Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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Subject: search.filters.subject.Convention on Biological Diversity

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    Importance of timely metadata curation to the global surveillance of genetic diversity
    (Wiley Periodicals LLC on behalf of Society for Conservation Biology, 2023-08) Crandall ED; Toczydlowski RH; Liggins L; Holmes AE; Ghoojaei M; Gaither MR; Wham BE; Pritt AL; Noble C; Anderson TJ; Barton RL; Berg JT; Beskid SG; Delgado A; Farrell E; Himmelsbach N; Queeno SR; Trinh T; Weyand C; Bentley A; Deck J; Riginos C; Bradburd GS; Toonen RJ
    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. Importancia de la curación oportuna de metadatos para la vigilancia mundial de ladiversidad genéticaResumen:La diversidad genética intraespecífica representa un nivel fundamental, pero ala vez subvalorado de la biodiversidad. La diversidad genética puede indicar la resilienciade una especie ante el clima cambiante, por lo que su medición es relevante para muchosobjetivos de la política de conservación mundial y nacional. Muchos estudios producenuna gran cantidad de datos sobre la diversidad a nivel genético de las poblaciones silvestres,aunque la mayoría (87%) no incluye los metadatos espaciales y temporales asociados paraque sean reutilizados en los programas de monitoreo o para reconocer la soberanía de lasnaciones o los pueblos indígenas. Realizamos un “datatón” distribuido para cuantificar ladisponibilidad de estos metadatos faltantes y para probar la hipótesis que supone que estadisponibilidad se deteriora con el tiempo. También trabajamos para reparar los metadatosfaltantes al extraerlos de los artículos asociados publicados, los repositorios en línea yla comunicación directa con los autores. Iniciamos con 838 candidatos de conjuntos dedatos genómicos (representación reducida y genoma completo) tomados de la colabo-ración internacional para la base de datos de secuencias de nucleótidos y determinamosque 561 incluían en su mayoría muestras tomadas de poblaciones silvestres. Restauramoscon éxito los metadatos espaciotemporales en el 78% de estos 561 conjuntos de datos (n=440 conjuntos de datos con información sobre 45,105 individuos de 762 especies en 17filos). El análisis de los artículos y los repositorios virtuales fue mucho más productivo quecontactar a los 351 autores, quienes tuvieron un 45% de respuesta a nuestros correos. Engeneral, el 23% de nuestras consultas descubrieron metadatos útiles. La probabilidad derecuperar metadatos espaciotemporales declinó de manera significativa conforme incre-mentó la antigüedad del conjunto de datos. Hubo una disminución anual del 13.5% enlos metadatos asociados con los artículos publicados y los repositorios virtuales y hastauna disminución anual del 22% en los metadatos que sólo estaban disponibles mediante lacomunicación con los autores. Este rápido deterioro en la disponibilidad de los metadatos,duplicado en estudios de otros tipos de datos biológicos, debería motivar la pronta actual-ización de las políticas del intercambio de datos y las prácticas de los investigadores paraasegurar que en las ciencias de la conservación no se pierda para siempre el contexto valiosoproporcionado por los metadatos.
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    Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved
    (Elsevier Ltd, 2020-08) Hoban S; Bruford M; D'Urban Jackson J; Lopes-Fernandes M; Heuertz M; Hohenlohe PA; Paz-Vinas I; Sjögren-Gulve P; Segelbacher G; Vernesi C; Aitken S; Bertola LD; Bloomer P; Breed M; Rodríguez-Correa H; Funk WC; Grueber CE; Hunter ME; Jaffe R; Liggins L; Mergeay J; Moharrek F; O'Brien D; Ogden R; Palma-Silva C; Pierson J; Ramakrishnan U; Simo-Droissart M; Tani N; Waits L; Laikre L
    The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.