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Andersen JC, Oboyski P, Davies N, Charlat S, Ewing C, Meyer C, Krehenwinkel H, Lim JY, Noriyuki S, Ramage T, Gillespie RG, Roderick GK. Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library. Ecol Appl 2019; 29:e01914. [PMID: 31050090 PMCID: PMC7079013 DOI: 10.1002/eap.1914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 05/26/2023]
Abstract
New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.
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Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - Peter Oboyski
- Essig Museum of EntomologyUniversity of California BerkeleyBerkeleyCalifornia94720USA
| | - Neil Davies
- Gump South Pacific Research StationUniversity of California BerkeleyMaharepaMooreaFrench Polynesia
| | - Sylvain Charlat
- Biométrie et Biologie ÉvolutiveUMR CNRS69622VilleurbanneFrance
| | - Curtis Ewing
- Komohana Research and Extension CenterUniversity of Hawai'i at MānoaHiloHawaii96720USA
| | | | | | - Jun Ying Lim
- Department of Integrated BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine ScienceKochi UniversityKochiJapan
| | | | - Rosemary G. Gillespie
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - George K. Roderick
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
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Ellwood ER, Kimberly P, Guralnick R, Flemons P, Love K, Ellis S, Allen JM, Best JH, Carter R, Chagnoux S, Costello R, Denslow MW, Dunckel BA, Ferriter MM, Gilbert EE, Goforth C, Groom Q, Krimmel ER, LaFrance R, Martinec JL, Miller AN, Minnaert-Grote J, Nash T, Oboyski P, Paul DL, Pearson KD, Pentcheff ND, Roberts MA, Seltzer CE, Soltis PS, Stephens R, Sweeney PW, von Konrat M, Wall A, Wetzer R, Zimmerman C, Mast AR. Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar. Bioscience 2018; 68:112-124. [PMID: 29599548 PMCID: PMC5862351 DOI: 10.1093/biosci/bix143] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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] [Indexed: 11/12/2022] Open
Abstract
The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institution's Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the event's effectiveness, and future directions—content now foundational to the growing WeDigBio event.
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Affiliation(s)
- Elizabeth R Ellwood
- La Brea Tar Pits & Museum, in Los Angeles, California, and was with the Department of Biological Science at Florida State University, in Tallahassee
| | - Paul Kimberly
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Robert Guralnick
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Kevin Love
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Shari Ellis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Julie M Allen
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Jason H Best
- Botanical Research Institute of Texas, in Fort Worth
| | - Richard Carter
- Biology Department at Valdosta State University, in Georgia
| | | | - Robert Costello
- Smithsonian Institution, National Museum of Natural History, in Washington, DC
| | - Michael W Denslow
- Florida Museum of Natural History at the University of Florida, in Gainesville, and the Department of Biology at Appalachian State University, in Boone, North Carolina
| | - Betty A Dunckel
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Meghan M Ferriter
- Smithsonian Institution Transcription Center at the Smithsonian Institution Office of the Chief Information Officer, in Washington, DC
| | | | | | | | - Erica R Krimmel
- Department of Biology at The Chicago Academy of Sciences and the Peggy Notebaert Nature Museum, in Chicago, Illinois
| | - Raphael LaFrance
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | - Joann Lacey Martinec
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Andrew N Miller
- Illinois Natural History Survey at the University of Illinois Urbana-Champaign
| | | | | | - Peter Oboyski
- Essig Museum of Entomology at the University of California, in Berkeley
| | - Deborah L Paul
- Institute for Digital Information and Scientific Communication at Florida State University, in Tallahassee
| | - Katelin D Pearson
- Department of Biological Science at Florida State University, in Tallahassee
| | - N Dean Pentcheff
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Mari A Roberts
- William and Lynda Steere Herbarium at the New York Botanical Garden
| | | | - Pamela S Soltis
- Florida Museum of Natural History at the University of Florida, in Gainesville
| | | | - Patrick W Sweeney
- Yale Peabody Museum of Natural History at Yale University, in New Haven, Connecticut
| | - Matt von Konrat
- Gantz Family Collections Center, Science and Education, at The Field Museum, in Chicago, Illinois
| | - Adam Wall
- Research and Collections at the Natural History Museum of Los Angeles County
| | - Regina Wetzer
- Research and Collections at the Natural History Museum of Los Angeles County
| | | | - Austin R Mast
- Department of Biological Science at Florida State University, in Tallahassee
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Hill A, Guralnick R, Smith A, Sallans A, Rosemary Gillespie, Denslow M, Gross J, Murrell Z, Tim Conyers, Oboyski P, Ball J, Thomer A, Prys-Jones R, de Torre J, Kociolek P, Fortson L. The notes from nature tool for unlocking biodiversity records from museum records through citizen science. Zookeys 2012:219-33. [PMID: 22859890 PMCID: PMC3406478 DOI: 10.3897/zookeys.209.3472] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [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: 06/06/2012] [Accepted: 07/16/2012] [Indexed: 11/12/2022] Open
Abstract
Legacy data from natural history collections contain invaluable and irreplaceable information about biodiversity in the recent past, providing a baseline for detecting change and forecasting the future of biodiversity on a human-dominated planet. However, these data are often not available in formats that facilitate use and synthesis. New approaches are needed to enhance the rates of digitization and data quality improvement. Notes from Nature provides one such novel approach by asking citizen scientists to help with transcription tasks. The initial web-based prototype of Notes from Nature is soon widely available and was developed collaboratively by biodiversity scientists, natural history collections staff, and experts in citizen science project development, programming and visualization. This project brings together digital images representing different types of biodiversity records including ledgers , herbarium sheets and pinned insects from multiple projects and natural history collections. Experts in developing web-based citizen science applications then designed and built a platform for transcribing textual data and metadata from these images. The end product is a fully open source web transcription tool built using the latest web technologies. The platform keeps volunteers engaged by initially explaining the scientific importance of the work via a short orientation, and then providing transcription “missions” of well defined scope, along with dynamic feedback, interactivity and rewards. Transcribed records, along with record-level and process metadata, are provided back to the institutions. While the tool is being developed with new users in mind, it can serve a broad range of needs from novice to trained museum specialist. Notes from Nature has the potential to speed the rate of biodiversity data being made available to a broad community of users.
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