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Importance of timely metadata curation to the global surveillance of genetic diversity |
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| Authors: | Eric D. Crandall Rachel H. Toczydlowski Libby Liggins Ann E. Holmes Maryam Ghoojaei Michelle R. Gaither Briana E. Wham Andrea L. Pritt Cory Noble Tanner J. Anderson Randi L. Barton Justin T. Berg Sofia G. Beskid Alonso Delgado Emily Farrell Nan Himmelsbach Samantha R. Queeno Thienthanh Trinh Courtney Weyand Andrew Bentley John Deck Cynthia Riginos Gideon S. Bradburd Robert J. Toonen |
| Affiliation: | 1. Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA;2. Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA;3. School of Natural Sciences, Massey University, Auckland, New Zealand;4. Department of Animal Science, University of California, Davis, Davis, California, USA;5. Department of Biology, University of Central Florida, Orlando, Florida, USA;6. Department of Research Informatics and Publishing, The Pennsylvania State University Libraries, Pennsylvania State University, University Park, Pennsylvania, USA;7. Madlyn L. Hanes Library, The Pennsylvania State University Libraries, Pennsylvania State University, Middletown, Pennsylvania, USA;8. Department of Anthropology, University of Oregon, Eugene, Oregon, USA;9. Department of Marine Science, California State University Monterey Bay, Seaside, California, USA;10. UOG Marine Laboratory, University of Guam, Mangilao, Guam;11. Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA;12. Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA;13. Department of Natural Science, Hawai‘i Pacific University, Honolulu, Hawaii, USA;14. Department of Biological Sciences, Auburn University, Auburn, Alabama, USA;15. Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA;16. Berkeley Natural History Museums, University of California, Berkeley, Berkeley, California, USA;17. School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia;18. Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kaneohe, Hawaii, USA |
| Abstract: | Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. |
| Keywords: | biodiversity conservation genetics Convention on Biological Diversity digital sequence information evolution genetic diversity metadata molecular ecology open data biodiversidad Convenio sobre la Diversidad Biológica datos abiertos diversidad genética ecología molecular evolución información de secuencia digital metadatos 演化 分子生态学 保护遗传学 元数据 遗传多样性 开放数据 数字序列信息 《生物多样性公约》 |