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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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    Studies of how to improve translocation outcomes of Apteryx mantelli focusing on breeding, hybrids, diversity, and telomeres : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University - Te Kunenga Ki Purehuroa, Palmerston North, New Zealand
    (Massey University, 2021) Undin, Malin
    Genetic diversity contributes to the resilience of populations and, thus, to their potential to adapt to change and rebound after episodes of population decline. At the same time, many threatened species are confined to small populations with severely reduced access to gene flow. Since lost connectivity can result in inbreeding, translocations have become an increasingly important tool used by conservationists. However, the relative risks associated with inbreeding are difficult to weigh against potential negative fitness effects of outcrossing and hybridization. North Island brown kiwi, Apteryx mantelli, have a long, documented history of management and many severely isolated populations. The goal of this thesis was to determine current gaps in knowledge for successful genetic management of A. mantelli, explore closing those gaps using established hybrid populations and make recommendations for future translocations. First, information from past studies of Apteryx genetics was synthesised, which drew attention to the fact that available genetic data are insufficient for informing genetic management, predicting translocation outcomes, and linking genetic diversity to population fitness and local adaptation. Genome science combined with a strategic sampling regime was identified as crucial for acquiring the missing data. Second, an in-depth theoretical and empirical analysis of A. mantelli breeding behaviour was conducted. The results of this analysis showed that A. mantelli have the potential for polygamy, shows no signs of assortative mating, and breed in groups in certain conditions. These features of A. mantelli behaviour increase the likelihood of successful genetic rescue after reinforcement translocations. Next, the genetic diversity of the mixed-origin A. mantelli population on Ponui Island was investigated. Genotyping-by-sequencing analyses showed that this population constitutes a hybrid swarm in which founding parental genomes remain represented and levels of diversity are high compared to reference mainland populations. In addition to these studies, I conducted the first investigation of Apteryx telomeres. My theoretical analyses and empirical findings showed that telomere analyses of as long-lived species as A. mantelli are challenging and that telomere length is unlikely to be a suitable marker for determining Apteryx age and viability. Taken together, I suggest that the success of the hybrid population on Ponui Island indicates that mixed origin translocations should be considered as part of Apteryx management. However, I stress the need to (1) determine the role of local adaptation in Apteryx diversification, (2) study the impact of inbreeding, and (3) undertake investigations into informative markers of age and fitness on the individual and population-level. Investigation of epigenetic regulation of gene expression will be highly interesting for both these quests.
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    skelesim: an extensible, general framework for population genetic simulation in R.
    (2017-01) Parobek CM; Archer FI; DePrenger-Levin ME; Hoban SM; Liggins L; Strand AE
    Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny).