• Inbreeding and inbreeding avoidance in wild giant pandas

      Hu, Yibo; Nie, Yonggang; Wei, Wei; Ma, Tianxiao; Van Horn, Russell C.; Zheng, Xiaoguang; Swaisgood, Ronald R.; Zhou, Zhixin; Zhou, Wenliang; Yan, Li; et al. (2017)
      Inbreeding can have negative consequences on population and individual fitness, which could be counteracted by inbreeding avoidance mechanisms. However, the inbreeding risk and inbreeding avoidance mechanisms in endangered species are less studied....
    • Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species

      Willoughby, Janna R.; Ivy, Jamie A.; Lacy, Robert C.; Doyle, Jacqueline M.; DeWoody, J. Andrew (2017)
      Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
    • Inbreeding, immune defence and ectoparasite load in different mockingbird populations and species in the Galápagos Islands

      Hoeck, Paquita E. A.; Keller, Lukas F. (2012)
      ...Using 26 microsatellite loci and genetic data from museum specimens and contemporary samples, we calculated short‐term and long‐term inbreeding in 13 different mockingbird populations covering the range of all 4 species in the Galápagos Islands and compared them with three different measures of innate immunity and ectoparasite load. We found no significant effect of either measure of inbreeding on natural antibody or complement enzyme titres, heterophil‐lymphocyte ratio or feather louse abundance....
    • Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

      Luan, P.T.; Ryder, Oliver A.; Davis, H.; Zhang, Y.P.; Yu, L. (2013)
      Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora)….
    • Incorporating mortality into habitat selection to identify secure and risky habitats for savannah elephants

      Roever, C. L.; van Aarde, R. J.; Chase, Michael J. (2013)
      Empirical models of habitat selection are increasingly used to guide and inform habitat-based management plans for wildlife species. However, habitat selection does not necessarily equate to habitat quality particularly if selection is maladaptive, so incorporating measures of fitness into estimations of occurrence is necessary to increase model robustness. Here, we incorporated spatially explicit mortality events with the habitat selection of elephants to predict secure and risky habitats in northern Botswana....
    • Increasing conservation translocation success by building social functionality in released populations

      Goldenberg, Shifra Z.; Owen, Megan A.; Brown, Janine L.; Wittemyer, George; Oo, Zaw Min; Leimgruber, Peter (2019)
      The importance of animal behavior to successful wildlife translocations has been acknowledged in recent decades, and it has been increasingly considered and more frequently incorporated into translocation management and research. However, explicit consideration of social behavior is often overlooked in this context. Social relationships take a variety of forms (e.g., cooperative partners, members of a dominance hierarchy, territorial neighbors) and play important roles in survival, reproduction, and resource exploitation. We review the ways in which concepts from studies of social behavior in wild populations may be leveraged to increase translocation success. Social structure and cohesion, social roles, social learning, and social competency may all be important to consider in building populations that are resilient and likely to persist. We argue that relevant data collected at all stages of translocation, including candidate selection, and during pre-release, release, and post-release monitoring, may inform the establishment of functional social structure post-release in species dependent on social processes. Integrating knowledge of social behavior into management decisions may be particularly useful when comparing the success of alternative release protocols or release candidate behavioral traits. Complementary datasets on a range of fitness-related metrics post-release will further leverage our understanding of social establishment in translocated populations. We illustrate the potential of these ideas using Asian and African elephants as a model. Both species are particularly challenging to manage but are translocated frequently; thus, evidence-based protocols for conservation translocations of elephants are urgently needed.
    • Increasing generations in captivity is associated with increased vulnerability of Tasmanian devils to vehicle strike following release to the wild

      Grueber, Catherine E.; Reid-Wainscoat, Elizabeth E.; Fox, Samantha; Belov, Katherine; Shier, Debra M.; Hogg, Carolyn J.; Pemberton, David (2017)
      Captive breeding of threatened species, for release to the wild, is critical for conservation. This strategy, however, risks producing captive-raised animals with traits poorly suited to the wild. We describe the first study to characterise accumulated consequences of long-term captive breeding on behaviour, by following the release of Tasmanian devils to the wild. We test the impact of prolonged captive breeding on the probability that captive-raised animals are fatally struck by vehicles. Multiple generations of captive breeding increased the probability that individuals were fatally struck, a pattern that could not be explained by other confounding factors (e.g. age or release site). Our results imply that long-term captive breeding programs may produce animals that are naïve to the risks of the post-release environment. Our analyses have already induced changes in management policy of this endangered species, and serve as model of productive synergy between ecological monitoring and conservation strategy.
    • Indeterminate growth in desert tortoises

      Nafus, Melia G. (2015)
      ...Using a captive colony of desert tortoises, I explored three questions about adult growth: 1) Do tortoises experience growth at reproductively mature size classes? 2) For those adults that experience growth, is growth continuous throughout adulthood? 3) Are there differences in growth and size between males and females...?
    • Individual identification of wild giant pandas from camera trap photos – a systematic and hierarchical approach

      Zheng, X.; Owen, Megan A.; Nie, Y.; Hu, Y.; Swaisgood, Ronald R.; Yan, L.; Wei, F. (2016)
      ...Here we tested the utility of an approach to individually identify wild giant pandas Ailuropoda melanoleuca from camera trap images, by cataloguing and careful scrutiny of numerous traits. We developed our identification strategy first by analyzing images of known (captive) individuals (N = 7). We then deployed camera traps at 23 control sites and at seven camera trap arrays ‘baited’ with conspecific decoys, in Foping Nature Reserve, China….
    • Induced pluripotent stem cells from highly endangered species

      Ben-Nun, Inbar Friedrich; Montague, Susanne C; Houck, Marlys L.; Tran, Ha T; Garitaonandia, Ibon; Leonardo, Trevor R; Wang, Yu-Chieh; Charter, Suellen J.; Laurent, Louise C; Ryder, Oliver A.; et al. (2011)
      For some highly endangered species there are too few reproductively capable animals to maintain adequate genetic diversity, and extraordinary measures are necessary to prevent extinction. We report generation of induced pluripotent stem cells (iPSCs) from two endangered species: a primate, the drill, Mandrillus leucophaeus and the nearly extinct northern white rhinoceros, Ceratotherium simum cottoni. iPSCs may eventually facilitate reintroduction of genetic material into breeding populations.
    • Induction of sperm hypermotility through membrane progestin receptor alpha (mPRα): A teleost model of rapid, multifaceted, nongenomic progestin signaling

      Tan, Wenxian; Pang, Yefei; Tubbs, Christopher W.; Thomas, Peter (2018)
      Rapid progestin effects on sperm physiology have been described in a variety of vertebrate species. Here, we briefly review the signaling pathways mediating rapid progestin induction of sperm hypermotility and increased fertility in two teleost species, Atlantic croaker and southern flounder....
    • 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.
    • Influences of sex, incubation temperature, and environmental quality on gonadal estrogen and androgen receptor messenger RNA expression in juvenile American alligators (Alligator mississippiensis)

      Moore, B.C.; Milnes, Mathew R.; Kohno, S.; Katsu, Y.; Iguchi, T.; LJ, Guilette, Jr; (2010)
      ...We have shown previously that gonads from wild-caught juvenile alligators express greater levels of estrogen receptor 1 (ESR1) than estrogen receptor 2 (ESR2).... These findings demonstrate that the mRNA expression of receptors required for steroid hormone signaling are modified by exposure to environmental factors, including temperature and contaminants.
    • Information sharing for gorilla conservation: a workshop in Ruhija.

      Imong, I.; Abwe, Ekwoge E.; Ikfuingei, R.; Onononga, J.R.; Makaga, L. (2012)
      Gorilla conservationists and researchers working on the ground at different sites often face the challenge of accessing valuable yet unpublished information about ongoing projects outside their immediate locality, and sharing experiences on their respective projects. Poor information sharing among field workers means that those planning or carrying out projects at one site may not be able to learn from the experiences of others who might have implemented similar projects at other sites.
    • Informing species conservation at multiple scales using data collected for marine mammal stock assessments

      Grech, Alana; Sheppard, James; Marsh, Helene (2011)
      Background Conservation planning and the design of marine protected areas (MPAs) requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments. Methodology and Results We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong) abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km2). We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia's National Representative System of Marine Protected Areas. Conclusion/Significance In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.
    • Initial sequence characterization of the rhabdoviruses of squamate reptiles including a novel rhabdovirus from a caiman lizard (Dracaena guianensis)

      Wellehan, J.F.X.; Pessier, Allan P.; Archer, L.; Childress, A.; Jacobson, E.R.; Tesh, R.B. (2012)
      Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis….
    • Insights for reducing the consumption of wildlife: The use of bear bile and gallbladder in Cambodia

      Davis, Elizabeth Oneita; Veríssimo, Diogo; Crudge, Brian; Lim, Thona; Roth, Vichet; Glikman, Jenny A. (2020)
      Unsustainable wildlife use is one of the leading threats to earth's biodiversity. Historically, efforts to address this issue have been focused on increasing enforcement and anti-poaching measures. However, recognition that such supply-reduction measures may be inefficient has spurred a movement towards consumer research and behaviour change. Here, we used consumer research to investigate the consumption of bear bile and gallbladder in Cambodia. Our aim was to gather key consumer insights such as demographics, beliefs and the identification of trusted individuals and communication channels, which could be used to underpin future behaviour change efforts to reduce the consumption of bear bile and gallbladder. To accomplish this, we conducted 4,512 structured quantitative interviews and 132 qualitative, semi-structured interviews across Cambodia. We found that although the level of bear bile and gallbladder consumption varied across the country, consumers were largely homogenous in their beliefs and choice of trusted messengers. This indicates that behaviour change interventions grounded in these results may be effective in any of the eight areas surveyed. We believe our study strategy can be adapted and followed by other conservation organizations to ensure they are capturing essential information necessary for designing effective behaviour change campaigns. A free Plain Language Summary can be found within the Supporting Information of this article.
    • Insights into hominid evolution from the gorilla genome sequence

      Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Gregory E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; et al. (2012)
      Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera....