Utilizing aquatic environmental DNA to address global biodiversity targets

Published: April 27, 2025

Language: Английский

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Empowering Regional Conservation: Genetic Diversity Assessments as a Tool for Eelgrass Management

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 12, 2025

To halt the loss of biodiversity, collaboration among scientists, managers and decision-makers is vital. Although biodiversity a global problem, management actions influencing diversity are often on local to regional scale. Our study an example conservation genomic assessment developed in between scientists managers. We used 2bRAD sequencing assess 18 eelgrass (Zostera marina) meadows northwestern Sweden, area that has experienced large losses since 1980s. Genetic was comparable other assessed Atlantic, but order magnitude lower than Pacific. All one meadow showed high rates sexual reproduction. Almost all were divergent grouped into five genetic clusters. Four clusters correspond geographic regions can be define units. Meadows areas with decline 1980s 2020s more inbred increase eelgrass. Overall, our results indicate striving protect number within each cluster important for maintaining connectivity Sweden likely beneficial wider ecosystem. estimate current indicators essential variables discuss their challenges marine facultative clonal species. showcase how regional-scale assessments serve as foundation protection restoration priority

Language: Английский

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A molecular specimen bank for contemporary and future study captures landscape-scale biodiversity baselines before Klamath River dam removal

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Global restoration and conservation of freshwater biodiversity are represented in practice by works such as the Klamath River Renewal Project (KRRP), largest dam removal river United States, which has reconnected 640 kilometers. With removals, many biological outcomes remain understudied due to a lack pre-impact data complex ecosystem recovery timeframes. To avoid this, we created KRRP molecular library, an environmental specimen bank, for long-term curation nucleic acids collected from project. We used these initial samples, DNA metabarcoding, generalized linear mixed-effects models evaluate patterns pre-dam fish richness diversity. Demonstrating suitability resolve differences, baseline shows that tributary mainstem streams had greater native diversity 2.3–10.7 times species than reservoirs. These future sampling efforts should, at minimum, allow tracking community response restoration. Anticipating acceleration omics innovation, preserved samples storage identified requisite phases sustained function adaptation library: securing physical facility genetic material, establishing governance structure, confirming support archive management.

Language: Английский

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Overture: an open-source genomics data platform

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Background Next-generation sequencing has created many new technological challenges in organizing and distributing genomics datasets, which now can routinely reach petabyte scales. Coupled with data-hungry artificial intelligence machine learning applications, findable, accessible, interoperable, reusable datasets have never been more valuable. While major archives like the Genomics Data Commons, Sequence Reads Archive, European Genome-Phenome Archive improved researchers’ ability to share reuse data, general-purpose repositories such as Zenodo Figshare provide valuable platforms for research data publication, diversity of precludes any one-size-fits-all approach. In cases, bespoke solutions are required, despite funding agencies journals increasingly mandating practices, researchers still lack technical support needed meet multifaceted reuse. Findings Overture bridges this gap by providing open-source software building deploying customizable platforms. Its architecture consists modular microservices, each is generalized narrow responsibilities that together combine create complete management systems. These systems enable organize, share, explore their at scale. Through Overture, connect both humans machines, fostering reproducibility enabling insights through controlled sharing Conclusions By making these tools freely available, we accelerate development reliable genomic across community quickly, flexibly, multiple an project licensed under AGPLv3.0 all source code publicly available from https://github.com/overture-stack documentation on development, deployment, usage www.overture.bio.

Language: Английский

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Principles in experimental design for evaluating genomic forecasts

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(9), P. 1466 - 1482

Published: July 10, 2024

Abstract Over the past decade, there has been a rapid increase in development of predictive models at intersection molecular ecology, genomics, and global change. The common goal these ‘genomic forecasting’ is to integrate genomic data with environmental ecological model make quantitative predictions about vulnerability populations climate Despite methodological growing number systems which forecasts are made, themselves rarely evaluated rigorous manner ground‐truth experiments. This study reviews evaluation experiments that have done, introduces important terminology regarding forecasting models, discusses elements design reporting To date, experimental evaluations found high variation accuracy forecasts, but it difficult compare studies on ground due different approaches designs. Additionally, some may be biased toward higher performance because training testing not independent. In addition independence between data, an experiment include construction parameterization model, choice fitness proxies measure for test metric(s), degree extrapolation novel environments or genotypes, sensitivity, uncertainty reproducbility forecasts. Although methods becoming more accessible, evaluating their limitations particular system requires careful planning experimentation. Meticulously designed can clarify robustness application management. Clear basic will improve rigour evaluations, turn our understanding why work cases others.

Language: Английский

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Conserving genetic diversity hotspots under climate change: Are protected areas helpful?

Biological Conservation, Journal Year: 2024, Volume and Issue: 299, P. 110828 - 110828

Published: Oct. 31, 2024

Language: Английский

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