Browsing by Author "Toonen RJ"
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- ItemA decade of seascape genetics: Contributions to basic and applied marine connectivity(2016-07-28) Selkoe KA; D'Aloia CC; Crandall ED; Iacchei M; Liggins L; Puritz JB; Von Der Heyden S; Toonen RJSeascape genetics, a term coined in 2006, is a fast growing area of population genetics that draws on ecology, oceanography and geography to address challenges in basic understanding of marine connectivity and applications to management. We provide an accessible overview of the latest developments in seascape genetics that merge exciting new ideas from the field of marine population connectivity with statistical and technical advances in population genetics. After summarizing the historical context leading to the emergence of seascape genetics, we detail questions and methodological approaches that are evolving the discipline, highlight applications to conservation and management, and conclude with a summary of the field's transition to seascape genomics. From 100 seascape genetic studies, we assess trends in taxonomic and geographic coverage, sampling and statistical design, and dominant seascape drivers. Notably, temperature, oceanography and geography show equal prevalence of influence on spatial genetic patterns, and tests of over 20 other seascape factors suggest that a variety of forces impact connectivity at distinct spatio-temporal scales. A new level of rigor in statistical analysis is critical for disentangling multiple drivers and spurious effects. Coupled with GIS data and genomic scale sequencing methods, this rigor is taking seascape genetics beyond an initial focus on identifying correlations to hypothesis-driven insights into patterns and processes of population connectivity and adaptation. The latest studies are illuminating differences between demographic, functional and neutral genetic connectivity, and informing applications to marine reserve design, fisheries science and strategies to assess resilience to climate change and other anthropogenic impacts.
- ItemBuilding a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.(2020-11) Riginos C; Crandall ED; Liggins L; Gaither MR; Ewing RB; Meyer C; Andrews KR; Euclide PT; Titus BM; Therkildsen NO; Salces-Castellano A; Stewart LC; Toonen RJ; Deck JGenetic 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.
- ItemPoor data stewardship will hinder global genetic diversity surveillance.(2021-08-24) Toczydlowski RH; Liggins L; Gaither MR; Anderson TJ; Barton RL; Berg JT; Beskid SG; Davis B; Delgado A; Farrell E; Ghoojaei M; Himmelsbach N; Holmes AE; Queeno SR; Trinh T; Weyand CA; Bradburd GS; Riginos C; Toonen RJ; Crandall EDGenomic 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 (86%) 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 33% (39% 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.