• A comparison of strategies for selecting breeding pairs to maximize genetic diversity retention in managed populations

      Ivy, Jamie A.; Lacy, Robert C. (2012)
      Captive breeding programs aim to maintain populations that are demographically self-sustaining and genetically healthy. It has been well documented that the best way for managed breeding programs to retain gene diversity (GD) and limit inbreeding is to select breeding pairs that minimize a population's average kinship....
    • Camera settings and biome influence the accuracy of citizen science approaches to camera trap image classification

      Egna, Nicole; O'Connor, David; Stacy-Dawes, Jenna; Tobler, Mathias W.; Pilfold, Nicholas W.; Neilson, Kristin; Simmons, Brooke; Davis, Elizabeth Oneita; Bowler, Mark; Fennessy, Julian; et al. (2020)
      Scientists are increasingly using volunteer efforts of citizen scientists to classify images captured by motion-activated trail cameras. The rising popularity of citizen science reflects its potential to engage the public in conservation science and accelerate processing of the large volume of images generated by trail cameras. While image classification accuracy by citizen scientists can vary across species, the influence of other factors on accuracy is poorly understood. Inaccuracy diminishes the value of citizen science derived data and prompts the need for specific best-practice protocols to decrease error. We compare the accuracy between three programs that use crowdsourced citizen scientists to process images online: Snapshot Serengeti, Wildwatch Kenya, and AmazonCam Tambopata. We hypothesized that habitat type and camera settings would influence accuracy. To evaluate these factors, each photograph was circulated to multiple volunteers. All volunteer classifications were aggregated to a single best answer for each photograph using a plurality algorithm. Subsequently, a subset of these images underwent expert review and were compared to the citizen scientist results. Classification errors were categorized by the nature of the error (e.g., false species or false empty), and reason for the false classification (e.g., misidentification). Our results show that Snapshot Serengeti had the highest accuracy (97.9%), followed by AmazonCam Tambopata (93.5%), then Wildwatch Kenya (83.4%). Error type was influenced by habitat, with false empty images more prevalent in open-grassy habitat (27%) compared to woodlands (10%). For medium to large animal surveys across all habitat types, our results suggest that to significantly improve accuracy in crowdsourced projects, researchers should use a trail camera set up protocol with a burst of three consecutive photographs, a short field of view, and determine camera sensitivity settings based on in situ testing. Accuracy level comparisons such as this study can improve reliability of future citizen science projects, and subsequently encourage the increased use of such data.
    • From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

      Wright, Belinda R.; Farquharson, Katherine A.; McLennan, Elspeth A.; Belov, Katherine; Hogg, Carolyn J.; Grueber, Catherine E. (2019)
      Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes.
    • Recent decline in suitable environmental conditions for African great apes

      Junker, Jessica; Blake, Stephen; Boesch, Christophe; Campbell, Geneviève; Toit, Louwrens du; Duvall, Chris; Ekobo, Atanga; Etoga, Gilles; Galat-Luong, Anh; Gamys, Joel; et al. (2012)
      To predict the distribution of suitable environmental conditions (SEC) for eight African great ape taxa for a first time period, the 1990s and then project it to a second time period, the 2000s; to assess the relative importance of factors influencing SEC distribution and to estimate rates of SEC loss, isolation and fragmentation over the last two decades....
    • Reproductive competition and fecal testosterone in wild male giant pandas (Ailuropoda melanoleuca)

      Nie, Yonggang; Swaisgood, Ronald R.; Zhang, Zejun; Liu, Xiaobin; Wei, Fuwen (2012)
      ...Using global positioning system/very high frequency radiocollars to locate mating aggregations, we used behavioral observations and fecal testosterone assays to gain insight into male panda reproductive effort and strategies, and test theories relating to reproductive competition. Male pandas initially competed fiercely for access to females that were about to be fertile, but once male competitive status was determined, aggression rates declined....
    • Tissue sampling methods and standards for vertebrate genomics

      Wong, P.B.Y.; Wiley, E.O.; Johnson, W.E.; Ryder, Oliver A.; O'Brien, S.J.; Haussler, C.; Koepfli, K.-P.; Houck, Marlys L.; Perelman, P.; Mastromonaco, G.; et al. (2012)
      The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 ?g of DNA); and one-star (ethanol-preserved tissue for 700 ?g of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.
    • Validating methods to determine walking rates of elephants within a zoological institution

      Miller, Lance J.; Andrews, J; Anderson, Matthew J. (2012)
      ...The purpose of the current research was to validate methods for examining the walking rates of elephants in a zoological facility. This included testing GPS units, examining walking rates of eight elephants at the San Diego Zoo Safari Park using collars and conducting trials on a subset of elephants wearing both a collar and anklet outfitted with GPS devices to determine reliability....