• Inference of gorilla demographic and selective history from whole-genome sequence data

      McManus, Kimberly F.; Kelley, Joanna L.; Song, Shiya; Veeramah, Krishna R.; Woerner, August E.; Stevison, Laurie S.; Ryder, Oliver A.; Great Ape Genome Project; Kidd, Jeffrey M.; Wall, Jeffrey D.; et al. (2015)
      Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
    • Inferring public interest from search engine data requires caution

      Correia, Ricardo A.; Di Minin, Enrico; Jarić, Ivan; Jepson, Paul; Ladle, Richard; Mittermeier, John; Roll, Uri; Soriano-Redondo, Andrea; Veríssimo, Diogo (2019)
    • Influence of season and social context on male giant panda (Ailuropoda melanoleuca) vocal behaviour

      Charlton, Benjamin D.; Owen, Megan A.; Zhou, Xiaoping; Zhang, Hemin; Swaisgood, Ronald R. (2019)
      Documenting the different social and behavioural contexts that vocalisations are produced in remains an important step towards understanding the functional relevance of specific call types in a given species’ vocal repertoire. In this study we investigated whether seasonal differences and the presence or absence of male and female conspecifics influence the production of male giant panda vocal signals. To this end, captive male giant pandas were observed during and outside of the breeding season in three social contexts: only male conspecific neighbours, only female conspecific neighbours, and a context with no neighbours. We found that males were more likely to bleat, chirp, honk and moan during the breeding season, and showed a tendency to growl more outside of the reproductive period. The contextual analysis revealed that bleats were more likely to be produced by males when opposite-sexed conspecifics are in close attendance during the breeding season. Conversely, males were more likely to chirp when neighboured by males than females or no neighbours. In addition, males were more likely to honk in the absence of neighbouring conspecifics during the breeding season, raising the possibility that these calls function to signal location and gain the attention of potential mates. Moans were produced more often when male giant pandas had male than female neighbours during the breeding season, which may reflect mild aggression towards these same-sexed rivals, whereas the production of barks and growls did not vary according to season or the sex of conspecific neighbours. Our findings underscore the importance of male giant panda bleats for coordinating reproduction and promoting contact with potential mating partners in this non-gregarious species, and yield fresh insights into the function of male honks that warrant further investigation. They also provide a basis for comparison with free-ranging giant panda vocal behaviour that could potentially inform conservation efforts.
    • Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

      Zimkus, Breda M; Hassapakis, Craig L; Houck, Marlys L. (2018)
      Global amphibian declines associated with anthropogenic causes, climate change, and amphibianspecific infectious diseases (e.g., chytridiomycosis) have highlighted the importance of biobanking amphibian genetic material. Genetic resource collections were the first to centralize the long-term storage of samples for use in basic science, including disciplines such as molecular evolution, molecular genetics, phylogenetics, and systematics. Biobanks associated with conservation breeding programs put a special emphasis on the cryopreservation of viable cells. These cell lines have a broader application, including the potential for genetic rescue and use in species propagation for population enhancement, such as captive breeding and reintroduction programs. We provide an overview of the most commonly used methods for the preservation of genetic resources, identify ways to standardize collection processes across biobanks, and provide decision trees to assist researchers in maximizing the potential use of their samples for both scientific research and the practice of species conservation. We hope that the collection and deposition of tissues preserved using methods that enable eventual cell line establishment will become routine practice among researchers, particularly herpetologists working in the field. While many major museums do not yet cryopreserve reproductive cells or cell lines, they contain the infrastructure and staff to maintain these collections if protocols and procedures are adapted. Collaboration between organizations can play an important future role in the conservation of amphibians, especially biobanks associated with research institutions and those pioneering techniques used in breeding programs.
    • Inter-aviary distance and visual access influence conservation breeding outcomes in a territorial, endangered bird

      Flanagan, Alison M.; Rutz, Christian; Farabaugh, Susan M.; Greggor, Alison L.; Masuda, Bryce M.; Swaisgood, Ronald R. (2020)
      Species extinctions are becoming a global crisis, affecting biodiversity and ecosystem services, with island populations being particularly vulnerable. In response, conservation managers are increasingly turning to ex situ conservation breeding programs to establish assurance populations and provide a source for release and re-establishment of wild populations. The 'Alalā (Hawaiian crow, Corvus hawaiiensis) is a critically endangered and territorial island corvid that became extinct in the wild in 2002, following a severe and prolonged population decline during the late 20th century....
    • Intestinal helminths in wild Peruvian red uakari monkeys (Cacajao calvus ucayalii) in the northeastern Peruvian Amazon

      Conga, David F.; Bowler, Mark; Tantalean, Manuel; Montes, Daniel; Serra-Freire, Nicolau Maués; Mayor, Pedro (2014)
      …We examined 36 fecal samples from Peruvian red uakari monkeys (Cacajao calvus ucayalii ) collected from wild animals in the northeastern Peruvian Amazon. Samples were positive for helminth infection. Nematodes egg: Strongyloididae, Trypanoxyuris sp., Spirurid, and a cestode egg were identified.
    • Into the night: camera traps reveal nocturnal activity in a presumptive diurnal primate, (Rhinopithecus brelichi)

      Tan, Chia L.; Yang, Yeqin; Niu, Kefeng (2013)
      Most living primates exhibit a daytime or nighttime activity pattern. Strict diurnality is thought to be the rule among anthropoids except for owl monkeys. Here we report the diel activity pattern of an Asian colobine, the Guizhou snub-nosed monkey Rhinopithecus brelichi, based on a methodology that relied on using 24-h continuously operating camera traps. We conducted the study in Fanjingshan National Nature Reserve in Guizhou, China from March 22 to May 19 and from June 17 to October 14, 2011. After standardizing all time elements to a meridian-based time according to the geographic coordinates of the study site, we showed unequivocally that the monkeys, though predominantly diurnal, exhibited activity beyond daylight hours throughout the study. Specifically, their activity at night and during twilight periods suggests a complex interplay of behavioral adaptations, among others, to living in a temperate environment where day length and food resources fluctuate substantially across seasons. We contend that, under prevailing ecological conditions, so-called strictly diurnal primates may adjust their activity schedule opportunistically in order to increase energy intake. We also discuss the advantages of using camera traps in primate studies, and how the standardized use of meridian-based time by researchers would benefit comparisons of diel activity patterns among primates.
    • Isolation of a Bohle-like iridovirus from boreal toads housed within a cosmopolitan aquarium collection

      Cheng, Kwang; Jones, Megan E. B.; Jancovich, James K.; Burchell, Jennifer; Schrenzel, Mark D.; Reavill, Drury R.; Imai, Denise M.; Urban, Abby; Kirkendall, Maryanne; Woods, Leslie W.; et al. (2014)
      A captive ‘survival assurance’ population of 56 endangered boreal toads Anaxyrus boreas boreas, housed within a cosmopolitan collection of amphibians originating from Southeast Asia and other locations, experienced high mortality (91%) in April to July 2010. Histological examination demonstrated lesions consistent with ranaviral disease, including multicentric necrosis of skin, kidney, liver, spleen, and hematopoietic tissue, vasculitis, and myriad basophilic intracytoplasmic inclusion bodies…. This finding has implications for the management of amphibians destined for use in reintroduction programs, as their release may inadvertently lead to viral dissemination.
    • IUCN Red List Assessment: Reticulated Giraffe (Giraffa camelopardalis ssp. reticulata)

      Muneza, A.; Doherty, J. B.; Ali, A. Hussein; Fennessy, J.; Marais, A.; O'Connor, David; Wube, T. (2018)
      Reticulated Giraffe is listed as Endangered under criterion A because of an estimated continuing of ~56% over the last 30 years (3 generations). The decline is most likely attributed to habitat loss, deterioration in habitat quality and illegal killing/poaching....
    • Jaguar persecution without “cowflict”: Insights from protected territories in the Bolivian Amazon

      Knox, Jillian; Negrões, Nuno; Marchini, Silvio; Barboza, Kathrin; Guanacoma, Gladys; Balhau, Patricia; Tobler, Mathias W.; Glikman, Jenny A. (2019)
      Persecution by humans is one of the most pressing threats to jaguars (Panthera onca) throughout the Americas, yet few studies have examined the killing of jaguars outside cattle-ranching communities. Although over one-third of the jaguar’s range is formally protected, relatively little is known about human-jaguar relationships within protected areas and indigenous territories. Protected land within the Bolivian Amazon, considered a stronghold for the jaguar, contains communities who differ economically, legally, and socially from previously-studied human populations living with jaguars. Using in-person structured interviews, we investigated attitudes and norms related to jaguars and jaguar killing, self-reported past killing of jaguars, and demographic variables in two protected areas and an indigenous territory: Integrated Management Area of Santa Rosa del Abuná (Santa Rosa, n=224), Indigenous Territory Tacana II (n=137), and Manuripi National Amazon Wildlife Reserve (MNAWR, n=169). Overall, people disliked (48.9%) or felt neutral (26.8%) toward jaguars. A relatively large number of people reported either being attacked or knowing someone who had been attacked by a jaguar: 15.45% in Santa Rosa, 14.20% in MNAWR, and 30.88% in Tacana II. Many respondents stated to have killed a jaguar, although the proportion differed among study areas: 20.39% of Santa Rosa, 55.47% of Tacana II, and 32.72% of MNAWR. People perceived jaguar persecution as relatively common: 44.9% of Santa Rosa, 90.8% of Tacana II, and 65.8% of MNAWR said their neighbors kill jaguars (i.e. descriptive norm). Also, 75.4% of Santa Rosa, 89.1% of Tacana II, and 69.1% of MNAWR said that some of their family members and neighbors thought jaguar killing was good (i.e. subjective norm). Descriptive and subjective norms positively influenced both attitudes toward killing and past killing of jaguars. This perception of jaguar killing being common and socially-accepted, combined with high rates of past killing and a growing illegal trade of jaguar parts, may create an atmosphere conducive to widespread jaguar persecution in the Bolivian Amazon. We recommend management strategies that focus on preventing jaguar depredation of small domestic animals, lessening the perception of carnivore encounters as dangerous to decrease safety-related fears, and making large carnivore killing socially unacceptable (e.g. through social marketing).
    • Jamaican Iguana (Cyclura collei) AZA Animal Program Population Viability Analysis Report.

      Mechak, L.; Grant, Tandora D.; Krebs, J. (Associaton of Zoos and Aquariums, 2015)
    • Jamaican Iguana (Cyclura collei) AZA Regional Studbook. AZA Yellow SSP Program.

      Grant, Tandora D. (Associaton of Zoos and Aquariums, 2017)
    • Jamaican Iguana: Species Recovery Plan, 2006-2013

      Grant, Tandora D.; Pagni, L; Wilson, B (IUCNGland, Switzerland, 2013)
      Thought to be extinct by the mid 1900s, the Jamaican Iguana was rediscovered in 1970, and again in 1990. The 1970 rediscovery generated surprisingly little interest, either within Jamaica or among international conservation organizations. But when pig hunter Edwin Duffus brought a live specimen to the Hope Zoo in 1990, the local Jamaican Iguana Research and Conservation Group (JIRCG) was rapidly formed, and international support quickly materialized. The renamed Jamaican Iguana Recovery Group (JIRG) is a consortium of local Jamaican organizations and international conservation groups that held a workshop in July 2006 to formulate the present Species Recovery Plan (SRP)...
    • Joint species distribution models with species correlations and imperfect detection

      Tobler, Mathias W.; Kéry, Marc; Hui, Francis K. C.; Guillera-Arroita, Gurutzeta; Knaus, Peter; Sattler, Thomas (2019)
      Spatiotemporal patterns in biological communities are typically driven by environmental factors and species interactions. Spatial data from communities are naturally described by stacking models for all species in the community....
    • Justifying and deciding whether to conduct a reintroduction or other conservation translocation

      Maschinski, Joyce; Albrecht, Matthew A.; Font, Jeremie; Monks, Leonie; Haskins, Kristin E.; Center for Plant Conservation (CPC) (Center for Plant ConservationEscondido, California, 2019)
      Reintroduction is not the first step toward the conservation of a species, but rather follows a careful process of gathering information about the species, threats, alternative actions, and future needs. There are several considerations for justifying a reintroduction.
    • Laboratory diagnostics

      Rideout, Bruce; Braun, Josephine; Pessier, Allan P.; Terio, Karen A.; McAloose, Denise; St. Leger, Judy (Academic PressSan Diego, CA, 2018)
      This chapter focuses on the challenges of using laboratory diagnostics in wildlife and how to choose an appropriate test and interpret the results. Very few diagnostic tests have been validated for use in wildlife, which creates challenges for the diagnostician because some of these tests must be used anyway, while others should be avoided....
    • Large carnivores and zoos as catalysts for engaging the public in the protection of biodiversity

      Consorte-McCrea, Adriana; Fernandez, Ana; Bainbridge, Alan; Moss, Andrew; Prévot, Anne-Caroline; Clayton, Susan; Glikman, Jenny A.; Johansson, Maria; López-Bao, José Vicente; Bath, Alistair J.; et al. (2019)
      Addressing the biodiversity crisis requires renewed collaborative approaches. Large carnivores are ambassador species, and as such they can aid the protection of a wide range of species, including evolutionarily distinct and threatened ones, while being popular for conservation marketing. However, conflicts between carnivores and people present a considerable challenge to biodiversity conservation. Our cross disciplinary essay brings together original research to discuss key issues in the conservation of large carnivores as keystone species for biodiversity rich, healthy ecosystems. Our findings suggest the need to promote coexistence through challenging ‘wilderness’ myths; to consider coexistence/conflict as a continuum; to include varied interest groups in decision making; to address fear through positive mediated experiences, and to explore further partnerships with zoos. As wide-reaching institutions visited by over 700 million people/year worldwide, zoos combine knowledge, emotion and social context creating ideal conditions for the development of care towards nature, pro-environmental behaviors and long-term connections between visitors and carnivores. Based on current research, we provide evidence that large carnivores and zoos are both powerful catalysts for public engagement with biodiversity conservation, recognizing barriers and suggesting future ways to collaborate to address biodiversity loss.
    • Large numbers of vertebrates began rapid population decline in the late 19th century

      Li, Haipeng; Xiang-Yu, Jinggong; Dai, Guangyi; Gu, Zhili; Ming, Chen; Yang, Zongfeng; Ryder, Oliver A.; Li, Wen-Hsiung; Fu, Yun-Xin; Zhang, Ya-Ping (2016)
      ...Here we analyzed the genetic diversity data of nuclear and mitochondrial loci of 2,764 vertebrate species and found that the mean genetic diversity is lower in threatened species than in related nonthreatened species. Our coalescence-based modeling suggests that in many threatened species the RPD began ∼123 y ago (a 95% confidence interval of 20–260 y)....
    • Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

      Chen, Lei; Qiu, Qiang; Jiang, Yu; Wang, Kun; Lin, Zeshan; Li, Zhipeng; Bibi, Faysal; Yang, Yongzhi; Wang, Jinhuan; Nie, Wenhui; et al. (2019)
      The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families....
    • Lead exposure risk from trash ingestion by the endangered California condor (Gymnogyps californianus)

      Finkelstein, Myra E.; Brandt, Joseph; Sandhaus, Estelle; Grantham, Jesse; Mee, Allan; Schuppert, Patricia Jill; Smith, Donald R. (2015)
      Lead poisoning from ingestion of spent lead ammunition is one of the greatest threats to the recovery of California Condors (Gymnogyps californianus) in the wild…. Our results suggest that trash ingestion of nonammunition items does not pose a significant lead exposure risk to the California Condor population in California.