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Essl F, García‐Rodríguez A, Lenzner B, Alexander JM, Capinha C, Gaüzère P, Guisan A, Kühn I, Lenoir J, Richardson DM, Rumpf SB, Svenning J, Thuiller W, Zurell D, Dullinger S. Potential sources of time lags in calibrating species distribution models. JOURNAL OF BIOGEOGRAPHY 2024; 51:89-102. [PMID: 38515765 PMCID: PMC10952696 DOI: 10.1111/jbi.14726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 03/23/2024]
Abstract
The Anthropocene is characterized by a rapid pace of environmental change and is causing a multitude of biotic responses, including those that affect the spatial distribution of species. Lagged responses are frequent and species distributions and assemblages are consequently pushed into a disequilibrium state. How the characteristics of environmental change-for example, gradual 'press' disturbances such as rising temperatures due to climate change versus infrequent 'pulse' disturbances such as extreme events-affect the magnitude of responses and the relaxation times of biota has been insufficiently explored. It is also not well understood how widely used approaches to assess or project the responses of species to changing environmental conditions can deal with time lags. It, therefore, remains unclear to what extent time lags in species distributions are accounted for in biodiversity assessments, scenarios and models; this has ramifications for policymaking and conservation science alike. This perspective piece reflects on lagged species responses to environmental change and discusses the potential consequences for species distribution models (SDMs), the tools of choice in biodiversity modelling. We suggest ways to better account for time lags in calibrating these models and to reduce their leverage effects in projections for improved biodiversity science and policy.
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Affiliation(s)
- Franz Essl
- Division of BioInvasions, Global Change & Macroecology, Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Adrián García‐Rodríguez
- Division of BioInvasions, Global Change & Macroecology, Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Bernd Lenzner
- Division of BioInvasions, Global Change & Macroecology, Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - César Capinha
- Centre of Geographical StudiesInstitute of Geography and Spatial Planning, University of LisbonLisboaPortugal
- Associate Laboratory TERRALisbonPortugal
| | - Pierre Gaüzère
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRSLECAGrenobleF‐38000France
| | | | - Ingolf Kühn
- Helmholtz Centre for Environmental Research – UFZHalleGermany
- Martin Luther University Halle‐WittenbergHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Jonathan Lenoir
- UMR CNRS 7058, Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN)Université de Picardie Jules VerneAmiensFrance
| | - David M. Richardson
- Department of Botany and Zoology, Centre for Invasion BiologyStellenbosch UniversityStellenboschSouth Africa
- Department of Invasion EcologyCzech Academy of Sciences, Institute of BotanyPrůhoniceCzech Republic
| | - Sabine B. Rumpf
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
| | - Jens‐Christian Svenning
- Department of Biology, Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Aarhus UniversityAarhusDenmark
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRSLECAGrenobleF‐38000France
| | - Damaris Zurell
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Stefan Dullinger
- Division of Biodiversity Dynamics and Conservation, Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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Catching the Drift of Marine Invertebrate Diversity through Digital Repositories—A Case Study of the Mangroves and Seagrasses of Maputo Bay, Mozambique. DIVERSITY 2023. [DOI: 10.3390/d15020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Mangroves and seagrasses present with high marine macroinvertebrate biodiversity that contributes to their structure and functioning. Macroinvertebrates possess a broad range of functional traits, making them excellent models for biodiversity and available-trait-based studies. This study aimed to characterize the biodiversity of marine macroinvertebrates as two different ecosystems situated along the coastline of Maputo Bay by compiling dispersed data from online databases. Specifically, this study addressed species richness, taxonomic and functional diversity based on two traits (habitat occupation and trophic guild), and the community structure of these traits. Mangroves presented with a higher species richness and taxonomic diversity than seagrasses. The functional diversity of mangroves was mostly explained by the trophic guild trait. In the case of seagrasses, functional diversity was mostly due to differences in habitat occupation in the 20th century, but the trophic guild accounted for this functional diversity from 2000 onwards. The comparison of community compositions between the two ecosystems showed low or no similarity. The use of digital databases revealed some limitations, mostly regarding the sampling methods and individual counts. The trends and data gaps presented in this study can be further used to inform subsequent systematic data acquisition and support the development of future research. A further step that may be taken to improve the use of digital data in future biodiversity studies is to fully incorporate functional traits, abundance and sampling methods into online databases.
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Mind the Gaps: Taxonomic, Geographic and Temporal Data of Marine Invertebrate Databases from Mozambique and São Tomé and Príncipe. DIVERSITY 2023. [DOI: 10.3390/d15010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
One of the best ways to share and disseminate biodiversity information is through the digitization of data and making it available via online databases. The rapid growth of publicly available biodiversity data is not without problems which may decrease the utility of online databases. In this study we analyze taxonomic, geographic and temporal data gaps, and bias related to existing data on selected marine invertebrate occurrences along the coastline of two African countries, Mozambique and São Tomé and Príncipe. The final marine invertebrate dataset comprises of 19.910 occurrences, but 32% of the original dataset occurrences were excluded due to data gaps. Most marine invertebrates in Mozambique were collected in seagrasses, whereas in São Tomé and Príncipe they were mostly collected offshore. The dataset has a temporal coverage from 1816 to 2019, with most occurrences collected in the last two decades. This study provides baseline information relevant to a better understanding of marine invertebrate biodiversity data gaps and bias in these habitats along the coasts of these countries. The information can be further applied to complete marine invertebrate data gaps contributing to design informed sampling strategies and advancing refined datasets that can be used in management and conservation plans in both countries.
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Sigler K, Warren D, Tracy B, Forrestel E, Hogue G, Dornburg A. Assessing temporal biases across aggregated historical spatial data: a case study of North Carolina’s freshwater fishes. Ecosphere 2021. [DOI: 10.1002/ecs2.3878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Kyra Sigler
- North Carolina Museum of Natural Sciences Raleigh North Carolina 27601 USA
- Department of Biological and Agricultural Engineering North Carolina State University Raleigh North Carolina 27695 USA
| | - Dan Warren
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Okinawa Japan
| | - Bryn Tracy
- North Carolina Museum of Natural Sciences Raleigh North Carolina 27601 USA
| | - Elisabeth Forrestel
- Department of Viticulture and Enology University of California Davis California 95616 USA
| | - Gabriela Hogue
- North Carolina Museum of Natural Sciences Raleigh North Carolina 27601 USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics University of North Carolina Charlotte Charlotte North Carolina 28223 USA
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Vaganov AV, Shmakov AI, Smirnov SV, Usik NA, Shibanova AA, Kechaykin AA, Kosachev PA, Kopytina TM, Zholnerova EA, Medvedeva KE, Zaikov VF, Sinitsyna TA, Shalimov AP, Antonyuk EV, Gudkova PD, Dmitriev DA, Batkin AA, Kasatkin DE, Belkin DL. Virtual Herbarium ALTB: collection of vascular plants of the Altai Mountain Country. Biodivers Data J 2021; 9:e67616. [PMID: 34316271 PMCID: PMC8292289 DOI: 10.3897/bdj.9.e67616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/06/2021] [Indexed: 12/03/2022] Open
Abstract
Background The herbarium of the South-Siberian Botanical Garden of Altai State University (ALTB) houses the largest collection of plants from the Altai Mountain Country (AMC), an area that extends across Russia, Kazakhstan, Mongolia and China. The collection of ALTB includes more than 450,00 specimens, making it the seventh largest in Russia and the fourth largest amongst Russian university herbaria. Altai State University (ASU), the home of ALTB, is one of the most important centres of academic education and research in Siberia and the Russian Far East. It is a sociocultural centre that provides a distinguished learning environment for undergraduate and graduate students in many scholarly and professional fields, meeting the needs of today's knowledge-based post-industrial society and contributing to regional development. It actively promotes international cooperation and strategic collaboration amongst countries of the AMC in the fields of science, education and culture. In particular, the activities of the South-Siberian Botanical Garden include: development of measures to protect rare and endangered plant species, research on the flora and vegetation of the AMC, preparation and publication of a multi-volume work "Flora Altaica", monographic study of individual plant groups, conducting laboratory classes, summer practicals and special courses. The main purpose of this article is to attract the attention of the scientific community to the botanical research of transboundary territory of the Altai Mountain Country (Russia, Kazakhstan, China and Mongolia) and to the future development of digital plant collections in partnership with Global Biodiversity Information Facility (GBIF). New information The Virtual Herbarium ALTB (Russian interface - altb.asu.ru) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country and the main source of primary material for the "Flora Altaica" project (http://altaiflora.asu.ru/en/). Since 2017, when Altai State University became a GBIF data publisher, data from the Virtual Herbarium ALTB has been exported to the dataset "Virtual Herbarium ALTB (South-Siberian Botanical Garden)" in GBIF. Currently, it includes images and data from 22,466 vascular plants, of which 67% have geographic coordinates (accessed on 30.03.2021). Most of the specimens have been collected since 1977, with the most intensive collecting years being 1995–2008. In 2019, the label-data table of the Virtual Herbarium ALTB was modified to bring it into conformity with the Darwin Core specification (http://altb.asu.ru/). This effectively solved the major impediment to sharing plant diversity data from the AMC and adjacent regions in a multilingual environment.
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Affiliation(s)
- Aleksey V Vaganov
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia.,Sakhalin Branch of the Botanical Garden-Institute FEB RAS, Yuzhno-Sakhalinsk, Russia Sakhalin Branch of the Botanical Garden-Institute FEB RAS Yuzhno-Sakhalinsk Russia
| | - Alexander I Shmakov
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Sergey V Smirnov
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Nadezda A Usik
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Alena A Shibanova
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Aleksey A Kechaykin
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Petr A Kosachev
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Tatyana M Kopytina
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | | | | | - Vladimir F Zaikov
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Tatyana A Sinitsyna
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | | | - Evgenij V Antonyuk
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Polina D Gudkova
- Tomsk University, Tomsk, Russia Tomsk University Tomsk Russia.,Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Denis A Dmitriev
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Alexander A Batkin
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Dmitry E Kasatkin
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
| | - Denis L Belkin
- Altai State University, Barnaul, Russia Altai State University Barnaul Russia
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Buzzetti FMM, Stancher G, Marangoni F. Sixty years of work on Italy's Orthopteroids biodiversity, the big data of Galvagni collection. Biodivers Data J 2021; 9:e65953. [PMID: 34257509 PMCID: PMC8263551 DOI: 10.3897/bdj.9.e65953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/20/2021] [Indexed: 11/12/2022] Open
Abstract
Background Historical natural history collections are very important for the study of nature and environmental protection of the environment, these being the depository of essential information. The Fondazione Museo Civico di Rovereto holds two major Orthopteroid insect collections that make this Museum a landmark on Italian and Mediterranean Orthoptera diversity. Databasing the Galvagni Collection allows considerations on geographic and taxonomic coverage by specialist researchers. New information Databasing of the Galvagni Collection makes possible considerations on the late specialist research, geographic and taxonomic coverage.
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Affiliation(s)
| | - Gionata Stancher
- Fondazione Museo Civico di Rovereto, Rovereto, Italy Fondazione Museo Civico di Rovereto Rovereto Italy
| | - Federico Marangoni
- Fondazione Museo Civico di Rovereto, Rovereto, Italy Fondazione Museo Civico di Rovereto Rovereto Italy
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Rønsted N, Grace OM, Carine MA. Editorial: Integrative and Translational Uses of Herbarium Collections Across Time, Space, and Species. FRONTIERS IN PLANT SCIENCE 2020; 11:1319. [PMID: 32973855 PMCID: PMC7472523 DOI: 10.3389/fpls.2020.01319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 06/01/2023]
Affiliation(s)
- Nina Rønsted
- Science and Conservation, National Tropical Botanical Garden, Kalaheo, HI, United States
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Olwen M. Grace
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Mark A. Carine
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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8
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Walton S, Livermore L, Dillen M, De Smedt S, Groom Q, Koivunen A, Phillips S. A cost analysis of transcription systems. RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e56211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compare different approaches to transcribing natural history data and summarise the advantages and disadvantages of each approach using six case studies from four different natural history collections. We summarise the main cost considerations when planning a transcription project and discuss the limitations we current have in understanding the costs behind transcription and data quality.
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9
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Schneider FD, Fichtmueller D, Gossner MM, Güntsch A, Jochum M, König‐Ries B, Le Provost G, Manning P, Ostrowski A, Penone C, Simons NK. Towards an ecological trait‐data standard. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13288] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Florian D. Schneider
- unaffiliated, c/o Birgitta König‐Ries Department of Mathematics and Computer Science Friedrich‐Schiller‐Universität Jena Jena Germany
| | - David Fichtmueller
- Botanic Garden and Botanical Museum Berlin Freie Universität Berlin Berlin Germany
| | - Martin M. Gossner
- Forest Entomology Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Anton Güntsch
- Botanic Garden and Botanical Museum Berlin Freie Universität Berlin Berlin Germany
| | - Malte Jochum
- Institute of Plant Sciences University of Bern Bern Switzerland
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Birgitta König‐Ries
- Department of Mathematics and Computer Science Friedrich‐Schiller‐Universität Jena Jena Germany
| | - Gaëtane Le Provost
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F) Frankfurt am Main Germany
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F) Frankfurt am Main Germany
| | - Andreas Ostrowski
- Department of Mathematics and Computer Science Friedrich‐Schiller‐Universität Jena Jena Germany
| | - Caterina Penone
- Institute of Plant Sciences University of Bern Bern Switzerland
| | - Nadja K. Simons
- Department of Ecology and Ecosystem Management Technische Universität München Freising Germany
- Ecological Networks Department of Biology Technische Universität Darmstadt Darmstadt Germany
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10
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Stöver BC, Wiechers S, Müller KF. JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. BMC Bioinformatics 2019; 20:402. [PMID: 31331268 PMCID: PMC6647125 DOI: 10.1186/s12859-019-2982-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats with a limited metadata model, it would be desirable to have support for the more advanced formats. This is necessary for users to produce richly annotated data that can be efficiently reused and make underlying workflows easily reproducible. A programming library that abstracts over the data and metadata models of the different formats and allows supporting all of them in one step would significantly simplify the development of new and the extension of existing software to address the need for better metadata annotation. RESULTS We developed the Java library JPhyloIO, which allows event-based reading and writing of the most common alignment and tree/network formats. It allows full access to all features of the nine currently supported formats. By implementing a single JPhyloIO-based reader and writer, application developers can support all of these formats. Due to the event-based architecture, JPhyloIO can be combined with any application data structure, and is memory efficient for large datasets. JPhyloIO is distributed under LGPL. Detailed documentation and example applications (available on http://bioinfweb.info/JPhyloIO/ ) significantly lower the entry barrier for bioinformaticians who wish to benefit from JPhyloIO's features in their own software. CONCLUSION JPhyloIO enables simplified development of new and extension of existing applications that support various standard formats simultaneously. This has the potential to improve interoperability between phylogenetic software tools and at the same time motivate usage of more recent metadata-rich formats such as NeXML or phyloXML.
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Affiliation(s)
- Ben C Stöver
- Institute for Evolution and Biodiversity, WWU Münster, Hüfferstraße 1, 48149, Münster, Germany.
| | - Sarah Wiechers
- Institute for Evolution and Biodiversity, WWU Münster, Hüfferstraße 1, 48149, Münster, Germany
| | - Kai F Müller
- Institute for Evolution and Biodiversity, WWU Münster, Hüfferstraße 1, 48149, Münster, Germany
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Affiliation(s)
- Joseph A Cook
- Biology Department and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, USA
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12
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Green DW, Watson JA, Jung HS, Watson GS. Natural History Collections as Inspiration for Technology. Bioessays 2019; 41:e1700238. [PMID: 30775795 DOI: 10.1002/bies.201700238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 11/08/2018] [Indexed: 12/30/2022]
Abstract
Living organisms are the ultimate survivalists, having evolved phenotypes with unprecedented adaptability, ingenuity, resourcefulness, and versatility compared to human technology. To harness these properties, functional descriptions and design principles from all sources of biodiversity information must be collated - including the hundreds of thousands of possible survival features manifest in natural history museum collections, which represent 12% of total global biodiversity. This requires a consortium of expert biologists from a range of disciplines to convert the observations, data, and hypotheses into the language of engineering. We hope to unite multidisciplinary biologists and natural history museum scientists to maximize the coverage of observations, descriptions, and hypotheses relating to adaptation and function across biodiversity, to make it technologically useful. This is to be achieved by developments in meta- taxonomic classification, phylogenetics, systematics, biological materials research, structure and morphological characterizations, and ecological data gathering from the collections - the aim being to identify and catalogue features essential for good biomimetic design.
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Affiliation(s)
- David W Green
- Dr. D. W. Green, Prof. H.-S. Jung, Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Jolanta A Watson
- Dr. J. A. Watson, Dr. G. S. Watson, School of Science and Engineering, University of the Sunshine Coast, Fraser Coast, Hervey Bay, QL, 4655, Australia
| | - Han-Sung Jung
- Dr. D. W. Green, Prof. H.-S. Jung, Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Gregory S Watson
- Dr. J. A. Watson, Dr. G. S. Watson, School of Science and Engineering, University of the Sunshine Coast, Fraser Coast, Hervey Bay, QL, 4655, Australia
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Meineke EK, Davies TJ, Daru BH, Davis CC. Biological collections for understanding biodiversity in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0386. [PMID: 30455204 DOI: 10.1098/rstb.2017.0386] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Department of Ecology and Evolutionary Biology, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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14
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Nelson G, Ellis S. The history and impact of digitization and digital data mobilization on biodiversity research. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170391. [PMID: 30455209 PMCID: PMC6282090 DOI: 10.1098/rstb.2017.0391] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2018] [Indexed: 11/12/2022] Open
Abstract
The first two decades of the twenty-first century have seen a rapid rise in the mobilization of digital biodiversity data. This has thrust natural history museums into the forefront of biodiversity research, underscoring their central role in the modern scientific enterprise. The advent of mobilization initiatives such as the United States National Science Foundation's Advancing Digitization of Biodiversity Collections (ADBC), Australia's Atlas of Living Australia (ALA), Mexico's National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil's Centro de Referência em Informação (CRIA) and China's National Specimen Information Infrastructure (NSII) has led to a rapid rise in data aggregators and an exponential increase in digital data for scientific research and arguably provide the best evidence of where species live. The international Global Biodiversity Information Facility (GBIF) now serves about 131 million museum specimen records, and Integrated Digitized Biocollections (iDigBio) in the USA has amassed more than 115 million. These resources expose collections to a wider audience of researchers, provide the best biodiversity data in the modern era outside of nature itself and ensure the primacy of specimen-based research. Here, we provide a brief history of worldwide data mobilization, their impact on biodiversity research, challenges for ensuring data quality, their contribution to scientific publications and evidence of the rising profiles of natural history collections.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Gil Nelson
- iDigBio, Florida State University, 142 Collegiate Loop, Tallahassee, FL 32306, USA
| | - Shari Ellis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
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15
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Haelewaters D, Rossi W. Laboulbeniales parasitic on American small carrion beetles: new species of Corethromyces, Diphymyces, and Rodaucea. Mycologia 2017; 109:655-666. [PMID: 29023208 DOI: 10.1080/00275514.2017.1379118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ten new species of Laboulbeniales parasitic on small carrion beetles (Coleoptera, Leiodidae, Cholevinae) from the American continent are described: Corethromyces bernardii on Dissochaetus spp. from Bolivia, Costa Rica, Ecuador, and the USA; Diphymyces anthracinus on Ptomaphagus brevior from the USA; D. blackwelliae on Ptomaphagus giaquintoi from Guatemala; D. costaricensis on Adelopsis sp. from Costa Rica; D. dichromus on Adelopsis marinae from Argentina; D. newtonii on Ptomaphagus fumosus from the USA; D. obesus on Ptomaphagus brevior from the USA; Diphymyces perreaui on Ptomaphagus nevadicus from the USA; D. polycarpus on Paulipalpina pillahuata from Peru; and Rodaucea hermanii on Adelopsis sp. from Costa Rica. The hosts for all 10 species have been retrieved from museum collections (1 was collected in the field as well). The following new combination is proposed: Rodaucea bruchii, bringing the number of species in the recently established genus Rodaucea to three.
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Affiliation(s)
- Danny Haelewaters
- a Farlow Reference Library and Herbarium of Cryptogamic Botany , Harvard University , 22 Divinity Avenue, Cambridge , Massachusetts 02138
| | - Walter Rossi
- b Section of Environmental Sciences , Department of Life, Health and Environmental Sciences, University of L'Aquila , 67100 Coppito (AQ) , Italy
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Pérez-Lachaud G, Lachaud JP. Hidden biodiversity in entomological collections: The overlooked co-occurrence of dipteran and hymenopteran ant parasitoids in stored biological material. PLoS One 2017; 12:e0184614. [PMID: 28926617 PMCID: PMC5604966 DOI: 10.1371/journal.pone.0184614] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/28/2017] [Indexed: 01/31/2023] Open
Abstract
Biological collections around the world are the repository of biodiversity on Earth; they also hold a large quantity of unsorted, unidentified, or misidentified material and can house behavioral information on species that are difficult to access or no longer available to science. Among the unsorted, alcohol-preserved material stored in the Formicidae Collection of the 'El Colegio de la Frontera Sur' Research Center (Chetumal, Mexico), we found nine colonies of the ponerine ant Neoponera villosa, that had been collected in bromeliads at Calakmul (Campeche, Mexico) in 1999. Ants and their brood were revised for the presence of any sign of parasitism. Cocoons were dissected and their content examined under a stereomicroscope. Six N. villosa prepupae had been attacked by the ectoparasitoid syrphid fly Hypselosyrphus trigonus Hull (Syrphidae: Microdontinae), to date the only known dipteran species of the Microdontinae with a parasitoid lifestyle. In addition, six male pupae from three colonies contained gregarious endoparasitoid wasps. These were specialized in parasitizing this specific host caste as no gyne or worker pupae displayed signs of having been attacked. Only immature stages (larvae and pupae) of the wasp could be obtained. Due to the long storage period, DNA amplification failed; however, based on biological and morphological data, pupae were placed in the Encyrtidae family. This is the first record of an encyrtid wasp parasitizing N. villosa, and the second example of an encyrtid as a primary parasitoid of ants. Furthermore, it is also the first record of co-occurrence of a dipteran ectoparasitoid and a hymenopteran endoparasitoid living in sympatry within the same population of host ants. Our findings highlight the importance of biological collections as reservoirs of hidden biodiversity, not only at the taxonomic level, but also at the behavioral level, revealing complex living networks. They also highlight the need for funding in order to carry out biodiversity inventories and manage existing collections.
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Affiliation(s)
- Gabriela Pérez-Lachaud
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
| | - Jean-Paul Lachaud
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, Université de Toulouse UPS, Toulouse, France
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17
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Garcia FH, Fischer G, Liu C, Audisio TL, Economo EP. Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics. Zookeys 2017; 693:33-93. [PMID: 29362522 PMCID: PMC5777420 DOI: 10.3897/zookeys.693.13012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/12/2017] [Indexed: 12/22/2022] Open
Abstract
New technologies for imaging and analysis of morphological characters offer opportunities to enhance revisionary taxonomy and better integrate it with the rest of biology. In this study, we revise the Afrotropical fauna of the ant genus Zasphinctus Wheeler, and use high-resolution X-ray microtomography (micro-CT) to analyse a number of morphological characters of taxonomic and biological interest. We recognise and describe three new species: Z. obamaisp. n., Z. sarowiwaisp. n., and Z. wilsonisp. n. The species delimitations are based on the morphological examination of all physical specimens in combination with 3D scans and volume reconstructions. Based on this approach, we present a new taxonomic discrimination system for the regional fauna that consists of a combination of easily observable morphological characters visible at magnifications of around 80-100 ×, less observable characters that require higher magnifications, as well as characters made visible through virtual dissections that would otherwise require destructive treatment. Zasphinctus are rarely collected ants and the material available to us is comparatively scarce. Consequently, we explore the use of micro-CT as a non-invasive tool for the virtual examination, manipulation, and dissection of such rare material. Furthermore, we delineate the treated species by providing a diagnostic character matrix illustrated by numerous images and supplement that with additional evidence in the form of stacked montage images, 3D PDFs and 3D rotation videos of scans of major body parts and full body (in total we provide 16 stacked montage photographs, 116 images of 3D reconstructions, 15 3D rotation videos, and 13 3D PDFs). In addition to the comparative morphology analyses used for species delimitations, we also apply micro-CT data to examine certain traits, such as mouthparts, cuticle thickness, and thoracic and abdominal muscles in order to assess their taxonomic usefulness or gain insights into the natural history of the genus. The complete datasets comprising the raw micro-CT data, 3D PDFs, 3D rotation videos, still images of 3D models, and coloured montage photos have been made available online as cybertypes (Dryad, http://dx.doi.org/10.5061/dryad.4s3v1).
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Affiliation(s)
- Francisco Hita Garcia
- Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
| | - Georg Fischer
- Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
| | - Cong Liu
- Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
| | - Tracy L. Audisio
- Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
| | - Evan P. Economo
- Okinawa Institute of Science and Technology Graduate University, 1919–1 Tancha, Onna-son 904–0495, Japan
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18
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Hita Garcia F, Fischer G, Liu C, Audisio TL, Alpert GD, Fisher BL, Economo EP. X-Ray microtomography for ant taxonomy: An exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar. PLoS One 2017; 12:e0172641. [PMID: 28328931 PMCID: PMC5362212 DOI: 10.1371/journal.pone.0172641] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022] Open
Abstract
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrogsp. n. and T. nymeriasp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution maps for both new species. In addition to conventional morphological examination, we have used virtual reconstructions based on volumetric μCT scanning data for the species descriptions. We also include 3D PDFs, still images of virtual reconstructions, and 3D rotation videos for both holotype workers and one paratype queen. The complete μCT datasets have been made available online (Dryad, https://datadryad.org) and represent the first cybertypes in ants (and insects). We discuss the potential of μCT scanning and critically assess the usefulness of cybertypes for ant taxonomy.
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Affiliation(s)
- Francisco Hita Garcia
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- * E-mail:
| | - Georg Fischer
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Cong Liu
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Tracy L. Audisio
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Gary D. Alpert
- Entomology Department, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Brian L. Fisher
- Entomology Department, California Academy of Sciences, San Francisco, California, United States of America
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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19
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Sosef MSM, Dauby G, Blach-Overgaard A, van der Burgt X, Catarino L, Damen T, Deblauwe V, Dessein S, Dransfield J, Droissart V, Duarte MC, Engledow H, Fadeur G, Figueira R, Gereau RE, Hardy OJ, Harris DJ, de Heij J, Janssens S, Klomberg Y, Ley AC, Mackinder BA, Meerts P, van de Poel JL, Sonké B, Stévart T, Stoffelen P, Svenning JC, Sepulchre P, Zaiss R, Wieringa JJ, Couvreur TLP. Exploring the floristic diversity of tropical Africa. BMC Biol 2017; 15:15. [PMID: 28264718 PMCID: PMC5339970 DOI: 10.1186/s12915-017-0356-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/25/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. RESULTS The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. CONCLUSIONS The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.
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Affiliation(s)
- Marc S M Sosef
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium.
| | - Gilles Dauby
- DIADE, Université Montpellier, IRD, Montpellier, France
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- CESAB/FRB, Domaine du Petit Arbois, Av. Louis Philibert, Aix-en-Provence, 13100, France
| | - Anne Blach-Overgaard
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | | | - Luís Catarino
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Theo Damen
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vincent Deblauwe
- DIADE, Université Montpellier, IRD, Montpellier, France
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Box 951496, Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture, BP 2008 (Messa), Yaounde, Cameroon
| | - Steven Dessein
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | | | - Vincent Droissart
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Henry Engledow
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Geoffrey Fadeur
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Rui Figueira
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- CEABN/InBio, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Roy E Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Olivier J Hardy
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Janneke de Heij
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Picturae, De Droogmakerij 12, 1851LX, Heiloo, The Netherlands
| | - Steven Janssens
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Yannick Klomberg
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague 2, Czech Republic
| | - Alexandra C Ley
- Institut für Geobotanik und Botanischer Garten, Im Neuwerk 21, University Halle-Wittenberg, 06108, Halle (Saale), Germany
| | - Barbara A Mackinder
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Pierre Meerts
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire d'Ecologie végétale et Biogéochimie, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Jeike L van de Poel
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Tariq Stévart
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Piet Stoffelen
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Rainer Zaiss
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Jan J Wieringa
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Thomas L P Couvreur
- DIADE, Université Montpellier, IRD, Montpellier, France.
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon.
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
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20
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Syfert MM, Serbina L, Burckhardt D, Knapp S, Percy DM. Emerging New Crop Pests: Ecological Modelling and Analysis of the South American Potato Psyllid Russelliana solanicola (Hemiptera: Psylloidea) and Its Wild Relatives. PLoS One 2017; 12:e0167764. [PMID: 28052088 PMCID: PMC5214844 DOI: 10.1371/journal.pone.0167764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
Food security is threatened by newly emerging pests with increased invasive potential accelerated through globalization. The Neotropical jumping plant louse Russelliana solanicola Tuthill is currently a localized potato pest and probable vector of plant pathogens. It is an unusually polyphagous species and is widely distributed in and along the Andes. To date, introductions have been detected in eastern Argentina, southern Brazil and Uruguay. Species distribution models (SDMs) and trait comparisons based on contemporary and historical collections are used to estimate the potential spread of R. solanicola worldwide. We also extend our analyses to all described species in the genus Russelliana in order to assess the value of looking beyond pest species to predict pest spread. We investigate the extent to which data on geographical range and environmental niche can be effectively extracted from museum collections for comparative analyses of pest and non-pest species in Russelliana. Our results indicate that R. solanicola has potential for invasion in many parts of the world with suitable environmental conditions that currently have or are anticipated to increase potato cultivation. Large geographical ranges are characteristic of a morphological subgeneric taxon group that includes R. solanicola; this same group also has a larger environmental breadth than other groups within the genus. Ecological modelling using museum collections provides a useful tool for identifying emerging pests and developing integrated pest management programs.
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Affiliation(s)
- Mindy M. Syfert
- Natural History Museum, Department of Life Sciences, London, United Kingdom
| | - Liliya Serbina
- Naturhistorisches Museum, Basel, Switzerland
- Institut für Natur-, Landschafts- und Umweltschutz der Universität Basel, Basel, Switzerland
| | | | - Sandra Knapp
- Natural History Museum, Department of Life Sciences, London, United Kingdom
| | - Diana M. Percy
- Natural History Museum, Department of Life Sciences, London, United Kingdom
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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21
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Keklikoglou K, Faulwetter S, Chatzinikolaou E, Michalakis N, Filiopoulou I, Minadakis N, Panteri E, Perantinos G, Gougousis A, Arvanitidis C. Micro-CT vlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT). Biodivers Data J 2016:e8740. [PMID: 27956848 PMCID: PMC5139143 DOI: 10.3897/bdj.4.e8740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/14/2016] [Indexed: 01/17/2023] Open
Abstract
Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices.
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Affiliation(s)
| | - Sarah Faulwetter
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
| | - Eva Chatzinikolaou
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
| | - Nikitas Michalakis
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
| | - Irene Filiopoulou
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
| | - Nikos Minadakis
- Institute of Computer Science (ICS), Foundation for Research and Technology - Hellas (FORTH), Science and Technology Park of Crete, Vassilika Vouton, Heraklion, Greece
| | - Emmanouela Panteri
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
| | - George Perantinos
- Hellenic Centre for Marine Research (HCMR), Gouves, Heraklion, Crete, Greece
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22
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Affiliation(s)
- Sven Buerki
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
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23
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Maldonado C, Molina CI, Zizka A, Persson C, Taylor CM, Albán J, Chilquillo E, Rønsted N, Antonelli A. Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases? GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2015; 24:973-984. [PMID: 27656106 PMCID: PMC5012125 DOI: 10.1111/geb.12326] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
AIM Massive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community - putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. LOCATION The American tropics. METHODS As test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. RESULTS Altitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. MAIN CONCLUSION Open databases and integrative bioinformatic tools allow a rapid approximation of large-scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be more explored, but under scrutiny and validation by taxonomic experts. We suggest that database managers implement easy ways of community feedback on data quality.
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Affiliation(s)
- Carla Maldonado
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Herbario Nacional de BoliviaUniversidad Mayor de San AndresLa PazBolivia
| | - Carlos I. Molina
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Instituto de EcologíaUniversidad Mayor de San AndresLa PazBolivia
| | - Alexander Zizka
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Claes Persson
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | | | - Joaquina Albán
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Eder Chilquillo
- Museo de Historia NaturalUniversidad Nacional Mayor de San MarcosLimaPeru
- Departamento de Biologia VegetalUniversidade Estadual de CampinasSao PauloBrazil
| | - Nina Rønsted
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Botanical GardenGothenburgSweden
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24
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Harrup LE, Bellis GA, Balenghien T, Garros C. Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:249-266. [PMID: 25535946 PMCID: PMC4330985 DOI: 10.1016/j.meegid.2014.12.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 11/23/2022]
Abstract
Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.
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Affiliation(s)
- L E Harrup
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
| | - G A Bellis
- University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - T Balenghien
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
| | - C Garros
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
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Capturing natural-colour 3D models of insects for species discovery and diagnostics. PLoS One 2014; 9:e94346. [PMID: 24759838 PMCID: PMC3997343 DOI: 10.1371/journal.pone.0094346] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/13/2014] [Indexed: 12/02/2022] Open
Abstract
Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity—past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens “from all angles” and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. (“Natural-colour” is used to contrast with “false-colour”, i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.
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Balke M, Schmidt S, Hausmann A, Toussaint EFA, Bergsten J, Buffington M, Häuser CL, Kroupa A, Hagedorn G, Riedel A, Polaszek A, Ubaidillah R, Krogmann L, Zwick A, Fikáček M, Hájek J, Michat MC, Dietrich C, La Salle J, Mantle B, Ng PKL, Hobern D. Biodiversity into your hands - A call for a virtual global natural history 'metacollection'. Front Zool 2013; 10:55. [PMID: 24044698 PMCID: PMC3848749 DOI: 10.1186/1742-9994-10-55] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 09/02/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis. DISCUSSION Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection.The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general.Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of "gems" of undescribed species hidden in museum accessions. SUMMARY Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world's natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.
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Affiliation(s)
- Michael Balke
- Zoologische Staatssammlung, Münchhausenstr. 21, 81247 Munich, Germany
- GeoBio Center, Ludwig-Maximilians-University, Munich, Germany
| | - Stefan Schmidt
- Zoologische Staatssammlung, Münchhausenstr. 21, 81247 Munich, Germany
| | - Axel Hausmann
- Zoologische Staatssammlung, Münchhausenstr. 21, 81247 Munich, Germany
| | - Emmanuel FA Toussaint
- Zoologische Staatssammlung, Münchhausenstr. 21, 81247 Munich, Germany
- GeoBio Center, Ludwig-Maximilians-University, Munich, Germany
| | | | - Matthew Buffington
- Systematic Entomology Lab, USDA-ARS, c/o NMNH, Smithsonian Institution, Washington DC, USA
| | | | | | - Gregor Hagedorn
- Museum für Naturkunde, Invalidenstr. 43, 10115 Berlin, Germany
| | - Alexander Riedel
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, 76133 Karlsruhe, Germany
| | - Andrew Polaszek
- Natural History Museum London, Cromwell Road, London SW7 5BD England
| | - Rosichon Ubaidillah
- LIPI Division of Zoology (Museum Zoologicum Bogoriense), Cibinong, West Java, Indonesia
| | - Lars Krogmann
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Andreas Zwick
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Martin Fikáček
- Department of Entomology, National Museum, Kunratice 1, 148 00 Praha 4, Czech Republic
| | - Jiří Hájek
- Department of Entomology, National Museum, Kunratice 1, 148 00 Praha 4, Czech Republic
| | - Mariano C Michat
- CONICET - Laboratorio de Entomologiá, Departamento de Biodiversidad y Biologá Experimental, Universidad de Buenos Aires, Av. Int. Guïraldes s/n, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Christopher Dietrich
- Illinois Natural History Survey, University of Illinois, 1816 S Oak St., Champaign, IL 61801, USA
| | - John La Salle
- Atlas of Living Australia, CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Beth Mantle
- Australian National Insect Collection, CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Peter KL Ng
- National University of Singapore and Raffles Museum of Biodiversity Research, Department of Biological Science, National University of Singapore, 14 Science Drive 4, 117543 Singapore, Singapore
| | - Donald Hobern
- GBIF Secretariat, Universitetsparken 15, 2100 Copenhagen, Denmark
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Faulwetter S, Vasileiadou A, Kouratoras M, Thanos Dailianis, Arvanitidis C. Micro-computed tomography: Introducing new dimensions to taxonomy. Zookeys 2013:1-45. [PMID: 23653515 PMCID: PMC3591762 DOI: 10.3897/zookeys.263.4261] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/28/2013] [Indexed: 12/13/2022] Open
Abstract
Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called “cybertypes”, and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information.
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Affiliation(s)
- Sarah Faulwetter
- Department of Zoology-Marine Biology, Faculty of Biology, National and Kapodestrian University of Athens, Panepistimiopolis, 15784, Athens, Greece, ; Institute for Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003 Heraklion, Crete, Greece
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Erwin T, Penev L, Stoev P, Georgiev T. Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys. Zookeys 2012; 251:1-10. [PMID: 23378804 PMCID: PMC3536320 DOI: 10.3897/zookeys.251.4516] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 12/17/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Terry Erwin
- Smithsonian Institution, Washington, DC, USA
| | - Lyubomir Penev
- Bulgarian Academy of Sciences & Pensoft Publishers, Sofia, Bulgaria
| | - Pavel Stoev
- Bulgarian Academy of Sciences & Pensoft Publishers, Sofia, Bulgaria
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