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Wu R, Zou Y, Liao S, Shi K, Nan X, Yan H, Luo J, Xiang Z, Bao Z. Shall we promote natural history collection today?-Answered by reviewing Ernest Henry Wilson's plant collection process in China. Sci Total Environ 2024; 915:170179. [PMID: 38246391 DOI: 10.1016/j.scitotenv.2024.170179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Plant diversity exploration needs to be accelerated because many species will go extinct before their discovery and description, and many species-rich regions remain poorly studied. However, most contemporary plant collections prefer to focus on a specific group, which hinders the exploration and conservation of plant diversity. Therefore, we need an alternative approach to the dilemma at hand. The comprehensive Natural History Collection (NHC), which existed throughout the pinnacle of biodiversity exploration in the 20th century could be considered. We explore Ernest Henry Wilson's (one of the most successful naturalists in the 20th) plant collections in China as a case to illustrate the advantages of NHC and discuss whether NHC deserves to be promoted again today. From multiple sources, we gathered 19,218 available specimen records of 11,884 collecting numbers assigned and analyzed the collected species, the collection's nature, and restored four routes of his explorations. Results reveal that Wilson's specimens were collected from 28 prefecture-level cities and 38 county-level regions of 7 provinces or municipalities, they belong to 200 families, 1046 genera, 3794 species, and 342 infraspecific taxa, approximately 41 %, 22 %, 10 %, 5 % of Chinese plant families, genera, species, and infraspecific taxa respectively. The Wilson case study shows that NHC is particularly effective in emphasizing species discovery and conservation, recording ecological information, understanding a region's flora, and developing landscape applications. Therefore, we strongly advocate for the expansion of natural history collections in species-rich regions. Furthermore, we recommend the employment of specialized collectors, the enlistment of international cooperation, and the standardization of guidelines for future NHCs.
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Affiliation(s)
- Renwu Wu
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yongxi Zou
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuai Liao
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ke Shi
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinge Nan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hai Yan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jifan Luo
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhoubing Xiang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiyi Bao
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
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Santos BS, Marques MP, Ceríaco LMP. Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation. AN ACAD BRAS CIENC 2024; 96:e20230622. [PMID: 38451598 DOI: 10.1590/0001-3765202420230622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/27/2023] [Indexed: 03/08/2024] Open
Abstract
Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.
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Affiliation(s)
- Bruna S Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
| | - Luis M P Ceríaco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
- Universidade Federal do Rio de Janeiro, Departamento de Vertebrados, Museu Nacional, Quinta da Boavista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
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Patten NN, Gaynor ML, Soltis DE, Soltis PS. Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data. Appl Plant Sci 2024; 12:e11575. [PMID: 38638614 PMCID: PMC11022233 DOI: 10.1002/aps3.11575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 04/20/2024]
Abstract
Premise Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs). Methods and Results The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps. Conclusions Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.
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Affiliation(s)
- Natalie N. Patten
- Department of MathematicsUniversity of FloridaGainesville32611FloridaUSA
- Present address:
Department of MathematicsThe Ohio State UniversityColumbus43210OhioUSA
| | - Michelle L. Gaynor
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
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Astudillo-Clavijo V, Mankis T, López-Fernández H. Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data. Am Nat 2024; 203:305-322. [PMID: 38358812 DOI: 10.1086/728422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.
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Delsett LL. Collecting whales: processes and biases in Nordic museum collections. PeerJ 2024; 12:e16794. [PMID: 38288462 PMCID: PMC10823993 DOI: 10.7717/peerj.16794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/24/2023] [Indexed: 02/01/2024] Open
Abstract
Whales are unique museum objects that have entered collections in many ways and for different reasons. This work studies three Nordic natural history museum collections in Norway and Denmark with more than 2,500 whale specimens in total, and gathers the available biological and collection data on the specimens, which include skeletal elements, foetuses and organs preserved in ethanol or formalin, and a few dry-preserved organs. It finds that influx of specimens, which were mainly locally common species that were hunted, to the collections, mainly happened in the latest 1800s and earliest 1900s, fuelled by research trends, nation building, local whaling, and colonial mechanisms. Norway was a major whaling nation, but the largest hunt for whales in the Southern Ocean in the mid-1900s is not reflected in the Norwegian museum collections, probably because of the commercial focus of the whaling industry and logistical challenges, combined with limited research interest in zoological specimens at that time. The results demonstrate that it is important to understand these processes and the resulting biases for future research, outreach, and conservation.
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Affiliation(s)
- Lene Liebe Delsett
- Department of Archaeology, Conservation and History, University of Oslo, Oslo, Norway
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6
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Rocha-Martínez N, López-Ordaz R, Rendón-Franco E, Muñoz-García CI. 3D wildlife skull models for wildlife veterinary training. Anat Sci Educ 2023; 16:1073-1078. [PMID: 37477190 DOI: 10.1002/ase.2321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/15/2023] [Accepted: 07/08/2023] [Indexed: 07/22/2023]
Abstract
Wildlife veterinarians are necessary for zoonotic diseases and species loss management, and there is a rising interest to enroll at veterinary schools with the wish to work in zoo and wildlife medicine. However, teaching wildlife is challenging due to the difficulty faced by universities to work with wild animal specimens. The aim of the present was to evaluate the understanding efficiency of some anatomical and behavioral aspects using 3D printed models of four wildlife species skulls, the kinkaju (Potos flavus), the white-nosed coati (Nasua narica), the northern anteater (Tamandua mexicana), and the nine-banded armadillo (Dasypus novemcinctus). This study was performed on 85 third-year veterinary students, divided into an experimental and a control group, who used and not used 3D printed skulls, respectively. Results show that the experimental group shows higher scores, in three of the four variables evaluated, than the control group. Then, 3D wildlife printed skulls constitute a promising teaching tool for veterinary students. In fact, it may be as good as real skulls, since new 3D printers can print on high endurance and firmness stock with high accuracy at reduced costs. In this context, it is important to encourage its use for the training of new generations and keep professionals up to date.
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Affiliation(s)
- Nadia Rocha-Martínez
- Maestría en Ecología Aplicada, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Reyes López-Ordaz
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Emilio Rendón-Franco
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Claudia I Muñoz-García
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
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Nanglu K, de Carle D, Cullen TM, Anderson EB, Arif S, Castañeda RA, Chang LM, Iwama RE, Fellin E, Manglicmot RC, Massey MD, Astudillo‐Clavijo V. The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education. Ecol Evol 2023; 13:e10621. [PMID: 37877102 PMCID: PMC10591213 DOI: 10.1002/ece3.10621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - Danielle de Carle
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Invertebrate ZoologyRoyal Ontario MuseumTorontoOntarioCanada
| | - Thomas M. Cullen
- Department of GeosciencesAuburn UniversityAuburnAlabamaUSA
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Erika B. Anderson
- The HunterianUniversity of GlasgowGlasgowUK
- Department of Earth and SpaceRoyal Ontario MuseumTorontoOntarioCanada
| | - Suchinta Arif
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Rowshyra A. Castañeda
- Ecosystems and Ocean SciencesPacific Region, Fisheries and Oceans CanadaSidneyBritish ColumbiaCanada
| | | | - Rafael Eiji Iwama
- Departamento de Genética e Biologia Evolutiva, Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Erica Fellin
- Department of BiologyMcGill UniversityMontrealQuebecCanada
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Speck O, Speck T. Biomimetics in Botanical Gardens-Educational Trails and Guided Tours. Biomimetics (Basel) 2023; 8:303. [PMID: 37504191 PMCID: PMC10807481 DOI: 10.3390/biomimetics8030303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
The first botanical gardens in Europe were established for the study of medicinal, poisonous, and herbal plants by students of medicine or pharmacy at universities. As the natural sciences became increasingly important in the 19th Century, botanical gardens additionally took on the role of public educational institutions. Since then, learning from living nature with the aim of developing technical applications, namely biomimetics, has played a special role in botanical gardens. Sir Joseph Paxton designed rainwater drainage channels in the roof of the Crystal Palace for the London World's Fair in 1881, having been inspired by the South American giant water lily (Victoria amazonica). The development of the Lotus-Effect® at the Botanical Garden Bonn was inspired by the self-cleaning leaf surfaces of the sacred lotus (Nelumbo nucifera). At the Botanic Garden Freiburg, a self-sealing foam coating for pneumatic systems was developed based on the self-sealing of the liana stems of the genus Aristolochia. Currently, botanical gardens are both research institutions and places of lifelong learning. Numerous botanical gardens provide biomimetics trails with information panels at each station for self-study and guided biomimetics tours with simple experiments to demonstrate the functional principles transferred from the biological model to the technical application. We present eight information panels suitable for setting up education about biomimetics and simple experiments to support guided garden tours about biomimetics.
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Affiliation(s)
- Olga Speck
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany;
- Plant Biomechanics Group@Botanic Garden Freiburg, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Thomas Speck
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany;
- Plant Biomechanics Group@Botanic Garden Freiburg, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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10
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Park DS, Feng X, Akiyama S, Ardiyani M, Avendaño N, Barina Z, Bärtschi B, Belgrano M, Betancur J, Bijmoer R, Bogaerts A, Cano A, Danihelka J, Garg A, Giblin DE, Gogoi R, Guggisberg A, Hyvärinen M, James SA, Sebola RJ, Katagiri T, Kennedy JA, Komil TS, Lee B, Lee SML, Magri D, Marcucci R, Masinde S, Melnikov D, Mráz P, Mulenko W, Musili P, Mwachala G, Nelson BE, Niezgoda C, Novoa Sepúlveda C, Orli S, Paton A, Payette S, Perkins KD, Ponce MJ, Rainer H, Rasingam L, Rustiami H, Shiyan NM, Bjorå CS, Solomon J, Stauffer F, Sumadijaya A, Thiébaut M, Thiers BM, Tsubota H, Vaughan A, Virtanen R, Whitfeld TJS, Zhang D, Zuloaga FO, Davis CC. The colonial legacy of herbaria. Nat Hum Behav 2023:10.1038/s41562-023-01616-7. [PMID: 37308536 DOI: 10.1038/s41562-023-01616-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
Abstract
Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.
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Affiliation(s)
- Daniel S Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
| | - Xiao Feng
- Department of Geography, Florida State University, Tallahassee, FL, USA
| | - Shinobu Akiyama
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Marlina Ardiyani
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Neida Avendaño
- Instituto Experimental Jardin Botánico 'Dr. Tobías Lasser', Avenida Salvador Allende, Ciudad Universitaria, Caracas, Venezuela
- Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Blandine Bärtschi
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | - Roxali Bijmoer
- Botany Section, Naturalis Biodiversity Center, Leiden, the Netherlands
| | | | - Asunción Cano
- Herbario San Marcos, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jiří Danihelka
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Arti Garg
- Central Regional Centre, Botanical Survey of India, Allahabad, India
| | - David E Giblin
- University of Washington Herbarium, Burke Museum, Seattle, WA, USA
| | - Rajib Gogoi
- Sikkim Himalayan Regional Centre, Botanical Survey of India, Gangtok, India
| | | | - Marko Hyvärinen
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Shelley A James
- Department of Biodiversity, Conservation and Attractions, Western Australian Herbarium, Kensington, Western Australia, Australia
| | - Ramagwai J Sebola
- South African National Biodiversity Institute, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tomoyuki Katagiri
- Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi, Japan
- Hattori Botanical Laboratory, Nichinan, Japan
| | | | - Tojibaev Sh Komil
- Institute of Botany, Uzbekistan Academy of Sciences, Tashkent, Uzbekistan
| | | | - Serena M L Lee
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Donatella Magri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | | | - Siro Masinde
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Denis Melnikov
- Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Patrik Mráz
- Herbarium Collections & Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Wieslaw Mulenko
- Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Paul Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | | | - Burrell E Nelson
- Rocky Mountain Herbarium, University of Wyoming, Laramie, WY, USA
| | | | - Carla Novoa Sepúlveda
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München, München, Germany
| | - Sylvia Orli
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Serge Payette
- Herbier Louis-Marie, Université Laval, Québec City, Québec, Canada
| | - Kent D Perkins
- University of Florida Herbarium, Florida Museum, Gainesville, FL, USA
| | - Maria Jimena Ponce
- Instituto Multidisciplinario de Biología Vegetal (UNC-CONICET), Córdoba, Argentina
| | - Heimo Rainer
- Naturhistorisches Museum Wien, Vienna, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - L Rasingam
- Deccan Regional Centre, Botanical Survey of India, Hyderabad, India
| | - Himmah Rustiami
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Natalia M Shiyan
- National Herbarium of Ukraine, M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | | | - Fred Stauffer
- Conservatory and Botanic Gardens of Geneva, Geneva, Switzerland
| | - Alex Sumadijaya
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mélanie Thiébaut
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Hiromi Tsubota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Miyajima Natural Botanical Garden, Hiroshima University, Hiroshima, Japan
| | - Alison Vaughan
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Risto Virtanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- University of Oulu Botanical Museum, Oulu, Finland
| | | | - Dianxiang Zhang
- South China Botanical Garden Herbarium, Chinese Academy of Sciences, Guangzhou, China
| | | | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, USA.
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11
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Ilechukwu I, Das RR, Reimer JD. Review of microplastics in museum specimens: An under-utilized tool to better understand the Plasticene. Mar Pollut Bull 2023; 191:114922. [PMID: 37068343 DOI: 10.1016/j.marpolbul.2023.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
This study summarises the status of microplastic research in marine and freshwater specimens in natural museum collections around the world. Abundances, distributions, and types of microplastics in the archived collections are discussed. Museum collections can fill knowledge gaps on evolution of microplastic pollution before and during the Plasticene era. The specimens in these studies, ranging from plankton to vertebrates, were collected and archived between 1900 and 2019, and are dominated by specimens from marine ecosystems. All the specimens included in this review were preserved by freezing or in ethanol/formaldehyde except for specimens in one study that were preserved via cryomilling. Microfibers were the most common microplastics in the reviewed studies. We recommend more microplastic studies over a wider taxonomic range of species and across a longer span of years utilizing archival specimen collections around the world in order to establish reference points and develop temporal trends for microplastic pollution of the environment.
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Affiliation(s)
- Ifenna Ilechukwu
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan; Department of Industrial Chemistry, Madonna University, Elele Campus, Rivers State, Nigeria.
| | - Rocktim Ramen Das
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan; Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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12
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Daru BH, Rodriguez J. Mass production of unvouchered records fails to represent global biodiversity patterns. Nat Ecol Evol 2023:10.1038/s41559-023-02047-3. [PMID: 37127769 DOI: 10.1038/s41559-023-02047-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.
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Affiliation(s)
- Barnabas H Daru
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Jordan Rodriguez
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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13
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Ringelberg JJ, Koenen EJ, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF, Jordão LS, Morales M, Bailey CD, Nageswara-Rao M, Nicholls JA, Loiseau O, Pennington RT, Dexter KG, Zimmermann NE, Hughes CE. Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. Sci Adv 2023; 9:eade4954. [PMID: 36800419 PMCID: PMC10957106 DOI: 10.1126/sciadv.ade4954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Benjamin Sauter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Anahita Aebli
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Juliana G. Rando
- Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia
- School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Joseph T. Miller
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil
| | - Lucas S. B. Jordão
- Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA
| | - Madhugiri Nageswara-Rao
- United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA
| | - James A. Nicholls
- Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Kyle G. Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Niklaus E. Zimmermann
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
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14
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Wood CL, Leslie KL, Claar D, Mastick N, Preisser W, Vanhove MPM, Welicky R. How to use natural history collections to resurrect information on historical parasite abundances. J Helminthol 2023; 97:e6. [PMID: 36633512 DOI: 10.1017/S0022149X2200075X] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many of the most contentious questions that concern the ecology of helminths could be resolved with data on helminth abundance over the past few decades or centuries, but unfortunately these data are rare. A new sub-discipline - the historical ecology of parasitism - is resurrecting long-term data on the abundance of parasites, an advancement facilitated by the use of biological natural history collections. Because the world's museums hold billions of suitable specimens collected over more than a century, these potential parasitological datasets are broad in scope and finely resolved in taxonomic, temporal and spatial dimensions. Here, we set out best practices for the extraction of parasitological information from natural history collections, including how to conceive of a project, how to select specimens, how to engage curators and receive permission for proposed projects, standard operating protocols for dissections and how to manage data. Our hope is that other helminthologists will use this paper as a reference to expand their own research programmes along the dimension of time.
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15
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Speed JDM, Evankow AM, Petersen TK, Ranke PS, Nilsen NH, Turner G, Aagaard K, Bakken T, Davidsen JG, Dunshea G, Finstad AG, Hassel K, Husby M, Hårsaker K, Koksvik JI, Prestø T, Vange V. A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections. Ecol Evol 2022; 12:e9471. [PMID: 36340816 PMCID: PMC9627063 DOI: 10.1002/ece3.9471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/02/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
Climate change has dramatic impacts on ecological systems, affecting a range of ecological factors including phenology, species abundance, diversity, and distribution. The breadth of climate change impacts on ecological systems leads to the occurrence of fingerprints of climate change. However, climate fingerprints are usually identified across broad geographical scales and are potentially influenced by publication biases. In this study, we used natural history collections spanning over 250 years, to quantify a range of ecological responses to climate change, including phenology, abundance, diversity, and distributions, across a range of taxa, including vertebrates, invertebrates, plants, and fungi, within a single region, Central Norway. We tested the hypotheses that ecological responses to climate change are apparent and coherent at a regional scale, that longer time series show stronger trends over time and in relation to temperature, and that ecological responses change in trajectory at the same time as shifts in temperature. We identified a clear regional coherence in climate signal, with decreasing abundances of limnic zooplankton (on average by 7691 individuals m-3 °C-1) and boreal forest breeding birds (on average by 1.94 territories km-2 °C-1), and earlier plant flowering phenology (on average 2 days °C-1) for every degree of temperature increase. In contrast, regional-scale species distributions and species diversity were largely stable. Surprisingly, the effect size of ecological response did not increase with study duration, and shifts in responses did not occur at the same time as shifts in temperature. This may be as the long-term studies include both periods of warming and temperature stability, and that ecological responses lag behind warming. Our findings demonstrate a regional climate fingerprint across a long timescale. We contend that natural history collections provide a unique window on a broad spectrum of ecological responses at timescales beyond most ecological monitoring programs. Natural history collections are thus an essential source for long-term ecological research.
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Affiliation(s)
- James D. M. Speed
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Ann M. Evankow
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Natural History MuseumUniversity of OsloOsloNorway
| | - Tanja K. Petersen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Peter S. Ranke
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Nellie H. Nilsen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Grace Turner
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Kaare Aagaard
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Torkild Bakken
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Jan G. Davidsen
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Glenn Dunshea
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Anders G. Finstad
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Kristian Hassel
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Magne Husby
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
- Section of ScienceNord UniversityLevangerNorway
| | - Karstein Hårsaker
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Jan Ivar Koksvik
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Tommy Prestø
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| | - Vibekke Vange
- Department of Natural HistoryNTNU University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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16
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Affiliation(s)
- Suzanne E. Pilaar Birch
- Department of Anthropology, Department of Geography, University of Georgia, Athens, GA 30602
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, K9L 0G2 ON, Canada
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17
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Andreone F, Boero F, Bologna MA, Carpaneto GM, Castiglia R, Gippoliti S, Massa B, Minelli A. Reconnecting research and natural history museums in Italy and the need of a national collection biorepository. Zookeys 2022; 1104:55-68. [PMID: 36761931 PMCID: PMC9848790 DOI: 10.3897/zookeys.1104.79823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
In Italy, differently from other countries, a national museum of natural history is not present. This absence is due, among other reasons, to its historical political fragmentation up to 1870, which led to the establishment of medium-sized museums, mostly managed by local administrations or universities. Moreover, a change of paradigm in biological research, at the beginning of the 20th century, contributed to privilege experimental studies in universities and facilitated the dismissal of descriptive and exploratory biology, which formed the basis of the taxonomic research carried out by natural history museums. Consequently, only a few museums have a provision of curatorial staff, space and material resources adequate to maintain their original mission of discovering the natural world, by conducting a regular research activity accompanied by field campaigns. The creation of a national research centre for the study of biodiversity, facilitating interconnections among the existing natural history museums could be a solution and is here supported, together with a centralised biorepository to host collections and vouchers, to the benefit of current and future taxonomic research and environmental conservation. Such an institution should find place and realisation within the recently proposed National Biodiversity Future Center (NBFC) planned within the National Plan of Recovery and Resilience (PNRR). Pending upon the creation of this new national centre, a network among the existing museums should coordinate their activities.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123 Torino, ItalyMuseo Regionale di Scienze NaturaliTorinoItaly
| | - Ferdinando Boero
- Università di Napoli Federico II, CNR-IAS, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, ItalyUniversità di Napoli Federico IINapoliItaly
| | - Marco A. Bologna
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Giuseppe M. Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università “La Sapienza” di Roma, Via A. Borelli, 50, I-00161 Roma, ItalyUniversità “La Sapienza” di RomaRomaItaly
| | - Spartaco Gippoliti
- Società Italiana per la Storia della Fauna “Giuseppe Altobello”, Viale Liegi, 48A, I-00198 Roma, ItalySocietà Italiana per la Storia della Fauna “Giuseppe Altobello”RomeItaly
| | - Bruno Massa
- Dipartimento di Scienze agrarie, alimentari e forestali, Università di Palermo, Viale Scienze, 13, I-90128 Palermo, ItalyUniversità di PalermoPalermoItaly
| | - Alessandro Minelli
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi, 58B, I-35131 Padova, ItalyUniversità di PadovaPadovaItaly
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18
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Affiliation(s)
- Marek L. Borowiec
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Plant and Wildlife Sciences Brigham Young University Provo UT USA
| | - Alexander McKeeken
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
| | | | - Alexander E. White
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Botany, National Museum of Natural History Smithsonian Institution Washington DC USA
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19
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Clewing C, Kehlmaier C, Stelbrink B, Albrecht C, Wilke T. Poor hDNA-Derived NGS Data May Provide Sufficient Phylogenetic Information of Potentially Extinct Taxa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Museum material is an important source of metadata for past and recent biological events. With current sequencing technologies, it is possible to obtain historical DNA (hDNA) from older material and/or endangered species to answer taxonomic, systematic, and biogeographical questions. However, hDNA from museum collections is often highly degraded, making it difficult to assess relationships at or above the species level. We therefore studied two probably extinct gastropod species of the genus Laevicaspia, which were collected ∼140 years ago in the Caspian Sea, to map “standard” mitochondrial and nuclear markers and assess both the sequencing depth and the proportion of ambiguous sites as an indicator for the phylogenetic quality of the NGS data. Our study resulted in the first phylogenetically informative mitochondrial and nuclear markers for L. caspia. Assessment of both sequencing depth (mean coverage) and proportion of ambiguous sites suggests that our assembled consensus sequences are reliable for this species. In contrast, no informative gastropod-specific DNA was obtained for L. conus, likely due to a high degree of tissue digestion and contamination with non-gastropod DNA. Nevertheless, our results show that hDNA may in principle yield high-quality sequences for species-level phylogenetic analyses, which underlines the importance of museum collections as valuable archives of the biological past.
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20
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Addison FI, Dally T, Duncan EJ, Rouse J, Evans WL, Hassall C, Neely RR. Simulation of the Radar Cross Section of a Noctuid Moth. Remote Sensing 2022; 14:1494. [DOI: 10.3390/rs14061494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Electromagnetic modelling may be used as a tool for understanding the radar cross section (RCS) of volant animals. Here, we examine this emerging method in detail and delve deeper into the specifics of the modelling process for a single noctuid moth, with the hope of illuminating the importance of different aspects of the process by varying the morphometric and compositional properties of the model. This was accomplished by creating a high-fidelity three-dimensional insect model by micro-CT scanning a gold-palladium-coated insect. Electromagnetic simulations of the insect model were conducted by applying different morphological and compositional configurations using the WiPL-D Pro 3D Electromagnetic Solver. The simulation results show that high-resolution modelling of insects has advantages compared to the simple ellipsoidal models used in previous studies. We find that the inclusion of wings and separating the composition of the body, wings, and legs and antennae have an impact on the resulting RCS of the specimen. Such modifications to the RCS are missed when a prolate spheroid model is used and should not be ignored in future studies. Finally, this methodology has been shown to be useful in exploring the changes in the RCS that result from variations in specimen size. As such, utilising this methodology further for more species will improve the ability to quantitatively interpret aeroecological observations of weather surveillance radars and special-purpose entomological radars.
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21
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Greeff M, Caspers M, Kalkman V, Willemse L, Sunderland B, Bánki O, Hogeweg L. Sharing taxonomic expertise between natural history collections using image recognition. RIO 2022. [DOI: 10.3897/rio.8.e79187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.
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de Lima Ferreira P, Batista R, Andermann T, Groppo M, Bacon CD, Antonelli A. Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses. Mol Phylogenet Evol 2022; 169:107432. [DOI: 10.1016/j.ympev.2022.107432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022]
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van Andel T, Vos RA, Michels E, Stefanaki A. Sixteenth-century tomatoes in Europe: who saw them, what they looked like, and where they came from. PeerJ 2022; 10:e12790. [PMID: 35111406 PMCID: PMC8772448 DOI: 10.7717/peerj.12790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Soon after the Spanish conquest of the Americas, the first tomatoes were presented as curiosities to the European elite and drew the attention of sixteenth-century Italian naturalists. Despite of their scientific interest in this New World crop, most Renaissance botanists did not specify where these 'golden apples' or 'pomi d'oro' came from. The debate on the first European tomatoes and their origin is often hindered by erroneous dating, botanical misidentifications and inaccessible historical sources. The discovery of a tomato specimen in the sixteenth-century 'En Tibi herbarium' kept at Leiden, the Netherlands, triggered research on its geographical provenance and morphological comparison to other tomato specimens and illustrations from the same time period. METHODS Recent digitization efforts greatly facilitate research on historic botanical sources. Here we provide an overview of the ten remaining sixteenth-century tomato specimens, early descriptions and 13 illustrations. Several were never published before, revealing what these tomatoes looked like, who saw them, and where they came from. We compare our historical findings with recent molecular research on the chloroplast and nuclear DNA of the 'En Tibi' specimen. RESULTS Our survey shows that the earliest tomatoes in Europe came in a much wider variety of colors, shapes and sizes than previously thought, with both simple and fasciated flowers, round and segmented fruits. Pietro Andrea Matthioli gave the first description of a tomato in 1544, and the oldest specimens were collected by Ulisse Aldrovandi and Francesco Petrollini in c. 1551, possibly from plants grown in the Pisa botanical garden by their teacher Luca Ghini. The oldest tomato illustrations were made in Germany and Switzerland in the early 1550s, but the Flemish Rembert Dodoens published the first image in 1553. The names of early tomatoes in contemporary manuscripts suggest both a Mexican and a Peruvian origin. The 'En Tibi' specimen was collected by Petrollini around 1558 and thus is not the oldest extant tomato. Recent molecular research on the ancient nuclear and chloroplast DNA of the En Tibi specimen clearly shows that it was a fully domesticated tomato, and genetically close to three Mexican landraces and two Peruvian specimens that probably also had a Mesoamerican origin. Molecular research on the other sixteenth-century tomato specimens may reveal other patterns of genetic similarity, past selection processes, and geographic origin. Clues on the 'historic' taste and pest resistance of the sixteenth-century tomatoes will be difficult to predict from their degraded DNA, but should be rather sought in those landraces in Central and South America that are genetically close to them. The indigenous farmers growing these traditional varieties should be supported to conserve these heirloom varieties in-situ.
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Affiliation(s)
- Tinde van Andel
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute for Biology, Leiden University, Leiden, the Netherlands
| | - Rutger A. Vos
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Ewout Michels
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute for Biology, Leiden University, Leiden, the Netherlands
| | - Anastasia Stefanaki
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Leiden, the Netherlands
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Brito RN, Souza RCM, Diotaitui L, Lima VS, Ferreira RA. Coleção de Vetores de Tripanosomatídeos (Fiocruz/COLVET) held at the institution Fiocruz Minas in Brazil: diversity of Triatominae (Hemiptera, Reduviidae) and relevance for research, education, and entomological surveillance. Zookeys 2021; 1074:17-42. [PMID: 34963751 PMCID: PMC8654810 DOI: 10.3897/zookeys.1074.69700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/13/2021] [Indexed: 11/12/2022] Open
Abstract
The Coleção de Vetores de Tripanosomatídeos (Fiocruz/COLVET), Minas Gerais, Brazil, stands out as one of the most important collections of blood-sucking triatomines, the vectors of Trypanosomacruzi that causes Chagas disease. The aim is to describe the collection and the services it provides to support scientific research, educational activities, and entomological surveillance between 2013-2019.The data associated with the specimens held in Fiocruz/COLVET is available from the Sistema de Informação sobre a Biodiversidade Brasileira (SiBBr). These specimen metadata were analyzed and either tabulated or plotted on graph and maps. The records of services provided by the collection between 2013-2019 were also categorized and analyzed. There are 12,568 triatomine specimens deposited in the collection that belong to 77 species and 11 genera, from 15 American countries. Of the ~ 65 species of triatomines found in Brazil, 38 (57.6%) are present in the collection, including specimens from all biomes and all but three Brazilian states. The occurrence of Triatomacostalimai, Triatomalenti, Rhodniusnasutus, and Panstrongyluslenti apparently collected beyond their known distribution ranges are reported and discussed. The collection provided 168 services, supporting educational activities (41.7%), scientific research (35.7%), and regional/national entomological surveillance of triatomines (22.6%). Between the years 2014 and 2020, the number of biological specimens deposited in the Fiocruz/COLVET repository increased from 4,778 to 12,568 triatomine specimens. In addition to its great value to biodiversity conservation, the collection is of great importance because of its support of research and educational activities, and contributions to entomological surveillance, and, therefore, to public health.
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Affiliation(s)
- Raíssa N. Brito
- Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz – IRR/Fiocruz Minas, Belo Horizonte, Minas Gerais, BrazilInstituto René RachouBelo HorizonteBrazil
- Programa de Pós-Graduação em Medicina Tropical, Núcleo de Medicina Tropical, Universidade de Brasília (UnB), Brasília, Distrito Federal, BrazilUniversidade de BrasíliaBrasíliaBrazil
| | - Rita C. M. Souza
- Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz – IRR/Fiocruz Minas, Belo Horizonte, Minas Gerais, BrazilInstituto René RachouBelo HorizonteBrazil
| | - Liléia Diotaitui
- Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz – IRR/Fiocruz Minas, Belo Horizonte, Minas Gerais, BrazilInstituto René RachouBelo HorizonteBrazil
| | - Valeria S. Lima
- Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz – IRR/Fiocruz Minas, Belo Horizonte, Minas Gerais, BrazilInstituto René RachouBelo HorizonteBrazil
| | - Raquel A. Ferreira
- Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz – IRR/Fiocruz Minas, Belo Horizonte, Minas Gerais, BrazilInstituto René RachouBelo HorizonteBrazil
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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Will K, Mendez PK. Mating marks on museum specimens reveal breeding patterns in species of Pterostichus Bonelli (Carabidae, Pterostichini). Biodivers Data J 2021; 9:e70897. [PMID: 34690517 PMCID: PMC8486734 DOI: 10.3897/bdj.9.e70897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 11/12/2022] Open
Abstract
We found distinct and consistently placed, species- and sex-specific abrasions of the cuticle on museum specimens of 14 species of the Pterostichus Bonelli, 1810 (Carabidae, Pterostichini) subgenusHypherpes Chaudoir, 1838. We deduced that these marks are generated during mating and, therefore, can be used to distinguish between preserved specimens of beetles that had previously mated at the time of capture and those that had not mated. In addition to describing and detailing the occurrence of the marks and providing evidence that they are the result of mating, we demonstrate their utility for inferring life history using a museum voucher collection. By scoring these indications of mating from pinned specimens, we describe life cycle patterns in two similar, relatively closely related and sympatric species of the subgenus Hypherpes, P.vicinus Mannerheim, 1843 and P.californicus (Dejean, 1828). Both were sampled during a pitfall trap study in Contra Costa, California, USA from 2014–2019 and deposited in the Essig Museum of Entomology, UC Berkeley. Both species had very low adult activity through the drought and end of drought period prior to the spring of 2017 and are significantly more abundant in the post-drought period. Based on mating marks, both species responded to accumulated precipitation ending the drought by the emergence of an active, mostly unmated cohort of adults. The spring activity peak, following the end of the drought, was dominated by unmarked and presumably unmated beetles, but samples from subsequent springs included a nearly equal mix of beetles showing mating marks and apparently unmated beetles. The beetle activity appears to correspond more with the accumulated rainfall of the preceding rainy season than with the rains of the sample year. Beetles sampled in autumn and winter (rainy season) predominantly show mating marks. The occurrence throughout the year of beetles that are marked as having mated is consistent with iteroparous beetles with a lifespan of more than one year and also consistent with dynamic phenotypic polyvariance in which the adult activity period is synchronised by adjusting development time. The dominant pattern fits with a life cycle that is typically annual univoltine, or possibly biennial semivoltine in dry years, rainy season breeding (autumn-winter) iteroparous, with adult summer aestivation and possibly facultative larval hibernation. However, unmarked and so apparently unmated individuals and teneral adults were captured during peak activity periods regardless of the season, suggesting that either the beetles diapause as teneral adults that then complete development and become active at various points during the year and/or there are multiple periods of breeding and oviposition each year in at least some portion of the population.
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Affiliation(s)
- Kipling Will
- University of California, Berkeley, ESPM Dept., Berkeley, CA, United States of America University of California, Berkeley, ESPM Dept. Berkeley, CA United States of America.,Essig Museum of Entomology, University of California, Berkeley, Berkeley, CA, United States of America Essig Museum of Entomology, University of California, Berkeley Berkeley, CA United States of America
| | - Patina K Mendez
- University of California, Berkeley, ESPM Dept., Berkeley, CA, United States of America University of California, Berkeley, ESPM Dept. Berkeley, CA United States of America.,Essig Museum of Entomology, University of California, Berkeley, Berkeley, CA, United States of America Essig Museum of Entomology, University of California, Berkeley Berkeley, CA United States of America
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Callahan S, Crowe‐Riddell JM, Nagesan RS, Gray JA, Davis Rabosky AR. A guide for optimal iodine staining and high-throughput diceCT scanning in snakes. Ecol Evol 2021; 11:11587-11603. [PMID: 34522326 PMCID: PMC8427571 DOI: 10.1002/ece3.7467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 01/10/2023] Open
Abstract
Diffusible iodine-based contrast-enhanced computed tomography (diceCT) visualizes soft tissue from micro-CT (µCT) scans of specimens to uncover internal features and natural history information without incurring physical damage via dissection. Unlike hard-tissue imaging, taxonomic sampling within diceCT datasets is currently limited. To initiate best practices for diceCT in a nonmodel group, we outline a guide for staining and high-throughput µCT scanning in snakes. We scanned the entire body and one region of interest (i.e., head) for 23 specimens representing 23 species from the clades Aniliidae, Dipsadinae, Colubrinae, Elapidae, Lamprophiidae, and Viperidae. We generated 82 scans that include 1.25% Lugol's iodine stained (soft tissue) and unstained (skeletal) data for each specimen. We found that duration of optimal staining time increased linearly with body size; head radius was the best indicator. Postreconstruction of scans, optimal staining was evident by evenly distributed grayscale values and clear differentiation among soft-tissue anatomy. Under and over stained specimens produced poor contrast among soft tissues, which was often exacerbated by user bias during "digital dissections" (i.e., segmentation). Regardless, all scans produced usable data from which we assessed a range of downstream analytical applications within ecology and evolution (e.g., predator-prey interactions, life history, and morphological evolution). Ethanol destaining reversed the known effects of iodine on the exterior appearance of physical specimens, but required substantially more time than reported for other destaining methods. We discuss the feasibility of implementing diceCT techniques for a new user, including approximate financial and temporal commitments, required facilities, and potential effects of staining on specimens. We present the first high-throughput workflow for full-body skeletal and diceCT scanning in snakes, which can be generalized to any elongate vertebrates, and increases publicly available diceCT scans for reptiles by an order of magnitude.
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Affiliation(s)
- Sean Callahan
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Department of BiologyEastern Michigan UniversityYpsilantiMIUSA
| | - Jenna M. Crowe‐Riddell
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | | | - Jaimi A. Gray
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Alison R. Davis Rabosky
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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Asase A, Mzumara‐Gawa TI, Owino JO, Peterson AT, Saupe E. Replacing “parachute science” with “global science” in ecology and conservation biology. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.517] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Alex Asase
- Department of Plant and Environmental Biology University of Ghana Accra Ghana
| | | | - Jesse O. Owino
- Rift Valley Eco‐Region Research Program Kenya Forestry Research Institute Londiani Kenya
| | | | - Erin Saupe
- Department of Earth Sciences University of Oxford Oxford UK
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Lopes RJ, Faria PMV, Gomes D, Freitas B, Málinger J. The Hummingbird Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP), Portugal. Biodivers Data J 2021; 9:e59913. [PMID: 34393580 PMCID: PMC8324581 DOI: 10.3897/bdj.9.e59913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The Hummingbird (Family Trochilidae) Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP) is one of the oldest collections of this family harboured in European museums. Almost 2,000 specimens, that encompass most of the taxonomic diversity of this family, were collected in the late 19th Century. The collection is relevant due its antiquity and because all specimens were bought from the same provider, mainly as mounted specimens, for a Portuguese private collection of Neotropical fauna. In the early 20th Century, it was donated to the Museum that is now the MHNC-UP. NEW INFORMATION The information about the majority of these specimens is now available for consultation on the GBIF platform after curation of all specimens and digital cleaning of the associated metadata. In the process, hundreds of non-catalogued specimens were found and taxonomic and spatial information was updated for many of the specimens.
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Affiliation(s)
- Ricardo Jorge Lopes
- MHNC-UP, Natural History and Science Museum of the University of Porto, Porto, PortugalMHNC-UP, Natural History and Science Museum of the University of PortoPortoPortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de VairãoVairãoPortugal
| | - Pedro Miguel Vieira Faria
- FCUP, Faculdade de Ciências da Universidade do Porto, Porto, PortugalFCUP, Faculdade de Ciências da Universidade do PortoPortoPortugal
| | - Daniela Gomes
- FCUP, Faculdade de Ciências da Universidade do Porto, Porto, PortugalFCUP, Faculdade de Ciências da Universidade do PortoPortoPortugal
| | - Bárbara Freitas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Vairão, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de VairãoVairãoPortugal
- FCUP, Faculdade de Ciências da Universidade do Porto, Porto, PortugalFCUP, Faculdade de Ciências da Universidade do PortoPortoPortugal
| | - Judit Málinger
- University of Pannonia, Veszprem, HungaryUniversity of PannoniaVeszpremHungary
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Colella JP, Bates J, Burneo SF, Camacho MA, Carrion Bonilla C, Constable I, D'Elía G, Dunnum JL, Greiman S, Hoberg EP, Lessa E, Liphardt SW, Londoño-Gaviria M, Losos E, Lutz HL, Ordóñez Garza N, Peterson AT, Martin ML, Ribas CC, Struminger B, Torres-Pérez F, Thompson CW, Weksler M, Cook JA. Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network. PLoS Pathog 2021; 17:e1009583. [PMID: 34081744 DOI: 10.1371/journal.ppat.1009583] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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de Almeida FG, Guimarães LSF, Fonseca ADO, de Oliveira PR, da Silva Mendes S. Influence of pesticides in reproductive aspects of Tropidurus torquatus in Minas Gerais, Brazil. Environ Sci Pollut Res Int 2021; 28:30070-30076. [PMID: 33582964 DOI: 10.1007/s11356-021-12712-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Intense agricultural activity in recent years has resulted in a greater use of pesticides in order to improve productivity. However, these pesticides may contain some pollutant component in their composition. Once present in the environment and/or in excess, they can cause damage to the local flora and fauna. The aim of this study was to evaluate the interference of pesticides in the reproductive aspects of male and female specimens collected in two distinct sampling sites and propose a methodology to investigate pesticide effects associated with the reproduction at a macroscopic level for reptile specimens from zoological collection. The results showed that males located in the area with the use of agricultural pesticides had a lower testicle volume compared with the ones located in the area that did not use pesticides. However, no difference was found regarding the volume of eggs compared at the same stage and the average clutch size of each population. Therefore, the present study indicates the analyzed pesticides might influence the reproduction of the studied males. Despite no evident alterations in egg volume and quantity in the area with pesticide use, our findings suggest further studies on the structure and composition of eggshell and yolk in order to assess the effects of pesticides on their viability.
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Affiliation(s)
- Filipe Gomes de Almeida
- Laboratório de Répteis, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, São Pedro, Juiz de Fora, Minas Gerais, Brazil
| | - Luiza Soares Ferreira Guimarães
- Laboratório de Répteis, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, São Pedro, Juiz de Fora, Minas Gerais, Brazil
| | - André de Oliveira Fonseca
- Laboratório de Répteis, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, São Pedro, Juiz de Fora, Minas Gerais, Brazil.
| | - Paola Rosa de Oliveira
- Programa de Pós-graduação em Biodiversidade e Conservação da natureza, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, São Pedro, Juiz de Fora, Minas Gerais, Brazil
| | - Sarah da Silva Mendes
- Laboratório de Répteis, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, 36036-900, São Pedro, Juiz de Fora, Minas Gerais, Brazil
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. New Phytol 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Blom MPK. Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing. Mol Ecol 2021; 30:5935-5948. [PMID: 33786900 DOI: 10.1111/mec.15909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
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Affiliation(s)
- Mozes P K Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
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Abstract
The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.
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Affiliation(s)
- J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213;
| | - Joseph T Miller
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
| | - Scott B Weingart
- Digital Humanities Program, University Libraries, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Secretariat, DK-2100 Copenhagen Ø, Denmark
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Mason SC, Betancourt IS, Gelhaus JK. Importance of building a digital species index (spindex) for entomology collections: A case study, results and recommendations. Biodivers Data J 2021; 8:e58310. [PMID: 33390759 PMCID: PMC7773715 DOI: 10.3897/bdj.8.e58310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/05/2020] [Indexed: 11/12/2022] Open
Abstract
The Entomology Collection at the Academy of Natural Sciences of Drexel University (ANSP) contains approximately four million insect specimens including some of the oldest in the Western Hemisphere. Like most large entomology collections, no complete inventory of the species represented in the collection was available and even a physical search for a species could not ensure that all available specimens would be recovered for study. Between 2010 and 2014, we created a species-level index (called here spindex) of all species and their specimen counts at ANSP, along with each species’ location in the collection. Additional data captured during the project included the higher level classification of each species and type of specimen preparation. The spindex is searchable online: http://symbiont.ansp.org/entomology/. The spindex project documented 96,126 species in the ANSP Entomology Collection, representing about 10% of the described insect fauna. Additionally, over 900 putative primary types were discovered outside the Primary Type Collection. The completion of this project has improved access to the collection by enabling scientists and other users worldwide to search these collection holdings remotely and has facilitated staff in curation, research, collection management and funding proposals. A spindex is an important tool that is overlooked for planning and carrying out specimen level digitisation. This project is a case study for building a species-level index. A detailed protocol is provided, along with recommendations for other collections, including cost estimates and strategies for tracking progress and avoiding common obstacles.
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Affiliation(s)
- Stephen C Mason
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
| | - Isabelle S Betancourt
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
| | - Jon K Gelhaus
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. Antimicrob Steward Healthc Epidemiol 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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Wilf P, Wing SL, Meyer HW, Rose JA, Saha R, Serre T, Cúneo NR, Donovan MP, Erwin DM, Gandolfo MA, González-Akre E, Herrera F, Hu S, Iglesias A, Johnson KR, Karim TS, Zou X. An image dataset of cleared, x-rayed, and fossil leaves vetted to plant family for human and machine learning. PhytoKeys 2021; 187:93-128. [PMID: 35068970 PMCID: PMC8702526 DOI: 10.3897/phytokeys.187.72350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/05/2021] [Indexed: 05/04/2023]
Abstract
Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.
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Affiliation(s)
- Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USAPennsylvania State UniversityUniversity ParkUnited States of America
| | - Scott L. Wing
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USADepartment of Paleobiology, Smithsonian InstitutionWashington, DCUnited States of America
| | - Herbert W. Meyer
- Florissant Fossil Beds National Monument, National Park Service, Florissant, CO 80816, USAFlorissant Fossil Beds National Monument, National Park ServiceFlorissantUnited States of America
| | - Jacob A. Rose
- School of Engineering, Brown University, Providence, RI 02912, USABrown UniversityProvidenceUnited States of America
| | - Rohit Saha
- Department of Cognitive, Linguistic and Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USAMuseo Paleontológico E. FeruglioTrelewArgentina
| | - Thomas Serre
- Department of Cognitive, Linguistic and Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USAMuseo Paleontológico E. FeruglioTrelewArgentina
| | - N. Rubén Cúneo
- CONICET-Museo Paleontológico Egidio Feruglio, Trelew 9100, Chubut, Argentinaepartment of Paleobotany and Paleoecology, Cleveland Museum of Natural HistoryClevelandUnited States of America
| | - Michael P. Donovan
- Department of Paleobotany and Paleoecology, Cleveland Museum of Natural History, Cleveland, OH 44106, USAUniversity of California-BerkeleyBerkeleyUnited States of America
| | - Diane M. Erwin
- University of California-Berkeley, Museum of Paleontology, Berkeley, CA 94720, USACornell UniversityIthacaUnited States of America
| | - María A. Gandolfo
- LH Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USASmithsonian Conservation Biology Institute, National Zoological Park,Front RoyalUnited States of America
| | - Erika González-Akre
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USANegaunee Integrative Research Center, Field Museum of Natural HistoryChicagoUnited States of America
| | - Fabiany Herrera
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USAYale UniversityNew HavenUnited States of America
| | - Shusheng Hu
- Division of Paleobotany, Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USAInstituto de Investigaciones en Biodiversidad y Ambiente INIBIOMA, CONICET-UNComaSan Carlos de BarilocheArgentina
| | - Ari Iglesias
- Instituto de Investigaciones en Biodiversidad y Ambiente INIBIOMA, CONICET-UNComa, San Carlos de Bariloche 8400, Río Negro, ArgentinaDepartment of Paleobiology, Smithsonian InstitutionWashingtonUnited States of America
| | - Kirk R. Johnson
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USADepartment of Paleobiology, Smithsonian InstitutionWashington, DCUnited States of America
| | - Talia S. Karim
- University of Colorado Museum of Natural History, Boulder, CO 80503, USAUniversity of Colorado Museum of Natural HistoryBoulderUnited States of America
| | - Xiaoyu Zou
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USAPennsylvania State UniversityUniversity ParkUnited States of America
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Shultz AJ, Adams BJ, Bell KC, Ludt WB, Pauly GB, Vendetti JE. Natural history collections are critical resources for contemporary and future studies of urban evolution. Evol Appl 2021; 14:233-247. [PMID: 33519967 PMCID: PMC7819571 DOI: 10.1111/eva.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.
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Affiliation(s)
- Allison J. Shultz
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Benjamin J. Adams
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Entomology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Department of Biological SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Kayce C. Bell
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Mammalogy DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - William B. Ludt
- Ichthyology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Gregory B. Pauly
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Herpetology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Jann E. Vendetti
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Malacology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
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Farooq H, Azevedo JAR, Soares A, Antonelli A, Faurby S. Mapping Africa's Biodiversity: More of the Same Is Just Not Good Enough. Syst Biol 2020; 70:623-633. [PMID: 33306123 PMCID: PMC8048386 DOI: 10.1093/sysbio/syaa090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 11/14/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Species distribution data are fundamental to the understanding of biodiversity patterns and processes. Yet, such data are strongly affected by sampling biases, mostly related to site accessibility. The understanding of these biases is therefore crucial in systematics, biogeography, and conservation. Here we present a novel approach for quantifying sampling effort and its impact on biodiversity knowledge, focusing on Africa. In contrast to previous studies assessing sampling completeness (percentage of species recorded in relation to predicted), we investigate whether the lack of knowledge of a site attracts scientists to visit these areas and collect samples of species. We then estimate the time required to sample 90% of the continent under a Weibull distributed biodiversity sampling rate and the number of sampling events required to record $ \ge $50% of the species. Using linear and spatial regression models, we show that previous sampling has been strongly influencing the resampling of areas, attracting repeated visits. This bias has existed for over two centuries, has increased in recent decades, and is most pronounced among mammals. It may take between 172 and 274 years, depending on the group, to achieve at least one sampling event per grid cell in the entire continent. Just one visit will, however, not be enough: in order to record $ \ge $50% of the current diversity, it will require at least 12 sampling events for amphibians, 13 for mammals, and 27 for birds. Our results demonstrate the importance of sampling areas that lack primary biodiversity data and the urgency with which this needs to be done. Current practice is insufficient to adequately classify and map African biodiversity; it can lead to incorrect conclusions being drawn from biogeographic analyses and can result in misleading and self-reinforcing conservation priorities. [Amphibians; birds; mammals; sampling bias; sampling gaps; Wallacean shortfall.].
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Affiliation(s)
- Harith Farooq
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden1.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden.,Departamento de Biologia e CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Faculty of Natural Sciences at Lúrio University, Campus universitário da Universidade Lúrio, Bairro Eduardo Mondlane, 3200, Pemba, Cabo Delgado, Moçambique
| | - Josué A R Azevedo
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden1.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden.,Coordenação de Pesquisa em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Caixa Postal 2223, CEP 69008-971, Manaus, Brazil
| | - Amadeu Soares
- Departamento de Biologia e CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden1.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden.,Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, U.K
| | - Søren Faurby
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden1.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
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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] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Monfils AK, Krimmel ER, Bates JM, Bauer JE, Belitz MW, Cahill BC, Caywood AM, Cobb NS, Colby JB, Ellis SA, Krejsa DM, Levine TD, Marsico TD, Mayfield-Meyer TJ, Miller-Camp JA, Nelson RM(G, Phillips MA, Revelez MA, Roberts DR, Singer RA, Zaspel JM. Regional Collections Are an Essential Component of Biodiversity Research Infrastructure. Bioscience 2020. [DOI: 10.1093/biosci/biaa102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anna K Monfils
- Department of Biology and the Institute for Great Lakes Research, Central Michigan University, Mount Pleasant
| | - Erica R Krimmel
- iDigBio, Institute for Digital Information and Scientific Communication, Florida State University, Tallahassee
| | - John M Bates
- Natural Science Collections Alliance and curator of birds and head of life sciences, Field Museum, in Chicago, Illinois
| | - Jennifer E Bauer
- Florida Museum of Natural History, University of Florida, Gainesville, and is currently, Museum of Paleontology, University of Michigan, Ann Arbor
| | - Michael W Belitz
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Blake C Cahill
- Department of Biology and the Institute for Great Lakes Research, Central Michigan University, Mount Pleasant
| | - Alyssa M Caywood
- Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
| | - Neil S Cobb
- Biodiversity Outreach Network, Phoenix, Arizona, and with Northern Arizona University, Flagstaff
| | - Julia B Colby
- Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
| | - Shari A Ellis
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Dianna M Krejsa
- Angelo State Natural History Collections, Angelo State University, San Angelo, Texas
| | - Todd D Levine
- Department of Life Sciences at Carroll University, Waukesha, Wisconsin
| | - Travis D Marsico
- Department of Biological Sciences, Arkansas State University, Jonesboro
| | | | - Jess A Miller-Camp
- Dept. of Earth and Atmospheric Sciencese, Indiana University, Bloomington
| | - Roy M (Gil) Nelson
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville
| | - Molly A Phillips
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville
| | - Marcia A Revelez
- Natural Science Research Laboratory, Texas Tech University, Lubbock
| | - Dawn R Roberts
- Chicago Academy of Sciences and the Peggy Notebaert Nature Museum, Chicago, Illinois
| | | | - Jennifer M Zaspel
- Natural Science Collections Alliance and is affiliated with the Department of Zoology, Milwaukee Public Museum, Milwaukee, Wisconsin
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45
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Sackton TB. Studying Natural Selection in the Era of Ubiquitous Genomes. Trends Genet 2020; 36:792-803. [DOI: 10.1016/j.tig.2020.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
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