An official website of the United States government
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.
more »
« less
Poor data stewardship will hinder global genetic diversity surveillance
Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic diversity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world’s largest genomic data repository, we found that most archived genomic datasets (87%) lacked the spatiotemporal metadata necessary for genetic biodiversity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 39% (51% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today’s genetic biodiversity and to plug the growing metadata gap.
more »
« less
- Award ID(s):
- 1764316
- PAR ID:
- 10420851
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 118
- Issue:
- 34
- ISSN:
- 0027-8424
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards‐compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.more » « less
-
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering — removing sequencing bases, reads, genetic variants and/or individuals from a dataset — to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomic data filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy–Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima’s D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne).more » « less
-
Over the past five decades, a large number of wild animals have been individually identified by various observation systems and/or temporary tracking methods, providing unparalleled insights into their lives over both time and space. However, so far there is no comprehensive record of uniquely individually identified animals nor where their data and metadata are stored, for example photos, physiological and genetic samples, disease screens, information on social relationships.Databases currently do not offer unique identifiers for living, individual wild animals, similar to the permanent ID labelling for deceased museum specimens.To address this problem, we introduce two new concepts: (1) a globally unique animal ID (UAID) available to define uniquely and individually identified animals archived in any database, including metadata archived at the time of publication; and (2) the digital ‘home’ for UAIDs, the Movebank Life History Museum (MoMu), storing and linking metadata, media, communications and other files associated with animals individually identified in the wild. MoMu will ensure that metadata are available for future generations, allowing permanent linkages to information in other databases.MoMu allows researchers to collect and store photos, behavioural records, genome data and/or resightings of UAIDed animals, encompassing information not easily included in structured datasets supported by existing databases. Metadata is uploaded through the Animal Tracker app, the MoMu website, by email from registered users or through an Application Programming Interface (API) from any database. Initially, records can be stored in a temporary folder similar to a field drawer, as naturalists routinely do. Later, researchers and specialists can curate these materials for individual animals, manage the secure sharing of sensitive information and, where appropriate, publish individual life histories with DOIs. The storage of such synthesized lifetime stories of wild animals under a UAID (unique identifier or ‘animal passport’) will support basic science, conservation efforts and public participation.more » « less
-
Abstract Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about datasets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1073/pnas.2107934118
