Don’t make genetic data disposable: Best practices for genetic and genomic data archiving DOI Creative Commons
Deborah M. Leigh, Amy G. Vandergast,

Maggie Hunter

et al.

Published: Sept. 25, 2023

In ecology and evolution, genetic genomic data are commonly collected for a vast array of scientific applied purposes. Despite mandates public archiving, such typically used only once by the data-generating authors. The repurposing datasets remains uncommon because it is often difficult, if not impossible, due to non-standard archiving practices lack contextual metadata. But as new research field macrogenetics demonstrating, their metadata were more accessible, they could be reused many additional purposes, far beyond initial intended impact. this review, we outline main challenges with existing archives, factors underlying challenges, current best data. Recognising that longstanding issue an absence formal management training within highlight key steps universities, funding bodies, publishers take ensure timely change towards good archiving.

Language: Английский

Global meta-analysis shows action is needed to halt genetic diversity loss DOI Creative Commons
Robyn E. Shaw, Katherine A. Farquharson, Michael W. Bruford

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

Mitigating loss of genetic diversity is a major global biodiversity challenge1-4. To meet recent international commitments to maintain within species5,6, we need understand relationships between threats, conservation management and change. Here conduct analysis change via meta-analysis all available temporal measures from more than three decades research. We show that within-population being lost over timescales likely have been impacted by human activities, some actions may mitigate this loss. Our dataset includes 628 species (animals, plants, fungi chromists) across terrestrial most marine realms on Earth. Threats two-thirds the populations analysed, less half analysed received management. Genetic occurs globally realistic prediction for many species, especially birds mammals, in face threats such as land use change, disease, abiotic natural phenomena harvesting or harassment. Conservation strategies designed improve environmental conditions, increase population growth rates introduce new individuals (for example, restoring connectivity performing translocations) even diversity. findings underscore urgent active, genetically informed interventions halt

Language: Английский

Citations

6
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics DOI Creative Commons
Ann M. Mc Cartney, Giulio Formenti, Alice Mouton

et al.

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: Sept. 17, 2024

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched Pilot establishing first distributed genome production infrastructure testing it on 98 from 33 countries. Here we outline explore its effectiveness scaling production, whilst considering equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational, national resource projects EBP.

Language: Английский

Citations

12
Redlisting genetics: towards inclusion of genetic data in IUCN Red List assessments DOI Creative Commons
Chloee M. McLaughlin, Chauncy Hinshaw, Stephania Sandoval-Arango

et al.

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract Genetic diversity is critical for adaptation in response to changing environments and provides a valuable metric predicting species’ extinction risk. The International Union Conservation of Nature (IUCN) broader scientific community have acknowledged that genetic component biodiversity conservation. However, there remain gaps the incorporation or application data risk assessments. Here, we describe how metrics can inform species Specifically, focus on information gained from metrics, temporal reporting changes complement existing IUCN Red List Threatened Species criteria. We conclude by advocating standardized sequence calculated facilitate use threat assessments List-assessed species. This perspective highlights need for, step towards, integration into expect our recommendations will ongoing work Survival Commission’s Genetics Specialist Group protect globally.

Language: Английский

Citations

1
Conservation macrogenetics: harnessing genetic data to meet conservation commitments DOI Creative Commons
Chloé Schmidt, Sean Hoban, Walter Jetz

et al.

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(11), P. 816 - 829

Published: Aug. 28, 2023

Language: Английский

Citations

18
Genomic Tools in Biological Invasions: Current State and Future Frontiers DOI Creative Commons
Angela McGaughran, Manpreet K. Dhami, Elahe Parvizi

et al.

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 16(1)

Published: Dec. 18, 2023

Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little how genomic processes facilitate the invasion process. Although most literature has focused on underlying phenotypic correlates invasiveness, advances in technologies showing a strong link between variation success. Here, consider ability tools to (i) inform mechanistic understanding (ii) solve real-world issues predicting managing invasions. For both, examine current state field discuss genomics can be leveraged future. In addition, make recommendations pertinent broader research issues, such as data sovereignty, metadata standards, collaboration, science communication best practices that will require concerted efforts from global community.

Language: Английский

Citations

18
Best practices for genetic and genomic data archiving DOI
Deborah M. Leigh, Amy G. Vandergast, Margaret E. Hunter

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(7), P. 1224 - 1232

Published: May 24, 2024

Language: Английский

Citations

6
The emerging picture of a diverse deep Arctic Ocean seafloor: From habitats to ecosystems DOI Creative Commons
Eva Ramírez-Llodra, Heidi Kristina Meyer, Bodil A. Bluhm

et al.

Elementa Science of the Anthropocene, Journal Year: 2024, Volume and Issue: 12(1)

Published: Jan. 1, 2024

Interest in the deep Arctic Ocean is rapidly increasing from governments, policy makers, industry, researchers, and conservation groups, accentuated by growing accessibility of this remote region surface vessel traffic. In review, our goal to provide an updated taxonomic inventory benthic taxa known occur relate habitat diversity. To achieve goal, we collected data for metazoan deep-sea open-access databases, information facilities, non-digitised scientific literature, limiting collection area north 66°N below 500 m depth (excluding all shelf seas). Although notable progress has been made understanding using novel technologies infrastructure, gathering shows that knowledge communities remains very limited. Yet, through compilation maps, show contains a high diversity geomorphological features, including slopes, basins, submarine canyons, ridges, seamounts, as well chemosynthesis-based biogenic (biologically engineered) ecosystems. analyse taxon richness density, both morphological molecular data, compiled 75,404 faunal records with 2,637 taxa. Phyla most were Arthropoda (21,405), Annelida (13,763) Porifera (12,591); phyla documented (956), (566) Mollusca (351). An overview dominant groups inhabiting different features highlights regions where are particularly scarce increased research efforts needed, basins central Ocean. This scarcity biodiversity creates bottleneck developing robust management measures changing region, leading call international collaboration shared ensure preservation these fragile

Language: Английский

Citations

5
A pragmatic approach for integrating molecular tools into biodiversity conservation DOI Creative Commons
Laura D. Bertola, Anna Brüniche‐Olsen, Francine Kershaw

et al.

Conservation Science and Practice, Journal Year: 2023, Volume and Issue: 6(1)

Published: Dec. 25, 2023

Abstract Molecular tools are increasingly applied for assessing and monitoring biodiversity informing conservation action. While recent developments in genetic genomic methods provide greater sensitivity analysis the capacity to address new questions, they not equally available all practitioners: There is considerable bias across institutions countries access technologies, funding, training. Consequently, many cases, more accessible traditional data (e.g., microsatellites) still utilized making decisions. Conservation approaches need be pragmatic by tackling clearly defined management questions using most appropriate available, while maximizing use of limited resources. Here we present some key consider when applying molecular toolbox actionable management. Finally, highlight a number important steps addressed collaborative way, which can facilitate broad integration into conservation.

Language: Английский

Citations

11
Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection DOI Creative Commons
Astrid Böhne, Rosa Fernández, Jennifer A. Leonard

et al.

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: Sept. 17, 2024

Abstract The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan-European network. To demonstrate community’s capability capacity realise ambitious ERGA Pilot project was initiated. In support effort genomes biodiversity, Sampling Sample Processing committee (SSP) formed by volunteer experts from member base. SSP aid participating researchers (i) establishing standards collecting sample/specimen metadata; (ii) prioritisation species sequencing; (iii) development taxon-specific collection guidelines including logistics support. serves as entry point sample providers genomic resource production infrastructure guarantees that high-quality upheld throughout processing. With volume researchers, projects, consortia, organisations with interests in genomics resources expanding, manuscript shares important experiences lessons learned during standardised operational procedures provider details our incorporating FAIR CARE principles, prioritisation, workflow development, which could be useful individuals well other initiatives.

Language: Английский

Citations

4
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics DOI Creative Commons
Ann M. Mc Cartney, Giulio Formenti, Alice Mouton

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 28, 2023

A global genome database of all Earth's species diversity could be a treasure trove scientific discoveries. However, regardless the major advances in sequencing technologies, only tiny fraction have genomic information available. To contribute to more complete planetary database, scientists and institutions across world united under Earth BioGenome Project (EBP), which plans sequence assemble high-quality reference genomes for ~1.5 million recognized eukaryotic through stepwise phased approach. As initiative transitions into Phase II, where 150,000 are sequenced just four years, worldwide participation project will fundamental success. European node EBP, Reference Genome Atlas (ERGA) seeks implement new decentralised, accessible, equitable inclusive model producing genomes, inform EBP as it scales. embark on this mission, ERGA launched Pilot establish network Europe develop test first infrastructure its kind coordinated distributed production 98 from sample providers 34 countries. Here we outline process challenges faced during development pilot resources, explore effectiveness approach terms production, considering also equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational national resource projects.

Language: Английский

Citations

10