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      Open data and digital morphology

      review-article
      1 ,   1 , 2 , 1 , 3 , 1 , 4 ,   5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 5 , 20 , 21 , 22 , 6 , 5 , 23 , 1 , 24 , 25 , 15 , 26 , 23 , 27 , 1 , 28 , 29 , 30 , 19 , 31 , 5 ,   32 , 33 , 34 , 35 , 36 , 37 , 1 , 38 , 1 , 1
      Proceedings of the Royal Society B: Biological Sciences
      The Royal Society
      digital data, three-dimensional models, phenotype, computed tomography, visualization, functional analysis

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          Abstract

          Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

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          NIH Image to ImageJ: 25 years of image analysis.

          For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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            Mega-evolutionary dynamics of the adaptive radiation of birds

            The origin and expansion of biological diversity is regulated by both developmental trajectories1,2 and limits on available ecological niches3–7. As lineages diversify an early, often rapid, phase of species and trait proliferation gives way to evolutionary slowdowns as new species pack into ever more densely occupied regions of ecological niche space6,8. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear9. Here we address this problem on a global scale by analysing a novel crowd-sourced dataset of 3D-scanned bill morphology from >2000 species. We find that bill diversity expanded early in extant avian evolutionary history before transitioning to a phase dominated by morphospace packing. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare but major discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian9 and Simpsonian4 ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.
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              Public Availability of Published Research Data in High-Impact Journals

              Background There is increasing interest to make primary data from published research publicly available. We aimed to assess the current status of making research data available in highly-cited journals across the scientific literature. Methods and Results We reviewed the first 10 original research papers of 2009 published in the 50 original research journals with the highest impact factor. For each journal we documented the policies related to public availability and sharing of data. Of the 50 journals, 44 (88%) had a statement in their instructions to authors related to public availability and sharing of data. However, there was wide variation in journal requirements, ranging from requiring the sharing of all primary data related to the research to just including a statement in the published manuscript that data can be available on request. Of the 500 assessed papers, 149 (30%) were not subject to any data availability policy. Of the remaining 351 papers that were covered by some data availability policy, 208 papers (59%) did not fully adhere to the data availability instructions of the journals they were published in, most commonly (73%) by not publicly depositing microarray data. The other 143 papers that adhered to the data availability instructions did so by publicly depositing only the specific data type as required, making a statement of willingness to share, or actually sharing all the primary data. Overall, only 47 papers (9%) deposited full primary raw data online. None of the 149 papers not subject to data availability policies made their full primary data publicly available. Conclusion A substantial proportion of original research papers published in high-impact journals are either not subject to any data availability policies, or do not adhere to the data availability instructions in their respective journals. This empiric evaluation highlights opportunities for improvement.
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                Author and article information

                Journal
                Proc Biol Sci
                Proc. Biol. Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                12 April 2017
                12 April 2017
                12 April 2017
                : 284
                : 1852
                : 20170194
                Affiliations
                [1 ]School of Earth Sciences, University of Bristol , Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
                [2 ]Oxford University Museum of Natural History , Parks Road, Oxford OX1 3PW, UK
                [3 ]School of Geography, Earth and Environmental Sciences, University of Birmingham , Birmingham B15 2TT, UK
                [4 ]Museum of Zoology, University of Cambridge , Downing Street, Cambridge CB2 3EJ, UK
                [5 ]Dept. Earth Sciences, Natural History Museum , Cromwell Road, London SW7 5BD, UK
                [6 ]Institute of Ageing and Chronic Disease, University of Liverpool , Liverpool L7 8TX, UK
                [7 ]Dept. Palaeobiology, Swedish Museum of Natural History , PO Box 50007, 104 05 Stockholm, Sweden
                [8 ]Dept. Earth Sciences, University of Oxford , South Parks Road, Oxford OX1 3AN, UK
                [9 ]Dept. Evolutionary Anthropology, Duke University , PO Box 90383, Biological Sciences Building, 130 Science Drive, Durham, NC 27708, USA
                [10 ]Computer-assisted Palaeoanthropology Team, UMR 5288 CNRS-Université de Toulouse (Paul Sabatier) , Toulouse, France
                [11 ]Evolutionary Studies Institute, University of Witwatersrand , Johannesburg, South Africa
                [12 ]School of Geosciences, University of South Florida , Tampa, FL 33620, USA
                [13 ]Center for Virtualization and Applied Spatial Technologies, University of South Florida , Tampa, FL 33620, USA
                [14 ]Dept. Biology, College of the Holy Cross , Worcester, MA 01610, USA
                [15 ]Dept. Archaeology and Hull York Medical School, University of York , York YO10 5DD, UK
                [16 ]School of Earth and Space Science, Peking University , Beijing 100871, People's Republic of China
                [17 ]School of Biological Sciences, Monash University , Victoria 3800, Australia
                [18 ]School of Natural Sciences and Psychology, Liverpool John Moores University , Liverpool, UK
                [19 ]Dept. Earth and Environmental Sciences and Museum of Paleontology, University of Michigan , Ann Arbor, MI 48109, USA
                [20 ]School of Earth and Environmental Sciences, University of Manchester , Manchester M13 9PL, UK
                [21 ]Dept. Genetics, Evolution and Environment, and Dept. Earth Sciences, University College London , Gower Street, London SW17 7PL, UK
                [22 ]Structure and Motion Lab, Dept. Comparative Biomedical Sciences, The Royal Veterinary College , Hawkshead Lane, Hatfield, Hertfordshire AL9 7TA, UK
                [23 ]Institut des Sciences de l'Evolution de Montpellier, CC64, Université de Montpellier , campus Triolet, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
                [24 ]Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia , 46980 Paterna, Spain
                [25 ]Unidad de Paleontología, Dpto. Biología, Universidad Autónoma de Madrid , 28049 Cantoblanco, Spain
                [26 ]Dept. Theoretical Biology, University of Vienna , Althanstrasse 14, 1090, Austria
                [27 ]Jackson School of Geosciences C1100, The University of Texas at Austin , Austin, TX 78712, USA
                [28 ]Naturalis Biodiversity Center , Postbus 9517, 2300 RA Leiden, The Netherlands
                [29 ]Paläontologisches Institut und Museum der Universität Zürich , Karl Schmid Strasse 4, 8006 Zürich, Switzerland
                [30 ]Dept. Organismal Biology & Anatomy, University of Chicago , Chicago, IL 60637, USA
                [31 ]Dept. Biology II, Ludwig-Maximilians University Munich (LMU) , Großhadernerstr. 2, 82152 Planegg-Martinsried, Germany
                [32 ]University of Washington , Friday Harbor Labs, Friday Harbor, WA 98250, USA
                [33 ]Dept. Earth Science and Engineering, Imperial College , London SW7 2AZ, UK
                [34 ]National Museums Scotland , Chambers Street, Edinburgh EH1 1JF, UK
                [35 ]School of Biological Sciences, The University of Queensland , St Lucia, Queensland 4072, Australia
                [36 ]Dept. Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine , Athens, OH 45701, USA
                [37 ]School of Environmental and Rural Science, University of New England , Armidale, New South Wales 2351, Australia
                [38 ]State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences , Nanjing 210008, People's Republic of China
                Author notes
                Author information
                http://orcid.org/0000-0001-6598-6534
                http://orcid.org/0000-0003-3472-814X
                http://orcid.org/0000-0003-0412-3000
                http://orcid.org/0000-0002-9284-9591
                http://orcid.org/0000-0002-1873-6070
                http://orcid.org/0000-0001-9782-2358
                http://orcid.org/0000-0003-1856-8377
                http://orcid.org/0000-0002-8444-6776
                http://orcid.org/0000-0002-3766-8560
                http://orcid.org/0000-0002-6514-4406
                http://orcid.org/0000-0002-7254-837X
                http://orcid.org/0000-0002-5923-0404
                http://orcid.org/0000-0002-2618-750X
                http://orcid.org/0000-0003-3116-7463
                Article
                rspb20170194
                10.1098/rspb.2017.0194
                5394671
                28404779
                201962d9-25cf-4227-99e9-7d645b88a15c
                © 2017 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : 30 January 2017
                : 10 March 2017
                Funding
                Funded by: Royal Commission for the Exhibition of 1851, http://dx.doi.org/10.13039/501100000700;
                Funded by: H2020 European Research Council, http://dx.doi.org/10.13039/100010663;
                Funded by: Vetenskapsrådet, http://dx.doi.org/10.13039/501100004359;
                Funded by: The Calleva Foundation;
                Funded by: Leverhulme Trust, http://dx.doi.org/10.13039/501100000275;
                Funded by: Human Origins Research Fund;
                Funded by: National Science Foundation, http://dx.doi.org/10.13039/100000001;
                Funded by: Royal Society, http://dx.doi.org/10.13039/501100000288;
                Funded by: Biotechnology and Biological Sciences Research Council, http://dx.doi.org/10.13039/501100000268;
                Categories
                1001
                70
                144
                25
                Morphology and Biomechanics
                Perspective
                Custom metadata
                April 12, 2017

                Life sciences
                digital data,three-dimensional models,phenotype,computed tomography,visualization,functional analysis

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