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Dillon EM, Dunne EM, Womack TM, Kouvari M, Larina E, Claytor JR, Ivkić A, Juhn M, Carmona PSM, Robson SV, Saha A, Villafaña JA, Zill ME. Challenges and directions in analytical paleobiology. PALEOBIOLOGY 2023; 49:377-393. [PMID: 37809321 PMCID: PMC7615171 DOI: 10.1017/pab.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.
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Affiliation(s)
- Erin M. Dillon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, U.S.A.; Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Emma M. Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tom M. Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Miranta Kouvari
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom; Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Ekaterina Larina
- Jackson School of Geosciences, University of Texas, Austin, Texas 78712, U.S.A
| | - Jordan Ray Claytor
- Department of Biology, University of Washington, Seattle, Washington 98195, U.S.A; Burke Museum of Natural History and Culture, Seattle, Washington 98195, U.S.A
| | - Angelina Ivkić
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2,1090 Vienna, Austria
| | - Mark Juhn
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, U.S.A
| | - Pablo S. Milla Carmona
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Geológicas, Buenos Aires C1428EGA, Argentina; Instituto de Estudios Andinos “Don Pablo Groeber” (IDEAN, UBA-CONICET), Buenos Aires C1428EGA, Argentina
| | - Selina Viktor Robson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Anwesha Saha
- Institute of Palaeobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818 Warsaw, Poland; Laboratory of Paleogenetics and Conservation Genetics, Centre of New Technologies (CeNT), University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Jaime A. Villafaña
- Department of Palaeontology, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria; Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O ‘Higgins, Santiago 8370993, Chile
| | - Michelle E. Zill
- Department of Earth and Planetary Sciences, University of California Riverside, Riverside, California 92521, U.S.A
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Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network. PLoS Pathog 2021; 17:e1009583. [PMID: 34081744 PMCID: PMC8174688 DOI: 10.1371/journal.ppat.1009583] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.
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Ferguson AW. On the role of (and threat to) natural history museums in mammal conservation: an African small mammal perspective. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Leveraging legacy archaeological collections as proxies for climate and environmental research. Proc Natl Acad Sci U S A 2020; 117:8287-8294. [PMID: 32284414 DOI: 10.1073/pnas.1914154117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Understanding the causes and consequences of previous climate changes is essential for testing present-day climate models and projections. Archaeological sites are paleoenvironmental archives containing unique ecological baselines with data on paleoclimate transformations at a human timescale. Anthropogenic and nonanthropogenic forces have destroyed many sites, and others are under immediate threat. In the face of this loss, previously excavated collections from these sites-referred to as legacy collections-offer a source of climate and other paleoenvironmental information that may no longer exist elsewhere. Here, we 1) review obstacles to systematically using data from legacy archaeological collections, such as inconsistent or unreported field methods, inadequate records, unsatisfactory curation, and insufficient public knowledge of relevant collections; 2) suggest best practices for integrating archaeological data into climate and environmental research; and 3) summarize several studies to demonstrate the benefits and challenges of using legacy collections as archives of local and regional environmental proxies. Data from archaeological legacy collections contribute regional ecological baselines as well as serve to correct shifting baselines. They also enable regional climate reconstructions at various timescales and corroborate or refine radiocarbon dates. Such uses of legacy collections raise ethical concerns regarding ownership of and responsibility for cultural resources and highlight the importance of Indigenous involvement in planning and executing fieldwork and stewardship of cultural heritage. Finally, we discuss methodologies, practices, and policies pertaining to archaeological legacy collections and support calls for discipline-wide shifts in collections management to ensure their long-term utility in multidisciplinary research and public engagement.
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Miller SE, Barrow LN, Ehlman SM, Goodheart JA, Greiman SE, Lutz HL, Misiewicz TM, Smith SM, Tan M, Thawley CJ, Cook JA, Light JE. Building Natural History Collections for the Twenty-First Century and Beyond. Bioscience 2020. [DOI: 10.1093/biosci/biaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
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Affiliation(s)
- Sara E Miller
- Cornell University Department of Neurobiology and Behavior, Ithaca, New York
| | - Lisa N Barrow
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Sean M Ehlman
- Ecology, Evolution, and Behavior Department, University of Minnesota—Twin Cities, Saint Paul
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, in Santa Barbara, California
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro Georgia
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Tracy M Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman
| | - Stephanie M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana–Champaign, Champaign
| | - Christopher J Thawley
- Department of Biological Sciences, University of Rhode Island, Kingston
- Department of Mathematics and Sciences, Neumann University, Aston, Pennsylvania
| | - Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Jessica E Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station
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6
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Scheele BC, Pasmans F, Skerratt LF, Berger L, Martel A, Beukema W, Acevedo AA, Burrowes PA, Carvalho T, Catenazzi A, De la Riva I, Fisher MC, Flechas SV, Foster CN, Frías-Álvarez P, Garner TWJ, Gratwicke B, Guayasamin JM, Hirschfeld M, Kolby JE, Kosch TA, La Marca E, Lindenmayer DB, Lips KR, Longo AV, Maneyro R, McDonald CA, Mendelson J, Palacios-Rodriguez P, Parra-Olea G, Richards-Zawacki CL, Rödel MO, Rovito SM, Soto-Azat C, Toledo LF, Voyles J, Weldon C, Whitfield SM, Wilkinson M, Zamudio KR, Canessa S. Response to Comment on "Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity". Science 2020; 367:367/6484/eaay2905. [PMID: 32193294 DOI: 10.1126/science.aay2905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/20/2020] [Indexed: 01/03/2023]
Abstract
Lambert et al question our retrospective and holistic epidemiological assessment of the role of chytridiomycosis in amphibian declines. Their alternative assessment is narrow and provides an incomplete evaluation of evidence. Adopting this approach limits understanding of infectious disease impacts and hampers conservation efforts. We reaffirm that our study provides unambiguous evidence that chytridiomycosis has affected at least 501 amphibian species.
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Affiliation(s)
- Ben C Scheele
- Fenner School of Environment and Society, Australian National University, Canberra, ACT 2601, Australia. .,National Environmental Science Programme, Threatened Species Recovery Hub, Canberra, ACT 2601, Australia.,One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia
| | - Frank Pasmans
- Wildlife Health Ghent, Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Lee F Skerratt
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia
| | - Lee Berger
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia
| | - An Martel
- Wildlife Health Ghent, Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Wouter Beukema
- Wildlife Health Ghent, Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Aldemar A Acevedo
- Programa de Doctorado en Ciencias Biológicas, Laboratorio de Biología Evolutiva, Pontificia Universidad Católica de Chile, Santiago, Chile.,Grupo de Investigación en Ecología y Biogeografía, Universidad de Pamplona, Barrio El Buque, Pamplona, Colombia
| | | | - Tamilie Carvalho
- Laboratório de História Natural de Anfíbios Brasileiros, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | | | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Sandra V Flechas
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Sede Venado de Oro, Bogotá, Colombia
| | - Claire N Foster
- Fenner School of Environment and Society, Australian National University, Canberra, ACT 2601, Australia
| | - Patricia Frías-Álvarez
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society London, Regents Park, London NW1 4RY, UK.,Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Brian Gratwicke
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | - Juan M Guayasamin
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Investigaciones Biológicas y Ambientales BIOSFERA, Laboratorio de Biología Evolutiva, Campus Cumbayá, Quito, Ecuador.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Ingeniería en Biodiversidad y Cambio Climático, Facultad de Medio Ambiente, Universidad Tecnológica Indoamérica, Calle Machala y Sabanilla, Quito, Ecuador.,Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mareike Hirschfeld
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Jonathan E Kolby
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia.,Honduras Amphibian Rescue and Conservation Center, Lancetilla Botanical Garden and Research Center, Tela, Honduras.,The Conservation Agency, Jamestown, RI 02835, USA
| | - Tiffany A Kosch
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, VIC 3030, Australia.,AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North 4442, New Zealand
| | - Enrique La Marca
- School of Geography, Faculty of Forestry Engineering and Environmental Sciences, University of Los Andes, Merida, Venezuela
| | - David B Lindenmayer
- Fenner School of Environment and Society, Australian National University, Canberra, ACT 2601, Australia.,National Environmental Science Programme, Threatened Species Recovery Hub, Canberra, ACT 2601, Australia
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Ana V Longo
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Raúl Maneyro
- Laboratorio de Sistemática e Historia Natural de Vertebrados, Facultad de Ciencias, Universidad de la República, CP 11400 Montevideo, Uruguay
| | - Cait A McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joseph Mendelson
- Zoo Atlanta, Atlanta, GA 30315, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Gabriela Parra-Olea
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | | | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Sean M Rovito
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato CP36824, México
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370251, Chile
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jamie Voyles
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Steven M Whitfield
- Conservation and Research Department, Zoo Miami, Miami, FL 33177, USA.,School of Earth, Environment, and Society, Florida International University, Miami, FL 33199, USA
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Stefano Canessa
- Wildlife Health Ghent, Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
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Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, Irestedt M, Lundin K, Larsson E, Matos-Maraví P, Müller J, von Proschwitz T, Roderick GK, Schliep A, Wahlberg N, Wiedenhoeft J, Källersjö M. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 2020; 8:e8225. [PMID: 32025365 PMCID: PMC6993751 DOI: 10.7717/peerj.8225] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
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Affiliation(s)
- Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Nuno Ferrand
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Magnus Gelang
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Rosemary G Gillespie
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Kennet Lundin
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Johannes Müller
- Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Ted von Proschwitz
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - George K Roderick
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander Schliep
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | | | - John Wiedenhoeft
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | - Mari Källersjö
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Botanical Garden, Göteborg, Sweden
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8
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Hackett RA, Belitz MW, Gilbert EE, Monfils AK. A data management workflow of biodiversity data from the field to data users. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11310. [PMID: 31890356 PMCID: PMC6923704 DOI: 10.1002/aps3.11310] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Heterogeneity of biodiversity data from the collections, research, and management communities presents challenges for data findability, accessibility, interoperability, and reusability. Workflows designed with data collection, standards, dissemination, and reuse in mind will generate better information across geopolitical, administrative, and institutional boundaries. Here, we present our data workflow as a case study of how we collected, shared, and used data from multiple sources. METHODS In 2012, we initiated the collection of biodiversity data relating to Michigan prairie fens, including data on plant communities and the federally endangered Poweshiek skipperling (Oarisma poweshiek). RESULTS Over 23,000 occurrence records were compiled in a database following Darwin Core standards. The records were linked with media and biological, chemical, and geometric measurements. We published the data as Global Biodiversity Information Facility data sets and in Symbiota SEINet portals. DISCUSSION We highlight data collection techniques that optimized transcription time, including the use of predetermined and controlled vocabulary, Darwin Core terms, and data dictionaries. The validity and longevity of our data were supported by voucher specimens, metadata with measurement records, and published manuscripts detailing methods and data sets. Key to our data dissemination was cooperation among partners and the utilization of dynamic tools. To increase data interoperability, we need flexible and customizable data collection templates, coding, and enhanced communication among communities using biodiversity data.
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Affiliation(s)
- Rachel A. Hackett
- Department of BiologyInstitute for Great Lakes ResearchCentral Michigan UniversityBioscience Building 2100, 1455 Calumet CourtMount PleasantMichigan48859USA
- Michigan Natural Features InventoryMichigan State University ExtensionP.O. Box 13036LansingMichigan48901‐3036USA
| | - Michael W. Belitz
- Department of BiologyInstitute for Great Lakes ResearchCentral Michigan UniversityBioscience Building 2100, 1455 Calumet CourtMount PleasantMichigan48859USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | | | - Anna K. Monfils
- Department of BiologyInstitute for Great Lakes ResearchCentral Michigan UniversityBioscience Building 2100, 1455 Calumet CourtMount PleasantMichigan48859USA
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9
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Conservation Genomics in a Changing Arctic. Trends Ecol Evol 2019; 35:149-162. [PMID: 31699414 DOI: 10.1016/j.tree.2019.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
Abstract
Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.
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10
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Heberling JM, Prather LA, Tonsor SJ. The Changing Uses of Herbarium Data in an Era of Global Change: An Overview Using Automated Content Analysis. Bioscience 2019. [DOI: 10.1093/biosci/biz094] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.
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Affiliation(s)
| | - L Alan Prather
- Department of Plant Biology at Michigan State University
| | - Stephen J Tonsor
- Director of Science & Research, Carnegie Museum of Natural History
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11
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Galbreath KE, Hoberg EP, Cook JA, Armién B, Bell KC, Campbell ML, Dunnum JL, Dursahinhan AT, Eckerlin RP, Gardner SL, Greiman SE, Henttonen H, Jiménez FA, Koehler AVA, Nyamsuren B, Tkach VV, Torres-Pérez F, Tsvetkova A, Hope AG. Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites. J Mammal 2019; 100:382-393. [PMID: 31043762 PMCID: PMC6479512 DOI: 10.1093/jmammal/gyz048] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.
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Affiliation(s)
- Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Eric P Hoberg
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Joseph A Cook
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Blas Armién
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Kayce C Bell
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mariel L Campbell
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Jonathan L Dunnum
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Altangerel T Dursahinhan
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Ralph P Eckerlin
- Mathematics, Science and Engineering Division, Northern Virginia Community College, Annandale, VA, USA
| | - Scott L Gardner
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Stephen E Greiman
- Biology Department, Georgia Southern University, Statesboro, GA, USA
| | | | - F Agustín Jiménez
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Anson V A Koehler
- Department of Veterinary Biosciences, The University of Melbourne, Cnr Flemington Road and Park Drive, Parkville, Victoria, Australia
| | | | - Vasyl V Tkach
- Biology Department, University of North Dakota, Grand Forks, ND, USA
| | - Fernando Torres-Pérez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Albina Tsvetkova
- Institute of Ecology and Evolution A.N. Severtsov RAS, Saratov Branch, Saratov, Russia
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS, USA
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12
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Douglass K, Walz J, Quintana Morales E, Marcus R, Myers G, Pollini J. Historical perspectives on contemporary human-environment dynamics in southeast Africa. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:260-274. [PMID: 30411404 DOI: 10.1111/cobi.13244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/25/2018] [Accepted: 11/05/2018] [Indexed: 05/13/2023]
Abstract
The human communities and ecosystems of island and coastal southeast Africa face significant and linked ecological threats. Socioecological conditions of concern to communities, governments, nongovernmental organizations, and researchers include declining agricultural productivity, deforestation, introductions of non-native flora and fauna, coastal erosion and sedimentation, damage to marine environments, illegal fishing, overfishing, waste pollution, salinization of freshwater supplies, and rising energy demands, among others. Human-environment challenges are connected to longer, often ignored, histories of social and ecological dynamics in the region. We argue that these challenges are more effectively understood and addressed within a longer-term historical ecology framework. We reviewed cases from Madagascar, coastal Kenya, and the Zanzibar Archipelago of fisheries, deforestation, and management of human waste to encourage increased engagement among historical ecologists, conservation scientists, and policy makers. These case studies demonstrate that by widening the types and time depths of data sets we used to investigate and address current socioecological challenges, our interpretations of their causes and strategies for their mitigation varied significantly.
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Affiliation(s)
- Kristina Douglass
- Department of Anthropology and Institutes for Energy and the Environment, The Pennsylvania State University, 321 Carpenter Building, University Park, PA, 16802, U.S.A
| | - Jonathan Walz
- SIT-Graduate Institute, 1 Kipling Road, Brattleboro, VT, 05301, U.S.A
| | - Eréndira Quintana Morales
- Department of Anthropology, Rice University, MS-20, 6100 Main Street, P.O. Box 1892, Houston, TX, 77251, U.S.A
| | - Richard Marcus
- The Global Studies Institute, College of Liberal Arts, California State University Long Beach, 1250 Bellflower Boulevard, F01, MS 1802, Long Beach, CA, 90840, U.S.A
| | - Garth Myers
- Urban International Studies, Trinity College, 70 Vernon Street, Hartford, CT, 06106, U.S.A
| | - Jacques Pollini
- The Institutional Canopy of Conservation (I-CAN): Governance & Environmentality, Department of Anthropology, McGill University, 845 Sherbrooke Street W., Montreal, QC, H3A 0G4, Canada
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Young MK, Smith RJ, Pilgrim KL, Fairchild MP, Schwartz MK. Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae). Ecol Evol 2019; 9:1364-1377. [PMID: 30805166 PMCID: PMC6374720 DOI: 10.1002/ece3.4852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/02/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Abstract
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological differences between certain life stages or sexes, and has added importance when taxa are a focus of conservation efforts. Here, we examine the taxonomic status of Arsapnia arapahoe, a winter stonefly in the family Capniidae that is a species of conservation concern because of its limited abundance and restricted range in northern Colorado, USA. Phylogenetic analyses of sequences of mitochondrial and nuclear genes of this and other capniid stoneflies from this region and elsewhere in western North America indicated extensive haplotype sharing, limited genetic differences, and a lack of reciprocal monophyly between A. arapahoe and the sympatric A. decepta, despite distinctive and consistent morphological differences in the sexual apparatus of males of both species. Analyses of autosomal and sex-linked single nucleotide polymorphisms detected using genotyping by sequencing indicated that all individuals of A. arapahoe consisted of F1 hybrids between female A. decepta and males of another sympatric stonefly, Capnia gracilaria. Rather than constitute a self-sustaining evolutionary lineage, A. arapahoe appears to represent the product of nonintrogressive hybridization in the limited area of syntopy between two widely distributed taxa. This offers a cautionary tale for taxonomists and conservation biologists working on the less-studied components of the global fauna.
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Affiliation(s)
- Michael K. Young
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Rebecca J. Smith
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Kristine L. Pilgrim
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | | | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
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Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen RS, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B. Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. RESEARCH IDEAS AND OUTCOMES 2018. [DOI: 10.3897/rio.4.e32449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.
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15
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Dunnum JL, McLean BS, Dowler RC. Mammal collections of the Western Hemisphere: a survey and directory of collections. J Mammal 2018; 99:1307-1322. [PMID: 30538340 PMCID: PMC6283736 DOI: 10.1093/jmammal/gyy151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/07/2018] [Indexed: 01/13/2023] Open
Abstract
As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Over the past decade, 43 collections have been lost or transferred and 38 new or unsurveyed collections were added. Growth in number of total specimens, expansion of genomic resource collections, and substantial gains in digitization and web accessibility were documented, as well as slight shifts in proportional representation of taxonomic groups owing to increasingly balanced geographic representation of collections relative to previous surveys. While we find the overall health of Western Hemisphere collections to be adequate in some areas, gaps in spatial and temporal coverage and clear threats to long-term growth and vitality of these resources have also been identified. Major expansion of the collective mammal collection resource along with a recommitment to appropriate levels of funding will be required to meet the challenges ahead for mammalogists and other users, and to ensure samples are broad and varied enough that unanticipated future needs can be powerfully addressed.
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Affiliation(s)
- Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Bryan S McLean
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Robert C Dowler
- Department of Biology, Angelo State University, San Angelo, TX, USA
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Schmitt CJ, Cook JA, Zamudio KR, Edwards SV. Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170387. [PMID: 30455205 PMCID: PMC6282080 DOI: 10.1098/rstb.2017.0387] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 11/12/2022] Open
Abstract
Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- C Jonathan Schmitt
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joseph A Cook
- Museum of Southwestern Biology & Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kelly R Zamudio
- Museum of Vertebrates and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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17
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Randall JM, Mceachern K, Knapp J, Power P, Junak S, Gill K, Knapp D, Guilliams M. Informing Our Successors: What Botanical Information for Santa Cruz Island will Researchers and Conservation Managers in the Century Ahead Need the Most? WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John M. Randall
- The Nature Conservancy, California Chapter, 201 Mission Street, San Francisco, CA 94105
| | - Kathryn Mceachern
- U.S. Geological Survey, WERC, Channel Islands Field Station, 1901 Spinnaker Drive, Ventura, CA 93001
| | - John Knapp
- The Nature Conservancy, California Chapter, 201 Mission Street, San Francisco, CA 94105
| | - Paula Power
- National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001
| | - Steve Junak
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Kristina Gill
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Denise Knapp
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
| | - Matt Guilliams
- Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, CA 93105
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18
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Heberling JM, Isaac BL. iNaturalist as a tool to expand the research value of museum specimens. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01193. [PMID: 30473939 PMCID: PMC6240452 DOI: 10.1002/aps3.1193] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/20/2018] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY Innovative approaches to specimen collection and curation are needed to maximize the utility of natural history collections in a new era of data use. Associated data, such as digital images from the field, are routinely collected with recent herbarium specimens. However, these data often remain inaccessible and are rarely curated alongside the associated physical specimens, which limits future data use. METHODS AND RESULTS We leveraged the widely used citizen science platform, iNaturalist, to permanently associate field-collected data to herbarium specimens, including information not well preserved in traditional specimens. This protocol improves the efficiency and accuracy of all steps from the collecting event to specimen curation and enhances the potential uses of specimens. CONCLUSIONS iNaturalist provides a standardized and cost-efficient enhancement to specimen collection and curation that can be easily adapted for specific research goals or other collection types beyond herbaria.
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Affiliation(s)
- J. Mason Heberling
- Section of BotanyCarnegie Museum of Natural History4400 Forbes AvenuePittsburghPennsylvania15213USA
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee37996USA
| | - Bonnie L. Isaac
- Section of BotanyCarnegie Museum of Natural History4400 Forbes AvenuePittsburghPennsylvania15213USA
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19
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Morrison SA, Sillett TS, Funk WC, Ghalambor CK, Rick TC. California Island Rediscovery: Building an Archive to Improve Conservation Today and Equip the Historical Ecologist of Tomorrow. WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Scott A. Morrison
- The Nature Conservancy, 201 Mission St., 4th Floor, San Francisco, CA 94105
| | - T. Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013
| | - W. Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Cameron K. Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Torben C. Rick
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013
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20
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Gleason MG, Caselle JE, Caldow C, Galipeau R, Heady W, Laverty C, Little A, Mazurkiewicz D, O'Byrne E, Rosen D, Whitaker S. Horizon Scanning: Survey and Research Priorities for Coastal and Marine Systems of the Northern Channel Islands, California. WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | | | - Chris Caldow
- Channel Islands National Marine Sanctuary, University of California, Santa Barbara, Ocean Science Education Building 514, MC 6155, Santa Barbara, CA 93106-6155
| | - Russell Galipeau
- Channel Islands National Park, 1901 Spinnaker Dr., Ventura, CA 93001
| | - Walter Heady
- The Nature Conservancy, 201 Mission St., San Francisco, CA
| | - Corinne Laverty
- Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007
| | - Annie Little
- United States Fish and Wildlife Service, 1901 Spinnaker Dr., Ventura, CA 93001
| | | | - Eamon O'Byrne
- The Nature Conservancy, 201 Mission St., San Francisco, CA
| | - Dirk Rosen
- Marine Applied Research and Exploration, 1230 Brickyard Cove Rd. #101, Richmond, CA 94801
| | - Stephen Whitaker
- Channel Islands National Park, 1901 Spinnaker Dr., Ventura, CA 93001
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21
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Boser CL, Sillett TS, Collins PW, Faulkner KR, Funk WC, Ghalambor CK, Laughrin L, Pauly GB, Robertson JM, Shea R, Vickers W. Equipping Tomorrow's Historical Ecologist: Priorities for Documenting Conditions of the Terrestrial Fauna of Santa Cruz Island, California. WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - T. Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20013
| | - Paul W. Collins
- Santa Barbara Museum of Natural History, Santa Barbara, CA 93105
| | | | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Cameron K. Ghalambor
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Lyndal Laughrin
- University of California Natural Reserve System, UCSB, Santa Barbara, CA 93106
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007
| | | | - Robyn Shea
- California State University Channel Islands, Camarillo, CA 93012
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22
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Malaney JL, Cook JA. A perfect storm for mammalogy: declining sample availability in a period of rapid environmental degradation. J Mammal 2018. [DOI: 10.1093/jmammal/gyy082] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jason L Malaney
- Department of Biology and David Snyder Museum of Zoology, Austin Peay State University, Clarksville, TN, USA
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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23
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James SA, Soltis PS, Belbin L, Chapman AD, Nelson G, Paul DL, Collins M. Herbarium data: Global biodiversity and societal botanical needs for novel research. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1024. [PMID: 29732255 PMCID: PMC5851569 DOI: 10.1002/aps3.1024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/30/2017] [Indexed: 05/11/2023]
Abstract
Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.
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Affiliation(s)
- Shelley A. James
- National Herbarium of New South WalesRoyal Botanic Gardens and Domain TrustMrs Macquaries RoadSydneyNew South Wales2000Australia
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Lee Belbin
- Atlas of Living AustraliaCSIROClunies Ross StreetActonAustralia Capital Territory2601Australia
| | - Arthur D. Chapman
- Australian Biodiversity Information ServicesBallanVictoria3342Australia
| | - Gil Nelson
- iDigBioFlorida State UniversityTallahasseeFlorida32306USA
| | | | - Matthew Collins
- Advanced Computing and Information SystemsUniversity of FloridaGainesvilleFlorida32611USA
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