable insights into the adaptation to high altitude in the snub-nosed monkeys.
    • Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala ( Phascolarctos cinereus ): a dietary-specialist species distributed across heterogeneous environments

      Kjeldsen, Shannon R.; Raadsma, Herman W.; Leigh, Kellie A.; Tobey, Jennifer R.; Phalen, David; Krockenberger, Andrew; Ellis, William A.; Hynes, Emily; Higgins, Damien P.; Zenger, Kyall R. (2018)
      The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL%?=?68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala’s ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.
    • Geographic comparison of plant genera used in frugivory among the pitheciids Cacajao, Callicebus, Chiropotes, and Pithecia

      Boyle, Sarah A.; Thompson, Cynthia L.; Deluycker, Anneke; Alvarez, Silvia J.; Alvim, Thiago H.G.; Aquino, Rolando; Bezerra, Bruna M.; Boubli, Jean P.; Bowler, Mark; Caselli, Christini Barbosa; et al. (2016)
      Pitheciids are known for their frugivorous diets, but there has been no broad-scale comparison of fruit genera used by these primates that range across five geographic regions in South America. We compiled 31 fruit lists from data collected from 18 species (three Cacajao, six Callicebus, five Chiropotes, and four Pithecia) at 26 study sites in six countries. Together, these lists contained 455 plant genera from 96 families. We predicted that 1) closely related Chiropotes and Cacajao would demonstrate the greatest similarity in fruit lists; 2) pitheciids living in closer geographic proximity would have greater similarities in fruit lists; and 3) fruit genus richness would be lower in lists from forest fragments than continuous forests. Fruit genus richness was greatest for the composite Chiropotes list, even though Pithecia had the greatest overall sampling effort. We also found that the Callicebus composite fruit list had lower similarity scores in comparison with the composite food lists of the other three genera (both within and between geographic areas). Chiropotes and Pithecia showed strongest similarities in fruit lists, followed by sister taxa Chiropotes and Cacajao. Overall, pitheciids in closer proximity had more similarities in their fruit list, and this pattern was evident in the fruit lists for both Callicebus and Chiropotes. There was no difference in the number of fruit genera used by pitheciids in habitat fragments and continuous forest. Our findings demonstrate that pitheciids use a variety of fruit genera, but phylogenetic and geographic patterns in fruit use are not consistent across all pitheciid genera. This study represents the most extensive examination of pitheciid fruit consumption to date, but future research is needed to investigate the extent to which the trends in fruit genus richness noted here are attributable to habitat differences among study sites, differences in feeding ecology, or a combination of both. Am. J. Primatol. 78:493–506, 2016. © 2015 Wiley Periodicals, Inc.
    • Giant otters: using knowledge of life history for conservation

      Groenendijk, Jessica; Hajek, Frank; Johnson, Paul; Macdonald, David W.; Macdonald, David W.; Newman, Chris; Harrington, Lauren A. (Oxford University PressOxford, UK, 2017)
    • Giant panda distributional and habitat-use shifts in a changing landscape

      Wei, Wei; Swaisgood, Ronald R.; Dai, Qiang; Yang, Zhisong; Yuan, Shibin; Owen, Megan A.; Pilfold, Nicholas W.; Yang, Xuyu; Gu, Xiaodong; Zhou, Hong; et al. (2018)
      Long‐term data on populations, threats, and habitat‐use changes are fundamentally important for conservation policy and management decisions affecting species, but these data are often in short supply. Here, we analyze survey data from 57,087 plots collected in approximately three‐fourths of the giant panda's (Ailuropoda melanoleuca) distributional range during China's national surveys conducted in 1999–2003 and 2011–2014. Pandas associated preferentially with several ecological factors and avoided areas impacted by human activities, such as roads, livestock, mining, and tourism. Promise is shown by dramatic declines in logging rates, but is counterbalanced with recently emerging threats. Pandas have increasingly utilized secondary forest as these forests recovered under protective measures. Pandas have undergone a distributional shift to higher elevations, despite the elevational stability of their bamboo food source, perhaps in response to a similar upward shift in the distribution of livestock. Our findings showcase robust on‐the‐ground data from one of the largest‐scale survey efforts worldwide for an endangered species and highlight how science and policy have contributed to this remarkable success story, and help frame future management strategies.
    • Giant pandas a beacon for hope at World Conservation Congress

      Garshelis, Dave; Swaisgood, Ronald R.; Dajun Wang; Steinmetz, Rob (2016)
    • Giant pandas use odor cues to discriminate kin from nonkin

      Gilad, Oranit; Swaisgood, Ronald R.; Owen, Megan A.; Zhou, Xiaoping (2016)
      Sociality is an important factor in both the mechanism and function of kin recognition, yet it is little explored in solitary species. While there may be future opportunities for nepotistic functions of kin discrimination among solitary species, the ability to discriminate kin from nonkin may still have important roles in social regulation. The solitary giant panda Ailuropoda melanoleuca offers a good model system to explore kin discrimination in a solitary mammal. As kin discrimination in many other mammals is olfactorily mediated, we investigated whether giant pandas are able to discriminate odor cues from daughters even after months and years of separation. Our results indicate that giant pandas are capable of discriminating between kin and nonkin using odor cues available in urine and body odor. Daughters preferentially investigated the odors of unrelated adult female pandas over the odors of their mothers, and mothers spent more time investigating the odors of unrelated age-matched female pandas over those from their daughters. Because these studies were conducted months or years after the mother–daughter period of dependency ended, it is still unclear what mechanism is used for recognition. Long-term olfactory memories and phenotype matching should both be considered, and further studies are required for such determination.
    • Glucocorticoid measurement in plasma, urates, and feathers from California condors (Gymnogyps californianus) in response to a human-induced stressor

      Glucs, Zeka E.; Smith, Donald R.; Tubbs, Christopher W.; Scherbinski, Jennie Jones; Welch, Alacia; Burnett, Joseph; Clark, Michael; Eng, Curtis; Finkelstein, Myra E. (2018)
      Vertebrates respond to stressful stimuli with the secretion of glucocorticoid (GC) hormones, such as corticosterone (CORT), and measurements of these hormones in wild species can provide insight into physiological responses to environmental and human-induced stressors. California condors (Gymnogyps californianus) are a critically endangered and intensively managed avian species for which information on GC response to stress is lacking. Here we evaluated a commercially available I125 double antibody radioimmunoassay (RIA) and an enzyme-linked immunosorbent assay (ELISA) kit for measurement of CORT and GC metabolites (GCM) in California condor plasma, urate, and feather samples. The precision and accuracy of the RIA assay outperformed the ELISA for CORT and GCM measurements, and CORT and GCM values were not comparable between the two assays for any sample type. RIA measurements of total CORT in condor plasma collected from 41 condors within 15 minutes of a handling stressor were highly variable (median = 70 ng/mL, range = 1–189 ng/mL) and significantly different between wild and captive condors (p = 0.02, two-tailed t-test, n = 10 wild and 11 captive). Urate GCM levels (median = 620 ng/g dry wt., range = 0.74–7200 ng/g dry wt., n = 216) significantly increased within 2 hr of the acute handling stressor (p = 0.032, n = 11 condors, one-tailed paired t-test), while feather section CORT concentrations (median = 18 pg/mm, range = 6.3–68 ng/g, n = 37) also varied widely within and between feathers. Comparison of multiple regression linear models shows condor age as a significant predictors of plasma CORT levels, while age, sex, and plasma CORT levels predicted GCM levels in urates collected within 30 min of the start of handling. Our findings highlight the need for validation when selecting an immunoassay for use with a new species, and suggest that non-invasively collected urates and feathers hold promise for assessing condor responses to acute or chronic environmental and human-induced stressors.