Ethical, legal, and social issues in the Earth BioGenome Project

A Latitudinal Gradient of Reference Genomes

Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes, while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state-of-the-art methods. Here, we ask whether a fundamental biogeographic pattern-the latitudinal gradient of species richness in tetrapods-is reflected in the available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last 5 years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes and that reduced representation and whole-genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.

Environmental DNA without borders : Let's embrace decentralised genomics to meet the UN's biodiversity targets

Towards the 10th anniversary of the Nagoya Protocol, it is time to embrace key technology developments and adapt existing red tape for genomic monitoring.

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Disruptive technology: Exploring the ethical, legal, political, and societal implications of nanopore sequencing technology: Exploring the ethical, legal, political, and societal implications of nanopore sequencing technology

Due to its low cost and easy handling, nanopore sequencing has great potential to become a consumer product. The widespread use of DNA sequencers would, however, create new social, legal, and ethical challenges.

Indigenous peoples and local communities as partners in the sequencing of global eukaryotic biodiversity

The aim to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity is the shared mission of many ongoing large-scale biodiversity genomics initiatives. Reference genomes of global flora and fauna have the potential to inform a broad range of major issues facing both biodiversity and humanity, such as the impact of climate change, the conservation of endangered species and ecosystems, public health crises, and the preservation and enhancement of ecosystem services. Biodiversity is dramatically declining: 28% of species being assessed by the IUCN are threatened with extinction, and recent reports suggest that a transformative change is needed to conserve and protect what remains. To provide a collective and global genomic response to the biodiversity crisis, many biodiversity genomics initiatives have come together, creating a network of networks under the Earth BioGenome Project. This network seeks to expedite the creation of an openly available, "public good" encyclopedia of high-quality eukaryotic reference genomes, in the hope that by advancing our basic understanding of nature, it can lead to the transformational scientific developments needed to conserve and protect global biodiversity. Key to completing this ambitious encyclopedia of reference genomes, is the ability to responsibly, ethically, legally, and equitably access and use samples from all of the eukaryotic species across the planet, including those that are under the custodianship of Indigenous Peoples and Local Communities. Here, the biodiversity genomics community is subject to the provisions codified in international, national, and local legislations and customary community norms, principles, and protocols. We propose a framework to support biodiversity genomic researchers, projects, and initiatives in building trustworthy and sustainable partnerships with communities, providing minimum recommendations on how to access, utilize, preserve, handle, share, analyze, and communicate samples, genomics data, and associated Traditional Knowledge obtained from, and in partnership with, Indigenous Peoples and Local Communities across the data-lifecycle.

Benefit sharing: Why inclusive provenance metadata matter

Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital Sequence Information (“DSI”), discussions are currently underway regarding to include such data through ongoing Convention on Biological Diversity (“CBD”) negotiations. While Indigenous Peoples and Local Communities (“IPLC”) expect the value generated from genomic data to be subject to benefit sharing arrangements, a range of views are currently being expressed by Nation States, IPLC and other stakeholders. The use of DSI gives rise to unique considerations, creating a gray area as to how it should be considered under the Nagoya Protocol’s Access and Benefit Sharing (“ABS”) principles. One way for benefit sharing to be enhanced is through the connection of data to proper provenance information. A significant development is the use of digital labeling systems to ensure that the origin of samples is appropriately disclosed. The Traditional Knowledge and Biocultural Labels initiative offers a practical option for data provided to genomic databases. In particular, the BioCultural Labels (“BC Labels”) are a mechanism for Indigenous communities to identify and maintain provenance, origin and authority over biocultural material and data generated from Indigenous land and waters held in research, cultural institutions and data repositories. This form of cultural metadata adds value to the research endeavor and the creation of Indigenous fields within databases adds transparency and accountability to the research environment.

Standards recommendations for the Earth BioGenome Project

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.