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      Digitization workflows for flat sheets and packets of plants, algae, and fungi 1

      research-article
      Author(s): 2 , 27 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 11 , 16 , 17 , 18 , 9 , 19 , 20 , 21 , 2 , 22 , 23 , 24 , 11 , 25 , 26 , 10
      Publication date (Electronic):
      Journal: Applications in Plant Sciences
      Publisher: Botanical Society of America
      Keywords: citizen science, digital imaging, digitization, herbarium, specimen database, workflow

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          Abstract

          Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation’s (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7–36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

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          Climate Change and the Future of California's Endemic Flora

          Scott Loarie, Benjamin Carter, Katharine Hayhoe … (2008)
          The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region's endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California's varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may persist. Protecting these potential future refugia and facilitating species dispersal will be essential to maintain biodiversity in the face of climate change.
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            Polyploidy and novelty: Gottlieb's legacy.

            Pamela Soltis, Xiaoxian Liu, D Blaine Marchant … (2014)
            Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818-830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity-the production of novel enzyme forms in the allopolyploids-can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes-with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity-may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.
            Article 0 comments Cited 69 times – based on 0 reviews     Review now
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              No specimen left behind: industrial scale digitization of natural history collections

              Vladimir Blagoderov, Ian J. Kitching, Laurence Livermore … (2012)
              Abstract Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.
              Article 0 comments Cited 62 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Appl Plant Sci
                Journal ID (iso-abbrev): Appl Plant Sci
                Journal ID (publisher-id): apps
                Title: Applications in Plant Sciences
                Publisher: Botanical Society of America
                ISSN (Electronic): 2168-0450
                Publication date Collection: September 2015
                Publication date (Electronic): 10 September 2015
                Volume: 3
                Issue: 9
                Electronic Location Identifier: apps.1500065
                Affiliations
                [2 ]Integrated Digitized Biocollections (iDigBio), Florida State University, Tallahassee, Florida 32306-2100 USA
                [3 ]Peabody Museum of Natural History, Yale University, New Haven, Connecticut, USA
                [4 ]Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
                [5 ]University of Michigan Herbarium–EEB, Ann Arbor, Michigan, USA
                [6 ]Department of Plant Biology, University of Vermont, Burlington, Vermont, USA
                [7 ]Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
                [8 ]Biology Department, Valdosta State University, Valdosta, Georgia, USA
                [9 ]Department of Biology, Appalachian State University, Boone, North Carolina, USA
                [10 ]Department of Biological Science, Florida State University, Tallahassee, Florida, USA
                [11 ]Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
                [12 ]School of Life Sciences, Arizona State University, Tempe, Arizona, USA
                [13 ]Department of Biological Sciences, Marshall University, Huntington, West Virginia, USA
                [14 ]Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
                [15 ]Burke Museum, University of Washington, Seattle, Washington, USA
                [16 ]Department of Biology, University of Florida, Gainesville, Florida, USA
                [17 ]Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
                [18 ]Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
                [19 ]Rancho Santa Ana Botanic Garden, Claremont, California, USA
                [20 ]Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, USA
                [21 ]University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
                [22 ]Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky, USA
                [23 ]Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, USA
                [24 ]Biological and Environmental Sciences, University of Tennessee, Chattanooga, Tennessee, USA
                [25 ]William and Lynda Steere Herbarium, The New York Botanical Garden, Bronx, New York, USA
                [26 ]Department of Biology and the Ted R. Bradley Herbarium, George Mason University, Fairfax, Virginia, USA
                Author notes
                [1]

                The authors thank the herbarium digitization efforts with which the authors are associated (Box 2) and previous work of iDigBio’s Flat Sheets and Packets Digitization Working Group. This material is based on work supported by the National Science Foundation under Cooperative Agreement no. EF-1115210. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

                [27 ]Author for correspondence: gnelson@ 123456bio.fsu.edu
                Article
                Publisher ID: apps1500065
                DOI: 10.3732/apps.1500065
                PMC ID: 4578381
                SO-VID: 96b65808-4a93-407d-bc2f-5266c0a54de0
                Copyright © © 2015 Nelson et al. Published by the Botanical Society of America
                License:

                This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA).

                History
                Date received : 8 June 2015
                Date accepted : 30 July 2015
                Categories
                Subject: Review Article

                Keywords: citizen science,digital imaging,digitization,herbarium,specimen database,workflow
                Data availability:
                Keywords: citizen science, digital imaging, digitization, herbarium, specimen database, workflow

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