• Validation of mercury tip-switch and accelerometer activity sensors for identifying resting and active behavior in bears

      Ware, Jasmine V.; Rode, Karyn D.; Pagano, Anthony M.; Bromaghin, Jeffrey F.; Robbins, Charles T.; Erlenbach, Joy; Jensen, Shannon; Cutting, Amy; Nicassio-Hiskey, Nicole; Hash, Amy; et al. (2015)
      In this study, we examined the performance of a mercury tip-switch and a tri-axial accelerometer housed in collars to determine whether sensor data can be accurately classified as resting and active behaviors and whether data are comparable for the 2 sensor types. Five captive bears (3 polar [Ursus maritimus] and 2 brown [U. arctos horribilis]) were fitted with a collar specially designed to internally house the sensors. The bears’ behaviors were recorded, classified, and then compared with sensor readings…
    • Variation in reproductive success across captive populations: Methodological differences, potential biases and opportunities

      Griffith, Simon C.; Crino, Ondi L.; Andrew, Samuel C.; Nomano, Fumiaki Y.; Adkins-Regan, Elizabeth; Alonso-Alvarez, Carlos; Bailey, Ida E.; Bittner, Stephanie S.; Bolton, Peri E.; Boner, Winnie; et al. (2017)
      ...The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency….
    • Viable cell culture banking for biodiversity characterization and conservation

      Ryder, Oliver A.; Onuma, Manabu (2018)
      Because living cells can be saved for indefinite periods, unprecedented opportunities for characterizing, cataloging, and conserving biological diversity have emerged as advanced cellular and genetic technologies portend new options for preventing species extinction. Crucial to realizing the potential impacts of stem cells and assisted reproductive technologies on biodiversity conservation is the cryobanking of viable cell cultures from diverse species, especially those identified as vulnerable to extinction in the near future. The advent of in vitro cell culture and cryobanking is reviewed here in the context of biodiversity collections of viable cell cultures that represent the progress and limitations of current efforts. The prospects for incorporating collections of frozen viable cell cultures into efforts to characterize the genetic changes that have produced the diversity of species on Earth and contribute to new initiatives in conservation argue strongly for a global network of facilities for establishing and cryobanking collections of viable cells.
    • Vocal behaviour predicts mating success in giant pandas

      Charlton, Benjamin D.; Martin-Wintle, Meghan S.; Owen, Megan A.; Zhang, Hemin; Swaisgood, Ronald R. (2018)
      Surprisingly little is known about how mammal vocal signals are used to achieve behavioural synchrony in the lead up to copulation. The ability to signal short-term fluctuations in arousal levels and behavioural intention is likely to be particularly important for synchronizing mating behaviour in asocial species, which must overcome their natural avoidance and aggressive tendencies to mate. Here, we examined vocal behaviour during breeding encounters in captive giant pandas (Ailuropoda melanoleuca) to gain a greater understanding of how close-range vocal signalling mediates reproduction in this asocial, and conservation-dependent species. Our results revealed that the occurrence of different giant panda vocalizations and acoustic variation within these calls is predictive of successful encounters leading to copulation, as opposed to unsuccessful encounters that do not. In addition, key differences were detected between vocalizations produced during and just prior to copulation. These findings illustrate that vocal exchanges are crucial for achieving behavioural synchrony and signalling intention to mate in giant pandas, and could also provide a valuable tool for breeding programmes, helping conservation managers to assess the likelihood of breeding introductions leading to copulation or potentially injurious failure.
    • Vocal repertoire and signal characteristics of 'Alalā, the Hawaiian Crow (Corvus hawaiiensis)

      Tanimoto, Ann M.; Hart, Patrick J.; Pack, Adam A.; Switzer, Richard A. (2017)
      The critically endangered Hawaiian Crow or ′Alalā (Corvus hawaiiensis) is currently extinct in the wild and the remaining 115 individuals are being captively managed on Hawai′i and Maui Islands by the Zoological Society of San Diego. Here we provide the first comprehensive analysis of the vocal repertoire of this species....
    • West Indian iguana Cyclura spp reintroduction and recovery programmes: Zoo support and involvement

      Grant, Tandora D.; Hudson, R. D. (2015)
      Many West Indian rock iguanas Cyclura spp comprise small restricted island populations that are threatened by habitat conversion and degradation, free-ranging domestic animals and invasive species. In the 1980s, concerted conservation efforts were initiated for Caribbean iguanas, using a combination of captive-breeding programmes and head-starting of wild-collected hatchlings for reintroduction, and habitat protection….
    • What evidence exists on the effectiveness of different types of olfactory lures as attractants for invasive mammalian predators? A systematic map protocol

      Price, Catherine J.; Banks, Peter B.; Greggor, Alison L. (2019)
      Alien mammalian predators are a major cause of species extinction and decline globally. Baits and lures, usually human-food based (for example meat, nuts or oils), are widely deployed in trapping programs to attract target species, but their effectiveness compared to other types of olfactory lures, for example social odours or prey odours, has never been systematically examined. Depending on the context, there can be high proportions of non-target captures, for example when targeting feral cats using cage traps, or low capture success, for example, when targeting introduced rats on tropical islands. Here we use a systematic process to map evidence on the effectiveness of different categories of olfactory attractants for invasive mammalian predators within different ecological contexts. We aim to look for where evidence clusters and knowledge gaps occur, for example, across different lure types or across different habitat-types, and highlight opportunities for future research into behaviourally-relevant olfactory lures.
    • Where to now? An uncertain future for Jamaica's largest endemic vertebrate

      Veen, Rick van; Wilson, Byron S.; Grant, Tandora D.; Hudson, Richard (2014)
    • Which parasites should we be most concerned about in wildlife translocations?

      Rideout, Bruce; Sainsbury, Anthony W.; Hudson, Peter J. (2017)
    • White-footed sportive lemur (Lepilemur leucopus)

      Eppley, Timothy M.; Ferguson, B; Louis, E.E.; Rakotondranary, S.J.; Ganzhorn, J. (2020)
      The extent of occurrence (EOO) of this species covers 2,315 km2. This geographic range is severely fragmented and undergoing continuing decline in area, extent and quality of habitat. The number of mature individuals is also suspected to be in decline. Based on these premises, the species is listed as Endangered
    • White-fronted lemur (Eulemur albifrons). The IUCN Red List of Threatened Species 2020

      Borgerson, C.; Eppley, Timothy M.; Donati, G; Colquhoun, I.C; Irwin, M; Johnson, S; Louis, E.E.; Patel, E.; Ralainasolo, F.B; Ravaloharimanitra, M.; et al. (2020)
      Listed as Vulnerable, Eulemur albifrons is suspected to have undergone a population decline greater than or equal to 30% over a period of 24 years (three generations), due primarily to unsustainable hunting pressure and continuing decline in area, extent and quality of habitat. These causes have not ceased, and will, to a large extent, not be easily reversible
    • Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations

      Koepfli, Klaus-Peter; Tamazian, Gaik; Wildt, David; Dobrynin, Pavel; Kim, Changhoon; Frandsen, Paul B.; Godinho, Raquel; Yurchenko, Andrey A.; Komissarov, Aleksey; Krasheninnikova, Ksenia; et al. (2019)
      Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.926 Gb draft genome consists of 136,532 contigs with an N50 of 45.5 Kbp and 16,931 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 21,276 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.
    • Whole-genome analyses resolve early branches in the tree of life of modern birds

      Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; Faircloth, Brant C.; Nabholz, Benoit; Howard, Jason T.; et al. (2014)
      To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships.....
    • Whole-genome analysis of mycobacteria from birds at the San Diego Zoo

      Pfeiffer, Wayne; Braun, Josephine; Burchell, Jennifer; Witte, Carmel L.; Rideout, Bruce (2017)
      Methods Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically. Results Nine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.
    • Why we know so little: The challenges of fieldwork on the Pitheciids

      Pinto, L.P.; Barnett, A.A.; Bezerra, B.M.; Boubli, J.P.; Bowler, Mark; Barnett, A.A.; Veiga, L.M.; Ferrari, S.F.; Norconk, M.A. (Cambridge University PressCambridge, 2013)
      Possessing a suite of unusual and interesting features, Pitheciids are at the extremes of many of primatology’s ecological and sociological continua (see Norconk 2011). Pitheciids should provide acute tests of many primatological models; however, this is frequently thwarted by the lack of even the most basic quantitative information concerning ecology, behavior and social organization....
    • Wild jackdaws are wary of objects that violate expectations of animacy

      Greggor, Alison L.; McIvor, Guillam E.; Clayton, Nicola S.; Thornton, Alex (2018)
      Nature is composed of self-propelled, animate agents and inanimate objects. Laboratory studies have shown that human infants and a few species discriminate between animate and inanimate objects. This ability is assumed to have evolved to support social cognition and filial imprinting, but its ecological role for wild animals has never been examined.....
    • Withered on the stem: is bamboo a seasonally limiting resource for giant pandas?

      Li, Youxu; Swaisgood, Ronald R.; Wei, Wei; Nie, Yonggang; Hu, Yibo; Yang, Xuyu; Gu, Xiaodong; Zhang, Zejun (2017)
      In response to seasonal variation in quality and quantity of available plant biomass, herbivorous foragers may alternate among different plant resources to meet nutritional requirements. Giant pandas (Ailuropoda melanoleuca) are reliant almost exclusively on bamboo which appears omnipresent in most occupied habitat, but subtle temporal variation in bamboo quality may still govern foraging strategies, with population-level effects....
    • X chromosome evolution in Cetartiodactyla

      Proskuryakova, Anastasia A.; Kulemzina, Anastasia I.; Perelman, Polina L.; Makunin, Alexey I.; Larkin, Denis M.; Farré, Marta; Kukekova, Anna V.; Lynn Johnson, Jennifer; Lemskaya, Natalya A.; Beklemisheva, Violetta R.; et al. (2017)
      The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere David’s deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups.
    • Xenogeneic transfer of adult quail (Coturnix coturnix) spermatogonial stem cells to embryonic chicken (Gallus gallus) hosts: a model for avian conservation

      Roe, Mandi; McDonald, Nastassja; Durrant, Barbara S.; Jensen, Thomas (2013)
      ...This is the first study to suggest that it is feasible to rescue adult germ stem cells of deceased birds to prolong the reproductive lifespan of critically endangered species or genetically valuable individuals by transferring them to an embryonic chicken host.
    • 2013 Reporte Manu

      San Diego Zoo Global PERU; Servicio Nacional de Áreas Naturales Protegidas (Peru); Groenendijk, Jessica; Tovar, Antonio; Wust Edicciones; San Diego Zoo Global PERU; Servicio Nacional de Áreas Naturales Protegidas (Peru) (San Diego Zoo Global Peru : SERNANPLima, 2013)
      Summarizes the main findings of research carried out at Cocha Cashu and the wider Manu Biosphere Reserve, roughly since 2000, with sections on forest and aquatic ecology, fauna, and the human dimension.