• 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 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....
    • 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....
    • Advancing laboratory-based zoo research to enhance captive breeding of southern white rhinoceros

      Tubbs, Christopher W.; Minteer, Ben A.; Maienschein, Jane; Collins, James P. (University of Chicago PressChicago, IL, 2018)
      The captive southern white rhinoceros (SWR) is not currently self-sustaining because of low fertility of captive-born females. The cause of this phenomenon is believed to be high dietary levels of phytoestrogens; endocrine disrupting chemicals (EDCs) produced by plants that can mimic the reproductive hormone estrogen....
    • An enigmatic mortality event in the only population of the Critically Endangered Cameroonian frog Xenopus longipes

      Blackburn, David C.; Evans, Ben J.; Pessier, Allan P.; Vredenburg, Vance T.; (2010)
      Contemporary global declines and mortality events in amphibian populations have been often attributed to infectious disease and climate change, separately and in combination. We report on an enigmatic mortality event in the only known population of the Critically Endangered frog species Xenopus longipes....
    • An optimal and near-optimal strategy to selecting individuals for transfer in captive breeding programs

      Allen, S.D.; Fathi, Y.; Gross, K.; Mace, Michael E.; (2010)
      As species extinction rates continue to rise, zoos have adopted a more active role in the conservation of endangered species. A central concern is to preserve genetic diversity of zoological populations....
    • Andros iguana: Conservation action plan, 2005-2011

      Knapp, Charles; Pagni, Lee (IUCN/SSC Iguana Specialist GroupGland, Switzerland, 2011)
      The endangered Andros iguana, Cyclura cychlura cychlura, is the largest native terrestrial vertebrate, and the only iguana (of 3 species) in the Bahamas that is not confined presently to small cays. The Andros iguana is unique to Andros Island and despite the recent formation of a national park on North Andros Island in 2002, the population is declining. This document presents a comprehensive plan for conservation measures considered essential to the long-term survival of this flagship species in the wild. It combines the knowledge and expertise of highly qualified experts from government and non-government organizations within The Bahamas with the collective conservation experience and scientific expertise of the IUCN/SSC Iguana Specialist Group.
    • Artificial propagation and neonatal care of passerines as an effective tool for in-situ species recovery programs

      Switzer, Richard A.; Cristinacce, A.; Ladkoo, A.; Goltz, T.; Ward, G.; Kuehler, Cyndi M.; Lieberman, Alan A.; Jones, C.; (2010)
    • Assessing California's Relocation Guidelines for Burrowing Owls Impacted by Renewable Energy Development.

      Hennessy, Sarah McCullough; Wisinski, Colleen; Ronan, Noelle; Gregory, Chris; Swaisgood, Ronald R.; Nordstrom, Lisa A. (California Energy Commission, 2020)
      Once common and widespread throughout the western United States and Canada, the western burrowing owl (Athene cunicularia hypugaea) population has declined to the point where the species is now designated as a Species of Special Concern in California. Their presence in development areas, including renewable energy facilities, necessitates an effective strategy for protecting them. This study is the first of its kind to test both passive and active relocation techniques with burrowing owls and evaluate their relative effectiveness with and without the addition of conspecific cues (such as acoustic playback of owl calls and imitation whitewash to attract the owls)....
    • Behavioral audiogram of the giant panda (Ailuropoda melanoleuca): Preliminary results

      Owen, Megan A.; Keating, Jennifer L.; Denes, Samuel L.; Hawk, Kathy; Boroski, Juli; Fiore, Angela; Swaisgood, Ronald R. (2011)
      We used behavioral techniques to assess the hearing sensitivity of four, critically endangered, giant pandas at the San Diego Zoo. Study subjects included one adult male (age 19), two adult females (ages 5 and 19), and one sub-adult female (age 3)…. Hearing sensitivity data will enhance the understanding of how anthropogenic noise may impact both free-ranging and captive giant pandas.
    • 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)....
    • Body size, demography, and body condition in Ctenosaura bakeri

      Pasachnik, Stesha A.; Montgomery, C.E.; Martinez, A.; Belal, N.; Clayson, S.; Faulkner, S. (2012)
      Abstract.—Utila Spiny-tailed Iguanas, Ctenosaura bakeri, are listed as Critically Endangered by the IUCN Redlist Assessment and are listed under Appendix II of CITES. This species occupies a portion of Utila, a small continental island located off the northern coast of Honduras, in the Bay Islands chain. Habitat destruction and overharvesting for consumption and the pet trade are among the top threats facing this species. Though first described in 1901 (Stejneger) and currently the focus of a local conservation program, little is known concerning that basic biology of this species. Combining data from six years we examined body size, sexual size dimorphism, and changes in demography and body condition over the study period. Our results indicate that males are larger and heavier than females on average, and have a longer tail for a given snout-vent length, as is the case with most iguanas. Over the study period we found an increase in the ratio of males to females, suggesting that female biased hunting pressure is increasing. This is consistent with an increase in the human population size and a preference for consuming gravid females. The body condition of both males and females declined over the duration of the study, which is suggestive of a decrease in habitat quality. These results indicate that the situation for this endangered species is becoming increasingly threatening. Conservation measures should focus on alleviating these threats through increased law enforcement, outreach, and education.
    • Body size, demography, and body condition in Utila spiny-tailed iguanas, Ctenosaura bakeri

      Pasachnik, Stesha A.; Montgomery, Chad E; Martinez, Andrea; Belal, Nardiah; Clayson, Steve; Faulkner, Shane (2012)
      Utila Spiny-tailed Iguanas, Ctenosaura bakeri, are listed as Critically Endangered by the IUCN Redlist Assessment and are listed under Appendix II of CITES. This species occupies a portion of Utila, a small continental island located off the northern coast of Honduras, in the Bay Islands chain. Habitat destruction and overharvesting for consumption and the pet trade are among the top threats facing this species. Though first described in 1901 (Stejneger) and currently the focus of a local conservation program, little is known concerning that basic biology of this species. Combining data from six years we examined body size, sexual size dimorphism, and changes in demography and body condition over the study period. Our results indicate that males are larger and heavier than females on average, and have a longer tail for a given snout-vent length, as is the case with most iguanas. Over the study period we found an increase in the ratio of males to females, suggesting that female biased hunting pressure is increasing. This is consistent with an increase in the human population size and a preference for consuming gravid females. The body condition of both males and females declined over the duration of the study, which is suggestive of a decrease in habitat quality. These results indicate that the situation for this endangered species is becoming increasingly threatening. Conservation measures should focus on alleviating these threats through increased law enforcement, outreach, and education.
    • Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates

      Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; et al. (2020)
      The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
    • California Condor Studbook

      Mace, Michael E. (Zoological Society of San DiegoSan Diego, 2011)
    • Can science save the giant panda (Ailuropoda melanoleuca)? Unifying science and policy in an adaptive management paradigm

      Swaisgood, Ronald R.; Wei, Fuwen; Mcshea, William J.; Wildt, David E.; Kouba, Andrew J.; Zhang, Zejun (2011)
      …Here, we review recent developments in giant panda conservation science and propose a strategic plan for moving panda conservation forward…. Specific threats, such as habitat destruction, anthropogenic disturbance and fragmented nonviable populations, need to be addressed simultaneously by researchers, managers and policy-makers working in concert to understand and overcome these obstacles to species recovery. With the backing of the Chinese Government and the conservation community, the giant panda can become a high-profile test species for this much touted, but rarely implemented, approach to conservation management….
    • Characterization of reproductive gene diversity in the endangered Tasmanian devil

      Brandies, Parice A.; Wright, Belinda R.; Hogg, Carolyn J.; Grueber, Catherine E.; Belov, Katherine (2020)
      ...We characterized single nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in 37 Tasmanian devils…. We will use this information in future to examine the interplay between reproductive gene variation and reproductive fitness in Tasmanian devil populations.
    • Clinical trials with itraconazole as a treatment for chytrid fungal infections in amphibians

      Brannelly, L.A.; Richards-Zawacki, C.L.; Pessier, Allan P. (2012)
      Due in large part to recent global declines and extinctions, amphibians are the most threatened vertebrate group. Captive assurance colonies may be the only lifeline for some rapidly disappearing species. Maintaining these colonies free of disease represents a challenge to effective amphibian conservation. The fungal disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is one of the major contributors to global amphibian declines and also poses a serious threat to captive assurance colonies. Many treatment options for Bd infection have not been experimentally tested and the commonly administered dosages of some drugs are known to have negative side effects, highlighting a need for clinical trials. The objective of this study was to clinically test the drug itraconazole as a method for curing Bd infection. We bathed Bd-positive juveniles of 2 anuran amphibian species, Litoria caerulea and Incilius nebulifer, in aqueous itraconazole, varying the concentration and duration of treatment, to find the combination that caused the fewest side effects while also reliably ridding animals of Bd. Our results suggest that a bath in 0.0025% itraconazole for 5 min d?1 for 6 d reliably cures Bd infection and causes fewer side effects than the longer treatment times and higher concentrations of this drug that are commonly administered.
    • Conservation assessment of Guaiacum sanctum and Guaiacum coulteri: Historic distribution and future trends in Mexico

      López-Toledo, Leonel; Gonzalez-Salazar, C.; Burslem, D.F.R.P.; Martinez-Ramos, M. (2011)
      Guaiacum sanctum and Guaiacum coulteri are long‐lived Mesoamerican timber tree species heavily exploited throughout their range and considered to be at risk of extinction. Both species are included on the IUCN Red List and on CITES Appendix II, but there has been no formal assessment of the conservation status of either species. We used ecological niche modeling and rapid assessments of local density and population size structure to provide such evaluations....